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

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    transmission_1-s2.0-S0378111921000901-main.pdf
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    Description:
    Accepted manuscript
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    Type
    Article
    Authors
    Hoshino, Kunikazu
    Maeshiro, Tatsuji
    Nishida, Nao cc
    Sugiyama, Masaya
    Fujita, Jiro cc
    Gojobori, Takashi cc
    Mizokami, Masashi
    KAUST Department
    Biological and Environmental Science and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
    Date
    2021-02-15
    Online Publication Date
    2021-02-15
    Print Publication Date
    2021-05
    Embargo End Date
    2022-02-15
    Submitted Date
    2020-10-16
    Permanent link to this record
    http://hdl.handle.net/10754/667532
    
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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.
    Citation
    Hoshino, K., Maeshiro, T., Nishida, N., Sugiyama, M., Fujita, J., Gojobori, T., & Mizokami, M. (2021). Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis. Gene, 145496. doi:10.1016/j.gene.2021.145496
    Publisher
    Elsevier BV
    Journal
    Gene
    DOI
    10.1016/j.gene.2021.145496
    PubMed ID
    33588037
    PubMed Central ID
    PMC7880849
    Additional Links
    https://linkinghub.elsevier.com/retrieve/pii/S0378111921000901
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.gene.2021.145496
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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