Investigation of the Molecular Epidemiology and Evolution of Circulating Severe Acute Respiratory Syndrome Coronavirus 2 in Thailand from 2020 to 2022 via Next-Generation Sequencing

Jiratchaya Puenpa; Vorthon Sawaswong; Pattaraporn Nimsamer; Sunchai Payungporn; Patthaya Rattanakomol; Nutsada Saengdao; Jira Chansaenroj; Ritthideach Yorsaeng; Kamol Suwannakarn; Yong Poovorawan

doi:10.3390/v15061394

Investigation of the Molecular Epidemiology and Evolution of Circulating Severe Acute Respiratory Syndrome Coronavirus 2 in Thailand from 2020 to 2022 via Next-Generation Sequencing

Viruses. 2023 Jun 19;15(6):1394. doi: 10.3390/v15061394.

Affiliations

¹ Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
² Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
³ Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
⁴ FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok 10300, Thailand.

Abstract

Coronavirus disease 2019 (COVID-19) is an infectious condition caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which surfaced in Thailand in early 2020. The current study investigated the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history. Complete genome sequencing of 210 SARS-CoV-2 samples collected from collaborating hospitals and the Institute of Urban Disease Control and Prevention over two years, from December 2020 to July 2022, was performed using next-generation sequencing technology. Multiple lineage introductions were observed before the emergence of the B.1.1.529 omicron variant, including B.1.36.16, B.1.351, B.1.1, B.1.1.7, B.1.524, AY.30, and B.1.617.2. The B.1.1.529 omicron variant was subsequently detected between January 2022 and June 2022. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated to be between 0.87 and 1.71 × 10^-3 substitutions per site per year. There was a substantial prevalence of the predominant mutations C25672T (L94F), C25961T (T190I), and G26167T (V259L) in the ORF3a gene during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes in viral genomes, which is crucial to ensuring that vaccine strains are protective against worldwide outbreaks.

Keywords: COVID-19; SARS-CoV-2; complete genome sequencing; evolution; molecular epidemiology; next-generation sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
High-Throughput Nucleotide Sequencing
Humans
Molecular Epidemiology
SARS-CoV-2* / genetics
Thailand / epidemiology

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

The research was financially supported by the Health Systems Research Institute, the National Research Council of Thailand, the Center of Excellence in Clinical Virology, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the MK Restaurant Group and Aunt Thongkam Foundation, and the BJC Big C Foundation. The Rachadapisek Sompote Fund of Chulalongkorn University awarded postdoctoral fellowships to Jiratchaya Puenpa.