Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan

Haruka Abe,Yuri Ushijima,Takaaki Kinoshita,Kouichi Morita,Jiro Yasuda,Koichi Izumikawa,Murasaki Amano,Katsunori Yanagihara,Yasuteru Sakurai,Yohei Kurosaki,Shigeru Kohno,Rokusuke Yoshikawa

doi:10.3390/microorganisms10010099

Haruka Abe, Yuri Ushijima + Show 10 more

Open Access

https://doi.org/10.3390/microorganisms10010099

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Journal: Microorganisms	Publication Date: Jan 4, 2022
Citations: 3	License type: CC BY 4.0

Affiliation: Nagasaki University, Nagasaki University Hospital

Abstract

In the initial phase of the novel coronavirus disease (COVID-19) pandemic, a large-scale cluster on the cruise ship Diamond Princess (DP) emerged in Japan. Genetic analysis of the DP strains has provided important information for elucidating the possible transmission process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on a cruise ship. However, genome-based analyses of SARS-CoV-2 detected in large-scale cruise ship clusters other than the DP cluster have rarely been reported. In the present study, whole-genome sequences of 94 SARS-CoV-2 strains detected in the second large cruise ship cluster, which emerged on the Costa Atlantica (CA) in Japan, were characterized to understand the evolution of the virus in a crowded and confined place. Phylogenetic and haplotype network analysis indicated that the CA strains were derived from a common ancestral strain introduced on the CA cruise ship and spread in a superspreading event-like manner, resulting in several mutations that might have affected viral characteristics, including the P681H substitution in the spike protein. Moreover, there were significant genetic distances between CA strains and other strains isolated in different environments, such as cities under lockdown. These results provide new insights into the unique evolution patterns of SARS-CoV-2 in the CA cruise ship cluster.

Highlights

IntroductionAs of 1 October 2021, more than 230 million cases of SARS-CoV-2 infections have been confirmed worldwide, with 4.8 million deaths [3]
Introduction iationsUnderstanding the evolutionary patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease (COVID-19) pandemic to identify significant mutation sites directly affecting viral characteristics is essential for establishing appropriate public health responses and developing effective countermeasures [1,2].As of 1 October 2021, more than 230 million cases of SARS-CoV-2 infections have been confirmed worldwide, with 4.8 million deaths [3]
Specimens were derived from crew members of a large cruise ship, Costa Atlantica, which had been in repair since January 2020 in Nagasaki, Japan

Summary

Introduction

As of 1 October 2021, more than 230 million cases of SARS-CoV-2 infections have been confirmed worldwide, with 4.8 million deaths [3]. Due to the proofreading function of the viral proteins, SARS-CoV-2 isolates display relatively small phylogenetic distances among each other in the phylogenetic tree, making it difficult to clarify the genetic relationships among strains [4]. Approximately four million complete genomes of SARS-CoV-2 have been deposited in the Global Initiative on Sharing All Influenza Data (GISAID) database (https://www.gisaid.org/ (accessed on 1 October 2021)).

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