SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise

Tsuyoshi Sekizuka; Sanae Kuramoto; Eri Nariai; Masakatsu Taira; Yushi Hachisu; Akihiko Tokaji; Michiyo Shinohara; Tsuyoshi Kishimoto; Kentaro Itokawa; Yusuke Kobayashi; Keisuke Kadokura; Hajime Kamiya; Tamano Matsui; Motoi Suzuki; Makoto Kuroda

doi:10.3389/fmicb.2020.01316

SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise

Front Microbiol. 2020 Jun 5:11:1316. doi: 10.3389/fmicb.2020.01316. eCollection 2020.

Authors

Affiliations

¹ Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.
² Ishikawa Prefectural Institute of Public Health and Environmental Science, Kanazawa, Japan.
³ Chiba Prefectural Institute of Public Health, Chiba, Japan.
⁴ Kochi Prefectural Institute of Public Health, Kochi, Japan.
⁵ Saitama Prefectural Institute of Public Health, Saitama, Japan.
⁶ Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.

Abstract

Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries.

Keywords: cruise ship; genome epidemiology; haplotype network; imported case; single-nucleotide variations.