{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,2]],"date-time":"2026-08-02T04:47:21Z","timestamp":1785646041795,"version":"3.56.0"},"reference-count":22,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T00:00:00Z","timestamp":1785456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2024A1515140152"],"award-info":[{"award-number":["2024A1515140152"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Foshan University 2025 Graduate Excellence and Innovation Program","award":["FOSU2025ZYCX-M04"],"award-info":[{"award-number":["FOSU2025ZYCX-M04"]}]},{"award":["FOSU2025ZYCX-M04"],"award-info":[{"award-number":["FOSU2025ZYCX-M04"]}],"id":[{"id":"https:\/\/ror.org\/02xvvvp28","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program Projects","doi-asserted-by":"publisher","award":["2023YFD1801302"],"award-info":[{"award-number":["2023YFD1801302"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program Projects","doi-asserted-by":"publisher","award":["2023YFD1801301"],"award-info":[{"award-number":["2023YFD1801301"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Funds for Rural Revitalization Strategy of Guangdong Provincial Department of Agriculture and Rural Affairs in 2026","award":["2026CXTD15"],"award-info":[{"award-number":["2026CXTD15"]}]},{"award":["2026CXTD15"],"award-info":[{"award-number":["2026CXTD15"]}],"id":[{"id":"https:\/\/ror.org\/040yejv90","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Open Foundation of Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding","award":["2024B03"],"award-info":[{"award-number":["2024B03"]}]},{"name":"Foshan University High Level Talents Research Start-up Project","award":["CGZ07465\/CGZ07001"],"award-info":[{"award-number":["CGZ07465\/CGZ07001"]}]},{"award":["CGZ07465\/CGZ07001"],"award-info":[{"award-number":["CGZ07465\/CGZ07001"]}],"id":[{"id":"https:\/\/ror.org\/02xvvvp28","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Key Research and Development Special Project of Henan Province","award":["251111113600"],"award-info":[{"award-number":["251111113600"]}]},{"name":"Joint Fund of Henan Province Science and Technology Research and Development Program","award":["242103810006"],"award-info":[{"award-number":["242103810006"]}]},{"name":"Key Scientific and Technological Grants in Henan Province","award":["24210211031"],"award-info":[{"award-number":["24210211031"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31902279"],"award-info":[{"award-number":["31902279"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["31902279"],"award-info":[{"award-number":["31902279"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains the predominant genotype circulating in China and continues to evolve through mutation and recombination. Although NSP1 is recognized as a multifunctional nonstructural protein involved in immune regulation, its genetic variation among PRRSV-2 strains circulating in China has not been comprehensively characterized. Methods: In this study, 425 complete NSP1 sequences, primarily representing PRRSV-2 strains circulating in China, were analyzed, and 48 representative strains were selected for pairwise percent-identity visualization. Results: Pairwise nucleotide identity among the 48 representative strains was found to range from 80.1% to 100.0%, with the lowest value detected between AHBZ and SD-R, whereas pairwise amino-acid identity ranged from 79.6% to 100.0%, with the lowest value detected between AHBZ and HNhx. Among the 425 aligned amino-acid sequences, 290 variable sites and 93 completely conserved sites were identified. The broad-lineage distribution was composed of Lineage 1 (n = 79), Lineage 3 (n = 4), Lineage 5 (n = 21), and Lineage 8 (n = 321). A global FEL dN\/dS of approximately 0.2979 was estimated from 379 non-recombinant unique haplotypes, and seven high-confidence candidate positively selected sites\u201442, 239, 255, 302, 367, 370, and 378\u2014were supported by MEME, FEL, and FUBAR. A descriptive lineage-biased pattern concentrated in Lineage 5 was observed for NSP1\u03b2 Val19Ile, corresponding to full-length NSP1 V199I. Eight candidate recombination events were identified using RDP4, and six representative events were further examined using SimPlot. Conclusions: Overall, NSP1 was found to be under predominant purifying selection while retaining localized variability, lineage-biased residue patterns, and candidate recombination signals that should be interpreted cautiously and validated experimentally.<\/jats:p>","DOI":"10.3390\/genes17080908","type":"journal-article","created":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T10:11:38Z","timestamp":1785492698000},"page":"908","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Variation Analysis of the NSP1 Gene of Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China"],"prefix":"10.3390","volume":"17","author":[{"given":"Tianyuan","family":"Nie","sequence":"first","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaman","family":"Li","sequence":"additional","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siqi","family":"Ye","sequence":"additional","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruining","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Animal Product Quality and Safety Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuyong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Animal Product Quality and Safety Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huawei","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Animal Product Quality and Safety Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0306-0327","authenticated-orcid":false,"given":"Keshan","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaqiong","family":"Ye","sequence":"additional","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4143-3606","authenticated-orcid":false,"given":"Mengmeng","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/030098589803500101","article-title":"Porcine Reproductive and Respiratory Syndrome","volume":"35","author":"Rossow","year":"1998","journal-title":"Vet. Pathol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev-animal-022114-111025","article-title":"Porcine Reproductive and Respiratory Syndrome Virus (PRRSV): Pathogenesis and Interaction with the Immune System","volume":"4","author":"Lunney","year":"2016","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zhang, Z., Zhang, H., Luo, Q., Zheng, Y., Kong, W., Huang, L., and Zhao, M. (2023). Variations in NSP1 of Porcine Reproductive and Respiratory Syndrome Virus Isolated in China from 1996 to 2022. Genes, 14.","DOI":"10.3390\/genes14071435"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Yu, J., Kang, R., Qing, Y., Xu, Q., Xie, J., Cao, Y., Ye, Y., Xiao, L., Xie, L., and Xiang, X. (2026). Molecular Epidemiology and Genetic Evolution of PRRSV ORF5 in Sichuan, Southwest China. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1753001"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s11262-022-01957-x","article-title":"Variations in the NSP4 Gene of the Type 2 Porcine Reproductive and Respiratory Syndrome Virus Isolated in China from 1996 to 2021","volume":"59","author":"Sha","year":"2023","journal-title":"Virus Genes"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1186\/s12985-015-0380-7","article-title":"Rescue and Evaluation of a Recombinant PRRSV Expressing Porcine Interleukin-4","volume":"12","author":"Li","year":"2015","journal-title":"Virol. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"10931","DOI":"10.1128\/JVI.02579-08","article-title":"Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Leader Protease Nsp1\u03b1","volume":"83","author":"Sun","year":"2009","journal-title":"J. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"6461","DOI":"10.1128\/JVI.00301-10","article-title":"The Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein Nsp1\u03b2 Reveals a Novel Metal-Dependent Nuclease","volume":"84","author":"Xue","year":"2010","journal-title":"J. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.virol.2016.07.008","article-title":"Nuclear Export Signal of PRRSV NSP1\u03b1 Is Necessary for Type I IFN Inhibition","volume":"499","author":"Chen","year":"2016","journal-title":"Virology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1089\/jir.2012.0100","article-title":"The Zinc-Finger Domain Was Essential for Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein-1\u03b1 to Inhibit the Production of Interferon-\u03b2","volume":"33","author":"Shi","year":"2013","journal-title":"J. Interferon Cytokine Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.cellimm.2012.10.003","article-title":"Amino Acid at Position 176 Was Essential for Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Non-Structural Protein 1\u03b1 (Nsp1\u03b1) as an Inhibitor to the Induction of IFN-\u03b2","volume":"280","author":"Shi","year":"2012","journal-title":"Cell. Immunol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5219","DOI":"10.1128\/JVI.02643-12","article-title":"Porcine Reproductive and Respiratory Syndrome Virus Nsp1\u03b2 Inhibits Interferon-Activated JAK\/STAT Signal Transduction by Inducing Karyopherin-\u03b11 Degradation","volume":"87","author":"Wang","year":"2013","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and Analysis of Recombination Patterns in Virus Genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Murrell, B., Wertheim, J.O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S.L. (2012). Detecting Individual Sites Subject to Episodic Diversifying Selection. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002764"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection","volume":"22","author":"Frost","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection","volume":"30","author":"Murrell","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.virol.2012.08.034","article-title":"Identification of Amino Acid Residues Important for Anti-IFN Activity of Porcine Reproductive and Respiratory Syndrome Virus Non-Structural Protein 1","volume":"433","author":"Beura","year":"2012","journal-title":"Virology"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1128\/JVI.03069-15","article-title":"Mutations in a Highly Conserved Motif of Nsp1\u03b2 Protein Attenuate the Innate Immune Suppression Function of Porcine Reproductive and Respiratory Syndrome Virus","volume":"90","author":"Li","year":"2016","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00469-19","DOI":"10.1128\/JVI.00469-19","article-title":"Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 1\u03b2 Interacts with Nucleoporin 62 To Promote Viral Replication and Immune Evasion","volume":"93","author":"Ke","year":"2019","journal-title":"J. Virol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/908\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,2]],"date-time":"2026-08-02T04:27:19Z","timestamp":1785644839000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,31]]},"references-count":22,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["genes17080908"],"URL":"https:\/\/doi.org\/10.3390\/genes17080908","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,31]]}}}