Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato

Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato S Kousalya, Li-mei Lee, Shang-yu Lin, Su-ling Shih, Srinivasan Ramasamy, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7403472/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Pepper veinal mottle virus (PVMV), a member of the Potyvirus genus, is primarily a pathogen of pepper, but its emerging impact on tomato poses a growing concern due to its broad host range, aphid transmission and potential for significant yield losses. Despite its economic importance, studies on the genomic characterization and host range of PVMV isolates are limited. This study characterizes, through host range analysis, complete genome sequencing and comparative analysis of two PVMV isolates Tom1 (from tomato) (PV476910) and EP1 (from eggplant) (PV476911) in Taiwan. Mechanical inoculation onto 20 plant species revealed distinct host responses: Tom1 induced severe mosaic and necrotic symptoms in tomato (PDI 100%), while EP1 caused milder symptoms in tomato (PDI 60%) but higher virulence in Capsicum species (PDI 100%). Full-length genomes (9,796 nt each) comprised a single open reading frame encoding a 3,073 amino acid polyprotein processed into ten characteristic potyviral proteins. Sequence Demarcation Tool (SDT) and sequence identity matrix analyses showed Tom1 and EP1 share 94.3% nucleotide identity, with highest identities (96%) to Japanese (Tom1) and Taiwanese (EP1) isolates. Both clustered with East/Southeast Asian isolates, sharing only 74–84% identity with African isolates and < 61% with non-PVMV potyviruses. Phylogenetic reconstruction revealed four major clades, placing Tom1 with East Asian isolates and EP1 with Taiwanese isolates, indicating regional diversification. Gene-wise comparison showed high conservation in the coat protein (99.3% nt, 100% aa) and greater variability in non-structural proteins (P1, HC-Pro, CI, VPg), suggesting roles in host adaptation. These findings enhance understanding of PVMV genetic diversity, phylogenetic relationships, and host specificity, providing a basis for targeted resistance breeding and regional disease management strategies. Pepper veinal µottle virus host range Full-length genome sequencing and viral genetic diversity Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 1. Introduction Tomato ( Solanum lycopersicum ) is one of the most important vegetable crops in the Solanaceae family, ranking as the ninth most cultivated crop globally [ 1 ]. According to the Food and Agriculture Organization [ 2 ], global tomato production was valued at approximately USD 19.5 billion in 2024. In Taiwan, tomatoes are grown on about 4,100 hectares, yielding 98,340 tons and contributing around USD 141 million to the national economy (Council of Agriculture, Executive Yuan) [ 2 ]. Pepper ( Capsicum spp.), another major solanaceous crop, is widely cultivated in tropical and subtropical regions and is highly susceptible to several viral diseases, including pepper veinal mottle virus (PVMV). According to ICTV (2024), PVMV has been renamed as Potyvirus capsivenae [ 3 ], a member of the Potyvirus genus within the Potyviridae family, is recognized for its aggressiveness in pepper, resulting in severe symptoms and substantial yield losses [ 4 ]. Potyvirus species possess a monopartite, single-stranded, positive-sense RNA genome of approximately 10 kb that encodes a polyprotein, which is processed into multiple functional proteins essential for replication, movement, and suppression of host defenses [ 4 , 5 ]. The virus is transmitted non-persistently by aphids and has a broad host range. Although PVMV primarily infects Capsicum species, recent reports have documented its occurrence in alternative solanaceous hosts, such as tomato ( S. lycopersicum ) and eggplant ( S. melongena ), in regions including Taiwan. This emerging host expansion raises concerns about the virus adaptability, potential for broader transmission, and the risk it poses to tomato production. Infected tomato plants often exhibit mottling, chlorosis, and stunting, with reported yield losses of up to 50% [ 6 , 7 ]. Such impacts are particularly problematic in mixed cropping systems, where management becomes more complex [ 8 ]. Despite its potential economic threat, the molecular characteristics, genetic variability, and pathogenicity of PVMV isolates infecting tomato remain poorly understood. To address this knowledge gap, the present study characterizes two PVMV isolates: Tom1, isolated from tomatoes and EP1, isolated from eggplants, were obtained from the Taiwan Agricultural Research Institute (TARI) and National Chung Hsing University (NCHU) and maintained at the World Vegetable Center in Taiwan. These isolates were selected based on their distinct host origins and differential symptom expression. Using full-length genome sequencing, phylogenetic analysis, and host range evaluation, this research aims to elucidate the evolutionary relationships, host-pathogen interactions, and pathogenic potential of these isolates. The findings will contribute to a better understanding of PVMV evolution and support the development of effective and sustainable management strategies for tomato cultivation in Taiwan, including the identification of potential sources of resistance for breeding programs. 2. Materials and Methods 2.1. Confirmation of PVMV isolates: Symptomatic N. benthamiana leaves of two isolates of pepper veinal mottle virus (PVMV) Tom1 (from tomato) and EP1 (from eggplant) were obtained from Taiwan Agricultural Research Institute (TARI) and National Chung Hsing University (NCHU) [ 8 ], respectively. The Tom1 isolate was maintained in tomato and Nicotiana benthamiana , whereas the EP1 isolate was maintained in eggplant and N. benthamiana under controlled greenhouse conditions at the World Vegetable Center, Taiwan. Total RNA was extracted from infected leaf tissues using the GenMark total RNA purification kit (Cat. No.: TR02-150), following the manufacturer’s protocol. The presence of PVMV was confirmed by reverse transcription PCR (RT-PCR) using PVMV specific primers targeting the coat protein (CP) gene (Forward: 5′- AATGCAGGAACACAGGGGAC − 3′ and Reverse: 5′ CGCGCTAATGACATATCGGT − 3′) designed by the Virology team at the World Vegetable Center. To assess the pathogenicity of the isolates, mechanical inoculation was performed on tomato ( Solanum lycopersicum ) . Inoculated plants were observed for symptom development, and the virus was reconfirmed in symptomatic tissues using RT-PCR. The amplified CP gene sequences of the two isolates were submitted to the NCBI GenBank database. 2.2. Host range study 2.2.1. Inoculation and observation PVMV isolates Tom1 and EP1 were mechanically inoculated onto 20 plant entries representing 12 species across six families. Each entry included 10 plants, while four plants per entries were maintained as healthy controls. The list of host species inoculated is provided in Table S1 . 1 g of infected leaf tissue was homogenized in 10 mL phosphate buffer (pH 7.0; 0.01 M Na₂HPO₄, 0.01 M KH₂PO₄) to obtain a 10% (w/v) crude sap extract. The homogenate was filtered through two layers of cheesecloth and used immediately without further dilution. The upper surface of the first two fully expanded leaves was dusted with 600-mesh carborundum, and ~ 100 µL of inoculum was gently rubbed onto each leaf using a soft cotton swab. Mock-inoculated control plants were treated with phosphate buffer alone following the same procedure. After inoculation, leaves were rinsed with distilled water to remove excess inoculum and abrasive. Inoculated and control plants were maintained in an insect-proof greenhouse at 25–30 ℃ and 50–60% relative humidity, watered regularly, and fertilized every two weeks with a balanced NPK (20:20:20) fertilizer. Symptom expression was recorded at 7-day intervals post inoculation (7th, 14th, 21st, and 28th day), observations such as leaf curling, mottling, and stunting were recorded and compared with controls. Disease severity was evaluated based on percent disease incidence (PDI) following the method described by BH Wheeler [ 9 ]. Following symptom observation, the presence of PVMV in the affected plants was confirmed through SDT- RT-PCR, ensuring accurate identification of virus infected individuals. $$\:\text{P}\text{e}\text{r}\text{c}\text{e}\text{n}\text{t}\text{a}\text{g}\text{e}\:\text{D}\text{i}\text{s}\text{e}\text{a}\text{s}\text{e}\:\text{I}\text{n}\text{c}\text{i}\text{d}\text{e}\text{n}\text{c}\text{e}=\frac{\text{T}\text{o}\text{t}\text{a}\text{l}\:\text{n}\text{u}\text{m}\text{b}\text{e}\text{r}\:\text{o}\text{f}\:\text{i}\text{n}\text{f}\text{e}\text{c}\text{t}\text{e}\text{d}\:\text{p}\text{l}\text{a}\text{n}\text{t}\text{s}}{\text{T}\text{o}\text{t}\text{a}\text{l}\:\text{n}\text{u}\text{m}\text{b}\text{e}\text{r}\:\text{o}\text{f}\:\text{p}\text{l}\text{a}\text{n}\text{t}\text{s}\:\text{o}\text{b}\text{s}\text{e}\text{r}\text{v}\text{e}\text{d}}\:\times\:100$$ 2.2.2. Simple Direct Tube- RT-PCR (SDT-RT-PCR) and gel electrophoresis The leaf samples of all the 20 plant entries after 28th DPI were homogenized in 500 µl of 1× PBST buffer, and the extract was incubated in PCR tubes at 37°C for 30 minutes[ 10 ]. Tubes were washed twice with 1× PBST and briefly spun down to remove residual buffer. cDNA was synthesized using M-MuLV Reverse Transcriptase (Invitrogen, Thermo Fisher Scientific) with a CP gene specific reverse primer following the manufacturer’s instructions. PCR amplification was subsequently carried out using Taq DNA Polymerase (Invitrogen, Thermo Fisher Scientific) with CP gene primers (Forward: 5′- AATGCAGGAACACAGGGGAC − 3′ and Reverse: 5′ CGCGCTAATGACATATCGGT − 3′) to amplify fragments of the PVMV genome. Thermal cycling conditions included an initial denaturation at 95°C, followed by 29 cycles of denaturation (95°C), annealing (52°C), and extension (72°C), with a final extension at 72°C for 5 minutes. PCR products were resolved on a 1% agarose gel prepared in 0.5x TBE buffer [ 11 ], stained with SYBR Green, and visualized under UV illumination using a 1 kb DNA ladder. Based on the assay host studies conducted, N. benthamiana was identified as suitable host to maintain both the isolates. 2.3. Full-length genome sequencing and analysis of PVMV isolates Tom1 and EP1 2.3.1. RNA extraction, cDNA synthesis and PCR amplification Total RNA was extracted from 100 mg of fresh Nicotiana benthamiana leaf tissue inoculated with PVMV using the GenMark plant total RNA purification kit (catalog no. TR02-150), following the manufacturer’s protocol. Tissues were ground in liquid nitrogen and lysed in buffer containing 2-mercaptoethanol. After incubation at 60°C for 3 minutes and centrifugation, the lysate was processed using spin filters and ethanol precipitation. Genomic DNA was removed by DNase I treatment [ 12 ]. RNA was eluted in 30–50 µL of nuclease-free water, quantified using a NanoDrop spectrophotometer (Invitrogen, Thermo Fisher Scientific), and stored at − 80°C. cDNA synthesis was performed as described in Section 2.2.2. PCR amplification was performed using Taq DNA polymerase (Invitrogen, Thermo Fisher Scientific) and primers designed to amplify overlapping fragments of the PVMV genome. Details of primer sequences, annealing temperatures, and expected product sizes are provided in Table S2. The assembled full-length genomes of PVMV Tom1 and EP1 were each 9,796 nucleotides (nt) in length, encoding a single large open reading frame (ORF) of 9,219nt corresponding to a polyprotein of 3,073 amino acids (aa), flanked by a 5′ untranslated region (UTR) and a 3′ UTR followed by a poly(A) tail. 2.3.3. Gel purification, cloning and sequencing PCR products were purified using the Wizard® SV Gel and PCR Clean-Up System (Promega) and then ligated into the pGEM®-T Easy Vector. Ligation mixtures were transformed into Escherichia coli DH5α competent cells via heat shock and plated on LB agar containing ampicillin, IPTG, and X-Gal [ 13 ]. White colonies were screened by colony PCR, and positive clones were cultured in LB broth supplemented with ampicillin. Plasmid DNA was isolated and submitted for Sanger sequencing (Genomics, Taiwan) [ 14 ]. Consensus sequences were manually assembled using ApE software[ 15 ], and gene annotation was performed using NCBI BLAST [ 16 ]. Each sequenced sample was submitted to the NCBI GenBank, USA, to acquire a GenBank accession number. Functional and comparative analyses were conducted using public databases, including NCBI and UniProt. Multiple sequence alignments were performed using ClustalW in BioEdit version 5.0.9. Phylogenetic trees were constructed using the Neighbor-Joining method with the Kimura 2-parameter model in MEGA version 11, with 1000 bootstrap replicates. The resulting trees were visualized and annotated using Interactive Tree of Life (iTOL) version 6. Pairwise sequence identity were assessed using two methods: (i) Sequence Demarcation Tool (SDT) (v1.2) for heatmap visualization and (2) sequence identity matrix for exact nucleotide and amino acid values. Gene-wise comparisons between PVMV Tom1 and EP1 were performed by aligning each coding region individually to determine nucleotide and amino acid identities, as well as to identify specific amino acid substitutions in functional domains[ 17 ]. 3. Results 3.1. Confirmation of PVMV isolates: In N. benthamiana , infection with both PVMV isolates produced veinal chlorosis, mild mottling and slight leaf deformation by 7–8 days post inoculation (DPI). These two isolates, Tom1 (from tomato) and EP1 (from eggplant), were maintained at the World Vegetable Center, Taiwan. Total RNA extracted from N. benthamiana infected plants showed high integrity and the presence of PVMV was confirmed by RT-PCR using coat protein (CP) specific primers, yielding amplicons of the expected size (~ 480 bp). Mechanical inoculation of both isolates onto tomato ( Solanum lycopersicum ) resulted in isolate specific symptom expression. In Tom1 infected plants, symptoms appeared at 7–8 DPI showed vein chlorosis, mild mottling and necrosis of leaves. In EP1 infected plants, symptoms appeared later 14–15 DPI and were comparatively milder, consisting of moderate mottle with necrosis rarely observed. Both isolates induced symptoms at the same time in N. benthamiana , but in tomato, EP1 caused delayed and milder symptoms compared to Tom1. RT-PCR analysis of symptomatic tomato leaves reconfirmed the presence of PVMV, and the pathogenicity of both isolates was proven (Fig. 1 ). The amplified coat protein gene sequences of the two isolates have been deposited in the NCBI GenBank database under the accession numbers PX119809 (PVMV Tom1) and PX119811 (PVMV EP1). 3.2. Host range study for PVMV isolates Tom1 and EP1 The host range study was conducted to determine the susceptibility of selected plant species to two isolates of pepper veinal mottle virus (PVMV), Tom1 and EP1. Twenty plant entries representing different species were mechanically inoculated, and symptom severity was measured using the percent disease incidence (PDI) formula, with observations recorded at 7, 14, 21, and 28 days post-inoculation (DPI). The symptom data compiled at 28 DPI were used to compare the responses of different hosts (Table 1 ). Table 1 Host range study for PVMV Tom1 and PVMV EP1 S. No Common Name Scientific Name PVMV Tom1 PVMV EP1 Symptoms observed* PCR reaction** Number of plants expressed symptoms/ total number of plants inoculated PDI (%) Number of plants expressed symptoms/ total number of plants inoculated PDI (%) PVMV Tom1 PVMV EP1 1. Tomato S. lycopersicum (ANT22) 10/10 100 (90) a 6/10 60 (50) c (Sm, Ns) + + 2. Tomato S. lycopersicum (CLN4680F1) 10/10 100 (90) a 6/10 60 (50) c Ns (Tom1) and Vmm (EP1) + + 3. Cherry tomato S. lycopersicum 0/10 0 0/10 0 (NVS) - - 4. Pepper Capsicum annuum (VC27a) 8/10 80 (63) b 10/10 100 (90) a (mm, Ld) + + 5. Pepper C. chinense (AVPP1932) 8/10 80 (63) b 10/10 100 (90) a (Vmm)- Tom1 and (mm)- EP1 + + 6. Pepper C. frutescens (VI040881) 8/10 80 (63) b 10/10 100 (90) a (mm) + + 7. Cucumber Cucumis sativus 0/10 0 0/10 0 (NVS) - - 8. Luffa Luffa aegyptiaca 0/10 0 0/10 0 (NVS) - - 9. Bitter gourd Momordica charantia 0/10 0 0/10 0 (NVS) - - 10. Okra Abelmoschus esculentus 0/10 0 0/10 0 (NVS) - - 11. Cowpea Vigna ungiculata 6/10 60 (50) c 0/10 0 Vmm (Tom1); NVS (EP1) + - 12. Green gram Vigna radiata (KPS 2) 10/10 100 (90) a 0/10 0 Ns (Tom1); NVS (EP 1) + - 13. Green gram Vigna radiata 0/10 0 0/10 0 (NVS) - - 14. Black gram Vigna mungo 0/10 0 0/10 0 (NVS) - - 15. Tobacco Nicotiana rustica 8/10 80 (63) b 8/10 80 (63) b (mm) + + 16. Tobacco N. tabacum white burley 0/10 0 0/10 0 (NVS) - - 17. Tobacco N. tabacum var. Xanthi 0/10 0 0/10 0 (NVS) - - 18. Quinoa Chenopodium quinoa 10/10 100 (90) a 10/10 100 (90) a (Cs) + + 19. Lambs quarters C. amaranticolor 10/10 100 (90) a 10/10 100 (90) a (Ns) + + 20. Indian thornapple Datura metel 10/10 100 (90) a 8/10 80 (63) b (mm) + + SE(d) 1.52 1.08 CD (P = 0.05) 3.09 2.20 Note: Symptom severity is reported as an overall score based on observations at 7, 14, 21, 28 DPI. Abbreviations: *(mm)- Mild mottle; (Vmm)- Very mild mottle; (NVS)- No visible symptoms; (Cs)- Chlorotic spot; (Ns)- Necrotic spot; (Sm, Ns) - Severe mosaic with necrotic spots; (mm, Ld)- mild mottle with leaf distortion. **PCR reaction indicates RT-PCR confirmation of PVMV infection in symptomatic hosts + Positive reaction, -Negative reaction in RT-PCR. Out of 20 plant entries tested, 13 showed infection with at least one of the virus isolates, as confirmed by both visible symptoms and SDT- RT-PCR results. A ~ 480 bp fragment specific to PVMV was amplified in infected plants, confirming the presence of the virus. Datura metel, Nicotiana rustica, Chenopodium quinoa , and Chenopodium amaranticolor exhibited 80–100% infection, characterized by clear symptoms, including mild mottling, chlorotic (yellow) spots, and necrotic (dead) spots. Both isolates infected these plants. In Solanum lycopersicum , Tom1 caused severe mosaic and necrotic spots within 7 days post inoculation (DPI), reaching 100% percent disease incidence (PDI) (most prominent in this host), while EP1 induced milder mosaic symptoms around 14 DPI with a 60% PDI. Cherry tomato plants remained symptomless throughout the observation period and tested negative in SDT-RT-PCR for both isolates. All three Capsicum species ( C. annuum , C. chinense , and C. frutescens ) were susceptible to both isolates, with EP1 producing more pronounced leaf curling, vein clearing, and mosaic within 7 DPI (most prominent in C. annuum ), and Tom1 causing comparatively milder symptoms appearing around 13–14 DPI. In the legume group, cowpea ( Vigna unguiculata ) and green gram variety KPS2 ( V. radiata ) developed mild mosaic and leaf distortion within 7 DPI with a 60% PDI and tested positive only with Tom1, with cowpea showing more visible symptoms, whereas EP1 failed to infect these hosts. Green gram variety Taiwan No. 5 and black gram ( V. mungo ) showed no symptoms and were SDT-RT-PCR negative for both isolates. Cucumber ( Cucumis sativus L.), luffa ( Luffa aegyptiaca ), bitter gourd ( Momordica charantia L.), okra ( Abelmoschus esculentus ), and two tobacco varieties ( Nicotiana tabacum var. white burley and var. Xanthi) showed no visible symptoms up to 28 DPI, and SDT-RT-PCR results confirmed the absence of both Tom1 and EP1(Fig. 2 , Fig. 3 , Table 1 ). 3.3. Genome organization of PVMV isolates Tom1 and EP1 The complete genome sequences for both PVMV isolates were obtained and assembled using ApE software, and annotated through NCBI BLAST. These sequences were deposited in NCBI GenBank, USA, and obtained accession numbers PV476910 (Tom1) and PV476911 (EP1). Each genome is 9,796nt in length, consisting of a 5′ untranslated region (UTR), a single large open reading frame (ORF) of 9,219nt encoding a polyprotein of 3,073 amino acids, and a 3′ UTR (nt 9415–9796) followed by a poly(A) tail. The polyprotein is predicted to be processed into ten functional proteins characteristic of the potyvirus genus: P1 (nt 196–1095), HC-Pro (1096–2466), P3 (2467–3498), 6K1 (3499–3660), CI (3661–5589), 6K2 (5590–5748), VPg (5749–6321), NIa-Pro (6322–7047), NIb (7048–8604), and CP (8605–9414). In addition, the frameshift product P3N-PIPO (nt 2926–3144) is encoded within the P3 region, as reported for potyviruses[ 3 ]. 3.4. Comparative sequence analysis with global PVMV isolates A comparative analysis was conducted with 18 globally reported PVMV isolates and four related potyviruses. Sequence alignment using the MUSCLE algorithm and pairwise identity analysis with the Sequence Demarcation Tool v1.2 (SDT) showed that both Tom1 and EP1 had the highest nucleotide identity (96%) with the Japanese isolate OKP2 (LC438540), followed by OKP3 (95%, LC438541) and OKC25 (94%, LC438542). Taiwanese isolates ns1 (FJ617225) and Tn (OR355467) also showed high identity (94–96%), suggesting regional conservation and potential shared ancestry. In contrast, moderate identity values (74–84%) were recorded with genetically distinct isolates from China (KR002568, MN082715), Nigeria (OP722584), Senegal (OK558747), and Korea (NC011918), suggesting significant divergence due to geographic and evolutionary separation. Low identities (57–61%) with distantly related potyviruses such as sugarcane mosaic virus (EU091075) and Vietnam wild tomato mosaic virus (NC009744), confirm that Tom1 and EP1 belong to the same species (PVMV) but represent distinct variants according to ICTV demarcation thresholds (< 76%). A heatmap generated using SDT v1.2 illustrates these relationships, showing Tom1 and EP1 clustering with closely related East Asian isolates, while more divergent isolates form separate groups (Fig. 4 ). The color gradient from red (> 90% identity) to blue (< 60% identity) visually highlights these genetic distinctions. 3.5. Sequence identity matrix: The nucleotide sequence identity between PVMV Tom1 and PVMV EP1 was 94.3%, indicating a close genetic relationship. At the amino acid level, the identity was 91.4%, indicating strong conservation in essential protein coding regions. Both Tom1 and EP1 isolates exhibited high nucleotide identity (98.0–99.5%) with the Japanese isolates (LC438541 and LC438544), and amino acid identities ranged from 95.1–96.4%, indicating functional stability across these isolates. The Taiwanese isolate OR355467 also exhibited high similarity, with nucleotide identities of 97.7% (Tom1) and 97.5% (EP1), and amino acid identities of 90.7% and 90.5%, respectively, indicating potential geographic and host-specific evolutionary influences. In contrast, comparison with other potyvirus species, such as chilli veinal mottle virus (ChiVMV), revealed much lower identities (67.1% nucleotide and 41.2% amino acid), underscoring significant divergence. Furthermore, PVMV isolates shared less than 50% nucleotide identity and less than 25% amino acid identity with non-potyvirus RNA viruses, confirming their distinct taxonomic placement within the potyvirus genus (Table 2 ). Table 2 Sequence identity matrix and comparative analysis of PVMV Tom1, PVMV EP1 and related complete genomes S. No. GenBank accession Host Country Virus-acronym PVMV (Complete genome) Nt (%) AA (%) 1. LC438540 Capsicum annuum Japan PVMV 99.5 99.2 2. LC438541 Capsicum annuum Japan PVMV 99.5 99.2 3. LC438542 Capsicum annuum Japan PVMV 98.6 97.3 4. LC438543 Capsicum annuum Japan PVMV 98.2 96.2 5. LC438544 Capsicum annuum Japan PVMV 99.3 98.7 6. LC438545 Capsicum frutescens Japan PVMV 98.2 96.3 7. FJ617225 Solanum nigrum Taiwan PVMV 97.9 96.3 8. OR355467 Solanum lycopersicum Taiwan PVMV 97.7 95 9. PV476911 (PVMV EP1) Solanum melongena Taiwan PVMV 94.2 92.1 10. PV476910 (PVMV Tom1) Solanum lycopersicum Taiwan PVMV 94.5 92.8 11. KR002568 Capsicum annuum China PVMV 98.2 96.5 12. MN082715 Capsicum chinense China PVMV 97.8 95.3 13. OR355466 Capsicum annuum Taiwan PVMV 97.3 94.6 14. OP722584 Solanum lycopersicum Nigeria PVMV 94.5 87.6 15. OK558747 Solanum lycopersicum Senegal PVMV 93.9 87.4 16. OQ102061 Capsicum annuum Nigeria PVMV 93.8 87 17. OK558746 Solanum lycopersicum Senegal PVMV 83.5 66.9 18. NC011918 Capsicum annuum Korea PVMV 98.5 97.2 19. PQ520507 Capsicum annuum Ethiopia EPMV 72.6 48.7 20. NC043537 Solanum aethiopicum Tanzania EMV 67.8 43.8 21. MK405594 Nicotiana tabacum China ChiVMV 67.1 41.2 22. NC009744 Solanum torvum Laichau WTMV 64.9 39.7 23. EU091075 Saccharum officinarum Mexico SCMV 49.7 21.9 3.6. Phylogenetic analysis of full-length PVMV isolates A phylogenetic tree was constructed based on multiple nucleotide sequence alignments of the study isolates and 18 full-length PVMV genomes, along with three other potyviruses were retrieved from the database. The analysis revealed four major clades (Fig. 5 ), highlighting the evolutionary diversity of PVMV across different geographic regions and host plants. Clade 1 included the PVMV Tom1 isolate grouped closely with East Asian isolates from Japan (LC438540–LC438545), Korea (NC011918), and China (KR002568), forming a strongly supported group suggestive of a common origin or recent introduction from this region. In clade II comprised the EP1 isolate grouped with Taiwanese isolates (OR355466, OR355467 and FJ617225), indicating regional diversification and potential local adaptation in Taiwan. Clade III consisted of West African isolates from Nigeria (OP722584, OQ102061) and Senegal (OK558746, OK558747) forming a geographically and genetically distinct lineage. Distant clustering of PMMoV (Ethiopia), ChiVMV (China and India), wild ToMV (Vietnam and China), and SCMV (Mexico) as outgroups confirmed the monophyly of PVMV and its separation from other potyviruses, consistent with ICTV species classification guidelines [ 18 , 19 ]. 3.7. Comparative nucleotide and amino acid variations between PVMV Tom1 and EP1 The coding regions of PVMV isolates Tom1 and EP1 exhibited strong nucleotide conservation across the polyprotein, with identities ranging from 97.6–99.3% per gene (Table 3 ). Among the structural proteins, the coat protein (CP) was highly conserved, reflecting its essential role in virion assembly and transmission. In contrast, non-structural proteins, including P1, HC-Pro, CI, and VPg, showed slightly lower nucleotide identities (97.6–98.8%), suggesting localized variability that may facilitate host adaptation, viral replication efficiency, or evasion of host defense mechanisms. Table 3 Gene-wise comparison of PVMV Tom1 and EP1 isolates: Gene Coordinates (NT)* Coordinates AA** Length (NT) Length (AA) Notable substitutions (Tom1, EP1) NT identity (%) AA identity (%) P1 196–1095 1-300 900 300 D68E, A74V, E117G, H149R, R245K 97.6 96 HC-Pro 1096–2466 301–850 1371 457 A319T, T488A, D503N, 97.9 99.1 P3 2467–3498 851–1140 1032 344 V872A, D923G, M980I, A984T, R986K 98.8 98.5 6K1 3499–3660 1141–1185 162 54 - 97.6 100 CI 3661–5589 1186–1835 1929 643 M1200T, V1303I, V1611I, R1642P, T1667S, V1788I 98.6 99.0 6K2 5590–5748 1836–1875 159 53 - 98.8 100 VPg 5749–6321 1876–2050 573 191 I1886V, A1893S, K1969I, N195S, M2003V, A2008V, M2019V 98.1 95.8 NIa-Pro 6322–7047 2051–2280 726 242 H2123Y, N2152I, L2153C 99.0 99.6 NIb 7048–8604 2281–2795 1557 519 I2351T, Q2421R, V2639I 98.6 98.7 CP 8605–9414 2796–3074 810 270 S2972N, R3049Q 99.3 100 The table shows genomic coordinates, lengths, amino acid (AA) positions, notable amino acid substitutions, and nucleotide (NT) and amino acid identity percentages for each predicted protein-coding region. Coordinates are based on the complete genome sequences of PVMV Tom1 (PV476910) and EP1 (PV476911). At the protein level, amino acid substitutions between PVMV Tom1 and PVMV EP1 revealed multiple variations across different functional domains of the viral polyprotein. In the P1 (1-300 aa) region, which is involved in replication and host defense suppression, notable mutations include Aspartic acid (D) to Glutamic acid (E) at position 68, Alanine (A) to Valine (V) at 74th position, and Glutamic acid (E) to Glycine (G) at 117th position. Several mutations in this region involve changes in charged and polar residues, such as the conversion of Histidine (H) to Arginine (R) at position 149 and the conversion of Arginine (R) to Lysine (K) at position 245, which could impact protein interactions. The HC-Pro (301–850 aa) region, crucial for RNA silencing suppression and aphid transmission, exhibits substitutions such as Alanine (A) to Threonine (T) at 319th position, Threonine (T) to Alanine (A) at 488th and Aspartic acid (D) to Asparagine (N) at 503th position. These changes could influence HC-Pro functionality in modulating host defenses. In the CI (1186–1835 aa) region, which functions as an RNA helicase, mutations such as Methionine (M) to Threonine (T) at 1200th position, Arginine (R) to Proline (P) at 1642, and Threonine (T) to Serine (S) at 1667th postion were observed, possibly affecting enzymatic activity. The VPg (1876–2050 aa) region, which plays a role in viral RNA binding and translation initiation, harbors mutations such as Alanine (A) to Serine (S) transition at 1893 and a Lysine (K) to Isoleucine (I) substitution at 1969, Methionine (M) to Valine (V) at positions 2003 and 2019, and Alanine (A) to Valine (V) at position 2008, possibly affecting viral genome stability. The NIa (2051–2280 aa) region, responsible for polyprotein processing, contains mutations such as Asparagine (N) to Isoleucine (I) at 2152th position, Leucine (L) to Cysteine (C) at 2153 th position, which could impact protease efficiency. The NIb (2281–2795 aa) region, encoding the RNA-dependent RNA polymerase, exhibits a conservative mutation from and Arginine (R) to Glycine (G) at 2612th position, Valine (V) to Isoleucine (I) at position 2639. Lastly, in the CP (2796–3074 aa) region, which is essential for encapsidation and transmission, mutations such as Serine (S) to Asparagine (N) at position 2972 and Arginine (R) to Glutamine (Q) at position 3049 were observed, which could affect virion stability and host interactions (Fig. 6 ). 4. Discussion Pepper veinal mottle virus (PVMV) is emerging as a significant production constraint. Infected tomato plants show mottling, chlorosis, leaf distortion and stunting, leading to yield reductions of up to 50% and compromised fruit quality, which limits marketability [ 5 , 8 ]. This study provides clear molecular and phylogenetic evidence of PVMV occurrence in tomato in Taiwan and highlights the genomic distinctions between isolates Tom1 and EP1. The host range study revealed that the two isolates differ in their ability to infect specific plant species. Some plants developed strong symptoms, such as necrotic (dead) spots or chlorotic (yellow) spots, while others did not show any signs of infection. This kind of variation is common among different virus strains, and it helps us to understand how viruses spread and survive in nature [ 20 ]. In assay hosts such as Chenopodium quinoa , C. amaranticolor , Datura metel , and Nicotiana rustica , both Tom1 and EP1 produced visible symptoms, but differences in expression were observed: Tom1 typically induced more necrotic lesions and extensive chlorosis, whereas EP1 symptoms were more localized and chlorotic. According to Hull [ 21 ], Chenopodium species are commonly used for detecting viruses, because they form distinct local lesions [ 21 ]. Tomato ( Solanum lycopersicum ) plants developed more severe symptoms with Tom1 compared to EP1, indicating that Tom1 may be a more aggressive strain. Similar symptom variability among potyvirus isolates has been reported earlier. For example, Tomitaka and Ohshima [ 22 ] reported that minor sequence variations in the HC-Pro and coat protein genes of turnip mosaic virus (TuMV) isolates were linked to differences in symptom severity and host specificity in Brassica species, illustrating how small genomic changes can produce distinct pathogenic profiles. Pepper plants ( Capsicum annuum , C. chinense , C. frutescens ) were infected by both virus isolates, but EP1 caused more severe symptoms. This suggests that EP1 may be better adapted to infect pepper. Such differences in how well a virus strain infects a specific plant are influenced by the virus’s ability to multiply, move inside the plant, and suppress the plant’s defenses [ 23 ]. Some plants, such as cherry tomato, bitter gourd, okra, luffa, cucumber, and tobacco varieties, did not show any symptoms and were also negative in RT-PCR tests. These plants are likely to be non-hosts for both virus isolates. Non-host resistance is a natural way for plants to prevent viruses from infecting them, usually because the virus cannot complete its life cycle in these plants [ 20 ]. The legume group showed an interesting pattern. Cowpea and green gram (KPS2) were infected only by Tom1, not by EP1. This again indicates that Tom1 has a broader ability to infect different hosts. The other legume varieties were not infected, showing the importance of testing multiple varieties when studying host range. These results are significant because they demonstrate that even strains of the same virus can exhibit distinct behaviours in different plant species. This type of knowledge helps us to understand how viruses spread and which plants might aid their survival between cropping seasons. It also helps to identify potential virus reservoirs[ 24 ]. Pairwise nucleotide identity analysis showed that PVMV isolates Tom1 and EP1 shared 94–96% between Tom1, EP1, and East Asian isolates from Japan (OKP2, OKP3, OKC25: LC438540–LC438542) and Taiwan (ns1: FJ617225, Tn: OR355467) indicates conserved regional lineages, likely reflecting historical dispersal or shared germplasm movement, as reported for zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV) in Southeast Asia [ 25 ]. In contrast, moderate identity (74–84%) with isolates from China (KR002568, MN082715), Nigeria (OP722584), Senegal (OK558747), and Korea (NC011918) suggests greater diversity from evolutionary divergence or limited gene flow, similar to patterns in potato virus Y (PVY) [ 26 ]. The high nucleotide (94.3%) and amino acid (91.4%) identity between PVMV Tom1 and EP1 confirms their close relationship as isolates of the same species, reflecting conserved functions despite ecological or host pressures. Similar patterns occur in other potyviruses, such as ChiVMV and PepMoV, where high coding sequence similarity coexists with minor host-linked variations [ 27 ]. Both isolates also show strong genetic similarity (97.5–99.5% nt; 90.5–96.4% aa) to Japanese (LC438541, LC438544) and Taiwanese (OR355467) strains, supporting a shared East–Southeast Asian lineage shaped by regional dispersal and localized evolution [ 28 , 29 ]. Slightly lower amino acid than nucleotide identities indicate predominance of synonymous mutations, with non-synonymous changes contributing to strain-level diversity. The coat protein (CP) is completely conserved (99.3% nt, 100% aa identity), underscoring its essential role in encapsidation and suitability for diagnostics and phylogenetic analysis [ 30 , 31 ]. In contrast, moderate variation in P1 (96%), HC-Pro (99.12%), CI (99.07%), and VPg (95.81%) likely reflects adaptation to host factors or environmental conditions, as these proteins function in proteolysis, RNA silencing suppression, replication complex formation, and host interactions[ 32 , 33 ]. Phylogenetic analysis placed Tom1 with East Asian isolates from Japan, Korea, and China, while EP1 clustered with Taiwanese strains suggesting localized adaptation or microevolution within the region. The distinct clustering of EP1 with Taiwanese isolate, despite high identity to Tom1, implies localized adaptation or microevolution driven by ecological or host-specific pressures reflecting the dynamic evolution of potyviruses influenced by hosts, vectors, and cultivation practices[ 29 , 34 ]. West African isolates formed a separate, genetically distinct clade, mirroring diversification patterns observed in yam mosaic virus and cassava brown streak virus [ 27 , 35 ] [ 36 , 37 ], highlighting the role of geographic and agroecological factors on PVMV evolution. The amino acid substitutions observed between PVMV Tom1 and EP1 across multiple functional domains of the viral polyprotein suggest ongoing molecular diversification, possibly driven by host adaptation or environmental selection pressures. Notably, variations in the P1 region (96% aa identity), such as D68E, A74V, and E117G, may impact viral replication and host defense suppression, aligning with earlier findings in pepper mottle virus (PepMoV) and chilli veinal mottle virus (ChiVMV), where substitutions in the P1 domain were linked to altered host specificity and pathogenicity[ 34 , 38 ]. Similarly, the HC-Pro region, known for its role in RNA silencing suppression and aphid transmission, exhibited mutations such as A319T and D503N, which may influence viral counter-defense mechanisms. Previous studies on zucchini yellow mosaic virus (ZYMV) and tobacco etch virus (TEV) have demonstrated that even conservative changes in HC-Pro can modulate RNA silencing suppression efficiency and systemic movement [ 33 , 39 ]. The CI domain, functioning as an RNA helicase, showed substitutions (e.g., M1200T, R1642P) that may affect enzymatic activity and replication fidelity. Such mutations have been associated with differential replication efficiencies in potyviruses, such as turnip mosaic virus (TuMV) [ 40 ]. Changes in 6K2 and VPg may impact membrane binding and genome linkage, respectively, which are critical for replication complex formation and translation initiation[ 41 , 42 ]. The observed substitutions in NIa-Pro and NIb regions, including proteolytically and polymerase related sites, may modulate polyprotein processing and replication accuracy, as noted in potato virus Y (PVY) and papaya ringspot virus (PRSV)[43]. Finally, mutations in the coat protein (S2972N, R3049Q) may influence particle stability and vector transmission efficiency, as seen in watermelon mosaic virus and PRSV, where CP variation was linked to altered virulence and transmission[44]. These cumulative changes, particularly within functionally essential domains, reinforce the adaptive potential of PVMV and its evolutionary divergence, which could influence epidemiological patterns and management strategies. The differences in host range, symptom severity, and molecular variation between Tom1 and EP1 have direct implications for virus monitoring and resistance breeding. High conservation in the coat protein supports its continued use for diagnostics and phylogenetic studies, while variable regions such as P1, HC-Pro, and VPg could be targeted for studying pathogenicity mechanisms and host adaptation. 5. Conclusion The observed differences in host range, symptom severity, and molecular variation between PVMV Tom1 and EP1 have direct implications for virus monitoring and resistance breeding strategies. The high conservation of the coat protein supports its continued use in diagnostics and phylogenetic studies, whereas variable regions such as P1, HC-Pro, and VPg provide valuable targets for elucidating pathogenicity mechanisms and host adaptation. Sustained genomic surveillance will be critical for the early detection of novel variants and the prevention of their spread. Declarations Acknowledgement: The author gratefully acknowledges the Taiwan Government for the fellowship support that made this research possible. We are deeply grateful to the World Vegetable Center, Shanhua, Taiwan, for providing the facilities, resources and technical assistance essential for carrying out this study. We also sincerely thank all colleagues and staff at the World Vegetable Center for their assistance, collaboration and valuable discussions that contributed to the success of this work. Data availability All data supporting the conclusion of this article are provided within the text and supplementary material. Funding: This work was funded by the World Vegetable Center, Taiwan, under the Golden Jubilee Year Student Research Fellowships 2024. Ethical approval During the study, principles of ethical and professional conduct have been followed and there were no Human participants and or Animals involvement. Declaration of competing interest The authors declare no conflict of interest. Authorship contribution: Kousalya S: Performance of research experiments. 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Journal of Agricultural Science and Technology A 8. https://doi.org/10.17265/2161-6256/2018.04.005 Supplementary Files Supplementaryfiles.docx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7403472","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":504029409,"identity":"b248ef69-97a1-4909-a511-01716f5f91b9","order_by":0,"name":"S Kousalya","email":"","orcid":"","institution":"Tamil Nadu Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"S","middleName":"","lastName":"Kousalya","suffix":""},{"id":504029410,"identity":"2f9840e2-dfaf-431f-9b52-a5d7619ca562","order_by":1,"name":"Li-mei Lee","email":"","orcid":"","institution":"AVRDC World Vegetable Center","correspondingAuthor":false,"prefix":"","firstName":"Li-mei","middleName":"","lastName":"Lee","suffix":""},{"id":504029411,"identity":"e6daad58-e636-4d40-bb88-5cf0a13a34a4","order_by":2,"name":"Shang-yu Lin","email":"","orcid":"","institution":"AVRDC World Vegetable Center","correspondingAuthor":false,"prefix":"","firstName":"Shang-yu","middleName":"","lastName":"Lin","suffix":""},{"id":504029412,"identity":"a3386658-dda1-4084-8830-cae36ab0a3b5","order_by":3,"name":"Su-ling Shih","email":"","orcid":"","institution":"AVRDC World Vegetable Center","correspondingAuthor":false,"prefix":"","firstName":"Su-ling","middleName":"","lastName":"Shih","suffix":""},{"id":504029413,"identity":"aa559ba0-433c-43ec-8b02-8bb53f59d739","order_by":4,"name":"Srinivasan Ramasamy","email":"","orcid":"","institution":"AVRDC World Vegetable Center","correspondingAuthor":false,"prefix":"","firstName":"Srinivasan","middleName":"","lastName":"Ramasamy","suffix":""},{"id":504029414,"identity":"f4cba8a8-51a5-48f7-a33b-c6ff5fcdf4d2","order_by":5,"name":"Renukadevi Perumal","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+klEQVRIiWNgGAWjYJACxgYGZgYQYvgAFzMgUgvjjASStAABM08CfpVgYN7ee0xyRo21nMFxBrbHtj/uyBscYH74gaHgDk4tMmfOpUluOJZubHCYgd04J+GZ4YYDbMYSDAbPcGqRkMgxk3zAdjhxZjMDm3ROwmHGDQcYzIB+OYxbi/wboJZ/h+vBWiwSDttvOMD+Db8WCR4zyY1thxP4mYFaGBIOJ244wEPAFp4cY8uZfemG/cyM7YY9aYeTZx7mKZZIwKeF/YzhzZ5v1vJs/IePPfhhc9i273j7xg8f/uDWggQY2yA0KI4SiNEABGxEqhsFo2AUjIKRBgAbzU2WsR3mTgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0001-9665-1681","institution":"Tamil Nadu Agricultural University","correspondingAuthor":true,"prefix":"","firstName":"Renukadevi","middleName":"","lastName":"Perumal","suffix":""},{"id":504029415,"identity":"78e0a651-b35b-4c71-b801-4dc3828cd074","order_by":6,"name":"Ricardo Oliva","email":"","orcid":"","institution":"Alliance of Bioversity International and CIAT: Alliance of Bioversity International and International Center for Tropical Agriculture","correspondingAuthor":false,"prefix":"","firstName":"Ricardo","middleName":"","lastName":"Oliva","suffix":""},{"id":504029416,"identity":"d887b900-4a15-499e-b42c-207f67c5a883","order_by":7,"name":"Hao-wen Cheng","email":"","orcid":"","institution":"AVRDC World Vegetable Center","correspondingAuthor":false,"prefix":"","firstName":"Hao-wen","middleName":"","lastName":"Cheng","suffix":""}],"badges":[],"createdAt":"2025-08-19 01:52:25","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7403472/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7403472/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":90293163,"identity":"bd2a3506-05f5-46c5-acea-a0630e4365df","added_by":"auto","created_at":"2025-09-01 07:40:11","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":94075,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSymptoms of pepper veinal mottle virus (PVMV Tom1 and PVMV EP1) and visualization of PVMV\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003e \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003efragments via gel electrophoresis: \u003c/strong\u003ea) Severe leaf blighting in PVMV Tom1 inoculated tomato on 28\u003csup\u003eth\u003c/sup\u003e DPI b) Necrotic spots in PVMV EP1 inoculated tomato on 28\u003csup\u003eth\u003c/sup\u003e DPI c) Lane M- 1 kb Ladder; Lane 1 to Lane 4 – PVMV inoculated samples amplified at ~480bp\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/fc6167669a2802beded2f24a.jpg"},{"id":90293167,"identity":"0530abd5-13be-4b53-9a3f-f6873e121564","added_by":"auto","created_at":"2025-09-01 07:40:12","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":163285,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSymptoms observed on various hosts inoculated with PVMV Tom1 at 28 DPI: \u003c/strong\u003eThis figure illustrates the host range results for PVMV Tom1 observed on the 28\u003csup\u003eth\u003c/sup\u003e day after inoculation. 2(a)\u003cem\u003e Solanum lycopersicum\u003c/em\u003e (severe mosaic with necrotic spots), (b)\u003cem\u003e Solanum lycopersicum\u003c/em\u003e (severe mosaic with necrotic spots), (c) \u003cem\u003eSolanum lycopersicum\u003c/em\u003e (no visible symptoms), (d) \u003cem\u003eCapsicum annuum\u003c/em\u003e (mild mottle with slight leaf distortion), \u0026nbsp;(e) \u003cem\u003eCapsicum frutescens\u003c/em\u003e (mild mottle with leaf curling), (f) \u003cem\u003eCapsicum chinense\u003c/em\u003e (very mild mottle), (g) \u003cem\u003eCucumis sativus L.\u003c/em\u003e (no visible symptoms), (h) \u003cem\u003eLuffa aegyptiaca\u003c/em\u003e (no visible symptoms), (i) \u003cem\u003eMomordica charantia L.\u003c/em\u003e (no visible symptoms), (j)\u003cem\u003e Abelmoschus esculentus\u003c/em\u003e (no visible symptoms), (k) \u003cem\u003eVigna unguiculata\u003c/em\u003e (very mild mottle), (l) \u003cem\u003eVigna radiata\u003c/em\u003e (necrotic spots), (m) \u003cem\u003eVigna radiata\u003c/em\u003e (no visible symptoms), (n) \u003cem\u003eVigna mungo\u003c/em\u003e (no visible symptoms), (o) \u003cem\u003eNicotiana rustica\u003c/em\u003e (mild mottle), (p) \u003cem\u003eN. tabacum white burley\u003c/em\u003e (no visible symptoms), (q)\u003cem\u003e N. tabacum var. Xanthi\u003c/em\u003e (no visible symptoms), (r) \u003cem\u003eChenopodium quinoa\u003c/em\u003e (chlorotic spots), (s) \u003cem\u003eC. amaranticolor\u003c/em\u003e (necrotic spots), (t) \u003cem\u003eDatura metel\u003c/em\u003e (mild mottle).\u003c/p\u003e","description":"","filename":"2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/a059b6067f7bd9147b283837.jpg"},{"id":90293136,"identity":"8d03ca76-f48f-443b-bef0-052c8e265aec","added_by":"auto","created_at":"2025-09-01 07:40:05","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":151078,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSymptoms observed on various hosts inoculated with PVMV EP1 at 28 DPI:\u003c/strong\u003e This figure shows the host range results for PVMV Pep1 observed on the 28th day after inoculation. 3(a) \u003cem\u003eSolanum lycopersicum\u003c/em\u003e (very mild mottle with necrotic spot), (b) \u003cem\u003eSolanum lycopersicum\u003c/em\u003e (very mild mottle), (c) \u003cem\u003eSolanum lycopersicum\u003c/em\u003e (no visible symptoms),\u003cem\u003e \u003c/em\u003e(d)\u003cem\u003e Capsicum chinense\u003c/em\u003e (mild mottle), (e)\u003cem\u003e Capsicum frutescens\u003c/em\u003e (mild mottle with leaf curling), (f)\u003cem\u003e Capsicum annuum\u003c/em\u003e(mild mottle with slight leaf distortion), (g) \u003cem\u003eCucumis sativus L.\u003c/em\u003e (no visible symptoms), (h) \u003cem\u003eLuffa aegyptiaca\u003c/em\u003e (no visible symptoms), (i) \u003cem\u003eMomordica charantia L.\u003c/em\u003e (no visible symptoms), (j) \u003cem\u003eAbelmoschus esculentus\u003c/em\u003e (no visible symptoms), (k) \u003cem\u003eVigna unguiculata\u003c/em\u003e (no visible symptoms), (L) \u003cem\u003eVigna radiata\u003c/em\u003e (no visible symptoms), (m) \u003cem\u003eVigna radiata\u003c/em\u003e (no visible symptoms), (n) \u003cem\u003eVigna mungo\u003c/em\u003e (no visible symptoms), (o)\u003cem\u003e Nicotiana rustica\u003c/em\u003e (mild mottle), (p) \u003cem\u003eN. tabacum white burley\u003c/em\u003e (no visible symptoms), (q)\u003cem\u003e N. tabacum var. Xanthi\u003c/em\u003e(no visible symptoms), (r) \u003cem\u003eChenopodium quinoa\u003c/em\u003e (chlorotic spots), (s) \u003cem\u003eC. amaranticolor\u003c/em\u003e (necrotic spots), (t)\u003cem\u003e Datura metel\u003c/em\u003e (mild mottle).\u003c/p\u003e","description":"","filename":"3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/6b213f71166eba33888fca7d.jpg"},{"id":90293142,"identity":"a264cb0f-689a-4278-9dbc-19d30eaf30f0","added_by":"auto","created_at":"2025-09-01 07:40:07","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":165701,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNucleotide identity comparison of PVMV isolates using SDT 2.0: \u003c/strong\u003eThe heatmap compares PVMV strains Tom1 and EP1 with 25 global isolates. The color gradient represents nucleotide identity percentages, with red (\u0026gt;90%) indicating the highest similarity and blue (\u0026lt;60%) indicating the lowest similarity.\u003c/p\u003e","description":"","filename":"4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/daeae6d319c4be7c5c4cbe70.jpg"},{"id":90293141,"identity":"adf8e245-7d7d-497f-a4f2-7df007430965","added_by":"auto","created_at":"2025-09-01 07:40:06","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":106476,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePhylogenetic relationship of PVMV isolates: \u003c/strong\u003ePhylogenetic tree of PVMV isolates constructed using MEGA version 11.0 and visualized with iTOL version 6.\u003c/p\u003e","description":"","filename":"5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/6d6305b696b3e3c8a0a5264b.jpg"},{"id":90293165,"identity":"d9722f7a-761c-4cc3-b322-85c309d5b8d3","added_by":"auto","created_at":"2025-09-01 07:40:12","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":76496,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eMapping of amino acid variations by hydrophobicity and charge\u003c/strong\u003e: Amino acid differences are indicated with each coloured according to physicochemical properties: green for hydrophobic (non-polar), blue for polar (uncharged), yellow for positively charged (basic), and red for negatively charged (acidic) residues.\u003c/p\u003e","description":"","filename":"6.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/7ed8fa29ccc48f01c37a5280.jpg"},{"id":91917211,"identity":"30c71166-ac60-4e6c-9016-29ad82694019","added_by":"auto","created_at":"2025-09-23 00:56:10","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2435238,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/5eec8455-3f09-4e25-83e8-305bf1a6b088.pdf"},{"id":90293556,"identity":"95148ddb-615a-40d9-a0e0-ee5cc38ec28e","added_by":"auto","created_at":"2025-09-01 07:48:09","extension":"docx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":20576,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementaryfiles.docx","url":"https://assets-eu.researchsquare.com/files/rs-7403472/v1/7e8fe101883c3c6a5bfd555a.docx"}],"financialInterests":"","formattedTitle":"Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003eTomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e) is one of the most important vegetable crops in the \u003cem\u003eSolanaceae\u003c/em\u003e family, ranking as the ninth most cultivated crop globally [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. According to the Food and Agriculture Organization [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e], global tomato production was valued at approximately USD 19.5\u0026nbsp;billion in 2024. In Taiwan, tomatoes are grown on about 4,100 hectares, yielding 98,340 tons and contributing around USD 141\u0026nbsp;million to the national economy (Council of Agriculture, Executive Yuan) [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e].\u003c/p\u003e\u003cp\u003ePepper (\u003cem\u003eCapsicum\u003c/em\u003e spp.), another major solanaceous crop, is widely cultivated in tropical and subtropical regions and is highly susceptible to several viral diseases, including \u003cem\u003epepper veinal mottle virus\u003c/em\u003e (PVMV). According to ICTV (2024), PVMV has been renamed as \u003cb\u003ePotyvirus capsivenae\u003c/b\u003e [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e], a member of the \u003cem\u003ePotyvirus\u003c/em\u003e genus within the \u003cem\u003ePotyviridae\u003c/em\u003e family, is recognized for its aggressiveness in pepper, resulting in severe symptoms and substantial yield losses [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. \u003cem\u003ePotyvirus\u003c/em\u003e species possess a monopartite, single-stranded, positive-sense RNA genome of approximately 10 kb that encodes a polyprotein, which is processed into multiple functional proteins essential for replication, movement, and suppression of host defenses [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. The virus is transmitted non-persistently by aphids and has a broad host range. Although PVMV primarily infects \u003cem\u003eCapsicum\u003c/em\u003e species, recent reports have documented its occurrence in alternative solanaceous hosts, such as tomato (\u003cem\u003eS. lycopersicum\u003c/em\u003e) and eggplant (\u003cem\u003eS. melongena\u003c/em\u003e), in regions including Taiwan. This emerging host expansion raises concerns about the virus adaptability, potential for broader transmission, and the risk it poses to tomato production. Infected tomato plants often exhibit mottling, chlorosis, and stunting, with reported yield losses of up to 50% [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Such impacts are particularly problematic in mixed cropping systems, where management becomes more complex [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eDespite its potential economic threat, the molecular characteristics, genetic variability, and pathogenicity of PVMV isolates infecting tomato remain poorly understood. To address this knowledge gap, the present study characterizes two PVMV isolates: Tom1, isolated from tomatoes and EP1, isolated from eggplants, were obtained from the Taiwan Agricultural Research Institute (TARI) and National Chung Hsing University (NCHU) and maintained at the World Vegetable Center in Taiwan. These isolates were selected based on their distinct host origins and differential symptom expression. Using full-length genome sequencing, phylogenetic analysis, and host range evaluation, this research aims to elucidate the evolutionary relationships, host-pathogen interactions, and pathogenic potential of these isolates. The findings will contribute to a better understanding of PVMV evolution and support the development of effective and sustainable management strategies for tomato cultivation in Taiwan, including the identification of potential sources of resistance for breeding programs.\u003c/p\u003e"},{"header":"2. Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003e2.1. Confirmation of PVMV isolates:\u003c/h2\u003e\u003cp\u003eSymptomatic \u003cem\u003eN. benthamiana\u003c/em\u003e leaves of two isolates of pepper veinal mottle virus (PVMV) Tom1 (from tomato) and EP1 (from eggplant) were obtained from Taiwan Agricultural Research Institute (TARI) and National Chung Hsing University (NCHU) [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e], respectively. The Tom1 isolate was maintained in tomato and \u003cem\u003eNicotiana benthamiana\u003c/em\u003e, whereas the EP1 isolate was maintained in eggplant and \u003cem\u003eN. benthamiana\u003c/em\u003e under controlled greenhouse conditions at the World Vegetable Center, Taiwan. Total RNA was extracted from infected leaf tissues using the GenMark total RNA purification kit (Cat. No.: TR02-150), following the manufacturer\u0026rsquo;s protocol. The presence of PVMV was confirmed by reverse transcription PCR (RT-PCR) using PVMV specific primers targeting the coat protein (CP) gene (Forward: 5\u0026prime;- AATGCAGGAACACAGGGGAC \u0026minus;\u0026thinsp;3\u0026prime; and Reverse: 5\u0026prime; CGCGCTAATGACATATCGGT \u0026minus;\u0026thinsp;3\u0026prime;) designed by the Virology team at the World Vegetable Center. To assess the pathogenicity of the isolates, mechanical inoculation was performed on tomato \u003cb\u003e(\u003c/b\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003cb\u003e)\u003c/b\u003e. Inoculated plants were observed for symptom development, and the virus was reconfirmed in symptomatic tissues using RT-PCR. The amplified CP gene sequences of the two isolates were submitted to the NCBI GenBank database.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e\u003ch2\u003e2.2. Host range study\u003c/h2\u003e\u003cdiv id=\"Sec5\" class=\"Section3\"\u003e\u003ch2\u003e2.2.1. Inoculation and observation\u003c/h2\u003e\u003cp\u003ePVMV isolates Tom1 and EP1 were mechanically inoculated onto 20 plant entries representing 12 species across six families. Each entry included 10 plants, while four plants per entries were maintained as healthy controls. The list of host species inoculated is provided in Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e. 1 g of infected leaf tissue was homogenized in 10 mL phosphate buffer (pH 7.0; 0.01 M Na₂HPO₄, 0.01 M KH₂PO₄) to obtain a 10% (w/v) crude sap extract. The homogenate was filtered through two layers of cheesecloth and used immediately without further dilution. The upper surface of the first two fully expanded leaves was dusted with 600-mesh carborundum, and ~\u0026thinsp;100 \u0026micro;L of inoculum was gently rubbed onto each leaf using a soft cotton swab. Mock-inoculated control plants were treated with phosphate buffer alone following the same procedure. After inoculation, leaves were rinsed with distilled water to remove excess inoculum and abrasive. Inoculated and control plants were maintained in an insect-proof greenhouse at 25\u0026ndash;30 ℃ and 50\u0026ndash;60% relative humidity, watered regularly, and fertilized every two weeks with a balanced NPK (20:20:20) fertilizer. Symptom expression was recorded at 7-day intervals post inoculation (7th, 14th, 21st, and 28th day), observations such as leaf curling, mottling, and stunting were recorded and compared with controls. Disease severity was evaluated based on percent disease incidence (PDI) following the method described by BH Wheeler [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Following symptom observation, the presence of PVMV in the affected plants was confirmed through SDT- RT-PCR, ensuring accurate identification of virus infected individuals.\u003cdiv id=\"Equa\" class=\"Equation\"\u003e\u003cdiv format=\"TEX\" class=\"mathdisplay\" id=\"FileID_Equa\" name=\"EquationSource\"\u003e\n$$\\:\\text{P}\\text{e}\\text{r}\\text{c}\\text{e}\\text{n}\\text{t}\\text{a}\\text{g}\\text{e}\\:\\text{D}\\text{i}\\text{s}\\text{e}\\text{a}\\text{s}\\text{e}\\:\\text{I}\\text{n}\\text{c}\\text{i}\\text{d}\\text{e}\\text{n}\\text{c}\\text{e}=\\frac{\\text{T}\\text{o}\\text{t}\\text{a}\\text{l}\\:\\text{n}\\text{u}\\text{m}\\text{b}\\text{e}\\text{r}\\:\\text{o}\\text{f}\\:\\text{i}\\text{n}\\text{f}\\text{e}\\text{c}\\text{t}\\text{e}\\text{d}\\:\\text{p}\\text{l}\\text{a}\\text{n}\\text{t}\\text{s}}{\\text{T}\\text{o}\\text{t}\\text{a}\\text{l}\\:\\text{n}\\text{u}\\text{m}\\text{b}\\text{e}\\text{r}\\:\\text{o}\\text{f}\\:\\text{p}\\text{l}\\text{a}\\text{n}\\text{t}\\text{s}\\:\\text{o}\\text{b}\\text{s}\\text{e}\\text{r}\\text{v}\\text{e}\\text{d}}\\:\\times\\:100$$\u003c/div\u003e\u003c/div\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec6\" class=\"Section3\"\u003e\u003ch2\u003e2.2.2. Simple Direct Tube- RT-PCR (SDT-RT-PCR) and gel electrophoresis\u003c/h2\u003e\u003cp\u003eThe leaf samples of all the 20 plant entries after 28th DPI were homogenized in 500 \u0026micro;l of 1\u0026times; PBST buffer, and the extract was incubated in PCR tubes at 37\u0026deg;C for 30 minutes[\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Tubes were washed twice with 1\u0026times; PBST and briefly spun down to remove residual buffer. cDNA was synthesized using M-MuLV Reverse Transcriptase (Invitrogen, Thermo Fisher Scientific) with a CP gene specific reverse primer following the manufacturer\u0026rsquo;s instructions. PCR amplification was subsequently carried out using Taq DNA Polymerase (Invitrogen, Thermo Fisher Scientific) with CP gene primers (Forward: 5\u0026prime;- AATGCAGGAACACAGGGGAC \u0026minus;\u0026thinsp;3\u0026prime; and Reverse: 5\u0026prime; CGCGCTAATGACATATCGGT \u0026minus;\u0026thinsp;3\u0026prime;) to amplify fragments of the PVMV genome. Thermal cycling conditions included an initial denaturation at 95\u0026deg;C, followed by 29 cycles of denaturation (95\u0026deg;C), annealing (52\u0026deg;C), and extension (72\u0026deg;C), with a final extension at 72\u0026deg;C for 5 minutes. PCR products were resolved on a 1% agarose gel prepared in 0.5x TBE buffer [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e], stained with SYBR Green, and visualized under UV illumination using a 1 kb DNA ladder. Based on the assay host studies conducted, \u003cem\u003eN. benthamiana\u003c/em\u003e was identified as suitable host to maintain both the isolates.\u003c/p\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e\u003ch2\u003e2.3. Full-length genome sequencing and analysis of PVMV isolates Tom1 and EP1\u003c/h2\u003e\u003cdiv id=\"Sec8\" class=\"Section3\"\u003e\u003ch2\u003e2.3.1. RNA extraction, cDNA synthesis and PCR amplification\u003c/h2\u003e\u003cp\u003eTotal RNA was extracted from 100 mg of fresh \u003cem\u003eNicotiana benthamiana\u003c/em\u003e leaf tissue inoculated with PVMV using the GenMark plant total RNA purification kit (catalog no. TR02-150), following the manufacturer\u0026rsquo;s protocol. Tissues were ground in liquid nitrogen and lysed in buffer containing 2-mercaptoethanol. After incubation at 60\u0026deg;C for 3 minutes and centrifugation, the lysate was processed using spin filters and ethanol precipitation. Genomic DNA was removed by DNase I treatment [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. RNA was eluted in 30\u0026ndash;50 \u0026micro;L of nuclease-free water, quantified using a NanoDrop spectrophotometer (Invitrogen, Thermo Fisher Scientific), and stored at \u0026minus;\u0026thinsp;80\u0026deg;C. cDNA synthesis was performed as described in Section 2.2.2. PCR amplification was performed using Taq DNA polymerase (Invitrogen, Thermo Fisher Scientific) and primers designed to amplify overlapping fragments of the PVMV genome. Details of primer sequences, annealing temperatures, and expected product sizes are provided in Table S2. The assembled full-length genomes of PVMV Tom1 and EP1 were each 9,796 nucleotides (nt) in length, encoding a single large open reading frame (ORF) of 9,219nt corresponding to a polyprotein of 3,073 amino acids (aa), flanked by a 5\u0026prime; untranslated region (UTR) and a 3\u0026prime; UTR followed by a poly(A) tail.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec9\" class=\"Section3\"\u003e\u003ch2\u003e2.3.3. Gel purification, cloning and sequencing\u003c/h2\u003e\u003cp\u003ePCR products were purified using the Wizard\u0026reg; SV Gel and PCR Clean-Up System (Promega) and then ligated into the pGEM\u0026reg;-T Easy Vector. Ligation mixtures were transformed into \u003cem\u003eEscherichia coli\u003c/em\u003e DH5α competent cells via heat shock and plated on LB agar containing ampicillin, IPTG, and X-Gal [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. White colonies were screened by colony PCR, and positive clones were cultured in LB broth supplemented with ampicillin. Plasmid DNA was isolated and submitted for Sanger sequencing (Genomics, Taiwan) [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eConsensus sequences were manually assembled using ApE software[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e], and gene annotation was performed using NCBI BLAST [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Each sequenced sample was submitted to the NCBI GenBank, USA, to acquire a GenBank accession number. Functional and comparative analyses were conducted using public databases, including NCBI and UniProt. Multiple sequence alignments were performed using ClustalW in BioEdit version 5.0.9. Phylogenetic trees were constructed using the Neighbor-Joining method with the Kimura 2-parameter model in MEGA version 11, with 1000 bootstrap replicates. The resulting trees were visualized and annotated using Interactive Tree of Life (iTOL) version 6. Pairwise sequence identity were assessed using two methods: (i) Sequence Demarcation Tool (SDT) (v1.2) for heatmap visualization and (2) sequence identity matrix for exact nucleotide and amino acid values. Gene-wise comparisons between PVMV Tom1 and EP1 were performed by aligning each coding region individually to determine nucleotide and amino acid identities, as well as to identify specific amino acid substitutions in functional domains[\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e].\u003c/p\u003e\u003c/div\u003e\u003c/div\u003e"},{"header":"3. Results","content":"\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003e3.1. Confirmation of PVMV isolates:\u003c/h2\u003e\u003cp\u003eIn \u003cem\u003eN. benthamiana\u003c/em\u003e, infection with both PVMV isolates produced veinal chlorosis, mild mottling and slight leaf deformation by 7\u0026ndash;8 days post inoculation (DPI). These two isolates, Tom1 (from tomato) and EP1 (from eggplant), were maintained at the World Vegetable Center, Taiwan. Total RNA extracted from \u003cem\u003eN. benthamiana\u003c/em\u003e infected plants showed high integrity and the presence of PVMV was confirmed by RT-PCR using coat protein (CP) specific primers, yielding amplicons of the expected size (~\u0026thinsp;480 bp). Mechanical inoculation of both isolates onto tomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e) resulted in isolate specific symptom expression. In Tom1 infected plants, symptoms appeared at 7\u0026ndash;8 DPI showed vein chlorosis, mild mottling and necrosis of leaves. In EP1 infected plants, symptoms appeared later 14\u0026ndash;15 DPI and were comparatively milder, consisting of moderate mottle with necrosis rarely observed. Both isolates induced symptoms at the same time in \u003cem\u003eN. benthamiana\u003c/em\u003e, but in tomato, EP1 caused delayed and milder symptoms compared to Tom1. RT-PCR analysis of symptomatic tomato leaves reconfirmed the presence of PVMV, and the pathogenicity of both isolates was proven (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The amplified coat protein gene sequences of the two isolates have been deposited in the NCBI GenBank database under the accession numbers PX119809 (PVMV Tom1) and PX119811 (PVMV EP1).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003e3.2. Host range study for PVMV isolates Tom1 and EP1\u003c/h2\u003e\u003cp\u003eThe host range study was conducted to determine the susceptibility of selected plant species to two isolates of pepper veinal mottle virus (PVMV), Tom1 and EP1. Twenty plant entries representing different species were mechanically inoculated, and symptom severity was measured using the percent disease incidence (PDI) formula, with observations recorded at 7, 14, 21, and 28 days post-inoculation (DPI). The symptom data compiled at 28 DPI were used to compare the responses of different hosts (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eHost range study for PVMV Tom1 and PVMV EP1\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"10\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c10\" colnum=\"10\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eS. No\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eCommon Name\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eScientific Name\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e\u003cp\u003ePVMV Tom1\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e\u003cp\u003ePVMV EP1\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c8\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eSymptoms observed*\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colspan=\"2\" nameend=\"c10\" namest=\"c9\"\u003e\u003cp\u003ePCR reaction**\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eNumber of plants expressed symptoms/ total number of plants inoculated\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePDI (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eNumber of plants expressed symptoms/ total number of plants inoculated\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c7\"\u003e\u003cp\u003ePDI (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c9\"\u003e\u003cp\u003ePVMV Tom1\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c10\"\u003e\u003cp\u003ePVMV EP1\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e1.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTomato\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eS. lycopersicum\u003c/em\u003e\u003c/p\u003e\u003cp\u003e(ANT22)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e6/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e60\u003c/p\u003e\u003cp\u003e(50)\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(Sm, Ns)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTomato\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eS. lycopersicum\u003c/em\u003e\u003c/p\u003e\u003cp\u003e(CLN4680F1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e6/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e60\u003c/p\u003e\u003cp\u003e(50)\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003eNs (Tom1) and Vmm (EP1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e3.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCherry tomato\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eS. lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e4.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePepper\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003cp\u003e(VC27a)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(mm, Ld)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e5.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePepper\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e\u003cp\u003e(AVPP1932)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(Vmm)- Tom1 and (mm)- EP1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e6.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePepper\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eC. frutescens\u003c/em\u003e\u003c/p\u003e\u003cp\u003e(VI040881)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(mm)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCucumber\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCucumis sativus\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLuffa\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eLuffa aegyptiaca\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e9.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eBitter gourd\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eMomordica charantia\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e10.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOkra\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eAbelmoschus esculentus\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e11.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCowpea\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eVigna ungiculata\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e6/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e60\u003c/p\u003e\u003cp\u003e(50)\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003eVmm (Tom1); NVS (EP1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e12.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGreen gram\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eVigna radiata\u003c/em\u003e (KPS 2)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003eNs (Tom1); NVS (EP 1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e13.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eGreen gram\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eVigna radiata\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e14.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eBlack gram\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eVigna mungo\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e15.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTobacco\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eNicotiana rustica\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(mm)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e16.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTobacco\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eN. tabacum white burley\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e17.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTobacco\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eN. tabacum var. Xanthi\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e0/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(NVS)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e18.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eQuinoa\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eChenopodium quinoa\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(Cs)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e19.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLambs quarters\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eC. amaranticolor\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(Ns)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e20.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eIndian thornapple\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eDatura metel\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e10/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e100\u003c/p\u003e\u003cp\u003e(90)\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e8/10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e80\u003c/p\u003e\u003cp\u003e(63)\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e(mm)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u003cp\u003e+\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e\u003cp\u003eSE(d)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e1.52\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e1.08\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e\u003cp\u003eCD (P\u0026thinsp;=\u0026thinsp;0.05)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e3.09\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e2.20\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c9\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c10\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003ctfoot\u003e\u003ctr\u003e\u003ctd colspan=\"10\"\u003eNote: Symptom severity is reported as an overall score based on observations at 7, 14, 21, 28 DPI. Abbreviations: *(mm)- Mild mottle; (Vmm)- Very mild mottle; (NVS)- No visible symptoms; (Cs)- Chlorotic spot; (Ns)- Necrotic spot; (Sm, Ns) - Severe mosaic with necrotic spots; (mm, Ld)- mild mottle with leaf distortion. **PCR reaction indicates RT-PCR confirmation of PVMV infection in symptomatic hosts\u0026thinsp;+\u0026thinsp;Positive reaction, -Negative reaction in RT-PCR.\u003c/td\u003e\u003c/tr\u003e\u003c/tfoot\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003eOut of 20 plant entries tested, 13 showed infection with at least one of the virus isolates, as confirmed by both visible symptoms and SDT- RT-PCR results. A\u0026thinsp;~\u0026thinsp;480 bp fragment specific to PVMV was amplified in infected plants, confirming the presence of the virus. \u003cem\u003eDatura metel, Nicotiana rustica, Chenopodium quinoa\u003c/em\u003e, and \u003cem\u003eChenopodium amaranticolor\u003c/em\u003e exhibited 80\u0026ndash;100% infection, characterized by clear symptoms, including mild mottling, chlorotic (yellow) spots, and necrotic (dead) spots. Both isolates infected these plants. In \u003cem\u003eSolanum lycopersicum\u003c/em\u003e, Tom1 caused severe mosaic and necrotic spots within 7 days post inoculation (DPI), reaching 100% percent disease incidence (PDI) (most prominent in this host), while EP1 induced milder mosaic symptoms around 14 DPI with a 60% PDI. Cherry tomato plants remained symptomless throughout the observation period and tested negative in SDT-RT-PCR for both isolates. All three \u003cem\u003eCapsicum\u003c/em\u003e species (\u003cem\u003eC. annuum\u003c/em\u003e, \u003cem\u003eC. chinense\u003c/em\u003e, and \u003cem\u003eC. frutescens\u003c/em\u003e) were susceptible to both isolates, with EP1 producing more pronounced leaf curling, vein clearing, and mosaic within 7 DPI (most prominent in \u003cem\u003eC. annuum\u003c/em\u003e), and Tom1 causing comparatively milder symptoms appearing around 13\u0026ndash;14 DPI. In the legume group, cowpea (\u003cem\u003eVigna unguiculata\u003c/em\u003e) and green gram variety KPS2 (\u003cem\u003eV. radiata\u003c/em\u003e) developed mild mosaic and leaf distortion within 7 DPI with a 60% PDI and tested positive only with Tom1, with cowpea showing more visible symptoms, whereas EP1 failed to infect these hosts. Green gram variety Taiwan No. 5 and black gram (\u003cem\u003eV. mungo\u003c/em\u003e) showed no symptoms and were SDT-RT-PCR negative for both isolates. Cucumber (\u003cem\u003eCucumis sativus\u003c/em\u003e L.), luffa (\u003cem\u003eLuffa aegyptiaca\u003c/em\u003e), bitter gourd (\u003cem\u003eMomordica charantia\u003c/em\u003e L.), okra (\u003cem\u003eAbelmoschus esculentus\u003c/em\u003e), and two tobacco varieties (\u003cem\u003eNicotiana tabacum\u003c/em\u003e var. white burley and var. Xanthi) showed no visible symptoms up to 28 DPI, and SDT-RT-PCR results confirmed the absence of both Tom1 and EP1(Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\u003ch2\u003e3.3. Genome organization of PVMV isolates Tom1 and EP1\u003c/h2\u003e\u003cp\u003eThe complete genome sequences for both PVMV isolates were obtained and assembled using ApE software, and annotated through NCBI BLAST. These sequences were deposited in NCBI GenBank, USA, and obtained accession numbers PV476910 (Tom1) and PV476911 (EP1). Each genome is 9,796nt in length, consisting of a 5\u0026prime; untranslated region (UTR), a single large open reading frame (ORF) of 9,219nt encoding a polyprotein of 3,073 amino acids, and a 3\u0026prime; UTR (nt 9415\u0026ndash;9796) followed by a poly(A) tail. The polyprotein is predicted to be processed into ten functional proteins characteristic of the potyvirus genus: P1 (nt 196\u0026ndash;1095), HC-Pro (1096\u0026ndash;2466), P3 (2467\u0026ndash;3498), 6K1 (3499\u0026ndash;3660), CI (3661\u0026ndash;5589), 6K2 (5590\u0026ndash;5748), VPg (5749\u0026ndash;6321), NIa-Pro (6322\u0026ndash;7047), NIb (7048\u0026ndash;8604), and CP (8605\u0026ndash;9414). In addition, the frameshift product P3N-PIPO (nt 2926\u0026ndash;3144) is encoded within the P3 region, as reported for potyviruses[\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\u003ch2\u003e3.4. Comparative sequence analysis with global PVMV isolates\u003c/h2\u003e\u003cp\u003eA comparative analysis was conducted with 18 globally reported PVMV isolates and four related potyviruses. Sequence alignment using the MUSCLE algorithm and pairwise identity analysis with the Sequence Demarcation Tool v1.2 (SDT) showed that both Tom1 and EP1 had the highest nucleotide identity (96%) with the Japanese isolate OKP2 (LC438540), followed by OKP3 (95%, LC438541) and OKC25 (94%, LC438542). Taiwanese isolates ns1 (FJ617225) and Tn (OR355467) also showed high identity (94\u0026ndash;96%), suggesting regional conservation and potential shared ancestry. In contrast, moderate identity values (74\u0026ndash;84%) were recorded with genetically distinct isolates from China (KR002568, MN082715), Nigeria (OP722584), Senegal (OK558747), and Korea (NC011918), suggesting significant divergence due to geographic and evolutionary separation. Low identities (57\u0026ndash;61%) with distantly related potyviruses such as sugarcane mosaic virus (EU091075) and Vietnam wild tomato mosaic virus (NC009744), confirm that Tom1 and EP1 belong to the same species (PVMV) but represent distinct variants according to ICTV demarcation thresholds (\u0026lt;\u0026thinsp;76%). A heatmap generated using SDT v1.2 illustrates these relationships, showing Tom1 and EP1 clustering with closely related East Asian isolates, while more divergent isolates form separate groups (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). The color gradient from red (\u0026gt;\u0026thinsp;90% identity) to blue (\u0026lt;\u0026thinsp;60% identity) visually highlights these genetic distinctions.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec15\" class=\"Section2\"\u003e\u003ch2\u003e3.5. Sequence identity matrix:\u003c/h2\u003e\u003cp\u003eThe nucleotide sequence identity between PVMV Tom1 and PVMV EP1 was 94.3%, indicating a close genetic relationship. At the amino acid level, the identity was 91.4%, indicating strong conservation in essential protein coding regions.\u003c/p\u003e\u003cp\u003eBoth Tom1 and EP1 isolates exhibited high nucleotide identity (98.0\u0026ndash;99.5%) with the Japanese isolates (LC438541 and LC438544), and amino acid identities ranged from 95.1\u0026ndash;96.4%, indicating functional stability across these isolates. The Taiwanese isolate OR355467 also exhibited high similarity, with nucleotide identities of 97.7% (Tom1) and 97.5% (EP1), and amino acid identities of 90.7% and 90.5%, respectively, indicating potential geographic and host-specific evolutionary influences. In contrast, comparison with other potyvirus species, such as chilli veinal mottle virus (ChiVMV), revealed much lower identities (67.1% nucleotide and 41.2% amino acid), underscoring significant divergence. Furthermore, PVMV isolates shared less than 50% nucleotide identity and less than 25% amino acid identity with non-potyvirus RNA viruses, confirming their distinct taxonomic placement within the potyvirus genus (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eSequence identity matrix and comparative analysis of PVMV Tom1, PVMV EP1 and related complete genomes\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"7\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eS. No.\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eGenBank accession\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eHost\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eCountry\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e\u003cp\u003eVirus-acronym\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e\u003cp\u003ePVMV (Complete genome)\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eNt (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c7\"\u003e\u003cp\u003eAA (%)\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e1.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438540\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e99.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e99.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438541\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e99.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e99.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e3.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438542\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e98.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e97.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e4.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438543\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e98.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e96.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e5.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438544\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e99.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e6.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC438545\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum frutescens\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eJapan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e98.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e96.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e7.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eFJ617225\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum nigrum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTaiwan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e97.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e96.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e8.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOR355467\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTaiwan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e97.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e95\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e9.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePV476911 (PVMV EP1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum melongena\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTaiwan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e94.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e92.1\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e10.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePV476910\u003c/p\u003e\u003cp\u003e(PVMV Tom1)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTaiwan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e94.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e92.8\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e11.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eKR002568\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eChina\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e98.2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e96.5\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e12.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eMN082715\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum chinense\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eChina\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e97.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e95.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e13.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOR355466\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTaiwan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e97.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e94.6\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e14.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOP722584\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eNigeria\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e94.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e87.6\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e15.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOK558747\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eSenegal\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e93.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e87.4\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e16.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOQ102061\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eNigeria\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e93.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e87\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e17.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eOK558746\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eSenegal\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e83.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e66.9\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e18.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNC011918\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eKorea\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003ePVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e98.5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e97.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e19.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003ePQ520507\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eEthiopia\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eEPMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e72.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e48.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e20.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNC043537\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum aethiopicum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eTanzania\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eEMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e67.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e43.8\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e21.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eMK405594\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eNicotiana tabacum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eChina\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eChiVMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e67.1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e41.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e22.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNC009744\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSolanum torvum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eLaichau\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eWTMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e64.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e39.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e23.\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eEU091075\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e\u003cem\u003eSaccharum officinarum\u003c/em\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003eMexico\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003eSCMV\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e49.7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e21.9\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec16\" class=\"Section2\"\u003e\u003ch2\u003e3.6. Phylogenetic analysis of full-length PVMV isolates\u003c/h2\u003e\u003cp\u003eA phylogenetic tree was constructed based on multiple nucleotide sequence alignments of the study isolates and 18 full-length PVMV genomes, along with three other potyviruses were retrieved from the database. The analysis revealed four major clades (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e), highlighting the evolutionary diversity of PVMV across different geographic regions and host plants.\u003c/p\u003e\u003cp\u003eClade 1 included the PVMV Tom1 isolate grouped closely with East Asian isolates from Japan (LC438540\u0026ndash;LC438545), Korea (NC011918), and China (KR002568), forming a strongly supported group suggestive of a common origin or recent introduction from this region. In clade II comprised the EP1 isolate grouped with Taiwanese isolates (OR355466, OR355467 and FJ617225), indicating regional diversification and potential local adaptation in Taiwan. Clade III consisted of West African isolates from Nigeria (OP722584, OQ102061) and Senegal (OK558746, OK558747) forming a geographically and genetically distinct lineage. Distant clustering of PMMoV (Ethiopia), ChiVMV (China and India), wild ToMV (Vietnam and China), and SCMV (Mexico) as outgroups confirmed the monophyly of PVMV and its separation from other potyviruses, consistent with ICTV species classification guidelines [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e, \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e].\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec17\" class=\"Section2\"\u003e\u003ch2\u003e3.7. Comparative nucleotide and amino acid variations between PVMV Tom1 and EP1\u003c/h2\u003e\u003cp\u003eThe coding regions of PVMV isolates Tom1 and EP1 exhibited strong nucleotide conservation across the polyprotein, with identities ranging from 97.6\u0026ndash;99.3% per gene (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). Among the structural proteins, the coat protein (CP) was highly conserved, reflecting its essential role in virion assembly and transmission. In contrast, non-structural proteins, including P1, HC-Pro, CI, and VPg, showed slightly lower nucleotide identities (97.6\u0026ndash;98.8%), suggesting localized variability that may facilitate host adaptation, viral replication efficiency, or evasion of host defense mechanisms.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eGene-wise comparison of PVMV Tom1 and EP1 isolates:\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"8\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGene\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eCoordinates (NT)*\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eCoordinates\u003c/p\u003e\u003cp\u003eAA**\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eLength (NT)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003eLength (AA)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eNotable substitutions (Tom1, EP1)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c7\"\u003e\u003cp\u003eNT identity (%)\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c8\"\u003e\u003cp\u003eAA identity (%)\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eP1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e196\u0026ndash;1095\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e1-300\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e900\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e300\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eD68E, A74V, E117G, H149R, R245K\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e97.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e96\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eHC-Pro\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1096\u0026ndash;2466\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e301\u0026ndash;850\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e1371\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e457\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eA319T, T488A, D503N,\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e97.9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e99.1\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eP3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e2467\u0026ndash;3498\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e851\u0026ndash;1140\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e1032\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e344\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eV872A, D923G, M980I, A984T, R986K\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e98.5\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e6K1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3499\u0026ndash;3660\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e1141\u0026ndash;1185\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e162\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e54\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e97.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e100\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eCI\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3661\u0026ndash;5589\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e1186\u0026ndash;1835\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e1929\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e643\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eM1200T, V1303I, V1611I, R1642P, T1667S, V1788I\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e99.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e6K2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e5590\u0026ndash;5748\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e1836\u0026ndash;1875\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e159\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e53\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003e-\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e100\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eVPg\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e5749\u0026ndash;6321\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e1876\u0026ndash;2050\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e573\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e191\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eI1886V, A1893S, K1969I, N195S, M2003V, A2008V, M2019V\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e95.8\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eNIa-Pro\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e6322\u0026ndash;7047\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2051\u0026ndash;2280\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e726\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e242\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eH2123Y, N2152I, L2153C\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e99.0\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e99.6\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eNIb\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e7048\u0026ndash;8604\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2281\u0026ndash;2795\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e1557\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e519\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eI2351T, Q2421R, V2639I\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e98.6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e98.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eCP\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e8605\u0026ndash;9414\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2796\u0026ndash;3074\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e\u003cp\u003e810\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e\u003cp\u003e270\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c6\"\u003e\u003cp\u003eS2972N, R3049Q\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c7\"\u003e\u003cp\u003e99.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c8\"\u003e\u003cp\u003e100\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003ctfoot\u003e\u003ctr\u003e\u003ctd colspan=\"8\"\u003eThe table shows genomic coordinates, lengths, amino acid (AA) positions, notable amino acid substitutions, and nucleotide (NT) and amino acid identity percentages for each predicted protein-coding region. Coordinates are based on the complete genome sequences of PVMV Tom1 (PV476910) and EP1 (PV476911).\u003c/td\u003e\u003c/tr\u003e\u003c/tfoot\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003eAt the protein level, amino acid substitutions between PVMV Tom1 and PVMV EP1 revealed multiple variations across different functional domains of the viral polyprotein. In the P1 (1-300 aa) region, which is involved in replication and host defense suppression, notable mutations include Aspartic acid (D) to Glutamic acid (E) at position 68, Alanine (A) to Valine (V) at 74th position, and Glutamic acid (E) to Glycine (G) at 117th position. Several mutations in this region involve changes in charged and polar residues, such as the conversion of Histidine (H) to Arginine (R) at position 149 and the conversion of Arginine (R) to Lysine (K) at position 245, which could impact protein interactions.\u003c/p\u003e\u003cp\u003eThe HC-Pro (301\u0026ndash;850 aa) region, crucial for RNA silencing suppression and aphid transmission, exhibits substitutions such as Alanine (A) to Threonine (T) at 319th position, Threonine (T) to Alanine (A) at 488th and Aspartic acid (D) to Asparagine (N) at 503th position. These changes could influence HC-Pro functionality in modulating host defenses. In the CI (1186\u0026ndash;1835 aa) region, which functions as an RNA helicase, mutations such as Methionine (M) to Threonine (T) at 1200th position, Arginine (R) to Proline (P) at 1642, and Threonine (T) to Serine (S) at 1667th postion were observed, possibly affecting enzymatic activity. The VPg (1876\u0026ndash;2050 aa) region, which plays a role in viral RNA binding and translation initiation, harbors mutations such as Alanine (A) to Serine (S) transition at 1893 and a Lysine (K) to Isoleucine (I) substitution at 1969, Methionine (M) to Valine (V) at positions 2003 and 2019, and Alanine (A) to Valine (V) at position 2008, possibly affecting viral genome stability. The NIa (2051\u0026ndash;2280 aa) region, responsible for polyprotein processing, contains mutations such as Asparagine (N) to Isoleucine (I) at 2152th position, Leucine (L) to Cysteine (C) at 2153 th position, which could impact protease efficiency. The NIb (2281\u0026ndash;2795 aa) region, encoding the RNA-dependent RNA polymerase, exhibits a conservative mutation from and Arginine (R) to Glycine (G) at 2612th position, Valine (V) to Isoleucine (I) at position 2639. Lastly, in the CP (2796\u0026ndash;3074 aa) region, which is essential for encapsidation and transmission, mutations such as Serine (S) to Asparagine (N) at position 2972 and Arginine (R) to Glutamine (Q) at position 3049 were observed, which could affect virion stability and host interactions (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e6\u003c/span\u003e).\u003c/p\u003e\u003c/div\u003e"},{"header":"4. Discussion","content":"\u003cp\u003ePepper veinal mottle virus (PVMV) is emerging as a significant production constraint. Infected tomato plants show mottling, chlorosis, leaf distortion and stunting, leading to yield reductions of up to 50% and compromised fruit quality, which limits marketability [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. This study provides clear molecular and phylogenetic evidence of PVMV occurrence in tomato in Taiwan and highlights the genomic distinctions between isolates Tom1 and EP1.\u003c/p\u003e\u003cp\u003eThe host range study revealed that the two isolates differ in their ability to infect specific plant species. Some plants developed strong symptoms, such as necrotic (dead) spots or chlorotic (yellow) spots, while others did not show any signs of infection. This kind of variation is common among different virus strains, and it helps us to understand how viruses spread and survive in nature [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. In assay hosts such as \u003cem\u003eChenopodium quinoa\u003c/em\u003e, \u003cem\u003eC. amaranticolor\u003c/em\u003e, \u003cem\u003eDatura metel\u003c/em\u003e, and \u003cem\u003eNicotiana rustica\u003c/em\u003e, both Tom1 and EP1 produced visible symptoms, but differences in expression were observed: Tom1 typically induced more necrotic lesions and extensive chlorosis, whereas EP1 symptoms were more localized and chlorotic. According to Hull [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e], \u003cem\u003eChenopodium\u003c/em\u003e species are commonly used for detecting viruses, because they form distinct local lesions [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eTomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e) plants developed more severe symptoms with Tom1 compared to EP1, indicating that Tom1 may be a more aggressive strain. Similar symptom variability among potyvirus isolates has been reported earlier. For example, Tomitaka and Ohshima [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e] reported that minor sequence variations in the HC-Pro and coat protein genes of turnip mosaic virus (TuMV) isolates were linked to differences in symptom severity and host specificity in Brassica species, illustrating how small genomic changes can produce distinct pathogenic profiles. Pepper plants (\u003cem\u003eCapsicum annuum\u003c/em\u003e, \u003cem\u003eC. chinense\u003c/em\u003e, \u003cem\u003eC. frutescens\u003c/em\u003e) were infected by both virus isolates, but EP1 caused more severe symptoms. This suggests that EP1 may be better adapted to infect pepper. Such differences in how well a virus strain infects a specific plant are influenced by the virus\u0026rsquo;s ability to multiply, move inside the plant, and suppress the plant\u0026rsquo;s defenses [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Some plants, such as cherry tomato, bitter gourd, okra, luffa, cucumber, and tobacco varieties, did not show any symptoms and were also negative in RT-PCR tests. These plants are likely to be non-hosts for both virus isolates. Non-host resistance is a natural way for plants to prevent viruses from infecting them, usually because the virus cannot complete its life cycle in these plants [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. The legume group showed an interesting pattern. Cowpea and green gram (KPS2) were infected only by Tom1, not by EP1. This again indicates that Tom1 has a broader ability to infect different hosts. The other legume varieties were not infected, showing the importance of testing multiple varieties when studying host range. These results are significant because they demonstrate that even strains of the same virus can exhibit distinct behaviours in different plant species. This type of knowledge helps us to understand how viruses spread and which plants might aid their survival between cropping seasons. It also helps to identify potential virus reservoirs[\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e].\u003c/p\u003e\u003cp\u003ePairwise nucleotide identity analysis showed that PVMV isolates Tom1 and EP1 shared 94\u0026ndash;96% between Tom1, EP1, and East Asian isolates from Japan (OKP2, OKP3, OKC25: LC438540\u0026ndash;LC438542) and Taiwan (ns1: FJ617225, Tn: OR355467) indicates conserved regional lineages, likely reflecting historical dispersal or shared germplasm movement, as reported for zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV) in Southeast Asia [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. In contrast, moderate identity (74\u0026ndash;84%) with isolates from China (KR002568, MN082715), Nigeria (OP722584), Senegal (OK558747), and Korea (NC011918) suggests greater diversity from evolutionary divergence or limited gene flow, similar to patterns in potato virus Y (PVY) [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe high nucleotide (94.3%) and amino acid (91.4%) identity between PVMV Tom1 and EP1 confirms their close relationship as isolates of the same species, reflecting conserved functions despite ecological or host pressures. Similar patterns occur in other potyviruses, such as ChiVMV and PepMoV, where high coding sequence similarity coexists with minor host-linked variations [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Both isolates also show strong genetic similarity (97.5\u0026ndash;99.5% nt; 90.5\u0026ndash;96.4% aa) to Japanese (LC438541, LC438544) and Taiwanese (OR355467) strains, supporting a shared East\u0026ndash;Southeast Asian lineage shaped by regional dispersal and localized evolution [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. Slightly lower amino acid than nucleotide identities indicate predominance of synonymous mutations, with non-synonymous changes contributing to strain-level diversity.\u003c/p\u003e\u003cp\u003eThe coat protein (CP) is completely conserved (99.3% nt, 100% aa identity), underscoring its essential role in encapsidation and suitability for diagnostics and phylogenetic analysis [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. In contrast, moderate variation in P1 (96%), HC-Pro (99.12%), CI (99.07%), and VPg (95.81%) likely reflects adaptation to host factors or environmental conditions, as these proteins function in proteolysis, RNA silencing suppression, replication complex formation, and host interactions[\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e, \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e].\u003c/p\u003e\u003cp\u003ePhylogenetic analysis placed Tom1 with East Asian isolates from Japan, Korea, and China, while EP1 clustered with Taiwanese strains suggesting localized adaptation or microevolution within the region. The distinct clustering of EP1 with Taiwanese isolate, despite high identity to Tom1, implies localized adaptation or microevolution driven by ecological or host-specific pressures reflecting the dynamic evolution of potyviruses influenced by hosts, vectors, and cultivation practices[\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]. West African isolates formed a separate, genetically distinct clade, mirroring diversification patterns observed in yam mosaic virus and cassava brown streak virus [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e, \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e, \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e], highlighting the role of geographic and agroecological factors on PVMV evolution.\u003c/p\u003e\u003cp\u003eThe amino acid substitutions observed between PVMV Tom1 and EP1 across multiple functional domains of the viral polyprotein suggest ongoing molecular diversification, possibly driven by host adaptation or environmental selection pressures. Notably, variations in the P1 region (96% aa identity), such as D68E, A74V, and E117G, may impact viral replication and host defense suppression, aligning with earlier findings in pepper mottle virus (PepMoV) and chilli veinal mottle virus (ChiVMV), where substitutions in the P1 domain were linked to altered host specificity and pathogenicity[\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eSimilarly, the HC-Pro region, known for its role in RNA silencing suppression and aphid transmission, exhibited mutations such as A319T and D503N, which may influence viral counter-defense mechanisms. Previous studies on zucchini yellow mosaic virus (ZYMV) and tobacco etch virus (TEV) have demonstrated that even conservative changes in HC-Pro can modulate RNA silencing suppression efficiency and systemic movement [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e, \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe CI domain, functioning as an RNA helicase, showed substitutions (e.g., M1200T, R1642P) that may affect enzymatic activity and replication fidelity. Such mutations have been associated with differential replication efficiencies in potyviruses, such as turnip mosaic virus (TuMV) [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. Changes in 6K2 and VPg may impact membrane binding and genome linkage, respectively, which are critical for replication complex formation and translation initiation[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe observed substitutions in NIa-Pro and NIb regions, including proteolytically and polymerase related sites, may modulate polyprotein processing and replication accuracy, as noted in potato virus Y (PVY) and papaya ringspot virus (PRSV)[43]. Finally, mutations in the coat protein (S2972N, R3049Q) may influence particle stability and vector transmission efficiency, as seen in watermelon mosaic virus and PRSV, where CP variation was linked to altered virulence and transmission[44]. These cumulative changes, particularly within functionally essential domains, reinforce the adaptive potential of PVMV and its evolutionary divergence, which could influence epidemiological patterns and management strategies.\u003c/p\u003e\u003cp\u003eThe differences in host range, symptom severity, and molecular variation between Tom1 and EP1 have direct implications for virus monitoring and resistance breeding. High conservation in the coat protein supports its continued use for diagnostics and phylogenetic studies, while variable regions such as P1, HC-Pro, and VPg could be targeted for studying pathogenicity mechanisms and host adaptation.\u003c/p\u003e"},{"header":"5. Conclusion","content":"\u003cp\u003eThe observed differences in host range, symptom severity, and molecular variation between PVMV Tom1 and EP1 have direct implications for virus monitoring and resistance breeding strategies. The high conservation of the coat protein supports its continued use in diagnostics and phylogenetic studies, whereas variable regions such as P1, HC-Pro, and VPg provide valuable targets for elucidating pathogenicity mechanisms and host adaptation. Sustained genomic surveillance will be critical for the early detection of novel variants and the prevention of their spread.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgement:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe author gratefully acknowledges the Taiwan Government for the fellowship support that made this research possible. We are deeply grateful to the World Vegetable Center, Shanhua, Taiwan, for providing the facilities, resources and technical assistance essential for carrying out this study. We also sincerely thank all colleagues and staff at the World Vegetable Center for their assistance, collaboration and valuable discussions that contributed to the success of this work.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll data supporting the conclusion of this article are provided within the text and supplementary material.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u0026nbsp;\u003c/strong\u003eThis work was funded by the World Vegetable Center, Taiwan, under the Golden Jubilee Year Student Research Fellowships 2024.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical approval\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDuring the study, principles of ethical and professional conduct have been followed and there were no Human participants and or Animals involvement.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDeclaration of competing interest\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthorship contribution:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eKousalya S: Performance of research experiments. Original draft preparations and Formal analysis; Hao-wen Cheng: Investigation, Methodology, Development, Conceptualization, Supervison and Contribution to research execution; Li-mei Lee, Shang Yu, Su-lin Shih: Methodology, Resources; Ricardo oliva: Resources, Supervision and Contribution to research execution; Renukadevi: Conceptualization, Supervision; Srinivasan Ramasamy: Resources and Facilitation of research activities\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAno CU, Ochwo-Ssemakula M, Ibanda A, Ozimati A, Gibson P, Onyeka J, et al. 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Despite its economic importance, studies on the genomic characterization and host range of PVMV isolates are limited. This study characterizes, through host range analysis, complete genome sequencing and comparative analysis of two PVMV isolates Tom1 (from tomato) (PV476910) and EP1 (from eggplant) (PV476911) in Taiwan. Mechanical inoculation onto 20 plant species revealed distinct host responses: Tom1 induced severe mosaic and necrotic symptoms in tomato (PDI 100%), while EP1 caused milder symptoms in tomato (PDI 60%) but higher virulence in \u003cem\u003eCapsicum\u003c/em\u003e species (PDI 100%). Full-length genomes (9,796 nt each) comprised a single open reading frame encoding a 3,073 amino acid polyprotein processed into ten characteristic potyviral proteins. Sequence Demarcation Tool (SDT) and sequence identity matrix analyses showed Tom1 and EP1 share 94.3% nucleotide identity, with highest identities (96%) to Japanese (Tom1) and Taiwanese (EP1) isolates. Both clustered with East/Southeast Asian isolates, sharing only 74\u0026ndash;84% identity with African isolates and \u0026lt;\u0026thinsp;61% with non-PVMV potyviruses. Phylogenetic reconstruction revealed four major clades, placing Tom1 with East Asian isolates and EP1 with Taiwanese isolates, indicating regional diversification. Gene-wise comparison showed high conservation in the coat protein (99.3% nt, 100% aa) and greater variability in non-structural proteins (P1, HC-Pro, CI, VPg), suggesting roles in host adaptation. These findings enhance understanding of PVMV genetic diversity, phylogenetic relationships, and host specificity, providing a basis for targeted resistance breeding and regional disease management strategies.\u003c/p\u003e","manuscriptTitle":"Genomic characterization and host range study of pepper veinal mottle virus (Potyvirus capsivenae) (PVMV) infecting tomato","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-01 07:38:58","doi":"10.21203/rs.3.rs-7403472/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"65c1dd66-2a2b-42f2-b418-c120f7b8ef3d","owner":[],"postedDate":"September 1st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-23T00:48:02+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-01 07:38:58","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7403472","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7403472","identity":"rs-7403472","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}