Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia

PeerJ. 2022 Jun 10:10:e13522. doi: 10.7717/peerj.13522. eCollection 2022.

Abstract

Introduction: A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health.

Methods: Data were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia.

Results: Phylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein).

Conclusion: Our findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health.

Keywords: COVID-19; D614G; N439K; SARS-CoV-2; Whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / epidemiology
  • Humans
  • Indonesia / epidemiology
  • Mutation / genetics
  • Phylogeny
  • SARS-CoV-2* / genetics

Grants and funding

This work is supported by the Ministry of Research and Technology/National Research and Innovation Agency of Republic Indonesia (Ristek-BRIN) in collaboration with Indonesia Endowment Fund for Education (Lembaga Pengelola Dana Pendidikan/LPDP) (Grant no. 13/FI/P-KCOVID-19.2B3/X/2020). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.