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Temporal lineage dynamics of the ORF5 gene of porcine reproductive and respiratory syndrome virus in Korea in 2014–2019
Archives of Virology ( IF 2.5 ) Pub Date : 2021-08-10 , DOI: 10.1007/s00705-021-05169-w
Seung-Chai Kim 1 , Chang-Gi Jeong 1 , Gyeong-Seo Park 1 , Ji-Young Park 2 , Hye-Young Jeoung 2 , Go-Eun Shin 2 , Mi-Kyeong Ko 2 , Seoung-Hee Kim 2 , Kyoung-Ki Lee 2 , Won-Il Kim 1
Affiliation  

Porcine reproductive and respiratory syndrome virus (PRRSV) is the most important pathogen in the Korean swine industry. Despite efforts including improved biosecurity and vaccination protocols, the virus continues to circulate and evolve. Based on phylogenetic analysis of open reading frame 5 (ORF5), Korean PRRSVs are known to form not only globally circulating lineages but also country-specific lineages (Lin Kor A, B, and C). To understand the recent epidemiological status of PRRSV in Korea, a total of 1349 ORF5 sequences of Korean PRRSV isolates from 2014 to 2019 were analyzed. Phylogenetic analysis was conducted using the maximum-likelihood method, and temporal changes in the relative prevalence of lineages were investigated. The analysis showed that PRRSV1 and PRRSV2 were both highly prevalent throughout the years examined. Among the PRRSV1 isolates, subgroup A (90.1%) and vaccine-like subgroup C (9.0%) composed most of the population. For PRRSV2 isolates, vaccine-like lineage 5 (36.3%) was dominant, followed by Lin Kor B (25.9%), Kor C (16.6%), lineage 1 (11.6%), and Kor A (9.1%). The PRRSV2 lineage 1 population increased from 2014 (1.8%) to 2019 (29.6%) in Korea due to the continual spread of sublineage 1.8 (NADC30-like) and introduction of sublineage 1.6 into the country. Additional genetic analysis, including analysis of non synonymous and synonymous mutations, revealed evidence of diversification and positive selection in immunologically important regions of the genome, suggesting that current vaccination is failing and promoting immune-mediated selection. Overall, these findings provide insights into the epidemiological and evolutionary dynamics of cocirculating viral lineages, and constant surveillance of PRRSV occurrence is needed.



中文翻译:

2014-2019年韩国猪繁殖与呼吸综合征病毒ORF5基因的时间谱系动态

猪繁殖与呼吸综合征病毒(PRRSV)是韩国养猪业最重要的病原体。尽管做出了包括改进生物安全和疫苗接种协议在内的努力,但该病毒仍在继续传播和进化。根据开放阅读框 5 (ORF5) 的系统发育分析,已知韩国 PRRSV 不仅形成全球流行的谱系,而且形成特定国家的谱系(Lin Kor A、B 和 C)。为了解韩国 PRRSV 的近期流行病学状况,对 2014 年至 2019 年韩国 PRRSV 分离株的 1349 个 ORF5 序列进行了分析。使用最大似然法进行系统发育分析,并调查了谱系相对流行率的时间变化。分析表明,PRRSV1 和 PRRSV2 在检查的年份中都非常流行。在 PRRSV1 分离株中,亚群 A (90.1%) 和疫苗样亚群 C (9.0%) 构成了大部分人群。对于 PRRSV2 分离株,疫苗样谱系 5 (36.3%) 占优势,其次是 Lin Kor B (25.9%)、Kor C (16.6%)、谱系 1 (11.6%) 和 Kor A (9.1%)。由于亚谱系 1.8(类似 NADC30)的持续传播和亚谱系 1.6 的引入,韩国的 PRRSV2 谱系 1 人口从 2014 年(1.8%)增加到 2019 年(29.6%)。额外的遗传分析,包括对非同义和同义突变的分析,揭示了基因组免疫学重要区域多样化和正选择的证据,表明当前的疫苗接种失败并促进了免疫介导的选择。总体,

更新日期:2021-09-07
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