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 −4 substitutions per site per year. Population dynamics and the effective reproductive number (R e ) 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 e 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.
【저자키워드】 SARS-CoV-2, COVID-19, Coronavirus disease 2019, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2, outbreak, Population dynamics, SARS, Severe acute respiratory syndrome, Cruise ship, MERS, Middle East respiratory syndrome, GISAID, Global Initiative on Sharing All Influenza Data, effective reproductive number, R0, Basic reproductive number, Nucleotide substitution rate, RT-PCR, reverse-transcription PCR, Re, effective reproductive number, MCMC, Markov chain Monte Carlo, GTR, general time-reversible, ML, maximum likelihood, ESS, effective sample size, HPD, highest posterior density, tMRCA, time to the most recent common ancestor, Confined settings,