Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus
Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus
复制标题
DOI：
10.3389/fmicb.2019.02486
复制
发表时间：
2019-11-01
影响因子：
5.2
通讯作者：
VanderWaal, Kimberly
中科院分区：
文献类型：
--
作者：
Paploski, Igor Adolfo Dexheimer;Corzo, Cesar;VanderWaal, Kimberly
猪繁殖与呼吸综合征病毒（PRRSV）是美国养猪业最重要的地方性病原体。尽管控制工作涉及改善生物安全和不同的疫苗接种方案，但该病毒仍在继续传播和进化。其控制的首要挑战之一是高水平的遗传和抗原多样性。在这里，我们量化了 9 年期间（2009-2017 年）美国单个养猪地区多个 PRRSV 谱系的共同循环、出现和连续更替。通过将 4,000 多个 PRRSV 序列（开放阅读框 5）分类为系统发育谱系和亚谱系，我们记录了 PRRSV 种群持续的多样化和时间动态，包括 2008 年之前全球范围内似乎不存在的新型亚谱系的迅速出现。此外，谱系9是2009年至2010年最普遍的谱系，但其出现率在2014年之后每年下降到所有序列的0.5%，与谱系1作为主要谱系的出现或重新出现同时发生。不同谱系以及谱系 1 内三个不同亚谱系的连续优势，与免疫介导的优势谱系连续更替的选择假说一致。随着宿主群体通过自然感染或针对最常见变异的疫苗接种建立免疫力，这种显性（亚）谱系可能会被群体更容易受到影响的新兴变异所取代。对非同义和同义突变模式的分析揭示了基因组免疫学重要区域的正向选择的证据，进一步支持免疫介导的选择塑造该病毒的进化和流行病学动态的潜力。这对于 PRRSV 基因变异的出现和重新出现模式具有重要意义，这些变异对养猪业产生负面影响。对 PRRSV 发生情况的持续监测对于更好地了解共循环病毒谱系的流行病学和进化动态至关重要。利用全基因组测序和探索异源 PRRS 病毒之间交叉免疫程度的进一步研究可以进一步阐明 PRRSV 免疫反应，并有助于制定可能能够减少疾病影响的策略。
Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009-2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact.