{"paper_id":"3a3d6f27-5103-4ca3-ac16-24fc95b4e51b","body_text":"Effect of Viral Abundance and Diversity Associated with Mycoplasma hyopneumoniae on the Severity of Lung Lesions in Slaughtered Pigs: A Case-Control Study | 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 Short Report Effect of Viral Abundance and Diversity Associated with Mycoplasma hyopneumoniae on the Severity of Lung Lesions in Slaughtered Pigs: A Case-Control Study Eduarda Pereira, Meilin de Osório, Andressa Saueressig, Laura Nienow, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8426575/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 Respiratory diseases in swine are mostly infectious sources, and Mycoplasma hyopneumoniae (Mhyo) is one of the most prevalent agents in pig farms, often associated with coinfections with viruses as well as other bacteria. This interaction results in the Porcine Respiratory Disease Complex (PRDC) that can lead to significant economic losses to the swine industry. In this study, bronchial swabs were collected from 30 slaughtered pigs, divided into three groups according to the lung lesion score and Mhyo detection by PCR: Control: without lesions and Mhyo negative; Group 1: mild lesions and Mhyo positive; Group 2: severe lesions and Mhyo positive. Ten samples per group were pooled and high-throughput sequencing (HTS) was performed. The analyses revealed the presence of the viral families: Anelloviridae, Circoviridae, Parvoviridae , and Picornaviridae. The number of identified viral reads was significantly higher (11.6x) in the group with severe lung lesions and Mhyo-positive compared to the group with mild lesions and Mhyo-positive. Also, group 2 presented the highest viral diversity. No viruses were detected in samples from the group without lesions. Based on these findings, the study suggests that the presence of Mhyo in lungs at slaughter may increase the susceptibility of pigs to viral infection, resulting in severe pulmonary lesions. HTS Enzootic pneumonia PRDC Virome Figures Figure 1 Figure 2 Introduction A primary agent in swine respiratory disease is Mycoplasma hyopneumoniae (Mhyo), the etiological agent of Enzootic Pneumonia (Simionatto et al. 2013 ). This chronic bronchopneumonia affects pigs of all ages, with a high prevalence in fattening herds, and often serves as a gateway for secondary infections. These complex interactions are classified under the term Porcine Respiratory Disease Complex (PRDC) (Fablet et al. 2012 ; Przyborowska et al. 2024 ). The PRDC involves co-infections with viral pathogens such as Influenza A Virus, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), which is the primary etiological agent for several diseases and syndromes, which are collectively referred to as porcine circovirus-associated disease (PCVAD). Such co-infections lead to significant production losses through impaired growth rates, poor feed conversion, and increased mortality (Przyborowska et al. 2024 ). The intensification of swine production has led to increased animal density per facility, larger herd sizes, and a higher geographical concentration of farms (Barcellos et al , 2008). While enhancing efficiency, this intensification has concurrently elevated the risk of infectious disease outbreaks. Respiratory diseases impose substantial economic burdens by reducing daily weight gain, increasing mortality rates, and leading to condemnations at slaughter due to conditions such as pneumonia, pleurisy, and abscesses (Li et al. 2020 ). Brazil is the fourth largest swine producer, with 4983 million tons of pork in 2022 (Brazilian Animal Protein Association, 2023). Respiratory diseases such as pleurisy, pneumonia, and pleural adhesions impose major economic losses, with severe pleural lesions frequently reported in finishing pigs (Malcher et al. 2024 ). Many carcasses with pulmonary injuries are condemned by the Federal Inspection Service (SIF), impacting the production chain. Although the pathological and economic relevance of these lesions was established, the virological composition of affected lungs and their correlation with lesion severity and Mycoplasma hyopneumoniae (Mhyo) status remain unclear. This study therefore investigates the virological profile in bronchial samples from slaughtered pigs and its association with lung lesions and Mhyo PCR positivity. Methods The study was conducted in 2022 at a slaughterhouse under the Federal Inspection Service in Santa Catarina, Brazil. Thirty pig lungs were examined for pneumonic lesions, with no pleuritis observed. Bronchial swabs (Copan®, USA) were collected, stored in UTM at − 80°C, and processed for DNA/RNA extraction using the MagMax kit. Real-time PCR for Mhyo (Takeuti et al. 2017 ). Lungs were classified into three groups: Control (10 lungs, no lesions, Mhyo-negative), Group 1 (10 lungs, mild lesions in apical/cardiac lobes, Mhyo-positive), and Group 2 (10 lungs, severe lesions in multiple lobes, Mhyo-positive). Metagenomic negative control was also included in the analysis. Sample pools were vortexed, filtered (0.45 µm), and viral nucleic acids extracted with the MagMAX™ CORE kit (Applied Biosystems) on KingFisher™ Duo Prime (Thermo Fisher). cDNA synthesis used Superscript IV and NEB Q5 polymerase (Demoliner et al. 2025 ). Libraries were prepared with Illumina DNA Prep and sequenced on MiSeq (V3 600-cycle kit). Bioinformatic analysis employed Genome Detective, with quality filtering, contig assembly via CZID, and taxonomic classification using BLASTn/BLASTx. Genome Detective efficiently detects known and novel viral genomes (Vilsker et al. 2019 ). Phylogenetic analysis included sequences of PCV2 (ORF1/ORF2), Copiparvovirus ungulate 4, Iotatorquevirus suida 1b, and Teschovirus . Assemblies were mapped in Geneious Prime (v2025.0.3), aligned with MAFFT (v7), and analyzed by maximum-likelihood with ultrafast bootstrap in IQ-TREE. Trees were visualized in MEGA (v11.0.13). Following HTS, all 30 samples were tested individually by PCR using GoTaq® DNA Polymerase. Targets included Torque teno virus genogroups 1 and 2 (Segalés et al. 2009 ), porcine circovirus (Drolet et al. 2003 ) porcine parvovirus (de Menezes Cruz et al. 2016 , p. 201), and porcine teschovirus (Kuberka et al. 2024 ). Products were resolved on agarose gels, stained, visualized under UV, purified, and sequenced by Sanger for confirmation. Statistical analysis applied Chi-square tests to assess viral read distribution across Control, Group 1, and Group 2. Significance was set at p < 0.05. Individually frequencies of viral agents detected by PCR were also tested to evaluate associations between pathogens and lesion severity. The samples analyzed in this study were collected as part of a research project approved by the Animal Use Ethics Committee of the Federal University of Rio Grande do Sul (Protocol No. 39866). Results Metagenomic sequencing yielded 252,215 reads in Group 1 (mild lesions, Mhyo-positive), 260,950 reads in Group 2 (severe lesions, Mhyo-positive), and 102,250 reads in Control Group (no pulmonary lesions Mhyo-negative). CZID analysis classified sequencing reads into five viral families, including ssDNA ( Circoviridae , Parvoviridae , Anelloviridae ) and ssRNA ( Picornaviridae ). Taxonomic assembly identified in Group 1: Circovirus (6 reads), Copiparvovirus ungulate4 (8 reads), and Teschovirus (18 reads). Group 2 showed higher abundance and diversity, with Circovirus (106 reads), Copiparvovirus ungulate4 (121 reads), Porcine parvovirus 5 (24 reads), Iotatorquevirus suida1b (19 reads), and Kappatorquevirus suidaK2b (42 reads) (Fig. 1 ). Chi-square analysis showed viral reads were 11.6-fold higher in Group 2 lungs (P < 0.0001). No reads were detected in Controls, while Group 1 had 32 and Group 2 had 312 (excluding phages). Thus, viral load was significantly greater in pigs with severe pneumonia. Circoviridae : Circovirus porcine2 (PCV2) From 30 pooled bronchial swabs analyzed by HTS, 6 PCV2 reads were detected in Group 1 and 106 in Group 2. Group 1 produced a contig covering the full replicase (REP, 946 bp), showing 90.19% identity with PCV2 isolate URU31 (GenBank MF616414.1). Phylogenetic analysis clustered this REP sequence with PCV2b strains from Germany and the USA (Fig. 2 a). In Group 2, a contig spanning the complete capsid (CAP, 696 bp) was assembled, also classified as PCV2b and grouped with a Brazilian sequence (Fig. 2 b). Conventional PCR revealed a PCV frequency of 30% (3/10) of samples positive in Group 1, and 60% (6/10) in Group 2. All positive sequences were submitted to Sanger sequencing, which confirmed the presence of PCV2. There was no significant difference between mild and severe injuries regarding the frequency of reads of PCV2 (p = 0.3698). Parvoviridae : Porcine Parvovirus5 (PPV5); Copiparvovirus ungulate4 (PPV6) In Group 1, one contig of Copiparvovirus ungulate4 (PPV6) was identified, measuring 694 bp. BLASTn analysis showed 100% nucleotide identity with the Copiparvovirus ungu-late4 strain K13-8, which includes the nonstructural and capsid protein coding regions, complete CDS (GenBank accession: KX384813.1, UK/2016). In Group 2, two contigs of Porcine parvovirus 5 (PPV5) were identified. The first contig, PPV5G2a (216 bp), showed 97.09% nucleotide identity to Porcine parvovirus 5 isolate PPV5/COL/Valle511/2021, partial genome (GenBank accession: OR355614.1, Colombia/2024), corresponding to the 5′ UTR region. The second contig, PPV5G2b (171 bp), showed 99.42% identity to the PPV5 non-structural polyprotein 1 gene (complete CDS) and VP1 gene (partial CDS) from Porcine parvovirus 5 isolate RS/BR/2020 (GenBank accession: MT671979.1), corresponding to the capsid region. Additionally, a complete genome of PPV6 was assembled in Group 2, measuring 5582 bp. This genome presented the classical organization of PPV6, with ORF1 encoding the nonstructural protein NS1 (663 aa) and ORF2 (3570 nt) encoding the capsid protein VP1 (1190 amino acids). A multiple alignment was performed using PPV sequences from all known types, and a phylogenetic tree was constructed ( Fig. S1 ). The analysis con-firmed the classification of this genome as PPV6 and indicated close genetic relationships with strains previously detected in the United States. Conventional PCR performed on individual samples resulted in 5% (1/20) positive in Group 1 for PPV [PPV5 (0/10–0%), PPV6 (1/10–10%)], and resulting in 20% (4/20) positive in Group 2 for PPV [PPV5 (2/10–20%), PPV6 (2/10–20%)]. There was no significant difference between mild and severe injuries regarding the frequency of reads of PPV6 (p = 1.000) and PPV5 (p = 0.4737). Anelloviridae: Kappatorquevirus suidaK2a (TTSuVK2a); Iotatorquevirus suida1b (TTSuV1b) In Group 2, two contigs belonging to Iotatorquevirus suida 1b were identified. The first contig, designated TTSuVI1b_G2a, measured 2,883 bp and exhibited 96.94% nucleotide identity to Torque teno sus virus 1 isolate TTV1Hlj5, complete genome (GenBank accession: HM633254.1, China/2010), based on BLASTn analysis. The second contig, TTSu-VI1b_G2b (2,725 bp), showed 92.95% identity to Torque teno sus virus 1b isolate TTSuV1 P1 OK/USA, which includes complete coding sequences for ORF1, ORF2, and ORF3 proteins (GenBank accession: MW080709.1, USA/2021. Multiple sequence alignment was performed using representative genomes of TTSu-VI1a, TTSuVI1b, and TTSuVK2a. The resulting phylogenetic tree ( Fig. S2 ) confirmed the BLAST-based classification, grouping both contigs within the TTSuVI1b clade. These sequences were phylogenetically related to strains previously identified in Brazil and the United States. Additionally, a single read of Kappatorquevirus suidaK2b was detected in Group 2. This read (approximately 80 bp in length) demonstrated 100% nucleotide identity with Torque teno sus virus k2b isolate BR/RS/2008 (GenBank accession: KY742732.1). Conventional PCR revealed that 25% (5/20) of samples were positive for TTSuV1b, no samples were positive 0% (0/10) in Group 1, but in Group 2, 50% 5/10) of the samples were positive. The association among groups and outcomes is statistically significant (P = 0,0325). Picornaviridae : Teschovirus asilesi (PTV) In Group 1, a contig of Teschovirus asilesi measuring 128 bp was identified. BLASTn analysis revealed 100% nucleotide identity with Teschovirus A isolate HNMY, complete genome (GenBank accession: KX686489.1, China/2017). The contig corresponds to the 5′ untranslated region of the viral genome. A multiple sequence alignment was performed, and a phylogenetic tree was constructed ( Fig. S3 ), which confirmed the BLAST classification, grouping the sequence within the Porcine Teschovirus asilesi (PTV) cluster, alongside previously reported isolates. Conventional PCR revealed PTVA frequency resulting in 5% (1/20) positive in Group 1, 10% (1/10) of the samples were positive, while in Group 2 no positive samples were detected 0% (0/10). There was no significant difference between mild and severe injuries regarding the frequency of reads of PTV (P = 1.000). Complete and individual PCR results were included in Table 1 . In the identification column, each sample (animal) is labeled with the codes G1, G2, or G3, corresponding to their respective experimental groups. Table 1 Individual results of conventional PCRs for Teschovirus asilesi , Copiparvovirus ungulat4 , Circovirus porcine2 , Porcine parvovirus 5 and Torque teno sus virus in samples from Group 1 and 2. ID Torque teno sus virus Circovirus porcine 2 Copiparvovirus ungulate 4 Porcine parvovirus 5 Teschovirus asilesi G1 137 A Negative Negative Negative Negative Negative G1 138 B Negative Negative Negative Negative Negative G1 22 A Negative Positive Negative Negative Negative G1 24 B Negative Positive Negative Negative Negative G1 41 A Negative Negative Negative Negative Negative G1 42 A Negative Positive Negative Negative Positive G1 51 B Negative Negative Positive Negative Negative G1 55 A Negative Negative Negative Negative Negative G1 85 B Negative Negative Negative Negative Negative G1 93 B Negative Negative Negative Negative Negative G2 03 A Negative Positive Negative Positive Negative G2 08 A Positive Positive Negative Negative Negative G2 125 A Positive Negative Positive Negative Negative G2 13 A Negative Negative Positive Negative Negative G2 27 A Positive Negative Negative Positive Negative G2 35 A Positive Positive Negative Negative Negative G2 54 A Positive Positive Negative Negative Negative G2 75 A Negative Positive Negative Negative Negative G2 76 A Negative Positive Negative Negative Negative G2 77 A Negative Negative Negative Negative Negative Discussion Respiratory diseases are one of the major concerns of the pig industry. Intensive production systems, characterized by large batches in confined environments, favor the persistence and spread of pathogenic microorganisms (Drolet et al. 2003 ; de Menezes Cruz et al. 2016 ; Kuberka et al. 2024 ; Przyborowska et al. 2024 ), contributing to the occurrence of PRDC in mostly of the commercial pig farms worlwide. In this study, metagenomic analysis of bronchial swabs from three groups revealed distinct viral profiles. Group 1 (mild lesions, Mhyo-positive) showed Teschovirus asilesi, PCV2, and PPV6. Group 2 (severe lesions, Mhyo-positive) exhibited greater diversity, including PCV2, PPV5, PPV6, Iotatorquevirus suida1b, and Kappatorquevirus suidaK2b. The Control Group (no lesions, Mhyo-negative) showed no viral agents. Statistical analysis indicated viral reads were 11.6-fold higher in Group 2 than Group 1, strongly associated viral load with lesion severity. Based on conventional individual PCR, although a statistically significant difference among groups was observed only for TTSuV1b detection (P = 0.0325), with 50% positivity in Group 2 and none in Group 1, all viral agents tended to show higher frequencies in groups with severe lesions. This pattern, however, did not reach statistical significance for the other agents, possibly due to the limited sample size (n = 10 per group), which may have constrained the power to detect meaningful differences. The presence of Mhyo in both affected groups reinforces its role as a primary agent in swine respiratory tract, acting as a facilitator of viral coinfections and contributing to the progression of lung lesions. Previous studies have shown that for each 1% of increase in lung affected area, a decrease has been observed in weight or average daily gain in the finishing phase (Hill et al. 1994 ; Ferraz et al. 2020 ), suggesting that pigs coinfected with Mhyo and viruses may present reduced productive performance up to slaughter. Coinfections with Mhyo likely contribute to respiratory conditions such as pleurisy and severe pneumonia, commonly associated with multiple pathogens and classified as PRDC (Saade et al. 2020 ). Studies have shown coinfection of M. hyopneumoniae and PCV2 impacts clinical disease and performance, especially when pigs are inoculated with both pathogens (Suh et al. 2024 ). HTS detected PCV2 in both groups (Group 2: 106 reads; Group 1: 6 reads), suggesting higher viral load or replication. PCV2b was identified as the circulating genotype, with REP gene variation (90.19% identity with a Uruguayan strain) and CAP gene evidence of persistent regional variants, indicating distinct strains in South America. PCV2b infection is linked to characteristic lung lesions, including firm, non-collapsed lungs with pale consolidation, interstitial pneumonia, and bronchiolitis (Suh et al. 2024 ). PCR confirmed 30% positives in Group 1 and 60% in Group 2, consistent with HTS, indicating significant viral frequency. Detection of PCV2b in both groups confirms active circulation in Brazilian herds and highlights the need for surveillance, prevention, and vaccination strategies. The study identified PPV5 , PPV6 , TTSuV1b , TTSuVK2b , and Teschovirus asilesi , confirming their diversity and circulation in South American swine herds. PPV6 (Group 1) showed 100% identity with UK and North American strains, suggesting a conserved lineage, while PPV5 (Group 2) aligned with Colombian and Brazilian strains, indicating regional variants (Cibulski et al. 2021 ). TTSuV1b , detected only in Group 2, clustered with strains from China and the USA, suggesting co-circulation or recombination, whereas a single read of TTSuVK2b matched a Brazilian strain from 2008, indicating sporadic circulation. Teschovirus asilesi (Group 1) showed 100% identity with a Chinese strain, supporting global genomic conservation. Although PTV infections are often subclinical, some strains may cause severe neurological disease (Palmquist et al. 2002 ). Respiratory tract infections continue to represent one of the major global health challenges, ranking collectively as the fourth leading cause of death in pigs worldwide (Yu and Li 2025 ). Both humans and animals serve as reservoirs for respiratory pathogens, creating ecological niches that favor microbial adaptation, persistence, and the emergence of novel variants. Among these infections, bacterial pneumonia stands out for its high morbidity and mortality, particularly affecting vulnerable populations such as young children, the elderly, and livestock. Several viral-mediated mechanisms have been implicated in facilitating bacterial colonization and proliferation, including epithelial disruption, neuraminidase activity, exposure of platelet-activating factor receptors, and impaired innate immune responses (Saade et al. 2020 ; Yu and Li 2025 ). These interactions underscore the complexity of respiratory disease pathogenesis and reinforce the importance of integrated surveillance and control strategies across species. Our results revealed that pig lungs with severe lesions and Mhyo detection presented approximately 11.6 times more viral abundance than lungs with mild lesions and Mhyo detection, suggesting that viruses may have contributed to the extension of pneumonic lesions. The only virus that showed a statistically significant difference when samples were tested individually was TTV. Moreover, our findings indicate a highly diverse population of Anelloviridae , Circoviridae , and Parvoviridae in pig lungs. It is important to note that PCV2 was detected in both groups with lung lesions and Mhyo detection, emphasizing its circulation in finishing pigs. Declarations Author Contribution E.L.P. and M.S.S. contributed to the conceptualization of the study. Methodology and practical analysis were carried out by E.L.P., M.L.O., A.S., L.N., A.S., M.D., M.F., V.M.A.G.P., and J.S.G. Formal analysis was performed by M.S.S., L.B.S., and K.L.T. Investigation was conducted by E.L.P., M.L.O., A.S., and L.N. Writing—review and editing were performed by M.S.S., E.L.P., K.L.T., and F.R.S. Supervision was provided by M.S.S. and K.L.T. Funding acquisition was secured by M.S.S. and F.R.S. All authors reviewed and approved the final version of the manuscript. Financial Support : Universidade Feevale, CAPES, Fapergs nº 23/2551-0002221-4, CNPq nº 405786/2022-0, Ouro do Sul, INCT One. References Cibulski, S. et al. (2021) “A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil,” Virology , 552, pp. 1–9. Available at: https://doi.org/10.1016/j.virol.2020.09.005. Demoliner, M. et al. (2025) “Comparison of metagenomic protocols for virome data generation from environmental matrices and stool samples: insights into viral diversity and fecal contamination indicators,” Total Environment Microbiology , 1(2), p. 100008. Available at: https://doi.org/10.1016/j.temicr.2025.100008. Drolet, R. et al. 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(2020) “Coinfections and their molecular consequences in the porcine respiratory tract,” Veterinary Research , 51(1), p. 80. Available at: https://doi.org/10.1186/s13567-020-00807-8. Segalés, J. et al. (2009) “Retrospective study on swine Torque teno virus genogroups 1 and 2 infection from 1985 to 2005 in Spain,” Veterinary Microbiology , 134(3), pp. 199–207. Available at: https://doi.org/10.1016/j.vetmic.2008.08.002. Simionatto, S. et al. (2013) “Mycoplasma hyopneumoniae: From disease to vaccine development,” Veterinary Microbiology , 165(3), pp. 234–242. Available at: https://doi.org/10.1016/j.vetmic.2013.04.019. Suh, J., Ham, S. and Chae, C. (2024) “Divergent clinical outcomes depending on the sequential infection order of porcine circovirus type 2 and Mycoplasma hyopneumoniae,” Veterinary Microbiology , 292, p. 110060. Available at: https://doi.org/10.1016/j.vetmic.2024.110060. Takeuti, K.L. et al. (2017) “Infection dynamics and genetic variability of Mycoplasma hyopneumoniae in self-replacement gilts,” Veterinary Microbiology , 208, pp. 18–24. Available at: https://doi.org/10.1016/j.vetmic.2017.07.007. Vilsker, M. et al. (2019) “Genome Detective: an automated system for virus identification from high-throughput sequencing data,” Bioinformatics . Edited by I. Birol, 35(5), pp. 871–873. Available at: https://doi.org/10.1093/bioinformatics/bty695. Yu, E. and Li, C. (2025) “Global Trends and Attributable Risk Factors in the Disease Burden of Lower Respiratory Infections,” Tropical Medicine and Infectious Disease , 10(7), p. 180. Available at: https://doi.org/10.3390/tropicalmed10070180. Additional Declarations No competing interests reported. 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Pereira\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Vyctoria\",\"middleName\":\"\",\"lastName\":\"Pereira\",\"suffix\":\"\"},{\"id\":568513966,\"identity\":\"2ab3342b-4123-48e5-b678-f74e194aa2fa\",\"order_by\":8,\"name\":\"Juliana Gularte\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Juliana\",\"middleName\":\"\",\"lastName\":\"Gularte\",\"suffix\":\"\"},{\"id\":568513967,\"identity\":\"bec0afbf-debb-4921-90d9-d3b1b256e21d\",\"order_by\":9,\"name\":\"Luciano da Silva\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Luciano\",\"middleName\":\"da\",\"lastName\":\"Silva\",\"suffix\":\"\"},{\"id\":568513968,\"identity\":\"b4711b75-86da-4c8f-94e4-86861d33cda3\",\"order_by\":10,\"name\":\"Fernando Spilki\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Fernando\",\"middleName\":\"\",\"lastName\":\"Spilki\",\"suffix\":\"\"},{\"id\":568513969,\"identity\":\"944c81cc-c142-453a-96b5-a802479dba34\",\"order_by\":11,\"name\":\"Karine Takeuti\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Karine\",\"middleName\":\"\",\"lastName\":\"Takeuti\",\"suffix\":\"\"},{\"id\":568513970,\"identity\":\"d5223ecb-dd9f-4981-a5e1-553f090cbd62\",\"order_by\":12,\"name\":\"Mariana da Silva\",\"email\":\"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABBklEQVRIiWNgGAWjYJCCAyCCjR1IfKiQA7EZD0AFCWhhBiqdccYYJoJfCwQAtTDzthGhRbf97MMDP3fY2fMx8xh+4J1nIMcvkfzgwAeGO/m4tJidSTc42HsmObGNmcdYQnKbgbHkjDSDgzMYnlk24NJyII3hAG8bcwIbM1uChOG2P4kbzhwwOMzDcNgApy3nnzEc/NtWbw/UkvwjcY5B/f4zxz8c/oNPy400hsO8bYcZ25iZj0kcbDBIMGDvMTjMgFfLM4bDsm3HE0FaLBuOGRjOON5TcLDH4Bkeh6Uxf3zbVm0v397YfPtPjYE8fzP7xgc/Ku7g1IILkKxhFIyCUTAKRgEyAAAttFx6DRFEswAAAABJRU5ErkJggg==\",\"orcid\":\"\",\"institution\":\"Universidade Feevale\",\"correspondingAuthor\":true,\"prefix\":\"\",\"firstName\":\"Mariana\",\"middleName\":\"da\",\"lastName\":\"Silva\",\"suffix\":\"\"}],\"badges\":[],\"createdAt\":\"2025-12-22 15:38:56\",\"currentVersionCode\":1,\"declarations\":\"\",\"doi\":\"10.21203/rs.3.rs-8426575/v1\",\"doiUrl\":\"https://doi.org/10.21203/rs.3.rs-8426575/v1\",\"draftVersion\":[],\"editorialEvents\":[],\"editorialNote\":\"\",\"failedWorkflow\":false,\"files\":[{\"id\":100757355,\"identity\":\"a5997f39-e5a9-4b26-9c6f-b0ffadf9258a\",\"added_by\":\"auto\",\"created_at\":\"2026-01-21 06:48:29\",\"extension\":\"png\",\"order_by\":1,\"title\":\"Figure 1\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":67141,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eNumber of reads identified per family across the different groups. Group 1 includes \\u003cem\\u003eCircoviridae\\u003c/em\\u003e detection by PCR in lungs with mild lesions, while Group 2 features M.\\u003cem\\u003ehyopneumoniae\\u003c/em\\u003e detection by PCR in severe lung lesions. The families represented in the figure include PTVA (\\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e), PPV6 (\\u003cem\\u003eCopiparvovirus ungulat4\\u003c/em\\u003e), PCV2 (\\u003cem\\u003eCircovirus porcine2\\u003c/em\\u003e), PPV5 (\\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e), TTSuVI1b (\\u003cem\\u003eIotatorquevirus suida1b\\u003c/em\\u003e), and TTSuVK2a (\\u003cem\\u003eKappatorquevirus suidaK2a\\u003c/em\\u003e).\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"1.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8426575/v1/1fb6b8cbad47598db5f7eb59.png\"},{\"id\":100757357,\"identity\":\"540e3ccb-eec0-4090-b41d-60babce09f83\",\"added_by\":\"auto\",\"created_at\":\"2026-01-21 06:48:49\",\"extension\":\"png\",\"order_by\":2,\"title\":\"Figure 2\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":824058,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eGenetic characterization of PCV2. Phylogenetic analysis of the complete genome of REP-ORF 1 in Group 1 was inferred using the maximum likelihood method, Kimura-2 model parameter. The sequence obtained in this study is indicated by the red dot (b) (GenBank access: PX092312). Phylogenetic analysis of the complete genome of CAP-ORF 2 in Group 2. The sequence obtained in this study is indicated by the red dot (GenBank access: PX092313). All analyses were performed with 1000 bootstrap replicates.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"2.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8426575/v1/097916e7d68361e3864a3eaa.png\"},{\"id\":102397199,\"identity\":\"463a7772-8554-4777-9797-1befc36bd7e4\",\"added_by\":\"auto\",\"created_at\":\"2026-02-11 10:10:00\",\"extension\":\"pdf\",\"order_by\":0,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"manuscript-pdf\",\"size\":1814647,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"manuscript.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8426575/v1/85b01828-dcf4-4c40-9855-abe97af4ac1b.pdf\"},{\"id\":100757336,\"identity\":\"75bd6d7e-d989-46cb-a240-524ba0806ce9\",\"added_by\":\"auto\",\"created_at\":\"2026-01-21 06:47:47\",\"extension\":\"pdf\",\"order_by\":0,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":275973,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryMaterial.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-8426575/v1/a7f78071d12b6e4f8d668f1b.pdf\"}],\"financialInterests\":\"No competing interests reported.\",\"formattedTitle\":\"Effect of Viral Abundance and Diversity Associated with Mycoplasma hyopneumoniae on the Severity of Lung Lesions in Slaughtered Pigs: A Case-Control Study\",\"fulltext\":[{\"header\":\"Introduction\",\"content\":\"\\u003cp\\u003eA primary agent in swine respiratory disease is \\u003cem\\u003eMycoplasma hyopneumoniae\\u003c/em\\u003e (Mhyo), the etiological agent of Enzootic Pneumonia (Simionatto et al. \\u003cspan citationid=\\\"CR15\\\" class=\\\"CitationRef\\\"\\u003e2013\\u003c/span\\u003e). This chronic bronchopneumonia affects pigs of all ages, with a high prevalence in fattening herds, and often serves as a gateway for secondary infections. These complex interactions are classified under the term Porcine Respiratory Disease Complex (PRDC) (Fablet et al. \\u003cspan citationid=\\\"CR5\\\" class=\\\"CitationRef\\\"\\u003e2012\\u003c/span\\u003e; Przyborowska et al. \\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e). The PRDC involves co-infections with viral pathogens such as Influenza A Virus, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), which is the primary etiological agent for several diseases and syndromes, which are collectively referred to as porcine circovirus-associated disease (PCVAD). Such co-infections lead to significant production losses through impaired growth rates, poor feed conversion, and increased mortality (Przyborowska et al. \\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e).\\u003c/p\\u003e \\u003cp\\u003eThe intensification of swine production has led to increased animal density per facility, larger herd sizes, and a higher geographical concentration of farms (Barcellos \\u003cem\\u003eet al\\u003c/em\\u003e, 2008). While enhancing efficiency, this intensification has concurrently elevated the risk of infectious disease outbreaks. Respiratory diseases impose substantial economic burdens by reducing daily weight gain, increasing mortality rates, and leading to condemnations at slaughter due to conditions such as pneumonia, pleurisy, and abscesses (Li et al. \\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e2020\\u003c/span\\u003e).\\u003c/p\\u003e \\u003cp\\u003eBrazil is the fourth largest swine producer, with 4983\\u0026nbsp;million tons of pork in 2022 (Brazilian Animal Protein Association, 2023). Respiratory diseases such as pleurisy, pneumonia, and pleural adhesions impose major economic losses, with severe pleural lesions frequently reported in finishing pigs (Malcher et al. \\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e). Many carcasses with pulmonary injuries are condemned by the Federal Inspection Service (SIF), impacting the production chain. Although the pathological and economic relevance of these lesions was established, the virological composition of affected lungs and their correlation with lesion severity and \\u003cem\\u003eMycoplasma hyopneumoniae\\u003c/em\\u003e (Mhyo) status remain unclear. This study therefore investigates the virological profile in bronchial samples from slaughtered pigs and its association with lung lesions and Mhyo PCR positivity.\\u003c/p\\u003e\"},{\"header\":\"Methods\",\"content\":\"\\u003cp\\u003eThe study was conducted in 2022 at a slaughterhouse under the Federal Inspection Service in Santa Catarina, Brazil. Thirty pig lungs were examined for pneumonic lesions, with no pleuritis observed. Bronchial swabs (Copan\\u0026reg;, USA) were collected, stored in UTM at \\u0026minus;\\u0026thinsp;80\\u0026deg;C, and processed for DNA/RNA extraction using the MagMax kit. Real-time PCR for Mhyo (Takeuti et al. \\u003cspan citationid=\\\"CR17\\\" class=\\\"CitationRef\\\"\\u003e2017\\u003c/span\\u003e). Lungs were classified into three groups: Control (10 lungs, no lesions, Mhyo-negative), Group 1 (10 lungs, mild lesions in apical/cardiac lobes, Mhyo-positive), and Group 2 (10 lungs, severe lesions in multiple lobes, Mhyo-positive). Metagenomic negative control was also included in the analysis. Sample pools were vortexed, filtered (0.45 \\u0026micro;m), and viral nucleic acids extracted with the MagMAX\\u0026trade; CORE kit (Applied Biosystems) on KingFisher\\u0026trade; Duo Prime (Thermo Fisher). cDNA synthesis used Superscript IV and NEB Q5 polymerase (Demoliner et al. \\u003cspan citationid=\\\"CR3\\\" class=\\\"CitationRef\\\"\\u003e2025\\u003c/span\\u003e). Libraries were prepared with Illumina DNA Prep and sequenced on MiSeq (V3 600-cycle kit).\\u003c/p\\u003e \\u003cp\\u003eBioinformatic analysis employed Genome Detective, with quality filtering, contig assembly via CZID, and taxonomic classification using BLASTn/BLASTx. Genome Detective efficiently detects known and novel viral genomes (Vilsker et al. \\u003cspan citationid=\\\"CR18\\\" class=\\\"CitationRef\\\"\\u003e2019\\u003c/span\\u003e). Phylogenetic analysis included sequences of PCV2 (ORF1/ORF2), \\u003cem\\u003eCopiparvovirus ungulate 4, Iotatorquevirus suida 1b, and Teschovirus\\u003c/em\\u003e. Assemblies were mapped in Geneious Prime (v2025.0.3), aligned with MAFFT (v7), and analyzed by maximum-likelihood with ultrafast bootstrap in IQ-TREE. Trees were visualized in MEGA (v11.0.13). Following HTS, all 30 samples were tested individually by PCR using GoTaq\\u0026reg; DNA Polymerase. Targets included Torque teno virus genogroups 1 and 2 (Segal\\u0026eacute;s et al. \\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e2009\\u003c/span\\u003e), porcine circovirus (Drolet et al. \\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e2003\\u003c/span\\u003e) porcine parvovirus (de Menezes Cruz et al. \\u003cspan citationid=\\\"CR2\\\" class=\\\"CitationRef\\\"\\u003e2016\\u003c/span\\u003e, p. 201), and porcine teschovirus (Kuberka et al. \\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e). Products were resolved on agarose gels, stained, visualized under UV, purified, and sequenced by Sanger for confirmation.\\u003c/p\\u003e \\u003cp\\u003eStatistical analysis applied Chi-square tests to assess viral read distribution across Control, Group 1, and Group 2. Significance was set at p\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.05. Individually frequencies of viral agents detected by PCR were also tested to evaluate associations between pathogens and lesion severity. The samples analyzed in this study were collected as part of a research project approved by the Animal Use Ethics Committee of the Federal University of Rio Grande do Sul (Protocol No. 39866).\\u003c/p\\u003e\"},{\"header\":\"Results\",\"content\":\"\\u003cp\\u003eMetagenomic sequencing yielded 252,215 reads in Group 1 (mild lesions, Mhyo-positive), 260,950 reads in Group 2 (severe lesions, Mhyo-positive), and 102,250 reads in Control Group (no pulmonary lesions Mhyo-negative). CZID analysis classified sequencing reads into five viral families, including ssDNA (\\u003cem\\u003eCircoviridae\\u003c/em\\u003e, \\u003cem\\u003eParvoviridae\\u003c/em\\u003e, \\u003cem\\u003eAnelloviridae\\u003c/em\\u003e) and ssRNA (\\u003cem\\u003ePicornaviridae\\u003c/em\\u003e). Taxonomic assembly identified in Group 1: \\u003cem\\u003eCircovirus\\u003c/em\\u003e (6 reads), \\u003cem\\u003eCopiparvovirus ungulate4\\u003c/em\\u003e (8 reads), and \\u003cem\\u003eTeschovirus\\u003c/em\\u003e (18 reads). Group 2 showed higher abundance and diversity, with \\u003cem\\u003eCircovirus\\u003c/em\\u003e (106 reads), \\u003cem\\u003eCopiparvovirus ungulate4\\u003c/em\\u003e (121 reads), \\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e (24 reads), \\u003cem\\u003eIotatorquevirus suida1b\\u003c/em\\u003e (19 reads), and \\u003cem\\u003eKappatorquevirus suidaK2b\\u003c/em\\u003e (42 reads) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e). Chi-square analysis showed viral reads were 11.6-fold higher in Group 2 lungs (P\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.0001). No reads were detected in Controls, while Group 1 had 32 and Group 2 had 312 (excluding phages). Thus, viral load was significantly greater in pigs with severe pneumonia.\\u003c/p\\u003e \\u003cp\\u003e \\u003cb\\u003eCircoviridae\\u003c/b\\u003e: \\u003cb\\u003eCircovirus porcine2 (PCV2)\\u003c/b\\u003e\\u003c/p\\u003e \\u003cp\\u003eFrom 30 pooled bronchial swabs analyzed by HTS, 6 PCV2 reads were detected in Group 1 and 106 in Group 2. Group 1 produced a contig covering the full replicase (REP, 946 bp), showing 90.19% identity with PCV2 isolate URU31 (GenBank MF616414.1). Phylogenetic analysis clustered this REP sequence with PCV2b strains from Germany and the USA (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003ea). In Group 2, a contig spanning the complete capsid (CAP, 696 bp) was assembled, also classified as PCV2b and grouped with a Brazilian sequence (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003eb).\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003cp\\u003eConventional PCR revealed a PCV frequency of 30% (3/10) of samples positive in Group 1, and 60% (6/10) in Group 2. All positive sequences were submitted to Sanger sequencing, which confirmed the presence of PCV2. There was no significant difference between mild and severe injuries regarding the frequency of reads of PCV2 (p\\u0026thinsp;=\\u0026thinsp;0.3698).\\u003c/p\\u003e \\u003cp\\u003e \\u003cb\\u003eParvoviridae\\u003c/b\\u003e: \\u003cb\\u003ePorcine Parvovirus5 (PPV5); Copiparvovirus ungulate4 (PPV6)\\u003c/b\\u003e\\u003c/p\\u003e \\u003cp\\u003eIn Group 1, one contig of \\u003cem\\u003eCopiparvovirus ungulate4\\u003c/em\\u003e (PPV6) was identified, measuring 694 bp. BLASTn analysis showed 100% nucleotide identity with the Copiparvovirus ungu-late4 strain K13-8, which includes the nonstructural and capsid protein coding regions, complete CDS (GenBank accession: KX384813.1, UK/2016). In Group 2, two contigs of \\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e (PPV5) were identified. The first contig, PPV5G2a (216 bp), showed 97.09% nucleotide identity to \\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e isolate PPV5/COL/Valle511/2021, partial genome (GenBank accession: OR355614.1, Colombia/2024), corresponding to the 5\\u0026prime; UTR region. The second contig, PPV5G2b (171 bp), showed 99.42% identity to the PPV5 non-structural polyprotein 1 gene (complete CDS) and VP1 gene (partial CDS) from \\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e isolate RS/BR/2020 (GenBank accession: MT671979.1), corresponding to the capsid region.\\u003c/p\\u003e \\u003cp\\u003eAdditionally, a complete genome of PPV6 was assembled in Group 2, measuring 5582 bp. This genome presented the classical organization of PPV6, with ORF1 encoding the nonstructural protein NS1 (663 aa) and ORF2 (3570 nt) encoding the capsid protein VP1 (1190 amino acids). A multiple alignment was performed using PPV sequences from all known types, and a phylogenetic tree was constructed (\\u003cb\\u003eFig. \\u003cspan refid=\\\"MOESM1\\\" class=\\\"InternalRef\\\"\\u003eS1\\u003c/span\\u003e\\u003c/b\\u003e). The analysis con-firmed the classification of this genome as PPV6 and indicated close genetic relationships with strains previously detected in the United States.\\u003c/p\\u003e \\u003cp\\u003eConventional PCR performed on individual samples resulted in 5% (1/20) positive in Group 1 for PPV [PPV5 (0/10\\u0026ndash;0%), PPV6 (1/10\\u0026ndash;10%)], and resulting in 20% (4/20) positive in Group 2 for PPV [PPV5 (2/10\\u0026ndash;20%), PPV6 (2/10\\u0026ndash;20%)]. There was no significant difference between mild and severe injuries regarding the frequency of reads of PPV6 (p\\u0026thinsp;=\\u0026thinsp;1.000) and PPV5 (p\\u0026thinsp;=\\u0026thinsp;0.4737).\\u003c/p\\u003e\\n\\u003ch3\\u003eAnelloviridae: Kappatorquevirus suidaK2a (TTSuVK2a); Iotatorquevirus suida1b (TTSuV1b)\\u003c/h3\\u003e\\n\\u003cp\\u003eIn Group 2, two contigs belonging to \\u003cem\\u003eIotatorquevirus suida 1b\\u003c/em\\u003e were identified. The first contig, designated TTSuVI1b_G2a, measured 2,883 bp and exhibited 96.94% nucleotide identity to Torque teno sus virus 1 isolate TTV1Hlj5, complete genome (GenBank accession: HM633254.1, China/2010), based on BLASTn analysis. The second contig, TTSu-VI1b_G2b (2,725 bp), showed 92.95% identity to Torque teno sus virus 1b isolate TTSuV1 P1 OK/USA, which includes complete coding sequences for ORF1, ORF2, and ORF3 proteins (GenBank accession: MW080709.1, USA/2021.\\u003c/p\\u003e \\u003cp\\u003eMultiple sequence alignment was performed using representative genomes of TTSu-VI1a, TTSuVI1b, and TTSuVK2a. The resulting phylogenetic tree (\\u003cb\\u003eFig. S2\\u003c/b\\u003e) confirmed the BLAST-based classification, grouping both contigs within the TTSuVI1b clade. These sequences were phylogenetically related to strains previously identified in Brazil and the United States. Additionally, a single read of Kappatorquevirus suidaK2b was detected in Group 2. This read (approximately 80 bp in length) demonstrated 100% nucleotide identity with Torque teno sus virus k2b isolate BR/RS/2008 (GenBank accession: KY742732.1).\\u003c/p\\u003e \\u003cp\\u003eConventional PCR revealed that 25% (5/20) of samples were positive for TTSuV1b, no samples were positive 0% (0/10) in Group 1, but in Group 2, 50% 5/10) of the samples were positive. The association among groups and outcomes is statistically significant (P\\u0026thinsp;=\\u0026thinsp;0,0325).\\u003c/p\\u003e \\u003cp\\u003e \\u003cb\\u003ePicornaviridae\\u003c/b\\u003e: \\u003cb\\u003eTeschovirus asilesi\\u003c/b\\u003e \\u003cb\\u003e(PTV)\\u003c/b\\u003e\\u003c/p\\u003e \\u003cp\\u003eIn Group 1, a contig of \\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e measuring 128 bp was identified. BLASTn analysis revealed 100% nucleotide identity with Teschovirus A isolate HNMY, complete genome (GenBank accession: KX686489.1, China/2017). The contig corresponds to the 5\\u0026prime; untranslated region of the viral genome. A multiple sequence alignment was performed, and a phylogenetic tree was constructed (\\u003cb\\u003eFig. S3\\u003c/b\\u003e), which confirmed the BLAST classification, grouping the sequence within the Porcine \\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e (PTV) cluster, alongside previously reported isolates.\\u003c/p\\u003e \\u003cp\\u003eConventional PCR revealed PTVA frequency resulting in 5% (1/20) positive in Group 1, 10% (1/10) of the samples were positive, while in Group 2 no positive samples were detected 0% (0/10). There was no significant difference between mild and severe injuries regarding the frequency of reads of PTV (P\\u0026thinsp;=\\u0026thinsp;1.000). Complete and individual PCR results were included in Table\\u0026nbsp;\\u003cspan refid=\\\"Tab1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e. In the identification column, each sample (animal) is labeled with the codes G1, G2, or G3, corresponding to their respective experimental groups.\\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\\u003eIndividual results of conventional PCRs for \\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e, \\u003cem\\u003eCopiparvovirus ungulat4\\u003c/em\\u003e, \\u003cem\\u003eCircovirus porcine2\\u003c/em\\u003e, \\u003cem\\u003ePorcine parvovirus 5\\u003c/em\\u003e and \\u003cem\\u003eTorque teno sus virus\\u003c/em\\u003e in samples from Group 1 and 2.\\u003c/p\\u003e \\u003c/div\\u003e \\u003c/caption\\u003e \\u003ccolgroup cols=\\\"6\\\"\\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 \\u003cthead\\u003e \\u003ctr\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eID\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cem\\u003eTorque teno sus virus\\u003c/em\\u003e\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eCircovirus porcine 2\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eCopiparvovirus ungulate 4\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003ePorcine parvovirus 5\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eTeschovirus asilesi\\u003c/p\\u003e \\u003c/th\\u003e \\u003c/tr\\u003e \\u003c/thead\\u003e \\u003ctbody\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 137 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 138 B\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 22 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 24 B\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 41 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 42 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 51 B\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 55 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 85 B\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG1 93 B\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 03 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 08 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 125 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 13 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 27 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 35 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 54 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 75 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 76 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003ePositive\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003e\\u003cb\\u003eG2 77 A\\u003c/b\\u003e\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eNegative\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003c/tbody\\u003e \\u003c/colgroup\\u003e \\u003c/table\\u003e\\u003c/div\\u003e \\u003c/p\\u003e\"},{\"header\":\"Discussion\",\"content\":\"\\u003cp\\u003eRespiratory diseases are one of the major concerns of the pig industry. Intensive production systems, characterized by large batches in confined environments, favor the persistence and spread of pathogenic microorganisms (Drolet et al. \\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e2003\\u003c/span\\u003e; de Menezes Cruz et al. \\u003cspan citationid=\\\"CR2\\\" class=\\\"CitationRef\\\"\\u003e2016\\u003c/span\\u003e; Kuberka et al. \\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e; Przyborowska et al. \\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e), contributing to the occurrence of PRDC in mostly of the commercial pig farms worlwide. In this study, metagenomic analysis of bronchial swabs from three groups revealed distinct viral profiles. Group 1 (mild lesions, Mhyo-positive) showed Teschovirus asilesi, PCV2, and PPV6. Group 2 (severe lesions, Mhyo-positive) exhibited greater diversity, including PCV2, PPV5, PPV6, Iotatorquevirus suida1b, and Kappatorquevirus suidaK2b. The Control Group (no lesions, Mhyo-negative) showed no viral agents. Statistical analysis indicated viral reads were 11.6-fold higher in Group 2 than Group 1, strongly associated viral load with lesion severity.\\u003c/p\\u003e \\u003cp\\u003eBased on conventional individual PCR, although a statistically significant difference among groups was observed only for TTSuV1b detection (P\\u0026thinsp;=\\u0026thinsp;0.0325), with 50% positivity in Group 2 and none in Group 1, all viral agents tended to show higher frequencies in groups with severe lesions. This pattern, however, did not reach statistical significance for the other agents, possibly due to the limited sample size (n\\u0026thinsp;=\\u0026thinsp;10 per group), which may have constrained the power to detect meaningful differences. The presence of Mhyo in both affected groups reinforces its role as a primary agent in swine respiratory tract, acting as a facilitator of viral coinfections and contributing to the progression of lung lesions. Previous studies have shown that for each 1% of increase in lung affected area, a decrease has been observed in weight or average daily gain in the finishing phase (Hill et al. \\u003cspan citationid=\\\"CR7\\\" class=\\\"CitationRef\\\"\\u003e1994\\u003c/span\\u003e; Ferraz et al. \\u003cspan citationid=\\\"CR6\\\" class=\\\"CitationRef\\\"\\u003e2020\\u003c/span\\u003e), suggesting that pigs coinfected with Mhyo and viruses may present reduced productive performance up to slaughter.\\u003c/p\\u003e \\u003cp\\u003eCoinfections with \\u003cem\\u003eMhyo\\u003c/em\\u003e likely contribute to respiratory conditions such as pleurisy and severe pneumonia, commonly associated with multiple pathogens and classified as PRDC (Saade et al. \\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e2020\\u003c/span\\u003e). Studies have shown coinfection of \\u003cem\\u003eM. hyopneumoniae\\u003c/em\\u003e and \\u003cem\\u003ePCV2\\u003c/em\\u003e impacts clinical disease and performance, especially when pigs are inoculated with both pathogens (Suh et al. \\u003cspan citationid=\\\"CR16\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e). HTS detected \\u003cem\\u003ePCV2\\u003c/em\\u003e in both groups (Group 2: 106 reads; Group 1: 6 reads), suggesting higher viral load or replication. \\u003cem\\u003ePCV2b\\u003c/em\\u003e was identified as the circulating genotype, with REP gene variation (90.19% identity with a Uruguayan strain) and CAP gene evidence of persistent regional variants, indicating distinct strains in South America. \\u003cem\\u003ePCV2b\\u003c/em\\u003e infection is linked to characteristic lung lesions, including firm, non-collapsed lungs with pale consolidation, interstitial pneumonia, and bronchiolitis (Suh et al. \\u003cspan citationid=\\\"CR16\\\" class=\\\"CitationRef\\\"\\u003e2024\\u003c/span\\u003e). PCR confirmed 30% positives in Group 1 and 60% in Group 2, consistent with HTS, indicating significant viral frequency. Detection of \\u003cem\\u003ePCV2b\\u003c/em\\u003e in both groups confirms active circulation in Brazilian herds and highlights the need for surveillance, prevention, and vaccination strategies.\\u003c/p\\u003e \\u003c/p\\u003e \\u003cp\\u003eThe study identified \\u003cem\\u003ePPV5\\u003c/em\\u003e, \\u003cem\\u003ePPV6\\u003c/em\\u003e, \\u003cem\\u003eTTSuV1b\\u003c/em\\u003e, \\u003cem\\u003eTTSuVK2b\\u003c/em\\u003e, and \\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e, confirming their diversity and circulation in South American swine herds. \\u003cem\\u003ePPV6\\u003c/em\\u003e (Group 1) showed 100% identity with UK and North American strains, suggesting a conserved lineage, while \\u003cem\\u003ePPV5\\u003c/em\\u003e (Group 2) aligned with Colombian and Brazilian strains, indicating regional variants (Cibulski et al. \\u003cspan citationid=\\\"CR1\\\" class=\\\"CitationRef\\\"\\u003e2021\\u003c/span\\u003e). \\u003cem\\u003eTTSuV1b\\u003c/em\\u003e, detected only in Group 2, clustered with strains from China and the USA, suggesting co-circulation or recombination, whereas a single read of \\u003cem\\u003eTTSuVK2b\\u003c/em\\u003e matched a Brazilian strain from 2008, indicating sporadic circulation. \\u003cem\\u003eTeschovirus asilesi\\u003c/em\\u003e (Group 1) showed 100% identity with a Chinese strain, supporting global genomic conservation. Although PTV infections are often subclinical, some strains may cause severe neurological disease (Palmquist et al. \\u003cspan citationid=\\\"CR11\\\" class=\\\"CitationRef\\\"\\u003e2002\\u003c/span\\u003e).\\u003c/p\\u003e \\u003cp\\u003eRespiratory tract infections continue to represent one of the major global health challenges, ranking collectively as the fourth leading cause of death in pigs worldwide (Yu and Li \\u003cspan citationid=\\\"CR19\\\" class=\\\"CitationRef\\\"\\u003e2025\\u003c/span\\u003e). Both humans and animals serve as reservoirs for respiratory pathogens, creating ecological niches that favor microbial adaptation, persistence, and the emergence of novel variants. Among these infections, bacterial pneumonia stands out for its high morbidity and mortality, particularly affecting vulnerable populations such as young children, the elderly, and livestock. Several viral-mediated mechanisms have been implicated in facilitating bacterial colonization and proliferation, including epithelial disruption, neuraminidase activity, exposure of platelet-activating factor receptors, and impaired innate immune responses (Saade et al. \\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e2020\\u003c/span\\u003e; Yu and Li \\u003cspan citationid=\\\"CR19\\\" class=\\\"CitationRef\\\"\\u003e2025\\u003c/span\\u003e). These interactions underscore the complexity of respiratory disease pathogenesis and reinforce the importance of integrated surveillance and control strategies across species.\\u003c/p\\u003e \\u003cp\\u003eOur results revealed that pig lungs with severe lesions and Mhyo detection presented approximately 11.6 times more viral abundance than lungs with mild lesions and Mhyo detection, suggesting that viruses may have contributed to the extension of pneumonic lesions. The only virus that showed a statistically significant difference when samples were tested individually was TTV. Moreover, our findings indicate a highly diverse population of \\u003cem\\u003eAnelloviridae\\u003c/em\\u003e, \\u003cem\\u003eCircoviridae\\u003c/em\\u003e, and \\u003cem\\u003eParvoviridae\\u003c/em\\u003e in pig lungs. It is important to note that PCV2 was detected in both groups with lung lesions and Mhyo detection, emphasizing its circulation in finishing pigs.\\u003c/p\\u003e \"},{\"header\":\"Declarations\",\"content\":\"\\u003ch2\\u003eAuthor Contribution\\u003c/h2\\u003e\\u003cp\\u003eE.L.P. and M.S.S. contributed to the conceptualization of the study. Methodology and practical analysis were carried out by E.L.P., M.L.O., A.S., L.N., A.S., M.D., M.F., V.M.A.G.P., and J.S.G. Formal analysis was performed by M.S.S., L.B.S., and K.L.T. Investigation was conducted by E.L.P., M.L.O., A.S., and L.N. Writing\\u0026mdash;review and editing were performed by M.S.S., E.L.P., K.L.T., and F.R.S. Supervision was provided by M.S.S. and K.L.T. Funding acquisition was secured by M.S.S. and F.R.S. All authors reviewed and approved the final version of the manuscript.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eFinancial Support\\u003c/strong\\u003e: Universidade Feevale, CAPES, Fapergs n\\u0026ordm; 23/2551-0002221-4, CNPq n\\u0026ordm; 405786/2022-0, Ouro do Sul, INCT One.\\u003c/p\\u003e\"},{\"header\":\"References\",\"content\":\"\\u003col\\u003e\\n\\u003cli\\u003eCibulski, S. \\u003cem\\u003eet al.\\u003c/em\\u003e (2021) \\u0026ldquo;A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil,\\u0026rdquo; \\u003cem\\u003eVirology\\u003c/em\\u003e, 552, pp. 1\\u0026ndash;9. Available at: https://doi.org/10.1016/j.virol.2020.09.005.\\u003c/li\\u003e\\n\\u003cli\\u003eDemoliner, M. \\u003cem\\u003eet al.\\u003c/em\\u003e (2025) \\u0026ldquo;Comparison of metagenomic protocols for virome data generation from environmental matrices and stool samples: insights into viral diversity and fecal contamination indicators,\\u0026rdquo; \\u003cem\\u003eTotal Environment Microbiology\\u003c/em\\u003e, 1(2), p. 100008. Available at: https://doi.org/10.1016/j.temicr.2025.100008.\\u003c/li\\u003e\\n\\u003cli\\u003eDrolet, R. \\u003cem\\u003eet al.\\u003c/em\\u003e (2003) \\u0026ldquo;Detection rates of porcine reproductive and respiratory syndrome virus, porcine circovirus type 2, and swine influenza virus in porcine proliferative and necrotizing pneumonia.,\\u0026rdquo; \\u003cem\\u003eVeterinary pathology\\u003c/em\\u003e, 40(2), pp. 143\\u0026ndash;148. Available at: https://doi.org/10.1354/vp.40-2-143.\\u003c/li\\u003e\\n\\u003cli\\u003eFablet, C. \\u003cem\\u003eet al.\\u003c/em\\u003e (2012) \\u0026ldquo;Infectious agents associated with respiratory diseases in 125 farrow-to-finish pig herds: A cross-sectional study,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 157(1\\u0026ndash;2), pp. 152\\u0026ndash;163. Available at: https://doi.org/10.1016/j.vetmic.2011.12.015.\\u003c/li\\u003e\\n\\u003cli\\u003eFerraz, M.E.S. \\u003cem\\u003eet al.\\u003c/em\\u003e (2020) \\u0026ldquo;Lung consolidation caused by Mycoplasma hyopneumoniae has a negative effect on productive performance and economic revenue in finishing pigs.,\\u0026rdquo; \\u003cem\\u003ePreventive veterinary medicine\\u003c/em\\u003e, 182, p. 105091. Available at: https://doi.org/10.1016/j.prevetmed.2020.105091.\\u003c/li\\u003e\\n\\u003cli\\u003eHill, M.A. \\u003cem\\u003eet al.\\u003c/em\\u003e (1994) \\u0026ldquo;Relationship between the indicators of performance and the weight of pneumonic lesions from pigs at slaughter,\\u0026rdquo; \\u003cem\\u003eResearch in Veterinary Science\\u003c/em\\u003e, 56(2), pp. 240\\u0026ndash;244. Available at: https://doi.org/10.1016/0034-5288(94)90110-4.\\u003c/li\\u003e\\n\\u003cli\\u003eKuberka, Z. \\u003cem\\u003eet al.\\u003c/em\\u003e (2024) \\u0026ldquo;Relationships between pig farm management and facilities and lung lesions\\u0026rsquo; scores and between lung lesions scores and carcass characteristics,\\u0026rdquo; \\u003cem\\u003eBMC Veterinary Research\\u003c/em\\u003e, 20(1), p. 124. Available at: https://doi.org/10.1186/s12917-024-03968-2.\\u003c/li\\u003e\\n\\u003cli\\u003eLi, J. \\u003cem\\u003eet al.\\u003c/em\\u003e (2020) \\u0026ldquo;Relationship between environment, management and respiratory diseases in pigs,\\u0026rdquo; \\u003cem\\u003eTransboundary and Emerging Diseases\\u003c/em\\u003e, 67(1), pp. 263\\u0026ndash;275. Available at: https://doi.org/10.1111/tbed.13347.\\u003c/li\\u003e\\n\\u003cli\\u003eMalcher, C.S. \\u003cem\\u003eet al.\\u003c/em\\u003e (2024) \\u0026ldquo;Health\\u0026ndash;Economic Impact Attributable to Occurrence of Pleurisy and Pneumonia Lesions in Finishing Pigs,\\u0026rdquo; \\u003cem\\u003eVeterinary Sciences\\u003c/em\\u003e, 11(12), p. 668. Available at: https://doi.org/10.3390/vetsci11120668.\\u003c/li\\u003e\\n\\u003cli\\u003ede Menezes Cruz, A.C. \\u003cem\\u003eet al.\\u003c/em\\u003e (2016) \\u0026ldquo;Clinical aspects and weight gain reduction in swine infected with porcine circovirus type 2 and torque teno sus virus in Brazil,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 195, pp. 154\\u0026ndash;157. Available at: https://doi.org/10.1016/j.vetmic.2016.09.012.\\u003c/li\\u003e\\n\\u003cli\\u003ePalmquist, J.M. \\u003cem\\u003eet al.\\u003c/em\\u003e (2002) \\u0026ldquo;Detection of porcine teschovirus and enterovirus type II by reverse transcription-polymerase chain reaction.,\\u0026rdquo; \\u003cem\\u003eJournal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc\\u003c/em\\u003e, 14(6), pp. 476\\u0026ndash;480. Available at: https://doi.org/10.1177/104063870201400605.\\u003c/li\\u003e\\n\\u003cli\\u003ePrzyborowska, P. \\u003cem\\u003eet al.\\u003c/em\\u003e (2024) \\u0026ldquo;Impact of porcine respiratory disease complex on carcass weight and meatiness: quantitative insights from a mixed-model analysis,\\u0026rdquo; \\u003cem\\u003eBMC Veterinary Research\\u003c/em\\u003e, 20(1), p. 554. Available at: https://doi.org/10.1186/s12917-024-04410-3.\\u003c/li\\u003e\\n\\u003cli\\u003eSaade, G. \\u003cem\\u003eet al.\\u003c/em\\u003e (2020) \\u0026ldquo;Coinfections and their molecular consequences in the porcine respiratory tract,\\u0026rdquo; \\u003cem\\u003eVeterinary Research\\u003c/em\\u003e, 51(1), p. 80. Available at: https://doi.org/10.1186/s13567-020-00807-8.\\u003c/li\\u003e\\n\\u003cli\\u003eSegal\\u0026eacute;s, J. \\u003cem\\u003eet al.\\u003c/em\\u003e (2009) \\u0026ldquo;Retrospective study on swine Torque teno virus genogroups 1 and 2 infection from 1985 to 2005 in Spain,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 134(3), pp. 199\\u0026ndash;207. Available at: https://doi.org/10.1016/j.vetmic.2008.08.002.\\u003c/li\\u003e\\n\\u003cli\\u003eSimionatto, S. \\u003cem\\u003eet al.\\u003c/em\\u003e (2013) \\u0026ldquo;Mycoplasma hyopneumoniae: From disease to vaccine development,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 165(3), pp. 234\\u0026ndash;242. Available at: https://doi.org/10.1016/j.vetmic.2013.04.019.\\u003c/li\\u003e\\n\\u003cli\\u003eSuh, J., Ham, S. and Chae, C. (2024) \\u0026ldquo;Divergent clinical outcomes depending on the sequential infection order of porcine circovirus type 2 and Mycoplasma hyopneumoniae,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 292, p. 110060. Available at: https://doi.org/10.1016/j.vetmic.2024.110060.\\u003c/li\\u003e\\n\\u003cli\\u003eTakeuti, K.L. \\u003cem\\u003eet al.\\u003c/em\\u003e (2017) \\u0026ldquo;Infection dynamics and genetic variability of Mycoplasma hyopneumoniae in self-replacement gilts,\\u0026rdquo; \\u003cem\\u003eVeterinary Microbiology\\u003c/em\\u003e, 208, pp. 18\\u0026ndash;24. Available at: https://doi.org/10.1016/j.vetmic.2017.07.007.\\u003c/li\\u003e\\n\\u003cli\\u003eVilsker, M. \\u003cem\\u003eet al.\\u003c/em\\u003e (2019) \\u0026ldquo;Genome Detective: an automated system for virus identification from high-throughput sequencing data,\\u0026rdquo; \\u003cem\\u003eBioinformatics\\u003c/em\\u003e. Edited by I. Birol, 35(5), pp. 871\\u0026ndash;873. Available at: https://doi.org/10.1093/bioinformatics/bty695.\\u003c/li\\u003e\\n\\u003cli\\u003eYu, E. and Li, C. (2025) \\u0026ldquo;Global Trends and Attributable Risk Factors in the Disease Burden of Lower Respiratory Infections,\\u0026rdquo; \\u003cem\\u003eTropical Medicine and Infectious Disease\\u003c/em\\u003e, 10(7), p. 180. Available at: https://doi.org/10.3390/tropicalmed10070180.\\u003c/li\\u003e\\n\\u003c/ol\\u003e\"}],\"fulltextSource\":\"\",\"fullText\":\"\",\"funders\":[],\"hasAdminPriorityOnWorkflow\":false,\"hasManuscriptDocX\":true,\"hasOptedInToPreprint\":true,\"hasPassedJournalQc\":\"\",\"hasAnyPriority\":false,\"hideJournal\":true,\"highlight\":\"\",\"institution\":\"\",\"isAcceptedByJournal\":false,\"isAuthorSuppliedPdf\":false,\"isDeskRejected\":\"\",\"isHiddenFromSearch\":false,\"isInQc\":false,\"isInWorkflow\":false,\"isPdf\":false,\"isPdfUpToDate\":true,\"isWithdrawnOrRetracted\":false,\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"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},\"keywords\":\"HTS, Enzootic pneumonia, PRDC, Virome\",\"lastPublishedDoi\":\"10.21203/rs.3.rs-8426575/v1\",\"lastPublishedDoiUrl\":\"https://doi.org/10.21203/rs.3.rs-8426575/v1\",\"license\":{\"name\":\"CC BY 4.0\",\"url\":\"https://creativecommons.org/licenses/by/4.0/\"},\"manuscriptAbstract\":\"\\u003cp\\u003eRespiratory diseases in swine are mostly infectious sources, and \\u003cem\\u003eMycoplasma hyopneumoniae\\u003c/em\\u003e (Mhyo) is one of the most prevalent agents in pig farms, often associated with coinfections with viruses as well as other bacteria. This interaction results in the Porcine Respiratory Disease Complex (PRDC) that can lead to significant economic losses to the swine industry. In this study, bronchial swabs were collected from 30 slaughtered pigs, divided into three groups according to the lung lesion score and Mhyo detection by PCR: Control: without lesions and Mhyo negative; Group 1: mild lesions and Mhyo positive; Group 2: severe lesions and Mhyo positive. Ten samples per group were pooled and high-throughput sequencing (HTS) was performed. The analyses revealed the presence of the viral families: \\u003cem\\u003eAnelloviridae, Circoviridae, Parvoviridae\\u003c/em\\u003e, and \\u003cem\\u003ePicornaviridae.\\u003c/em\\u003e The number of identified viral reads was significantly higher (11.6x) in the group with severe lung lesions and Mhyo-positive compared to the group with mild lesions and Mhyo-positive. Also, group 2 presented the highest viral diversity. No viruses were detected in samples from the group without lesions. Based on these findings, the study suggests that the presence of Mhyo in lungs at slaughter may increase the susceptibility of pigs to viral infection, resulting in severe pulmonary lesions.\\u003c/p\\u003e\",\"manuscriptTitle\":\"Effect of Viral Abundance and Diversity Associated with Mycoplasma hyopneumoniae on the Severity of Lung Lesions in Slaughtered Pigs: A Case-Control Study\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2026-01-21 06:38:29\",\"doi\":\"10.21203/rs.3.rs-8426575/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"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\":\"31a85586-610a-43b7-b169-da5ed5f9cc25\",\"owner\":[],\"postedDate\":\"January 21st, 2026\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"posted\",\"subjectAreas\":[],\"tags\":[],\"updatedAt\":\"2026-02-03T23:08:56+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2026-01-21 06:38:29\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-8426575\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-8426575\",\"identity\":\"rs-8426575\",\"version\":[\"v1\"]},\"buildId\":\"XKTyCvWXoU3ODBz1xrDgd\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}