{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T05:05:29Z","timestamp":1780635929315,"version":"3.54.1"},"reference-count":35,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Central Public-interest Scientific Institution Basal Research Fund","award":["MARA-ORDC-AH06"],"award-info":[{"award-number":["MARA-ORDC-AH06"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Three species of suid herpesviruses (SuHVs) have been reported in pigs, specifically pseudorabies virus (PRV), porcine cytomegalovirus (PoCMV), and porcine lymphotropic herpesvirus (PLHV). However, their genetic diversity and epidemic circulating status in China remain largely unclear. In this study, 7200 nasal swabs and 2571 serum samples were collected from pigs across 17 provincial regions in China in 2017. All samples were pooled into 22 libraries based on sample type and geographic origin for high-throughput next-generation sequencing. Metaviromic analysis identified all three SuHV species, revealing marked variations in their detection rates and viral abundance. Notably, PoCMV and PRV were detected in all 17 sampled provinces, accompanied by high viral genome sequence abundance (RPM &gt; 1 \u00d7 102), while PLHV was only found in nasal swabs from 10 provinces, with extremely low sequence abundance (RPM &lt; 2). Further phylogenetic and genetic diversity analyses revealed notable molecular characteristics of the three circulating SuHVs: PoCMV exhibited substantial genetic diversity with at least two major evolutionary clades identified in Chinese pig populations; variant genotype II PRV strains were confirmed as the predominant circulating lineage; and potential PLHV variants with partial sequence divergence from the reference strain were also found to circulate in China. These findings enrich the molecular epidemiological data of SuHVs in Chinese pig populations and highlight the previously overlooked, highly widespread circulation of PoCMV, warranting attention to its potential impacts on swine health and production performance.<\/jats:p>","DOI":"10.3390\/v18060625","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:17:31Z","timestamp":1780467451000},"page":"625","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Metaviromic Profiling of Genetic Diversity and Prevalence of Suid Herpesviruses Circulating in China"],"prefix":"10.3390","volume":"18","author":[{"given":"Jing","family":"Wang","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhibin","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China"},{"name":"Observation and Research Data Center for Animal Health, Ministry of Agriculture and Rural Affairs, Harbin 150069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shida","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China"},{"name":"Observation and Research Data Center for Animal Health, Ministry of Agriculture and Rural Affairs, Harbin 150069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaisi","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China"},{"name":"Observation and Research Data Center for Animal Health, Ministry of Agriculture and Rural Affairs, Harbin 150069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China"},{"name":"Observation and Research Data Center for Animal Health, Ministry of Agriculture and Rural Affairs, Harbin 150069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1035-1069","authenticated-orcid":false,"given":"Jingfei","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China"},{"name":"State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China"},{"name":"Observation and Research Data Center for Animal Health, Ministry of Agriculture and Rural Affairs, Harbin 150069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"001673","DOI":"10.1099\/jgv.0.001673","article-title":"ICTV Virus Taxonomy Profile: Herpesviridae 2021","volume":"102","author":"Gatherer","year":"2021","journal-title":"J. Gen. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/s12985-025-02779-7","article-title":"Herpesviruses: Overview of systematics, genomic complexity and life cycle","volume":"22","author":"Arzul","year":"2025","journal-title":"Virol. J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/s11262-024-02122-2","article-title":"Pseudorabies virus as a zoonosis: Scientific and public health implications","volume":"61","author":"Chen","year":"2025","journal-title":"Virus Genes"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1007\/s12250-020-00340-0","article-title":"Current Status and Challenge of Pseudorabies Virus Infection in China","volume":"36","author":"Tan","year":"2021","journal-title":"Virol. Sin."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.virol.2014.05.014","article-title":"Genomic organization and molecular characterization of porcine cytomegalovirus","volume":"460\u2013461","author":"Gu","year":"2014","journal-title":"Virology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1023\/A:1008156017758","article-title":"Characterization of the DNA polymerase loci of porcine cytomegaloviruses from diverse geographic origins","volume":"21","author":"Goltz","year":"2000","journal-title":"Virus Genes"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e81","DOI":"10.4142\/jvs.2021.22.e81","article-title":"Porcine lymphotropic herpesvirus (Gammaherpesvirinae) DNA in free-living wild boars (Sus scrofa Linnaeus, 1758) in Brazil","volume":"22","author":"Porto","year":"2021","journal-title":"J. Vet. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Denner, J. (2021). Porcine Lymphotropic Herpesviruses (PLHVs) and Xenotranplantation. Viruses, 13.","DOI":"10.3390\/v13061072"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Wu, J., Zhang, J., Zhou, J., Luo, Y., Wang, X., Yang, R., Zhu, J., Jia, M., Zhang, L., and Fu, L. (2024). Prevalence and Genetic Variation Investigation of the Pseudorabies Virus in Southwest China. Animals, 14.","DOI":"10.3390\/ani14213103"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Tan, L., Zhou, Y., Qiu, Y., Lei, L., Wang, C., Zhu, P., Duan, D., Lei, H., Yang, L., and Wang, N. (2022). Pseudorabies in pig industry of China: Epidemiology in pigs and practitioner awareness. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.973450"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1007\/s00705-011-1189-3","article-title":"Seroprevalence of porcine cytomegalovirus and sapovirus infection in pigs in Hunan province, China","volume":"157","author":"Liu","year":"2012","journal-title":"Arch. Virol."},{"key":"ref_12","first-page":"325","article-title":"Molecular detection of Porcine cytomegalovirus (PCMV) in wild boars from Northeastern Patagonia, Argentina","volume":"53","author":"Winter","year":"2021","journal-title":"Rev. Argent. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R.P., Banday, S., Mishra, A.K., and Das, G. (2023). Next-Generation Sequencing Technology: Current Trends and Advancements. Biology, 12.","DOI":"10.3390\/biology12070997"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1038\/s41559-024-02365-0","article-title":"Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity","volume":"8","author":"Pan","year":"2024","journal-title":"Nat. Ecol. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nature19094","article-title":"Uncovering Earth\u2019s virome","volume":"536","author":"Pavlopoulos","year":"2016","journal-title":"Nature"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s12250-020-00232-3","article-title":"Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China","volume":"36","author":"Shi","year":"2021","journal-title":"Virol. Sin."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Sun, W., Shi, Z., Wang, P., Zhao, B., Li, J., Wei, X., Wei, L., and Wang, J. (2023). Metavirome Analysis Reveals a High Prevalence of Porcine Hemagglutination Encephalomyelitis Virus in Clinically Healthy Pigs in China. Pathogens, 12.","DOI":"10.3390\/pathogens12040510"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/bioinformatics\/btg192","article-title":"ClustalW-MPI: ClustalW analysis using distributed and parallel computing","volume":"19","author":"Li","year":"2003","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3118","DOI":"10.1093\/bioinformatics\/btac287","article-title":"SimPlot++: A Python application for representing sequence similarity and detecting recombination","volume":"38","author":"Samson","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"qzae047","DOI":"10.1093\/gpbjnl\/qzae047","article-title":"GenBase: A Nucleotide Sequence Database","volume":"22","author":"Bu","year":"2024","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_24","unstructured":"(2025). CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Res., 53, D30\u2013D44."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Liu, H., Shi, Z., Liu, C., Wang, P., Wang, M., Wang, S., Liu, Z., Wei, L., Sun, Z., and He, X. (2020). Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.612474"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.vetmic.2010.02.014","article-title":"Herpesvirus systematics","volume":"143","author":"Davison","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1146\/annurev-virology-092917-043227","article-title":"How Host Specific Are Herpesviruses? Lessons from Herpesviruses Infecting Wild and Endangered Mammals","volume":"5","author":"Azab","year":"2018","journal-title":"Annu. Rev. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.tim.2016.11.009","article-title":"Herpesviruses and Their Host Cells: A Successful Liaison","volume":"25","author":"Adler","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Bo, Z., and Li, X. (2022). A Review of Pseudorabies Virus Variants: Genomics, Vaccination, Transmission, and Zoonotic Potential. Viruses, 14.","DOI":"10.3390\/v14051003"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Tan, L., Yao, J., Lei, L., Xu, K., Liao, F., Yang, S., Yang, L., Shu, X., Duan, D., and Wang, A. (2022). Emergence of a Novel Recombinant Pseudorabies Virus Derived From the Field Virus and Its Attenuated Vaccine in China. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.872002"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Liu, X., Liao, S., Zhu, L., Xu, Z., and Zhou, Y. (2013). Molecular epidemiology of porcine Cytomegalovirus (PCMV) in Sichuan Province, China: 2010\u20132012. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0064648"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Cybulski, P., Socha, W., Jablonski, A., Kondratiuk, R., Rybkowska, W., Stadejek, T., and Larska, M. (2025). First Molecular Detection of Porcine Cytomegalovirus (PCMV) and Porcine Lymphotropic Herpesvirus (PLHV) in Domestic Pigs in Poland. Pathogens, 14.","DOI":"10.3390\/pathogens14040396"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s00705-022-05690-6","article-title":"Presence of porcine cytomegalovirus, a porcine roseolovirus, in wild boars in Italy and Germany","volume":"168","author":"Hansen","year":"2023","journal-title":"Arch. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1007\/s42770-020-00335-9","article-title":"Porcine lymphotropic herpesvirus DNA detection in multiple organs of pigs in Brazil","volume":"51","author":"Leme","year":"2020","journal-title":"Braz. J. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1006\/viro.2002.1390","article-title":"Sequence analysis of the genome of porcine lymphotropic herpesvirus 1 and gene expression during posttransplant lymphoproliferative disease of pigs","volume":"294","author":"Goltz","year":"2002","journal-title":"Virology"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/6\/625\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T04:44:49Z","timestamp":1780634689000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/6\/625"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,29]]},"references-count":35,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["v18060625"],"URL":"https:\/\/doi.org\/10.3390\/v18060625","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,29]]}}}