Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.
Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA.
Science. 2021 Apr 23;372(6540):412-417. doi: 10.1126/science.abf8003. Epub 2021 Mar 18.
Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated before the time of the most recent common ancestor of all sequenced SARS-CoV-2 genomes. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province, China. By characterizing the likely dynamics of the virus before it was discovered, we show that more than two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.
了解严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）何时出现对于评估我们目前监测新型人畜共患病原体的方法以及理解 COVID-19 早期控制和缓解努力的失败至关重要。我们使用合并框架将回顾性分子钟推断与前瞻性流行病学模拟相结合，以确定 SARS-CoV-2 在所有测序 SARS-CoV-2 基因组的最近共同祖先出现之前可以传播多长时间。我们的结果将 2019 年 10 月中旬至 11 月中旬定义为在中国湖北省出现首例 SARS-CoV-2 的可能时间段。通过描述在被发现之前病毒的可能动态，我们表明，超过三分之二的 SARS-CoV-2 样人畜共患病事件将是自限性的，在没有引发大流行的情况下自行消失。我们的研究结果强调了人畜共患病监测方法在检测具有中等死亡率的高传染性病原体方面的不足。
