Li Yang, Zhang Yunjun, Liang Mifang, Zhang Yi, Ma Xuejun, Zhang Yong, Zhou Xiaohua
NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400020, China.
Biosaf Health. 2022 Feb;4(1):1-5. doi: 10.1016/j.bsheal.2021.12.001. Epub 2021 Dec 25.
Although significant achievements have shown that the coronavirus disease 2019 (COVID-19) resurgence in Beijing, China, was initiated by contaminated frozen products and transported via cold chain transportation, international travelers with asymptomatic symptoms or false-negative nucleic acid may have another possible transmission mode that spread the virus to Beijing. One of the key differences between these two assumptions was whether the virus actively replicated since, so far, no reports showed viruses could stop evolution in alive hosts. We studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences in this outbreak by a modified leaf-dating method with the Bayes factor. The numbers of single nucleotide variants (SNVs) found in SARS-CoV-2 sequences were significantly lower than those called from B.1.1 records collected at the matching time worldwide ( = 0.047). In addition, results of the leaf-dating method showed ages of viruses sampled from this outbreak were earlier than their recorded dates of collection (Bayes factors > 10), while control sequences (selected randomly with ten replicates) showed no differences in their collection dates (Bayes factors < 10). Our results which indicated that the re-emergence of SARS-CoV-2 in Beijing in June 2020 was caused by a virus that exhibited a lack of evolutionary changes compared to viruses collected at the corresponding time, provided evolutionary evidence to the contaminated imported frozen food should be responsible for the reappearance of COVID-19 cases in Beijing. The method developed here might also be helpful to provide the very first clues for potential sources of COVID-19 cases in the future.
尽管重大研究成果表明，中国北京2019年冠状病毒病（COVID-19）的再次出现是由受污染的冷冻产品引发，并通过冷链运输传播，但无症状或核酸检测呈假阴性的国际旅行者可能存在另一种将病毒传播到北京的潜在传播方式。这两种假设的关键区别之一在于病毒是否会主动复制，因为到目前为止，尚无报告显示病毒能在活体宿主中停止进化。我们采用一种经过改进的带有贝叶斯因子的叶龄推断方法，研究了此次疫情中严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的序列。在SARS-CoV-2序列中发现的单核苷酸变异（SNV）数量显著低于全球同期收集的B.1.1记录中的变异数量（P = 0.047）。此外，叶龄推断方法的结果显示，此次疫情中采样的病毒年龄早于其记录的采集日期（贝叶斯因子>10），而对照序列（随机选取十个重复样本）在采集日期上没有差异（贝叶斯因子<10）。我们的研究结果表明，2020年6月北京SARS-CoV-2的再次出现是由一种与同期收集的病毒相比缺乏进化变化的病毒引起的，这为受污染的进口冷冻食品导致北京出现COVID-19病例提供了进化证据。这里开发的方法可能也有助于为未来COVID-19病例的潜在来源提供最初线索。
