State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
J Virol. 2020 Feb 28;94(6). doi: 10.1128/JVI.01813-19.
Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs ( = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014-2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991-2013 data and the 2014-2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014-2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries. Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.
猪繁殖与呼吸综合征病毒（PRRSV）是一种影响养猪业的重要病原体，属于高度遗传多样化的 RNA 病毒。然而，该病毒的系统发育和基因组重组特性尚未完全阐明。本研究对中国和美国在 2014-2018 年期间的所有北美（NA）型 PRRSV 基因组序列（ = 355 个，包括本研究中测序的 138 个 PRRSV 基因组）进行了比较分析，结果显示非结构蛋白 9（NSP9）和 GP2 到 GP3 区域存在高频的谱系间重组热点。研究发现，在中国和美国，1 型（L1）PRRSV 易受到 PRRSV 之间的重组影响。1991-2013 年数据和 2014-2018 年数据之间的重组主要亲本显示出从复杂到简单的趋势。2014-2018 年，中国 PRRSV 的主要重组模式由 L8 到 L1 转变，而美国 PRRSV 一直以 L1 为主干。谱系内重组热点不像谱系间重组热点那样集中。在 L1 中具有不同多样性的两个主要分支中，NADC30 样 PRRSV 的群体遗传多样性呈下降趋势，NADC34 样 PRRSV 的群体遗传多样性多年来一直相对稳定。对 NSP2 插入和缺失（indel）多态性的系统分析将 PRRSV 分为 25 种模式，可为 PRRSV 的分类提供新的参考依据。本研究结果有助于加深对 PRRSV 重组的理解，并表明需要在国家间开展协调的流行病学调查。猪繁殖与呼吸综合征（PRRS）是最重要的猪病之一。然而，PRRS 病毒（PRRSV）的系统发育和基因组重组特性尚未完全阐明。本研究系统比较了中国和美国的北美（NA）型 PRRSV 在线系分布、重组、NSP2 多态性和进化动态方面的差异。值得注意的是，我们在非结构蛋白 9（NSP9）和 GP2 到 GP3 区域发现了高频的谱系间重组热点。此外，中国和美国的毒株之间的基因组内重组热点分散在整个基因组中。进一步的，我们基于 NSP2 indel 模式提出了 PRRSV 的分类新方法。进化动态分析表明，NADC30 样 PRRSV 的群体遗传多样性呈下降趋势，这表明可能会出现优势种群并引发疫情。本研究结果为 PRRSV 的重组提供了重要的见解，并表明需要开展国际流行病学调查。
