Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis.
Name:
transmission_1-s2.0-S0378111921000901-main.pdf
Size:
1012.Kb
Format:
PDF
Description:
Accepted manuscript
Type
ArticleAuthors
Hoshino, KunikazuMaeshiro, Tatsuji
Nishida, Nao

Sugiyama, Masaya
Fujita, Jiro

Gojobori, Takashi

Mizokami, Masashi
KAUST Department
Biological and Environmental Science and Engineering (BESE) DivisionBioscience Program
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
Date
2021-02-15Online Publication Date
2021-02-15Print Publication Date
2021-05Embargo End Date
2022-02-15Submitted Date
2020-10-16Permanent link to this record
http://hdl.handle.net/10754/667532
Metadata
Show full item recordAbstract
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.2021.145496Publisher
Elsevier BVJournal
GenePubMed ID
33588037PubMed Central ID
PMC7880849Additional Links
https://linkinghub.elsevier.com/retrieve/pii/S0378111921000901ae974a485f413a2113503eed53cd6c53
10.1016/j.gene.2021.145496
Scopus Count
Related articles
- Coronavirus Disease 2019 (COVID-19) in Americans Aboard the Diamond Princess Cruise Ship.
- Authors: Plucinski MM, Wallace M, Uehara A, Kurbatova EV, Tobolowsky FA, Schneider ZD, Ishizumi A, Bozio CH, Kobayashi M, Toda M, Stewart A, Wagner RL, Moriarty LF, Murray R, Queen K, Tao Y, Paden C, Mauldin MR, Zhang J, Li Y, Elkins CA, Lu X, Herzig CTA, Novak R, Bower W, Medley AM, Acosta AM, Knust B, Cantey PT, Pesik NT, Halsey ES, Cetron MS, Tong S, Marston BJ, Friedman CR
- Issue date: 2021 May 18
- Haplotype networks of SARS-CoV-2 infections in the <i>Diamond Princess</i> cruise ship outbreak.
- Authors: Sekizuka T, Itokawa K, Kageyama T, Saito S, Takayama I, Asanuma H, Nao N, Tanaka R, Hashino M, Takahashi T, Kamiya H, Yamagishi T, Kakimoto K, Suzuki M, Hasegawa H, Wakita T, Kuroda M
- Issue date: 2020 Aug 18
- Preparation for Quarantine on the Cruise Ship Diamond Princess in Japan due to COVID-19.
- Authors: Yamahata Y, Shibata A
- Issue date: 2020 May 11
- Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine.
- Authors: Yeh TY, Contreras GP
- Issue date: 2021 Jul 1
- SARS-CoV-2 infections among Australian passengers on the Diamond Princess cruise ship: A retrospective cohort study.
- Authors: Walker LJ, Codreanu TA, Armstrong PK, Goodwin S, Trewin A, Spencer E, Colquhoun SM, Stephens DM, Baird RW, Douglas NM, Cribb D, Owen R, Kelly P, Kirk MD
- Issue date: 2021