Journal
VIRUSES-BASEL
Volume 15, Issue 6, Pages -Publisher
MDPI
DOI: 10.3390/v15061394
Keywords
SARS-CoV-2; COVID-19; evolution; complete genome sequencing; molecular epidemiology; next-generation sequencing
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This study conducted complete genome sequencing of 210 samples to investigate the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history, revealing multiple lineage introductions before the emergence of the omicron variant. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated, and certain predominant mutations in the ORF3a gene were identified during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes and is crucial for vaccine strain development.
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 x 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.
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