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

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

doi:10.3389/fmicb.2020.01316

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.

Highlights

The current pandemic of coronavirus disease 20191 (COVID-19) is caused by a positive-sense RNA virus, named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronaviridae Study Group of the International Committee on Taxonomy of V., 2020)
We found two SARS-CoV-2 genome lineages from Egypt-related imported cases
The Egypt-related isolates described in this study are divided into two distinct SARS-CoV-2 haplotype lineages, with two or three additional single-nucleotide variations (SNVs) from the major indexed isolates; one lineage, including P1–P3, included most haplotypes isolated from France and Egypt (Figure 3), whereas the other lineage, including P4 and P5, included the Netherlands/Belgium/ Switzerland isolates

Summary

Introduction

The current pandemic of coronavirus disease 20191 (COVID-19) is caused by a positive-sense RNA virus, named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronaviridae Study Group of the International Committee on Taxonomy of V., 2020). From the beginning of March 2020, 46 travelers who returned to Japan from abroad were suspected to have imported COVID-19; these cases account for roughly 10% of all new cases recorded in Japan Among these imported cases, as many as 26 have been linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Most of the travelers visited Egypt from late February to early March and embarked on Nile River cruise ship tours between Cairo and Luxor for 3–4 days. Soon after they returned to Japan, they experienced the onset of fever and sore throat.

Methods

Results

Conclusion