Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.

Kunikazu Hoshino; Tatsuji Maeshiro; Nao Nishida; Masaya Sugiyama; Jiro Fujita; Takashi Gojobori; Masashi Mizokami

doi:10.1016/j.gene.2021.145496

Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.

Kunikazu Hoshino, Tatsuji Maeshiro, Nao Nishida, Masaya Sugiyama, Jiro Fujita, Takashi Gojobori, Masashi Mizokami

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English (US)
Pages (from-to)	145496
Journal	Gene
DOIs	https://doi.org/10.1016/j.gene.2021.145496
State	Published - Feb 15 2021

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10.1016/j.gene.2021.145496

https://repository.kaust.edu.sa/bitstream/10754/667532/1/transmission_1-s2.0-S0378111921000901-main.pdf

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@article{171beccb2faf471da2c0578916174142,

title = "Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.",

abstract = "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.",

author = "Kunikazu Hoshino and Tatsuji Maeshiro and Nao Nishida and Masaya Sugiyama and Jiro Fujita and Takashi Gojobori and Masashi Mizokami",

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doi = "10.1016/j.gene.2021.145496",

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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

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DO - 10.1016/j.gene.2021.145496

M3 - Article

C2 - 33588037

SN - 0378-1119

SP - 145496

JO - Gene

JF - Gene

ER -

Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.

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