Identification and Genetic Evolution Analysis of Muscovy Duck Parvovirus in Guangdong Province

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The GD2407 strain was isolated from these samples. Genomic analysis revealed that the complete genome of GD2407 is 5067 bp in length, encoding both non-structural (NS) and structural proteins (VP). Identity analysis demonstrated that GD2407 shares 99.9% homology with the GDZJ1901 strain. Recombination analysis indicated that GD2407 originated from a recombination event between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV). Genetic evolution analysis showed that GD2407 is genetically closely related to GDZJ1901 but distinct from the pre-2020 prevalent GD201911 strain. These findings suggest that the circulation of MDPV in this region may contribute to illness and mortality in ducks. Figures Figure 1 Figure 2 Figure 3 Full Text Muscovy duck parvovirus (MDPV), a member of the Dependoparvovirus genus within the Parvovirinae subfamily, is a significant pathogen primarily affecting Muscovy ducklings under three weeks of age. MDPV infection is characterized by severe clinical symptoms, including growth retardation, diarrhea, and mortality. Notably, the virus induces pathological changes in vital organs such as the liver and pancreas. The mortality rate associated with MDPV infection can be as high as 22%-43%, underscoring its substantial impact on duckling health and production [2; 17; 20] .The virus was first identified in China and has subsequently been reported in several countries, including the United States, France, and Japan. This widespread distribution poses a significant threat to the global waterfowl industry [3; 4; 13; 20] .Although vaccination has demonstrated the potential to partially mitigate the incidence of MDPV infection, this acute infectious disease continues to pose a significant challenge to the waterfowl farming industry. The MDPV genome is a single-stranded linear DNA molecule, approximately 5 kb in length, and is characterized by the presence of inverted terminal repeats (ITRs) at both ends. The genome encompasses two major open reading frames (ORFs). The left ORF encodes the non-structural proteins NS1 and NS2, which share a common stop codon. These proteins are pivotal in facilitating viral DNA replication and regulating gene expression. The right ORF harbors the VP gene, which is responsible for encoding the viral capsid proteins. The VP proteins constitute essential structural components of the virus particle and play a critical role in eliciting an immune response within the host [7; 10; 14] . The VP gene is further subdivided into three distinct capsid proteins: VP1, VP2, and VP3. Among these, VP3 serves as the predominant capsid protein, constituting approximately 80% of the total capsid protein content [6; 21] .Notably, genetic recombination has been observed between Goose Parvovirus (GPV) and MDPV, which can potentially lead to the emergence of novel viral variants with altered pathogenicity and host range [8; 11; 16; 19; 22] . Analyzing such recombination events is crucial for gaining insights into viral evolution and for developing effective disease prevention and control strategies [12] . This study was conducted from 2020 to 2023 across multiple duck farms in Foshan and its surrounding areas, Guangdong, China. We collected 137 liver tissue samples from deceased Muscovy ducks displaying symptoms such as diarrhea, respiratory distress, anorexia, and lameness. Necropsy findings included swollen and friable livers with white necrotic foci in the pancreas, as well as inflammatory changes, hemorrhage, and sloughing of the intestinal mucosa. The samples were promptly placed in sterile containers, transported on ice to the laboratory, and processed under biosafety level 2 conditions. They were dissected into smaller pieces and stored at -80℃ for subsequent analysis. The collected organ tissues were minced and transferred into 2 ml centrifuge tubes, with 1 ml of PBS buffer added to each tube. The samples were homogenized using a tissue grinder for 2-5 minutes and then centrifuged at 5000 rpm for 10 minutes. The supernatant was carefully transferred into new 1.5 ml centrifuge tubes. For viral DNA extraction, 200 µL of supernatant was collected from each sample and processed using the FastPure® Viral DNA/RNA Mini Kit (Vazyme Biotech Co., Ltd., Nanjing, China) according to the manufacturer's protocol. The extracted DNA was eluted in 50 µL of elution buffer and stored at -20℃ for further analysis. To confirm the presence of MDPV in the collected samples, a real-time quantitative PCR (qPCR) assay was performed using SYBR Green chemistry. Primers specific for MDPV were designed based on publicly available MDPV gene sequences in GenBank using Primer Premier 5 software. The primers, designated as YG-MDPV-F1 (5'-GGGAGGAGCTAGAGGAGATATT-3') and YG-MDPV-R1 (5'-CATAGCACAGCGTACCTGATAG-3'), were synthesized to amplify a 131-base pair (bp) fragment of the MDPV genome. This fragment spans nucleotide positions 2070 to 2200. The qPCR reaction mixture consisted of 10 µL of 2× qPCR premix, 1 µL of each primer (YG-MDPV-F1 and YG-MDPV-R1), 4 µL of template DNA, and 4 µL of nuclease-free water, totaling 20 µL. The amplification program was set as follows: an initial denaturation step at 95℃ for 3 min, followed by 40 cycles of denaturation at 95℃ for 5 s and annealing/extension at 60℃ for 20 s.Viral DNA was extracted from the samples using the HiPure Viral DNA Kit (Magen，China). Subsequently, the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme Biotech Co., Ltd. China) was employed to construct DNA libraries from the extracted samples. These libraries were then subjected to high-throughput sequencing on the Illumina HiSeq 2500 platform to obtain the viral genome sequence information. Following sequencing, the raw sequencing reads were processed through quality control and filtering using the fastp software. The filtered reads were assembled into the complete viral genome sequence using Megahit.For genetic analysis, homology analysis of the nucleotide and amino acid sequences of NS and VP genes from 34 MDPV strains in GenBank was performed using DNAStar software. Recombination analysis of the MDPV genome was conducted using RDP4 and SimPlot. Phylogenetic analysis was performed using the Neighbor-Joining method in the MEGA11 software package. Real-time PCR assays were performed on 137 samples using MDPV-specific primers. The qPCR results indicated that 6 out of 137 samples detected positive for MDPV, corresponding to an infection rate of 4.38% (6/137). This finding confirms the presence of MDPV in the analyzed samples.The complete genome sequence of a novel viral strain GD2407 was successfully determined by metagenomic sequencing and assembly of MDPV positive samples, and submitted to GenBank (Accession Number: PQ820738).The GD2407 genome consists of 5067 bp and includes both the complete NS and VP genes. The NS gene, spanning 1884 bp, encodes two non-structural proteins: NS1 (1884 bp) and NS2 (1356 bp). The VP gene, comprising 2199 bp, encodes the structural proteins of the viral particle, including VP1 (2199 bp), VP2 (1764 bp), and VP3 (1605 bp). A systematic genomic alignment was executed through pairwise comparison of the Muscovy duck parvovirus (MDPV) strain GD2407 (PQ820738) whole-genome sequence against 34 reference avian parvovirus genomes curated from GenBank (Table 1). This analysis demonstrated complete genome sequence identities ranging from 85.0% to 99.9% between GD2407 and comparator strains. Notably, GD2407 exhibited maximum genomic congruence (99.9%) with the MDPV strain GDZJ1901 (MN824419), while displaying substantial divergence (85.0%) from the goose parvovirus (GPV) strain SYG61v (KC996729).The NS gene of GD2407 (PQ820738) showed high homology with several MDPV isolates, including 99.8% identity with Guangdong's GDZJ1901 (MN824419), 99.7% with Fujian's M8 (KR029614), 99.6% with Shanghai's SAAS-SHNH (KC171936), and 99.5% with Anhui's AH1401 (MH807445). Comprehensive pairwise alignment analysis identified GPV strain SYG61v (KC996729) as having the lowest homology with GD2407 (PQ820738), exhibiting only 81.9% identity in the NS gene sequence. This represents the lowest conservation level observed across all analyzed parvovirus lineages. For the VP gene, GD2407 (PQ820738) showed remarkably high sequence identity with Fujian M8 (KR029614; 99.9%), Guangdong GDZJ1901 (MN824419; 99.9%), and Guangdong GDNX (MH204100; 99.7%). Conversely, the lowest identity was observed with GPV strain SYG61v (KC996729; 87.9%), followed by MDPV strains FZ91-30 (KT865605) and P (KU844281) at 89.0% identity.Notably, the high identity of GD2407(PQ820738) with Guangdong's pathogenic GD201911 (MT450871) at 99.6% and with GDZJ1901 (MN824419) at 99.9% [11] . Phylogenetic analysis positioned GD2407 in a distinct evolutionary clade, showing maximal genetic distance from GPV SYG61v (KC996729). Within the DPV/MDPV cluster, GD2407 demonstrated significant divergence from the Fujian FJM5 isolate (KR075689), suggesting potential regional evolutionary patterns (Figure 1).A phylogenetic analysis of the VP gene, conducted to validate these results, yielded consistent outcomes, further confirming the close evolutionary link between GD2407(PQ820738) and GDZJ1901(MN824419)(Figure 2).Through complete genome recombination screening against 34 parvovirus references (Table 1) using SimPlot-RDP4 integration (Figure 3), we identified GD2407 (PQ820738) as a novel recombinant variant containing mosaic genomic segments from multiple MDPV/GPV lineages. The chimeric architecture features:A regulatory region recombination between Eurasian MDPV and GPV strains.A structural gene recombination event preserving MDPV backbone while incorporating GPV-derived sequences.These findings position GD2407 as an evolutionary intermediate demonstrating active cross-species parvoviral genetic exchange. Sequence alignment of NS and VP proteins from GD2407 with reference strains listed in Table 1 was conducted using the Clustal W algorithm implemented in MegAlign Pro software (version 17.2.1, DNASTAR), followed by comprehensive mutational analysis. Four characterized MDPV strains (JH10 [MH807698], LH [KY069274], GD201911 [MT450871], and YY [KX000918] exhibit differential pathogenicity in Muscovy ducks (Cairina moschata) [2; 11; 15; 18] . The JH10 strain (MH807698) demonstrated 100% mortality with acute necrotic lesions in lymphoid organs. Strain LH (KY069274) induced characteristic short beak and dwarfism syndrome accompanied by intestinal villus atrophy. GD201911 (MT450871) caused 86.7% mortality presenting with pathognomonic neurological symptoms including depression and open-mouth breathing. Notably, the YY strain (KX000918), originally isolated during the 2015 Zhejiang outbreak, showed moderate virulence with 62.5% mortality and multi-systemic hemorrhagic manifestations. Compared to these pathogenic strain, GD2407(PQ820738) has two NS protein mutations at positions 603 (F→L) and 608 (R→K). When compared to these pathogenic strains, GD2407(PQ820738) exhibited two notable mutations in the NS protein at amino acid positions 603 (F→L) and 608 (R→K) (Table 2). These pathological manifestations confirm the high virulence profile of 04Nb(DQ250134) in waterfowl. Importantly, the F603L mutation represents a conserved pathogenic marker, as evidenced by its presence in virulent strains like 04Nb(DQ250134) [5] . Furthermore, the VP protein of GD2407 (PQ820738)displayed two distinct mutations when compared to the classical MDPV-YY strain and the recombinant strain JH10(MH807698). These mutations were located at positions 42 (R→G), 490 (D→E) (Table 3). MDPV disease poses a serious threat to the poultry industry, particularly in China, causing significant economic losses in duck farming due to reduced egg production and increased mortality. In this study, we employed qPCR and metagenomic sequencing to comprehensively investigate MDPV infection in Foshan and its surrounding areas, Guangdong. Consequently, we obtained the complete genome sequence of a new MDPV strain, named GD2407(PQ820738), encompassing the full-length NS and VP gene sequences. This study provides a comprehensive analysis of the amino acid homology and mutation sites within the NS and VP genes of the MDPV strain GD2407. The results demonstrate a high degree of amino acid sequence identity between GD2407(PQ820738) and the recombinant strain GDZJ1901(MN824419), with the NS and VP regions of GD2407(PQ820738) exhibiting 99.8% and 99.9% identity with GDZJ1901(MN824419), respectively.Mutation analysis of the NS protein in GD2407 identified two notable amino acid substitutions. The first mutation, occurring at position 603, involved the substitution of phenylalanine (F) with leucine (L).This specific substitution has rarely been reported in other MDPV strains. The replacement of phenylalanine with leucine at this critical position may induce significant changes in the protein's structure and function. Such alterations could potentially impact the virus's ability to evade the host immune response, modify its virulence, or affect the efficacy of existing vaccines [9] . In the NS protein of MDPV strain GD2407(PQ820738), the amino acid at position 608 was found to have changed from arginine (R) to lysine (K). This mutation is not unique to GD2407; it is also present in nine other MDPV strains, including YY(KX000918) and FM(U22967). Although arginine and lysine are chemically similar, they have distinct biochemical properties. The impact of this amino acid change on GD2407's antigenicity and virulence needs further study. The VP protein, serving as the principal immunogenic antigen, displays significant sequence variability. In MDPV strain GD2407 (PQ820738), two critical amino acid substitutions (R42G and D489E) were identified within the VP gene.The VP gene encodes surface-exposed structural proteins, which are primary targets for neutralizing antibodies. The variability in these regions has the potential to impact the virus's antigenicity and its ability to evade the immune system. In summary, whether the amino acid mutations at the two sites observed in the VP protein of GD2407 will affect its antigenicity and the ability to evade the immune system requires further verification on our part. The MDPV GD2407(PQ820738) strain is a recombinant virus, arising from genetic recombination events involving MDPV strains YY(KX000918) and FM(U22967), as well as the GPV strain SYG61v(KC996729). Notably, the recombination in the VP3 region incorporated homologous sequences from the GPV strain. In previously reported literature, it was found that this genetic exchange may confer the ability to induce GPV-specific symptoms, such as intestinal embolism, during infection, potentially leading to increased mortality rates in young Muscovy ducks [17; 18] .Compared to previously reported recombinant strains in China, such as GDZJ1901(MN824419，prevalent in Guangdong) and JH10 (MH807698，a highly pathogenic strain in Zhejiang), the MDPV GD2407 strain exhibits distinct recombination patterns. While GDZJ1901(MN824419) and JH10(MH807698) arose from recombination between one MDPV strain (YY，KX000918) and three GPV strains (LH KY069274, the Hungarian virulent strain B GPU25749, and SYG61v KC996729), GD2407's recombination events involved two MDPV strains (YY KX000918 and FM U22967) and one GPV strain (SYG61v KC996729). The involvement of multiple MDPV and GPV strains in the recombination events of GD2407(PQ820738) may result in a more complex antigenic structure. As the virus evolves through recombination, it may acquire new antigenic properties that allow it to evade the immune response elicited by current vaccines [1] . GD2407 (PQ820738) was detected and isolated from Muscovy ducks that succumbed to illness in multiple farms around Foshan, China, between 2020 and 2023. The extended time frame of detection suggests an increasing prevalence of this strain. Phylogenetic analysis reveals that GD2407 (PQ820738) is genetically closely related to the highly virulent strain GD201911 (MT450871), which was isolated from an outbreak in Muscovy duck flocks in Yunfu City, Guangdong Province, China, in 2019. This genetic proximity indicates a potential high risk of transmission.Furthermore, amino acid mutations were identified in both the NS and VP proteins of GD2407 (PQ820738). These mutations may significantly influence the virus's pathogenicity and its strategies for immune evasion. It should be noted that the present study focused on molecular characterization rather than empirical pathogenicity evaluation. Subsequent investigations employing duck models under BSL-2 containment are required to establish clinical endpoints including mortality rates and histopathological scoring. While the epidemic potential of GD2407 (PQ820738) requires further validation, its temporal and spatial distribution, along with its genetic characteristics, underscore the necessity for heightened vigilance against the transmission risks associated with this strain. In summary, while we have successfully elucidated the genomic characteristics of the MDPV strain GD2407 (PQ820738), this knowledge alone is insufficient for the effective prevention and control of the epidemic. Given the substantial economic impact that MDPV has on the Muscovy duck industry in China, our future research will focus on conducting comprehensive pathogenicity assessments of GD2407 (PQ820738) and implementing molecular epidemiological monitoring to track its prevalence. Declarations Acknowledgments We thank Professors Chang Li at Military Veterinary Institute, Academy of Military Medical Sciences and Liang Zong Huang at School of Animal Science and Technology, Foshan University for their discussions and suggestions. Ethics Statement This study was approved by the Research Ethics Committee of the College of Life Science and Engineering, Foshan University. Experimental protocols for acquiring clinical samples were performed in strict accordance with the Chinese Regulations of Laboratory Animals. The study was conducted in accordance with the local legislation and institutional requirements. Disclosures The authors declare no conflicts of interest. Funding The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Sciences Foundation of China (32273097), Forestry Science and Technology Innovation of project in Guangdong Province (2024KJCX006), and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, P. R. China; Key Laboratory of Livestock Disease Prevention of Guangdong Province (YDWS202205). References Fan, W, Sun, Z, Shen, T, Xu, D, Huang, K, Zhou, J, Song, S, & Yan, L. (2017). Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus. Front Microbiol , 8 , 421. https://doi.org/10.3389/fmicb.2017.00421 Fu, Q, Huang, Y, Wan, C, Fu, G, Qi, B, Cheng, L, Shi, S, Chen, H, Liu, R, & Chen, Z. (2017). Genomic and pathogenic analysis of a Muscovy duck parvovirus strain causing short beak and dwarfism syndrome without tongue protrusion. Res Vet Sci , 115 , 393-400. https://doi.org/10.1016/j.rvsc.2017.07.006 Glávits, R, Zolnai, A, Szabó, E, Ivanics, E, Zarka, P, Mató, T, & Palya, V. (2005). Comparative pathological studies on domestic geese (Anser anser domestica) and Muscovy ducks (Cairina moschata) experimentally infected with parvovirus strains of goose and Muscovy duck origin. Acta Vet Hung , 53 (1), 73-89. https://doi.org/10.1556/AVet.53.2005.1.8 Jestin, V, Le Bras, M, Cherbonnel, M, Le Gall, G, & Bennejean, G. (1991). Mise en évidence de parvovirus (virus de la maladie de Derzsy) très pathogènes dans les élevages de canards de Barbarie. Rec Med Vet , 167 , 849-857. Jing, L, Zheng, K, Sheng-liang, C, Zhao-jun, F, & Tian-xian, L. (2006). Isolation and Identification of Duck Parvovirus 04Nb Strain and Sequence Analysis of rep Gene. Virologica Sinica , 21 (2), 173-177. Le Gall-Reculé, G, & Jestin, V. (1994). Biochemical and genomic characterization of muscovy duck parvovirus. Arch Virol , 139 (1-2), 121-131. https://doi.org/10.1007/bf01309459 Le Gall-Reculé, G, Jestin, V, Chagnaud, P, Blanchard, P, & Jestin, A. (1996). Expression of muscovy duck parvovirus capsid proteins (VP2 and VP3) in a baculovirus expression system and demonstration of immunity induced by the recombinant proteins. J Gen Virol , 77 ( Pt 9) , 2159-2163. https://doi.org/10.1099/0022-1317-77-9-2159 Liu, R, Chen, C, Huang, Y, Cheng, L, Lu, R, Fu, G, Shi, S, Chen, H, Wan, C, Fu, Q, & Lin, J. (2018). Microbiological identification and analysis of waterfowl livers collected from backyard farms in southern China. J Vet Med Sci , 80 (4), 667-671. https://doi.org/10.1292/jvms.17-0452 Madsen, E S, Madsen, K G, Nielsen, J, Jensen, M H, Lei, J C, & Have, P. (1997). Detection of antibodies against porcine parvovirus nonstructural protein NS1 may distinguish between vaccinated and infected pigs. Vet Microbiol , 54 (1), 1-16. https://doi.org/10.1016/s0378-1135(96)01270-9 Saliki, J T, Mizak, B, Flore, H P, Gettig, R R, Burand, J P, Carmichael, L E, Wood, H A, & Parrish, C R. (1992). Canine parvovirus empty capsids produced by expression in a baculovirus vector: use in analysis of viral properties and immunization of dogs. J Gen Virol , 73 ( Pt 2) , 369-374. https://doi.org/10.1099/0022-1317-73-2-369 Shen, H, Huang, J, Yan, Z, Yin, L, Li, Q, Zhou, Q, & Chen, F. (2020). Isolation and characterization of a recombinant Muscovy duck parvovirus circulating in Muscovy ducks in South China. Arch Virol , 165 (12), 2931-2936. https://doi.org/10.1007/s00705-020-04829-7 Simmonds, P. (2006). Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses. J Virol , 80 (22), 11124-11140. https://doi.org/10.1128/jvi.01076-06 Takehara, K, Hyakutake, K, Imamura, T, Mutoh, K, & Yoshimura, M. (1994). Isolation, identification, and plaque titration of parvovirus from Muscovy ducks in Japan. Avian Dis , 38 (4), 810-815. Tullis, G E, Burger, L R, & Pintel, D J. (1993). The minor capsid protein VP1 of the autonomous parvovirus minute virus of mice is dispensable for encapsidation of progeny single-stranded DNA but is required for infectivity. J Virol , 67 (1), 131-141. https://doi.org/10.1128/jvi.67.1.131-141.1993 Wang, J, Huang, Y, Zhou, M, & Zhu, G. (2016). Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats. Archives of virology , 161 (9), 2589-2594. Wang, J, Ling, J, Wang, Z, Huang, Y, Zhu, J, & Zhu, G. (2017). Molecular characterization of a novel Muscovy duck parvovirus isolate: evidence of recombination between classical MDPV and goose parvovirus strains. BMC Vet Res , 13 (1), 327. https://doi.org/10.1186/s12917-017-1238-6 Wang, J, Mi, Q, Wang, Z, Jia, J, Li, Y, & Zhu, G. (2020). Sole recombinant Muscovy duck parvovirus infection in Muscovy ducklings can form characteristic intestinal embolism. Vet Microbiol , 242 , 108590. https://doi.org/10.1016/j.vetmic.2020.108590 Wang, J, Wang, Z, Jia, J, Ling, J, Mi, Q, & Zhu, G. (2019). Retrospective investigation and molecular characteristics of the recombinant Muscovy duck parvovirus circulating in Muscovy duck flocks in China. Avian Pathol , 48 (4), 343-351. https://doi.org/10.1080/03079457.2019.1605145 Wang, S, Cheng, X X, Chen, S Y, Zhu, X L, Chen, S L, Lin, F Q, & Li, Z L. (2013). Genetic characterization of a potentially novel goose parvovirus circulating in Muscovy duck flocks in Fujian Province, China. J Vet Med Sci , 75 (8), 1127-1130. https://doi.org/10.1292/jvms.12-0527 Woolcock, P R, Jestin, V, Shivaprasad, H L, Zwingelstein, F, Arnauld, C, McFarland, M D, Pedersen, J C, & Senne, D A. (2000). Evidence of Muscovy duck parvovirus in Muscovy ducklings in California. Vet Rec , 146 (3), 68-72. https://doi.org/10.1136/vr.146.3.68 Zádori, Z, Stefancsik, R, Rauch, T, & Kisary, J. (1995). Analysis of the complete nucleotide sequences of goose and muscovy duck parvoviruses indicates common ancestral origin with adeno-associated virus 2. Virology , 212 (2), 562-573. https://doi.org/10.1006/viro.1995.1514 Zhu, Y, Zhou, Z, Huang, Y, Yu, R, Dong, S, Li, Z, & Zhang, Y. (2014). Identification of a recombinant Muscovy Duck parvovirus (MDPV) in Shanghai, China. Vet Microbiol , 174 (3-4), 560-564. https://doi.org/10.1016/j.vetmic.2014.10.032 Tables Tables 1 to 3 are available in the Supplementary Files section Supplementary Files renamed4a540.docx SupplementaryInformation.docx Cite Share Download PDF Status: Published Journal Publication published 29 Jul, 2025 Read the published version in Archives of Virology → Version 1 posted Editorial decision: Accept 30 Jun, 2025 Reviewers agreed at journal 22 Apr, 2025 Reviewers invited by journal 22 Apr, 2025 Editor assigned by journal 22 Apr, 2025 First submitted to journal 21 Apr, 2025 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. 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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-5792667","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":446430930,"identity":"ce351f44-8c2d-460b-9611-a664466820ce","order_by":0,"name":"Hao Liu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAz0lEQVRIiWNgGAWjYBACPmYGNhDNA+Z9MLCRI6iFDVkL44yCNGPCWhggWsCAmefD4UTCWth5zB78qDgsYy7dfOyzjQFzAgP74aMb8DuMx9yw58xhHss5x5Jn5xiw5THwpKXdIKDFTIK37TaPwY0cY+YcA55iBgkeM4JaJP+CteR/ZrYwkEhsIEaLNNQWZmYGAwNitLCVScuc+Q/UkmbM2GOQYMxGyC/8/Ie3Sb6pSLM3uJH8mOHHn/9y/OyHj+HVgsVe0pSPglEwCkbBKMAGANt4PN/QQrQrAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-7434-8697","institution":"the School of Animal Science and Technology, Foshan university","correspondingAuthor":true,"prefix":"","firstName":"Hao","middleName":"","lastName":"Liu","suffix":""},{"id":446430931,"identity":"4bc5cff0-c405-4701-a3e7-1d74052a1b94","order_by":1,"name":"Yao Qin","email":"","orcid":"","institution":"Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Yao","middleName":"","lastName":"Qin","suffix":""},{"id":446430932,"identity":"2ecd0dbc-62b0-4864-b7b1-fc727202ea1d","order_by":2,"name":"Yuan-yuan Hu","email":"","orcid":"","institution":"Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Yuan-yuan","middleName":"","lastName":"Hu","suffix":""},{"id":446430933,"identity":"9f1c447b-fef4-444c-bd8d-2f2446382640","order_by":3,"name":"Ling Zhang","email":"","orcid":"","institution":"Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Ling","middleName":"","lastName":"Zhang","suffix":""},{"id":446430934,"identity":"9f57df3b-54f0-461e-870f-a01f9de33dca","order_by":4,"name":"Xin-yu Zhang","email":"","orcid":"","institution":"Foshan University School of Life Science: Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Xin-yu","middleName":"","lastName":"Zhang","suffix":""},{"id":446430935,"identity":"6c646f64-d2ad-45c7-a35d-af82875343e0","order_by":5,"name":"Jieyu Xie","email":"","orcid":"","institution":"Foshan University School of Life Science: Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Jieyu","middleName":"","lastName":"Xie","suffix":""},{"id":446430936,"identity":"7b8d5ab8-087c-4cba-9160-54c15fd24f2b","order_by":6,"name":"Shu-ting Chen","email":"","orcid":"","institution":"Foshan University School of Life Science: Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Shu-ting","middleName":"","lastName":"Chen","suffix":""},{"id":446430937,"identity":"402ac9ff-86f7-482e-873a-fc2f68e07228","order_by":7,"name":"Jia-fan Liu","email":"","orcid":"","institution":"Foshan University School of Life Science: Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Jia-fan","middleName":"","lastName":"Liu","suffix":""},{"id":446430938,"identity":"57598bda-9b61-4d7f-8578-3c9df5f760d9","order_by":8,"name":"Lixia Li","email":"","orcid":"","institution":"Foshan University School of Life Science: Foshan University School of Life Science and Engineering","correspondingAuthor":false,"prefix":"","firstName":"Lixia","middleName":"","lastName":"Li","suffix":""}],"badges":[],"createdAt":"2025-01-09 02:55:52","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5792667/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5792667/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00705-025-06371-w","type":"published","date":"2025-07-29T16:38:15+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":81191337,"identity":"bd3facf4-fada-4e0a-ba89-bc0f605d5991","added_by":"auto","created_at":"2025-04-23 09:16:28","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":184057,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic tree for the NS gene of the MDPV.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis of 35 strains is carried out based on the nucleotide sequence of NS gene using the neighbor-joining method in MEGA 11. Bootstrap analysis with 1000 replicates.The genetic distance in nucleotide substitutions per site is shown by the scale bar. And the Bootstrap values are marked at each branch.The triangle represents the isolate GD2407.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/e197f091b89b05d742b5d865.png"},{"id":81191344,"identity":"4a68261f-ec47-49a6-9595-97e81b882709","added_by":"auto","created_at":"2025-04-23 09:16:28","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":225733,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic tree for the VP gene of the MDPV.\u003c/p\u003e\n\u003cp\u003eA phylogenetic tree of 35 strains was constructed using the neighbor-joining method based on the nucleotide sequences of the VP gene. The scale bar indicates the genetic distance in nucleotide substitutions per site, and bootstrap values are shown at each branch.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/7a93164c87fd5494e3715687.png"},{"id":81191354,"identity":"3bfab7f4-dd2a-472a-b4e1-364ae5d9dd83","added_by":"auto","created_at":"2025-04-23 09:16:29","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":291678,"visible":true,"origin":"","legend":"\u003cp\u003eMDPV isolate recombination analysis\u003c/p\u003e\n\u003cp\u003eThe X-axis showing the nucleotide position along the MDPV genome.The Y-axis indicates the amount of similarity of each reference sequence to the GD2407 query sequence.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/3e4de9e95ef2ff5d21d9f753.png"},{"id":88268440,"identity":"5d320132-e431-4959-9719-f353176867e3","added_by":"auto","created_at":"2025-08-04 16:51:43","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1054814,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/c2f9722d-7c16-4a32-972e-500301e899d9.pdf"},{"id":81192410,"identity":"676ab712-6ef2-4562-8c38-7655615f4c14","added_by":"auto","created_at":"2025-04-23 09:24:28","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":34178,"visible":true,"origin":"","legend":"","description":"","filename":"renamed4a540.docx","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/e2339a1a0eaf4bb5433c5a5c.docx"},{"id":81191335,"identity":"791e1be3-097a-40af-99ba-5fc7810c5279","added_by":"auto","created_at":"2025-04-23 09:16:28","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":25428,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryInformation.docx","url":"https://assets-eu.researchsquare.com/files/rs-5792667/v1/66ea9c2735ffa36a08643d02.docx"}],"financialInterests":"","formattedTitle":"Identification and Genetic Evolution Analysis of Muscovy Duck Parvovirus in Guangdong Province","fulltext":[{"header":"Full Text","content":"\u003cp\u003eMuscovy duck parvovirus (MDPV), a member of the \u003cem\u003eDependoparvovirus\u003c/em\u003e genus within the \u003cem\u003eParvovirinae\u003c/em\u003e subfamily, is a significant pathogen primarily affecting Muscovy ducklings under three weeks of age. MDPV infection is characterized by severe clinical symptoms, including growth retardation, diarrhea, and mortality. Notably, the virus induces pathological changes in vital organs such as the liver and pancreas. The mortality rate associated with MDPV infection can be as high as 22%-43%, underscoring its substantial impact on duckling health and production\u003csup\u003e[2; 17; 20]\u003c/sup\u003e.The virus was first identified in China and has subsequently been reported in several countries, including the United States, France, and Japan. This widespread distribution poses a significant threat to the global waterfowl industry\u003csup\u003e[3; 4; 13; 20]\u003c/sup\u003e.Although vaccination has demonstrated the potential to partially mitigate the incidence of MDPV infection, this acute infectious disease continues to pose a significant challenge to the waterfowl farming industry.\u003c/p\u003e\n\u003cp\u003eThe MDPV genome is a single-stranded linear DNA molecule, approximately 5 kb in length, and is characterized by the presence of inverted terminal repeats (ITRs) at both ends. The genome encompasses two major open reading frames (ORFs). The left ORF encodes the non-structural proteins NS1 and NS2, which share a common stop codon. These proteins are pivotal in facilitating viral DNA replication and regulating gene expression. The right ORF harbors the VP gene, which is responsible for encoding the viral capsid proteins. The VP proteins constitute essential structural components of the virus particle and play a critical role in eliciting an immune response within the host\u003csup\u003e[7; 10; 14]\u003c/sup\u003e. The VP gene is further subdivided into three distinct capsid proteins: VP1, VP2, and VP3. Among these, VP3 serves as the predominant capsid protein, constituting approximately 80% of the total capsid protein content\u003csup\u003e[6; 21]\u003c/sup\u003e.Notably, genetic recombination has been observed between Goose Parvovirus (GPV) and MDPV, which can potentially lead to the emergence of novel viral variants with altered pathogenicity and host range\u003csup\u003e[8; 11; 16; 19; 22]\u003c/sup\u003e. Analyzing such recombination events is crucial for gaining insights into viral evolution and for developing effective disease prevention and control strategies\u003csup\u003e[12]\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003eThis study was conducted from 2020 to 2023 across multiple duck farms in Foshan\u0026nbsp;and its surrounding areas, Guangdong, China. We collected 137 liver tissue samples from deceased Muscovy ducks displaying symptoms such as diarrhea, respiratory distress, anorexia, and lameness. Necropsy findings included swollen and friable livers with white necrotic foci in the pancreas, as well as inflammatory changes, hemorrhage, and sloughing of the intestinal mucosa. The samples were promptly placed in sterile containers, transported on ice to the laboratory, and processed under biosafety level 2 conditions. They were dissected into smaller pieces and stored at -80℃ for subsequent analysis. The collected organ tissues were minced and transferred into 2 ml centrifuge tubes, with 1 ml of PBS buffer added to each tube. The samples were homogenized using a tissue grinder for 2-5 minutes and then centrifuged at 5000 rpm for 10 minutes. The supernatant was carefully transferred into new 1.5 ml centrifuge tubes.\u0026nbsp;For viral DNA extraction, 200 \u0026micro;L of supernatant was collected from each sample and processed using the FastPure\u0026reg; Viral DNA/RNA Mini Kit (Vazyme Biotech Co., Ltd., Nanjing, China) according to the manufacturer\u0026apos;s protocol. The extracted DNA was eluted in 50 \u0026micro;L of elution buffer and stored at -20℃ for further analysis.\u003c/p\u003e\n\u003cp\u003eTo confirm the presence of MDPV in the collected samples, a real-time quantitative PCR (qPCR) assay was performed using SYBR Green chemistry. Primers specific for MDPV were designed based on publicly available MDPV gene sequences in GenBank using Primer Premier 5 software. The primers, designated as YG-MDPV-F1 (5\u0026apos;-GGGAGGAGCTAGAGGAGATATT-3\u0026apos;) and YG-MDPV-R1 (5\u0026apos;-CATAGCACAGCGTACCTGATAG-3\u0026apos;), were synthesized to amplify a 131-base pair (bp) fragment of the MDPV genome. This fragment spans nucleotide positions 2070 to 2200. The qPCR reaction mixture consisted of 10 \u0026micro;L of 2\u0026times;\u0026nbsp;qPCR premix, 1 \u0026micro;L of each primer (YG-MDPV-F1 and YG-MDPV-R1), 4 \u0026micro;L of template DNA, and 4 \u0026micro;L of nuclease-free water, totaling 20 \u0026micro;L. The amplification program was set as follows: an initial denaturation step at 95℃ for 3 min, followed by 40 cycles of denaturation at 95℃ for 5 s and annealing/extension at 60℃ for 20 s.Viral DNA was extracted from the samples using the HiPure Viral DNA Kit (Magen，China).\u0026nbsp;Subsequently, the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme Biotech Co., Ltd. China) was employed to construct DNA libraries from the extracted samples. These libraries were then subjected to high-throughput sequencing on the Illumina HiSeq 2500 platform to obtain the viral genome sequence information. Following sequencing, the raw sequencing reads were processed through quality control and filtering using the fastp software. The filtered reads were assembled into the complete viral genome sequence using Megahit.For genetic analysis, homology analysis of the nucleotide and amino acid sequences of NS and VP genes from 34 MDPV strains in GenBank was performed using DNAStar software. Recombination analysis of the MDPV genome was conducted using RDP4 and SimPlot. Phylogenetic analysis was performed using the Neighbor-Joining method in the MEGA11 software package.\u003c/p\u003e\n\u003cp\u003eReal-time PCR assays were performed on 137 samples using MDPV-specific primers. The qPCR results indicated that 6 out of 137 samples detected positive for MDPV, corresponding to an infection rate of 4.38% (6/137). This finding confirms the presence of MDPV in the analyzed samples.The complete genome sequence of a novel viral strain GD2407 was successfully determined by metagenomic sequencing and assembly of MDPV positive samples, and submitted to GenBank (Accession Number: PQ820738).The GD2407 genome consists of 5067 bp and includes both the complete NS and VP genes. The NS gene, spanning 1884 bp, encodes two non-structural proteins: NS1 (1884 bp) and NS2 (1356 bp). The VP gene, comprising 2199 bp, encodes the structural proteins of the viral particle, including VP1 (2199 bp), VP2 (1764 bp), and VP3 (1605 bp).\u003c/p\u003e\n\u003cp\u003eA systematic genomic alignment was executed through pairwise comparison of the Muscovy duck parvovirus (MDPV) strain GD2407 (PQ820738) whole-genome sequence against 34 reference avian parvovirus genomes curated from GenBank (Table 1). This analysis demonstrated complete genome sequence identities ranging from 85.0% to 99.9% between GD2407 and comparator strains. Notably, GD2407 exhibited maximum genomic congruence (99.9%) with the MDPV strain GDZJ1901 (MN824419), while displaying substantial divergence (85.0%) from the goose parvovirus (GPV) strain SYG61v (KC996729).The NS gene of GD2407 (PQ820738) showed high homology with several MDPV isolates, including 99.8% identity with Guangdong\u0026apos;s GDZJ1901 (MN824419), 99.7% with Fujian\u0026apos;s M8 (KR029614), 99.6% with Shanghai\u0026apos;s SAAS-SHNH (KC171936), and 99.5% with Anhui\u0026apos;s AH1401 (MH807445). Comprehensive pairwise alignment analysis identified GPV strain SYG61v (KC996729) as having the lowest homology with GD2407 (PQ820738), exhibiting only 81.9% identity in the NS gene sequence. This represents the lowest conservation level observed across all analyzed parvovirus lineages. For the VP gene, GD2407 (PQ820738) showed remarkably high sequence identity with Fujian M8 (KR029614; 99.9%), Guangdong GDZJ1901 (MN824419; 99.9%), and Guangdong GDNX (MH204100; 99.7%). Conversely, the lowest identity was observed with GPV strain SYG61v (KC996729; 87.9%), followed by MDPV strains FZ91-30 (KT865605) and P (KU844281) at 89.0% identity.Notably, the high identity of GD2407(PQ820738) with Guangdong\u0026apos;s pathogenic GD201911 (MT450871) at 99.6% and with GDZJ1901 (MN824419) at 99.9% \u003csup\u003e[11]\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis positioned GD2407 in a distinct evolutionary clade, showing maximal genetic distance from GPV SYG61v (KC996729). Within the DPV/MDPV cluster, GD2407 demonstrated significant divergence from the Fujian FJM5 isolate (KR075689), suggesting potential regional evolutionary patterns (Figure 1).A phylogenetic analysis of the VP gene, conducted to validate these results, yielded consistent outcomes, further confirming the close evolutionary link between GD2407(PQ820738) and GDZJ1901(MN824419)(Figure 2).Through complete genome recombination screening against 34 parvovirus references (Table 1) using SimPlot-RDP4 integration (Figure 3), we identified GD2407 (PQ820738) as a novel recombinant variant containing mosaic genomic segments from multiple MDPV/GPV lineages. The chimeric architecture features:A regulatory region recombination between Eurasian MDPV and GPV strains.A structural gene recombination event preserving MDPV backbone while incorporating GPV-derived sequences.These findings position GD2407 as an evolutionary intermediate demonstrating active cross-species parvoviral genetic exchange.\u003c/p\u003e\n\u003cp\u003eSequence alignment of NS and VP proteins from GD2407 with reference strains listed in Table 1 was conducted using the Clustal W algorithm implemented in MegAlign Pro software (version 17.2.1, DNASTAR), followed by comprehensive mutational analysis.\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003eFour characterized MDPV strains (JH10 [MH807698], LH [KY069274], GD201911 [MT450871], and YY [KX000918] exhibit differential pathogenicity in Muscovy ducks (Cairina moschata)\u003csup\u003e[2; 11; 15; 18]\u003c/sup\u003e. The JH10 strain (MH807698) demonstrated 100% mortality with acute necrotic lesions in lymphoid organs. Strain LH (KY069274) induced characteristic short beak and dwarfism syndrome accompanied by intestinal villus atrophy. GD201911 (MT450871) caused 86.7% mortality presenting with pathognomonic neurological symptoms including depression and open-mouth breathing. Notably, the YY strain (KX000918), originally isolated during the 2015 Zhejiang outbreak, showed moderate virulence with 62.5% mortality and multi-systemic hemorrhagic manifestations. Compared to these\u0026nbsp;pathogenic strain, GD2407(PQ820738) has two NS protein mutations at positions 603 (F\u0026rarr;L) and 608 (R\u0026rarr;K). When compared to these\u0026nbsp;pathogenic strains,\u0026nbsp;GD2407(PQ820738) exhibited two notable mutations in the NS protein at amino acid positions 603 (F\u0026rarr;L) and 608 (R\u0026rarr;K) (Table 2).\u0026nbsp;These pathological manifestations confirm the high virulence profile of 04Nb(DQ250134) in waterfowl. Importantly, the F603L mutation represents a conserved pathogenic marker, as evidenced by its presence in virulent strains like 04Nb(DQ250134)\u003csup\u003e[5]\u003c/sup\u003e.\u0026nbsp;Furthermore, the VP protein of GD2407 (PQ820738)displayed two distinct mutations when compared to the classical MDPV-YY strain and the recombinant strain JH10(MH807698). These mutations were located at positions 42 (R\u0026rarr;G), 490 (D\u0026rarr;E) (Table 3).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eMDPV disease poses a serious threat to the poultry industry, particularly in China, causing significant economic losses in duck farming due to reduced egg production and increased mortality. In this study, we employed qPCR and metagenomic sequencing to comprehensively investigate MDPV infection in Foshan and its surrounding areas, Guangdong. Consequently, we obtained the complete genome sequence of a new MDPV strain, named GD2407(PQ820738), encompassing the full-length NS and VP gene sequences. This study provides a comprehensive analysis of the amino acid homology and mutation sites within the NS and VP genes of the MDPV strain GD2407. The results demonstrate a high degree of amino acid sequence identity between GD2407(PQ820738) and the recombinant strain GDZJ1901(MN824419), with the NS and VP regions of GD2407(PQ820738) exhibiting 99.8% and 99.9% identity with GDZJ1901(MN824419), respectively.Mutation analysis of the NS protein in GD2407 identified two notable amino acid substitutions. The first mutation, occurring at position 603, involved the substitution of phenylalanine (F) with leucine (L).This specific substitution has rarely been reported in other MDPV strains. The replacement of phenylalanine with leucine at this critical position may induce significant changes in the protein\u0026apos;s structure and function. Such alterations could potentially impact the virus\u0026apos;s ability to evade the host immune response, modify its virulence, or affect the efficacy of existing vaccines\u003csup\u003e[9]\u003c/sup\u003e. In the NS protein of MDPV strain GD2407(PQ820738), the amino acid at position 608 was found to have changed from arginine (R) to lysine (K). This mutation is not unique to GD2407; it is also present in nine other MDPV strains, including YY(KX000918)\u0026nbsp;and FM(U22967). Although arginine and lysine are chemically similar, they have distinct biochemical properties. The impact of this amino acid change on GD2407\u0026apos;s antigenicity and virulence needs further study.\u003c/p\u003e\n\u003cp\u003eThe VP protein, serving as the principal immunogenic antigen, displays significant sequence variability. In MDPV strain GD2407 (PQ820738), two critical amino acid substitutions (R42G and D489E) were identified within the VP gene.The VP gene encodes surface-exposed structural proteins, which are primary targets for neutralizing antibodies. The variability in these regions has the potential to impact the virus\u0026apos;s antigenicity and its ability to evade the immune system.\u0026nbsp;In summary, whether the amino acid mutations at the two sites observed in the VP protein of GD2407 will affect its antigenicity and the ability to evade the immune system requires further verification on our part.\u003c/p\u003e\n\u003cp\u003eThe MDPV GD2407(PQ820738) strain is a recombinant virus, arising from genetic recombination events involving MDPV strains YY(KX000918)\u0026nbsp;and FM(U22967), as well as the GPV strain SYG61v(KC996729). Notably, the recombination in the VP3 region incorporated homologous sequences from the GPV strain. In previously reported literature, it was found that this genetic exchange may confer the ability to induce GPV-specific symptoms, such as intestinal embolism, during infection, potentially leading to increased mortality rates in young Muscovy ducks\u003csup\u003e[17; 18]\u003c/sup\u003e.Compared to previously reported recombinant strains in China, such as GDZJ1901(MN824419，prevalent in Guangdong) and JH10 (MH807698，a highly pathogenic strain in Zhejiang), the MDPV GD2407 strain exhibits distinct recombination patterns. While GDZJ1901(MN824419)\u0026nbsp;and JH10(MH807698) arose from recombination between one MDPV strain (YY，KX000918) and three GPV strains (LH\u0026nbsp;KY069274, the Hungarian virulent strain B\u0026nbsp;GPU25749, and SYG61v KC996729), GD2407\u0026apos;s recombination events involved two MDPV strains (YY KX000918 and FM U22967) and one GPV strain (SYG61v KC996729). The involvement of multiple MDPV and GPV strains in the recombination events of GD2407(PQ820738) may result in a more complex antigenic structure. As the virus evolves through recombination, it may acquire new antigenic properties that allow it to evade the immune response elicited by current vaccines\u003csup\u003e[1]\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003eGD2407 (PQ820738) was detected and isolated from Muscovy ducks that succumbed to illness in multiple farms around Foshan, China, between 2020 and 2023. The extended time frame of detection suggests an increasing prevalence of this strain. Phylogenetic analysis reveals that GD2407 (PQ820738) is genetically closely related to the highly virulent strain GD201911 (MT450871), which was isolated from an outbreak in Muscovy duck flocks in Yunfu City, Guangdong Province, China, in 2019. This genetic proximity indicates a potential high risk of transmission.Furthermore, amino acid mutations were identified in both the NS and VP proteins of GD2407 (PQ820738). These mutations may significantly influence the virus\u0026apos;s pathogenicity and its strategies for immune evasion. It should be noted that the present study focused on molecular characterization rather than empirical pathogenicity evaluation. Subsequent investigations employing duck models under BSL-2 containment are required to establish clinical endpoints including mortality rates and histopathological scoring. While the epidemic potential of GD2407 (PQ820738) requires further validation, its temporal and spatial distribution, along with its genetic characteristics, underscore the necessity for heightened vigilance against the transmission risks associated with this strain. In summary, while we have successfully elucidated the genomic characteristics of the MDPV strain GD2407 (PQ820738), this knowledge alone is insufficient for the effective prevention and control of the epidemic. Given the substantial economic impact that MDPV has on the Muscovy duck industry in China, our future research will focus on conducting comprehensive pathogenicity assessments of GD2407 (PQ820738) and implementing molecular epidemiological monitoring to track its prevalence.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe thank Professors Chang Li at Military Veterinary Institute, Academy of Military Medical Sciences and Liang Zong Huang at School of Animal Science and Technology, Foshan University for their discussions and suggestions.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was approved by the Research Ethics Committee of the College of Life Science and Engineering, Foshan University. Experimental protocols for acquiring clinical samples were performed in strict accordance with the Chinese Regulations of Laboratory Animals. The study was conducted in accordance with the local legislation and institutional requirements.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDisclosures\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no conflicts of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Sciences Foundation of China (32273097), Forestry Science and Technology Innovation of project in Guangdong Province (2024KJCX006), and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, P. R. China; Key Laboratory of Livestock Disease Prevention of Guangdong Province (YDWS202205).\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eFan, W, Sun, Z, Shen, T, Xu, D, Huang, K, Zhou, J, Song, S, \u0026amp; Yan, L. (2017). Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus. \u003cem\u003eFront Microbiol\u003c/em\u003e,\u003cem\u003e 8\u003c/em\u003e, 421. https://doi.org/10.3389/fmicb.2017.00421 \u003c/li\u003e\n\u003cli\u003eFu, Q, Huang, Y, Wan, C, Fu, G, Qi, B, Cheng, L, Shi, S, Chen, H, Liu, R, \u0026amp; Chen, Z. (2017). Genomic and pathogenic analysis of a Muscovy duck parvovirus strain causing short beak and dwarfism syndrome without tongue protrusion. \u003cem\u003eRes Vet Sci\u003c/em\u003e,\u003cem\u003e 115\u003c/em\u003e, 393-400. https://doi.org/10.1016/j.rvsc.2017.07.006 \u003c/li\u003e\n\u003cli\u003eGl\u0026aacute;vits, R, Zolnai, A, Szab\u0026oacute;, E, Ivanics, E, Zarka, P, Mat\u0026oacute;, T, \u0026amp; Palya, V. (2005). Comparative pathological studies on domestic geese (Anser anser domestica) and Muscovy ducks (Cairina moschata) experimentally infected with parvovirus strains of goose and Muscovy duck origin. \u003cem\u003eActa Vet Hung\u003c/em\u003e,\u003cem\u003e 53\u003c/em\u003e(1), 73-89. https://doi.org/10.1556/AVet.53.2005.1.8 \u003c/li\u003e\n\u003cli\u003eJestin, V, Le Bras, M, Cherbonnel, M, Le Gall, G, \u0026amp; Bennejean, G. (1991). Mise en \u0026eacute;vidence de parvovirus (virus de la maladie de Derzsy) tr\u0026egrave;s pathog\u0026egrave;nes dans les \u0026eacute;levages de canards de Barbarie. \u003cem\u003eRec Med Vet\u003c/em\u003e,\u003cem\u003e 167\u003c/em\u003e, 849-857. \u003c/li\u003e\n\u003cli\u003eJing, L, Zheng, K, Sheng-liang, C, Zhao-jun, F, \u0026amp; Tian-xian, L. (2006). Isolation and Identification of Duck Parvovirus 04Nb Strain and Sequence Analysis of rep Gene. \u003cem\u003eVirologica Sinica\u003c/em\u003e,\u003cem\u003e 21\u003c/em\u003e(2), 173-177. \u003c/li\u003e\n\u003cli\u003eLe Gall-Recul\u0026eacute;, G, \u0026amp; Jestin, V. (1994). Biochemical and genomic characterization of muscovy duck parvovirus. \u003cem\u003eArch Virol\u003c/em\u003e,\u003cem\u003e 139\u003c/em\u003e(1-2), 121-131. https://doi.org/10.1007/bf01309459 \u003c/li\u003e\n\u003cli\u003eLe Gall-Recul\u0026eacute;, G, Jestin, V, Chagnaud, P, Blanchard, P, \u0026amp; Jestin, A. (1996). Expression of muscovy duck parvovirus capsid proteins (VP2 and VP3) in a baculovirus expression system and demonstration of immunity induced by the recombinant proteins. \u003cem\u003eJ Gen Virol\u003c/em\u003e,\u003cem\u003e 77 ( Pt 9)\u003c/em\u003e, 2159-2163. https://doi.org/10.1099/0022-1317-77-9-2159 \u003c/li\u003e\n\u003cli\u003eLiu, R, Chen, C, Huang, Y, Cheng, L, Lu, R, Fu, G, Shi, S, Chen, H, Wan, C, Fu, Q, \u0026amp; Lin, J. (2018). Microbiological identification and analysis of waterfowl livers collected from backyard farms in southern China. \u003cem\u003eJ Vet Med Sci\u003c/em\u003e,\u003cem\u003e 80\u003c/em\u003e(4), 667-671. https://doi.org/10.1292/jvms.17-0452 \u003c/li\u003e\n\u003cli\u003eMadsen, E S, Madsen, K G, Nielsen, J, Jensen, M H, Lei, J C, \u0026amp; Have, P. (1997). Detection of antibodies against porcine parvovirus nonstructural protein NS1 may distinguish between vaccinated and infected pigs. \u003cem\u003eVet Microbiol\u003c/em\u003e,\u003cem\u003e 54\u003c/em\u003e(1), 1-16. https://doi.org/10.1016/s0378-1135(96)01270-9 \u003c/li\u003e\n\u003cli\u003eSaliki, J T, Mizak, B, Flore, H P, Gettig, R R, Burand, J P, Carmichael, L E, Wood, H A, \u0026amp; Parrish, C R. (1992). Canine parvovirus empty capsids produced by expression in a baculovirus vector: use in analysis of viral properties and immunization of dogs. \u003cem\u003eJ Gen Virol\u003c/em\u003e,\u003cem\u003e 73 ( Pt 2)\u003c/em\u003e, 369-374. https://doi.org/10.1099/0022-1317-73-2-369 \u003c/li\u003e\n\u003cli\u003eShen, H, Huang, J, Yan, Z, Yin, L, Li, Q, Zhou, Q, \u0026amp; Chen, F. (2020). Isolation and characterization of a recombinant Muscovy duck parvovirus circulating in Muscovy ducks in South China. \u003cem\u003eArch Virol\u003c/em\u003e,\u003cem\u003e 165\u003c/em\u003e(12), 2931-2936. https://doi.org/10.1007/s00705-020-04829-7 \u003c/li\u003e\n\u003cli\u003eSimmonds, P. (2006). Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses. \u003cem\u003eJ Virol\u003c/em\u003e,\u003cem\u003e 80\u003c/em\u003e(22), 11124-11140. https://doi.org/10.1128/jvi.01076-06 \u003c/li\u003e\n\u003cli\u003eTakehara, K, Hyakutake, K, Imamura, T, Mutoh, K, \u0026amp; Yoshimura, M. (1994). Isolation, identification, and plaque titration of parvovirus from Muscovy ducks in Japan. \u003cem\u003eAvian Dis\u003c/em\u003e,\u003cem\u003e 38\u003c/em\u003e(4), 810-815. \u003c/li\u003e\n\u003cli\u003eTullis, G E, Burger, L R, \u0026amp; Pintel, D J. (1993). The minor capsid protein VP1 of the autonomous parvovirus minute virus of mice is dispensable for encapsidation of progeny single-stranded DNA but is required for infectivity. \u003cem\u003eJ Virol\u003c/em\u003e,\u003cem\u003e 67\u003c/em\u003e(1), 131-141. https://doi.org/10.1128/jvi.67.1.131-141.1993 \u003c/li\u003e\n\u003cli\u003eWang, J, Huang, Y, Zhou, M, \u0026amp; Zhu, G. (2016). Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats. \u003cem\u003eArchives of virology\u003c/em\u003e,\u003cem\u003e 161\u003c/em\u003e(9), 2589-2594. \u003c/li\u003e\n\u003cli\u003eWang, J, Ling, J, Wang, Z, Huang, Y, Zhu, J, \u0026amp; Zhu, G. (2017). Molecular characterization of a novel Muscovy duck parvovirus isolate: evidence of recombination between classical MDPV and goose parvovirus strains. \u003cem\u003eBMC Vet Res\u003c/em\u003e,\u003cem\u003e 13\u003c/em\u003e(1), 327. https://doi.org/10.1186/s12917-017-1238-6 \u003c/li\u003e\n\u003cli\u003eWang, J, Mi, Q, Wang, Z, Jia, J, Li, Y, \u0026amp; Zhu, G. (2020). Sole recombinant Muscovy duck parvovirus infection in Muscovy ducklings can form characteristic intestinal embolism. \u003cem\u003eVet Microbiol\u003c/em\u003e,\u003cem\u003e 242\u003c/em\u003e, 108590. https://doi.org/10.1016/j.vetmic.2020.108590 \u003c/li\u003e\n\u003cli\u003eWang, J, Wang, Z, Jia, J, Ling, J, Mi, Q, \u0026amp; Zhu, G. (2019). Retrospective investigation and molecular characteristics of the recombinant Muscovy duck parvovirus circulating in Muscovy duck flocks in China. \u003cem\u003eAvian Pathol\u003c/em\u003e,\u003cem\u003e 48\u003c/em\u003e(4), 343-351. https://doi.org/10.1080/03079457.2019.1605145 \u003c/li\u003e\n\u003cli\u003eWang, S, Cheng, X X, Chen, S Y, Zhu, X L, Chen, S L, Lin, F Q, \u0026amp; Li, Z L. (2013). Genetic characterization of a potentially novel goose parvovirus circulating in Muscovy duck flocks in Fujian Province, China. \u003cem\u003eJ Vet Med Sci\u003c/em\u003e,\u003cem\u003e 75\u003c/em\u003e(8), 1127-1130. https://doi.org/10.1292/jvms.12-0527 \u003c/li\u003e\n\u003cli\u003eWoolcock, P R, Jestin, V, Shivaprasad, H L, Zwingelstein, F, Arnauld, C, McFarland, M D, Pedersen, J C, \u0026amp; Senne, D A. (2000). Evidence of Muscovy duck parvovirus in Muscovy ducklings in California. \u003cem\u003eVet Rec\u003c/em\u003e,\u003cem\u003e 146\u003c/em\u003e(3), 68-72. https://doi.org/10.1136/vr.146.3.68 \u003c/li\u003e\n\u003cli\u003eZ\u0026aacute;dori, Z, Stefancsik, R, Rauch, T, \u0026amp; Kisary, J. (1995). Analysis of the complete nucleotide sequences of goose and muscovy duck parvoviruses indicates common ancestral origin with adeno-associated virus 2. \u003cem\u003eVirology\u003c/em\u003e,\u003cem\u003e 212\u003c/em\u003e(2), 562-573. https://doi.org/10.1006/viro.1995.1514 \u003c/li\u003e\n\u003cli\u003eZhu, Y, Zhou, Z, Huang, Y, Yu, R, Dong, S, Li, Z, \u0026amp; Zhang, Y. (2014). Identification of a recombinant Muscovy Duck parvovirus (MDPV) in Shanghai, China. \u003cem\u003eVet Microbiol\u003c/em\u003e,\u003cem\u003e 174\u003c/em\u003e(3-4), 560-564. https://doi.org/10.1016/j.vetmic.2014.10.032 \u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp\u003eTables 1 to 3 are available in the Supplementary Files section\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5792667/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5792667/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eIn this study, we analyzed 137 liver samples collected from deceased Muscovy ducks in Guangdong, China, between 2020 and 2023. The GD2407 strain was isolated from these samples. Genomic analysis revealed that the complete genome of GD2407 is 5067 bp in length, encoding both non-structural (NS) and structural proteins (VP). Identity analysis demonstrated that GD2407 shares 99.9% homology with the GDZJ1901 strain. Recombination analysis indicated that GD2407 originated from a recombination event between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV). Genetic evolution analysis showed that GD2407 is genetically closely related to GDZJ1901 but distinct from the pre-2020 prevalent GD201911 strain. These findings suggest that the circulation of MDPV in this region may contribute to illness and mortality in ducks.\u003c/p\u003e","manuscriptTitle":"Identification and Genetic Evolution Analysis of Muscovy Duck Parvovirus in Guangdong Province","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-23 09:16:23","doi":"10.21203/rs.3.rs-5792667/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Accept","date":"2025-06-30T16:55:50+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2025-04-22T14:48:01+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-04-22T14:46:37+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-04-22T07:18:12+00:00","index":"","fulltext":""},{"type":"submitted","content":"Archives of Virology","date":"2025-04-22T00:53:46+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"fd2197a8-f37d-4893-a475-702f3ec780f9","owner":[],"postedDate":"April 23rd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-08-04T16:46:39+00:00","versionOfRecord":{"articleIdentity":"rs-5792667","link":"https://doi.org/10.1007/s00705-025-06371-w","journal":{"identity":"archives-of-virology","isVorOnly":false,"title":"Archives of Virology"},"publishedOn":"2025-07-29 16:38:15","publishedOnDateReadable":"July 29th, 2025"},"versionCreatedAt":"2025-04-23 09:16:23","video":"","vorDoi":"10.1007/s00705-025-06371-w","vorDoiUrl":"https://doi.org/10.1007/s00705-025-06371-w","workflowStages":[]},"version":"v1","identity":"rs-5792667","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5792667","identity":"rs-5792667","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}