Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022.

The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10-3 (95% highest posterior density [HPD], 1.72 × 10-3 to 3.62 × 10-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.

Molecular characterisation and tracking of the severe acute respiratory syndrome coronavirus 2, Thailand, 2020–2022 (preprint)

Coronavirus disease 2019 (COVID-19) is a severe and frequently lethal disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that surfaced in Thailand in early 2020. As of this writing, there have been 3,303,169 reported cases and 24,075 deaths in Thailand. This study investigated molecular characterisation and the evolution of the SARS-CoV-2 identified during 2020–2022 in Thailand. Two hundred and sixty-eight SARS-CoV-2 strains, collected mostly in Bangkok during 2020–2022 from COVID-19 patients, were characterised by partial genome sequencing. Moreover, 5,627 positive SARS-CoV-2 samples were identified as variants of the virus (GRY/Alpha, GK/delta, GRA/Omicron BA.1 and GRA/Omicron BA.2) by multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR) assays. The results revealed that clade GH caused the predominant outbreak in the second wave (December 2020–January 2021), clade GRY/Alpha in the third wave (April–June 2021), clade GK/delta in the fourth wave (July–December 2021), and clade GRA/Omicron in the fifth wave (January–March 2022). The evolutionary rate in the outbreak was 2.60×10 − 3 (95% highest posterior density [HPD], 1.72×10 − 3 to 3.62×10 − 3 ) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants to prevent possible new COVID-19 outbreaks.