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
Affiliations
Jiratchaya Puenpa
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Vorthon Sawaswong
Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Pattaraporn Nimsamer
Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Sunchai Payungporn
Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Patthaya Rattanakomol
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Nutsada Saengdao
Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
Jira Chansaenroj
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Ritthideach Yorsaeng
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
Kamol Suwannakarn
Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
Yong Poovorawan
Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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.
