Whole-genome-scale analysis of circulating SARS-CoV-2 during the first COVID-19 wave in an international tourist destination, Bali, Indonesia

Abstract

Background: The emergence of severe acute respiratory syndromes coronavirus 2 (SARS-CoV-2) variants such as B.1.17 (alpha), B.1351 (beta), and B.1.617.2 (delta) have caused a significant rise in coronavirus disease 2019 (COVID-19) cases worldwide. In response, the Indonesian government imposed restrictions on international and domestic travel, especially in areas with a high number of COVID-19 cases including Java Island and Bali. The aim of this study was to investigate the mutation patterns of indigenous SARS-CoV-2 strains in Bali. Methods: We conducted whole-genome sequencing on isolates collected from COVID-19-confirmed patients at the end of the first wave (January – March 2021). The sequencing was carried out at the 1st BASE Pte Ltd Laboratory (Singapore) using Oxford Nanopore Platform (GridION) using IDT ARTIC nCoV-2019 V3 Panel. The phylogenetic tree was constructed on MEGA 7.0 with hCoV-19/Wuhan/WIV04/2019 as the genomic reference. Results: Our data revealed that none of the isolates were variants of concern. Among the five lineages tracked, the viral isolates were most likely from B.1.466.2 (n=4). All viruses had D614G mutation in the spike protein with clade GH being most predominant (n=10) and followed by GR (n=1) and O (n=1). Additionally, mutations at NS3, NSP3, NSP12, and NSP6 were found. Conclusion: At the end of the first COVID-19 wave in Bali, variants of concern were not detected which could be attributed to the heavy mobility restrictions.