{"title":"基于全基因组分析剖析中国 PRRSV-1 的遗传多样性和进化趋势","authors":"Bangjun Gong, Hu Xu, Qi Sun, Chao Li, Lirun Xiang, Jing Zhao, Wansheng Li, Zhenyang Guo, Jinhao Li, Qian Wang, Jinmei Peng, Guohui Zhou, Chaoliang Leng, Yan-Dong Tang, Jianan Wu, Huairan Liu, Tong-Qing An, Xuehui Cai, Zhi-Jun Tian, Hongliang Zhang","doi":"10.1155/2024/9705539","DOIUrl":null,"url":null,"abstract":"<div>\n <p>Porcine reproductive and respiratory syndrome (PRRS) poses a serious threat to the Chinese swine industry. The etiological agent PRRSV can be classified as either PRRSV-1 or PRRSV-2. Recent studies have revealed an increase in the rates of PRRSV-1 detection and a wider PRRSV-1 distribution. However, the PRRSV-1 genome in China has yet to be fully characterized. In this study, 24 whole PRRSV-1 genomes from different swine farms were assembled and subjected to whole-genome analysis. A phylogenetic analysis based on the complete genome and ORF5 sequences revealed that the PRRSV-1 strains from China belonged to Western European Subtype I and could be classified into seven subgroups. Statistical analysis revealed that BJEU06-1-Like PRRSV is currently the predominant PRRSV-1 strain. Moreover, a similarity analysis showed low pairwise similarity between most PRRSV-1 genomes from different pig farms. Amino acid alignments of the Nsp2 gene revealed that the BJEU06-1-Like subgroup had five discontinued aa deletions (4 + 1). The new subgroup 1 had 11 continued aa deletions and an aa insertion, the new subgroup 2 had two discontinued aa deletions (1 + 1), and, except for in the case of HKEU16, the HKEU16-Like subgroup had five discontinuous aa deletions (1 + 4). Recombination analysis revealed that the BJEU06-1-Like and NMEU09-1-Like strains participated extensively in recent recombination events. The analysis of positive selection suggested that there were 15 positively selected codons in site model, and there were five sites under positive selection in the BJEU06-1-Like subgroup in the branch-site model. The mean rate and tMRCA for PRRSV-1 strains from China were 4.11 × 10<sup>−3</sup> substitutions/site/year and 1,969.63, respectively. Thus, it is crucial to strengthen epidemiological surveys of PRRSV-1 in China, especially those monitoring BJEU06-1-Like PRRSV.</p>\n </div>","PeriodicalId":234,"journal":{"name":"Transboundary and Emerging Diseases","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/9705539","citationCount":"0","resultStr":"{\"title\":\"Dissecting Genetic Diversity and Evolutionary Trends of Chinese PRRSV-1 Based on Whole-Genome Analysis\",\"authors\":\"Bangjun Gong, Hu Xu, Qi Sun, Chao Li, Lirun Xiang, Jing Zhao, Wansheng Li, Zhenyang Guo, Jinhao Li, Qian Wang, Jinmei Peng, Guohui Zhou, Chaoliang Leng, Yan-Dong Tang, Jianan Wu, Huairan Liu, Tong-Qing An, Xuehui Cai, Zhi-Jun Tian, Hongliang Zhang\",\"doi\":\"10.1155/2024/9705539\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n <p>Porcine reproductive and respiratory syndrome (PRRS) poses a serious threat to the Chinese swine industry. The etiological agent PRRSV can be classified as either PRRSV-1 or PRRSV-2. Recent studies have revealed an increase in the rates of PRRSV-1 detection and a wider PRRSV-1 distribution. However, the PRRSV-1 genome in China has yet to be fully characterized. In this study, 24 whole PRRSV-1 genomes from different swine farms were assembled and subjected to whole-genome analysis. A phylogenetic analysis based on the complete genome and ORF5 sequences revealed that the PRRSV-1 strains from China belonged to Western European Subtype I and could be classified into seven subgroups. Statistical analysis revealed that BJEU06-1-Like PRRSV is currently the predominant PRRSV-1 strain. Moreover, a similarity analysis showed low pairwise similarity between most PRRSV-1 genomes from different pig farms. Amino acid alignments of the Nsp2 gene revealed that the BJEU06-1-Like subgroup had five discontinued aa deletions (4 + 1). The new subgroup 1 had 11 continued aa deletions and an aa insertion, the new subgroup 2 had two discontinued aa deletions (1 + 1), and, except for in the case of HKEU16, the HKEU16-Like subgroup had five discontinuous aa deletions (1 + 4). Recombination analysis revealed that the BJEU06-1-Like and NMEU09-1-Like strains participated extensively in recent recombination events. The analysis of positive selection suggested that there were 15 positively selected codons in site model, and there were five sites under positive selection in the BJEU06-1-Like subgroup in the branch-site model. The mean rate and tMRCA for PRRSV-1 strains from China were 4.11 × 10<sup>−3</sup> substitutions/site/year and 1,969.63, respectively. Thus, it is crucial to strengthen epidemiological surveys of PRRSV-1 in China, especially those monitoring BJEU06-1-Like PRRSV.</p>\\n </div>\",\"PeriodicalId\":234,\"journal\":{\"name\":\"Transboundary and Emerging Diseases\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-06-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/9705539\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Transboundary and Emerging Diseases\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1155/2024/9705539\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Transboundary and Emerging Diseases","FirstCategoryId":"97","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1155/2024/9705539","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Dissecting Genetic Diversity and Evolutionary Trends of Chinese PRRSV-1 Based on Whole-Genome Analysis
Porcine reproductive and respiratory syndrome (PRRS) poses a serious threat to the Chinese swine industry. The etiological agent PRRSV can be classified as either PRRSV-1 or PRRSV-2. Recent studies have revealed an increase in the rates of PRRSV-1 detection and a wider PRRSV-1 distribution. However, the PRRSV-1 genome in China has yet to be fully characterized. In this study, 24 whole PRRSV-1 genomes from different swine farms were assembled and subjected to whole-genome analysis. A phylogenetic analysis based on the complete genome and ORF5 sequences revealed that the PRRSV-1 strains from China belonged to Western European Subtype I and could be classified into seven subgroups. Statistical analysis revealed that BJEU06-1-Like PRRSV is currently the predominant PRRSV-1 strain. Moreover, a similarity analysis showed low pairwise similarity between most PRRSV-1 genomes from different pig farms. Amino acid alignments of the Nsp2 gene revealed that the BJEU06-1-Like subgroup had five discontinued aa deletions (4 + 1). The new subgroup 1 had 11 continued aa deletions and an aa insertion, the new subgroup 2 had two discontinued aa deletions (1 + 1), and, except for in the case of HKEU16, the HKEU16-Like subgroup had five discontinuous aa deletions (1 + 4). Recombination analysis revealed that the BJEU06-1-Like and NMEU09-1-Like strains participated extensively in recent recombination events. The analysis of positive selection suggested that there were 15 positively selected codons in site model, and there were five sites under positive selection in the BJEU06-1-Like subgroup in the branch-site model. The mean rate and tMRCA for PRRSV-1 strains from China were 4.11 × 10−3 substitutions/site/year and 1,969.63, respectively. Thus, it is crucial to strengthen epidemiological surveys of PRRSV-1 in China, especially those monitoring BJEU06-1-Like PRRSV.
期刊介绍:
Transboundary and Emerging Diseases brings together in one place the latest research on infectious diseases considered to hold the greatest economic threat to animals and humans worldwide. The journal provides a venue for global research on their diagnosis, prevention and management, and for papers on public health, pathogenesis, epidemiology, statistical modeling, diagnostics, biosecurity issues, genomics, vaccine development and rapid communication of new outbreaks. Papers should include timely research approaches using state-of-the-art technologies. The editors encourage papers adopting a science-based approach on socio-economic and environmental factors influencing the management of the bio-security threat posed by these diseases, including risk analysis and disease spread modeling. Preference will be given to communications focusing on novel science-based approaches to controlling transboundary and emerging diseases. The following topics are generally considered out-of-scope, but decisions are made on a case-by-case basis (for example, studies on cryptic wildlife populations, and those on potential species extinctions):
Pathogen discovery: a common pathogen newly recognised in a specific country, or a new pathogen or genetic sequence for which there is little context about — or insights regarding — its emergence or spread.
Prevalence estimation surveys and risk factor studies based on survey (rather than longitudinal) methodology, except when such studies are unique. Surveys of knowledge, attitudes and practices are within scope.
Diagnostic test development if not accompanied by robust sensitivity and specificity estimation from field studies.
Studies focused only on laboratory methods in which relevance to disease emergence and spread is not obvious or can not be inferred (“pure research” type studies).
Narrative literature reviews which do not generate new knowledge. Systematic and scoping reviews, and meta-analyses are within scope.