Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus
Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus
复制标题
DOI：
10.1093/molbev/msaa117
复制
发表时间：
2020-09-01
影响因子：
10.7
通讯作者：
Su, Shuo
中科院分区：
文献类型：
--
作者：
He, Wan-Ting;Ji, Xiang;Su, Shuo
严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的出现再次表明，动物冠状病毒（CoV）是人类流行病的潜在来源。猪三角洲冠状病毒（Porcine deltacoronavirus，PDCoV）是一种新发现的猪肠道病原体，在世界范围内均有分布。在这里，我们实施并描述了一种方法来分析PDCoV在猪群中出现后的流行病学。我们对21种新测序病毒的全基因组序列数据进行了综合分析，沿着过去15年在全球收集的全面流行病学监测数据。我们发现四个不同的系统发育谱系的PDCoV，这在他们的地理循环模式不同。有趣的是，我们发现，与美国血统相比，中国血统中的猪在不同的养殖系统和生态环境中饲养，更频繁的系内和系间重组和更高的病毒遗传多样性。大多数重组断裂点位于ORF 1ab基因中，而不是编码结构蛋白的基因中。我们还确定了5个氨基酸的刺突蛋白的正选择下，适应性进化的作用。根据结构图，三个正选择的位点位于S1亚基的N-末端结构域，这是最有可能参与结合碳水化合物受体，而其他两个位于或接近S2亚基的融合肽，因此可能影响膜融合。最后，我们的地理分布调查强调了显著的南北传播以及中国频繁的远距离传播事件，这些事件可能涉及人为介导的传播。我们的研究结果为PDCoV的进化和传播提供了新的见解，有助于我们理解CoV出现的关键因素。
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.