Department of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan.
Department of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan.
Gene. 2021 May 5;779:145496. doi: 10.1016/j.gene.2021.145496. Epub 2021 Feb 13.
An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred aboard the Diamond Princess cruise ship between her January 20 departure and late February 2020. Here, we used phylodynamic analyses to investigate the transmission dynamics of SARS-CoV-2 during the outbreak. Using a Bayesian coalescent-based method, the estimated mean nucleotide substitution rate of 240 SARS-CoV-2 whole-genome sequences was approximately 7.13 × 10 substitutions per site per year. Population dynamics and the effective reproductive number (R) of SARS-CoV-2 infections were estimated using a Bayesian framework. The estimated origin of the outbreak was January 21, 2020. The infection spread substantially before quarantine on February 5. The R peaked at 6.06 on February 4 and gradually declined to 1.51, suggesting that transmission continued slowly even after quarantine. These findings highlight the high transmissibility of SARS-CoV-2 and the need for effective measures to control outbreaks in confined settings.
一起由严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）引起的 2019 年冠状病毒病（COVID-19）疫情于 2020 年 1 月 20 日钻石公主号游轮启航和 2 月下旬期间爆发。在这里，我们使用系统发育动力学分析来研究疫情期间 SARS-CoV-2 的传播动态。使用基于贝叶斯合并的方法，240 个 SARS-CoV-2 全基因组序列的估计平均核苷酸取代率约为每年每个位点 7.13×10 个取代。使用贝叶斯框架估计 SARS-CoV-2 感染的种群动态和有效繁殖数（R）。估计疫情的起源是 2020 年 1 月 21 日。在 2 月 5 日隔离之前，感染已经大量传播。R 在 2 月 4 日达到 6.06，然后逐渐下降到 1.51，这表明即使在隔离之后，传播仍在缓慢继续。这些发现强调了 SARS-CoV-2 的高传染性以及在封闭环境中控制疫情爆发的需要采取有效措施。
