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.

The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology

“…We then infer a decrease in reproductive number, which remains near or below 1 in the last 23 days of the time period of interest, suggesting that the epidemic was mostly contained by measures taken. These trends agree with other studies in magnitude, and although estimates ranging from 2.28 to 14.8 have been reported for the first time period, most analyses infer a reproductive number below 2 in the subsequent time periods ( Hoshino et al 2021 ; Zhang et al 2020 ; Rocklöv et al 2020 ). Interestingly, we note that in our results the decrease in reproductive number is driven by the sampling and removal of individuals from the infectious population, with the total sampling rate going up from 1.76 to 2.14 days \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$^{-1}$\end{document} , after February 11th (see Supplementary Fig.…”

Transmission of SARS-CoV-2 Associated with Cruise Ship Travel: A Systematic Review

“…We excluded 53 studies (see Supplementary Materials File S3 and File S4 for the reasons for exclusion). In total, we included 26 articles: 2 environmental studies [ 15 , 16 ], 23 papers considering transmission of SARS-CoV-2 aboard cruise ships [ 6 , 7 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ], and one systematic review [ 38 ] ( Supplementary Materials File S5 ). The main characteristics of the included studies are presented in Table 1 and Table 2 .…”

“…Among 23 papers reporting on onboard transmission of SARS-CoV-2, 15 articles presented different aspects of the outbreak on the Diamond Princess (DP) cruise ship [ 7 , 17 , 19 , 20 , 21 , 23 , 24 , 25 , 26 , 27 , 29 , 30 , 31 , 35 , 37 ]. Nine articles reported on other international ships [ 6 , 7 , 18 , 22 , 28 , 32 , 33 , 34 , 36 ].…”

“…Fifteen studies reported different aspects of the SARS-CoV-2 outbreak from the DP [ 7 , 17 , 19 , 20 , 21 , 23 , 24 , 25 , 26 , 27 , 29 , 30 , 31 , 35 , 37 ]. Six studies detailed the ship’s technical specifications [ 23 , 25 , 26 , 30 , 31 , 35 ], focusing mainly on cabin capacity and occupancy, and distribution of cases according to different decks.…”

“…The total number of people onboard the DP was reported to be 3711 [ 7 , 19 , 21 , 25 , 26 , 27 , 31 , 35 , 37 ] or 3713 [ 30 ]. The number of passengers was reported to be 2666 [ 7 , 19 , 25 , 27 , 31 ] or 2645 [ 30 ]. The number of crew was reported to be 1045 [ 7 , 19 , 25 , 27 , 31 ] or 1068 [ 23 , 30 ].…”