Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America

Ming-Jr Jian; Hsing-Yi Chung; Chih-Kai Chang; Shan-Shan Hsieh; Jung-Chung Lin; Kuo-Ming Yeh; Chien-Wen Chen; Feng-Yee Chang; Kuo-Sheng Hung; Ming-Tsan Liu; Ji-Rong Yang; Tein-Yao Chang; Sheng-Hui Tang; Cherng-Lih Perng; Hung-Sheng Shang

doi:10.7717/peerj.11991

Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America

PeerJ. 2021 Sep 2:9:e11991. doi: 10.7717/peerj.11991. eCollection 2021.

Authors

Affiliations

¹ Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Taipei city, Taiwan.
² Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Taipei city, Taiwan.
³ Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Taipei city, Taiwan.
⁴ Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Taipei City, Taiwan.
⁵ Centers for Disease Control, Taipei, Taiwan, Taipei city, Taiwan.
⁶ Institute of Preventive Medicine, National Defense Medical Center, Taipei city, Taiwan.

Abstract

Background: There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from five travelers who returned to Taiwan from the United States of America (USA) between March and April 2020.

Methods: Haplotype network analysis was performed using genome-wide single-nucleotide variations to trace potential infection routes. To determine the genetic variations and evolutionary trajectory of the isolates, the genomes of isolates were compared to those of global virus strains from GISAID. Pharyngeal specimens were confirmed to be SARS-CoV-2-positive by RT-PCR. Direct whole-genome sequencing was performed, and viral assemblies were subsequently uploaded to GISAID. Comparative genome sequence and single-nucleotide variation analyses were performed.

Results: The D614G mutation was identified in imported cases, which separated into two clusters related to viruses originally detected in the USA. Our findings highlight the risk of spreading SARS-CoV-2 variants through air travel and the need for continued genomic tracing for the epidemiological investigation and surveillance of SARS-CoV-2 using viral genomic data.

Conclusions: Continuous genomic surveillance is warranted to trace virus circulation and evolution in different global settings during future outbreaks.

Keywords: COVID-19; Imported case; Phylogenetic analysis; SARS-CoV-2; Whole-genome sequencing.

Grants and funding

This study was supported by the Tri-Service General Hospital, Taipei, Taiwan, ROC (grant number: TSGH-D-110100). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.