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

Affiliation

Hoshino K(1), Maeshiro T(2), Nishida N(3), Sugiyama M(4), Fujita J(5), Gojobori T(6), Mizokami M(7).
Author information:
(1)Department of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan. Electronic address: [Email]
(2)Department of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan. Electronic address: [Email]
(3)Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan. Electronic address: [Email]
(4)Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan. Electronic address: [Email]
(5)Department of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan. Electronic address: [Email]
(6)Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, 23955-6900, Saudi Arabia. Electronic address: [Email]
(7)Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan. Electronic address: [Email]

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 (Re) 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 Re 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.