TY - JOUR
T1 - Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.
AU - Hoshino, Kunikazu
AU - Maeshiro, Tatsuji
AU - Nishida, Nao
AU - Sugiyama, Masaya
AU - Fujita, Jiro
AU - Gojobori, Takashi
AU - Mizokami, Masashi
N1 - KAUST Repository Item: Exported on 2021-02-23
PY - 2021/2/15
Y1 - 2021/2/15
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/667532
UR - https://linkinghub.elsevier.com/retrieve/pii/S0378111921000901
U2 - 10.1016/j.gene.2021.145496
DO - 10.1016/j.gene.2021.145496
M3 - Article
C2 - 33588037
SN - 0378-1119
SP - 145496
JO - Gene
JF - Gene
ER -