Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for the COVID-19 pandemic declared by World Health Organization (WHO) on 11 March 2020, continues to cause deleterious public health and socioeconomic impacts . As of 26 December 2021, there have been over 278 million confirmed COVID-19 cases, with over 5 million fatal cases globally . SARS-CoV-2 is an enveloped virus harbouring a positive-sense, single-stranded RNA genome of approximately 27–32 kb in size encoding for four structural proteins, spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, and 16 nonstructural proteins (nsp1-nsp16) participating in several functional processes and viral replication . The massive circulation of SARS-CoV-2 worldwide and inequitable global vaccine distribution allow the virus to experience evolutionary pressures, leading to an emergence of new variants [4, 5]. High volumes of SARS-CoV-2 genomes have been generated rapidly and deposited in the global archive, namely the Global Initiative on Sharing All Influenza (GISAID) database. As of 2 March 2021, classified by significant mutations, there were nine clades consisting of S, L, V, G, GH, GK, GR, GV, and GRY . The epidemiologically relevant phylogenetic cluster of SARS-CoV-2 is further defined as a lineage by the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) tool . Based on the enhanced transmissibility, increase in virulence, and decrease in the natural infection- and vaccine-mediated neutralisation attributed to significant amino acid substitutions, SARS-CoV-2 variants are classified as Variants of Concern (VOC) .
By December 2021, Thailand experienced its fifth COVID-19 wave. The cumulative number of confirmed COVID-19 cases was 3,398,792, with 24,417 deaths recorded by 22 March 2022 . The first confirmed COVID-19 case was reported on 12 January 2020, detected in a traveller from China . The number of the infected individuals rapidly surged during March–May 2020 because of viral spreading linked to boxing events and entertainment venues in Bangkok, then disseminated on a nationwide level and was considered the first COVID-19 wave in Thailand . To grapple with the virus spreading effectively, public health and social measures, including wearing masks, physical distancing, movement restriction, workplace and school closures, and city lockdowns were implemented mandatorily. The second wave occurred during October–March 2021, triggered by the spread among Myanmar migrants working at the seafood market in Samut Sakhon. The third wave began in early April 2021 with the upsurge of COVID-19 cases linked to the entertainment venue at Thonglor, Bangkok . This worse and deadlier wave was driven by the emergence of a more transmissible B.1.1.7 SARS-CoV-2 variant of concern (VOC), leading to rising hospitalisations and overwhelming healthcare facilities . Protective measures were still stringent. Moreover, field hospitals and hospitals were set up for isolation. Amid the third wave, the mass vaccination campaign was rolled out on 7 June 2021 to slow down the transmission. However, the supply of vaccines was limited, and only two brands of vaccines, the CorovaVac and ChAdOx1-S vaccines, were available at that time. As of 1 July 2021, there were 52,052 confirmed COVID-19 cases with 1,971 patients classified as having severe illness, of which 566 patients required ventilatory support . As of 8 July 2021, COVID-19 cases were reported in all 77 provinces of Thailand. The Centre for COVID-19 Situation Administration (CCSA) declared the emergence of the fourth wave of COVID-19 pandemic in Thailand from the highly contagious delta variant, whose transmissibility is faster than that of the previous SARS-CoV-2 variant .
As part of the molecular epidemiological investigation of SARS-CoV-2 in Thailand during the first wave of the outbreak in 2020, 40 nasopharyngeal and/or throat swab specimens from 40 samples were found infected with SARS-CoV-2 types L, GH, GR, O, and S . Our study aimed to monitor and track emerging new variants of SARS-CoV2 circulating in Thailand between March 2020 and March 2022. To assist public communication and avoid stigmatisation, the Greek alphabet, i.e. alpha, beta, gamma, delta, omicron, is used to designate SARS-CoV-2 variants. Monitoring and tracking mutations of the viral genome were conducted along with deciphering the molecular mechanism of the virus-host interaction, providing information for managing countermeasures, including vaccines, therapeutic medicines, diagnostic tools, and public health and social policy.