Yu De, Zhao Zhuang-Yan, Yang Yong-Le, Qin Yu, Pan Dan, Yuan Li-Xia, Huang Yao-Wei, Wang Bin
Department of Veterinary Medicine, Zhejiang University, Hangzhou, China.
Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
J Med Virol. 2023 Mar;95(3):e28672. doi: 10.1002/jmv.28672.
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly discovered alphacoronavirus with zoonotic potential that causes diarrhea and vomiting mainly in piglets. Having emerged suddenly in 2017, the prevailing opinion is that the virus originated from HKU2, an alphacoronavirus whose primary host is bats, and at some unknown point achieved interspecies transmission via some intermediate. Here, we further explore the evolutionary history and possible cross-species transmission event for SADS-CoV. Coevolutionary analysis demonstrated that HKU2 may have achieved host switch via SADS-related (SADSr)-CoV, which was isolated from the genus Rhinolophus in 2017. SADS-CoV, HKU2, and SADSr-CoV share similar codon usage patterns and showed a lower tendency to use CpG, which may reflect a method of immune escape. The analyses of virus-host coevolution and recombination support SADSr-CoV is the direct source of SADS-CoV that may have undergone recombination events during its formation. Structure-based spike glycoprotein variance analysis revealed a more nuanced evolutionary pathway to receptor recognition for host switch. We did not find a possible positive selection site, and the dN/dS of the S gene was only 0.29, which indicates that the current SADS-CoV is slowly evolving. These results provide new insights that may help predict future cross-species transmission, and possibly surveil future zoonotic outbreaks and associated public health emergencies.
猪急性腹泻综合征冠状病毒（SADS-CoV）是一种新发现的具有人畜共患病潜力的甲型冠状病毒，主要导致仔猪腹泻和呕吐。该病毒于2017年突然出现，普遍观点认为它起源于HKU2，一种以蝙蝠为主要宿主的甲型冠状病毒，在某个未知时间点通过某种中间宿主实现了跨物种传播。在此，我们进一步探讨SADS-CoV的进化历史和可能的跨物种传播事件。共进化分析表明，HKU2可能通过2017年从菊头蝠属分离出的SADS相关（SADSr）-CoV实现了宿主转换。SADS-CoV、HKU2和SADSr-CoV具有相似的密码子使用模式，且使用CpG的倾向较低，这可能反映了一种免疫逃逸方式。病毒-宿主共进化和重组分析支持SADSr-CoV是SADS-CoV的直接来源，SADSr-CoV在形成过程中可能经历了重组事件。基于结构的刺突糖蛋白变异分析揭示了宿主转换受体识别的更细微进化途径。我们未发现可能的正选择位点，S基因的dN/dS仅为0.29，这表明当前的SADS-CoV正在缓慢进化。这些结果提供了新的见解，可能有助于预测未来的跨物种传播，并可能监测未来的人畜共患病爆发及相关公共卫生紧急情况。
