Detection and characterization of SARS-CoV-2 variants in Thailand from 2020-2023 using next-generation sequencing

Background: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to multiple variants with significant public health implications. Objective: This study aimed to detect and characterize SARS-CoV-2 genomic variants in Thailand using next-generation sequencing (NGS) from 2020 to 2023. Materials and methods: A total of 2,592 oro/nasopharyngeal swab specimens with high viral loads (cycle threshold; Ct≤25.0) were collected from SARS-CoV2-positive patients in Nonthaburi, Nakhon Phanom, and Tak Provinces. NGS was performed using Ion Torrent, Oxford Nanopore Technologies, and Illumina platforms to identify and analyze SARS-CoV-2 variants. Results: The sequencing revealed various SARS-CoV-2 variants circulating in Thailand, with 2,592 lineages identified. The Omicron variant was predominant, accounting for 93.44% (2,422/2,592). The most common Omicron subvariants were BA.2 (54.86%, 1,422/2,592), BA.5 (20.22%, 524/2,592), and XBB (14.51%, 376/2,592). The Delta variant constituted 2.66% (69/2,592) of the cases, with AY.30 (1.20%, 31/2,592) and AY.85 (1.27%, 33/2,592) being the most frequent sub-lineages. The Alpha variant (B.1.1.7) was detected in 33 cases (1.27%), and the Beta variant (B.1.351) in 1 case (0.04%). Conclusion: The findings reveal a significant shift in the SARS-CoV-2 variant landscape in Thailand, with Omicron becoming the dominant strain post-2022. Continuous genomic surveillance is critical for tracking viral evolution, informing public health strategies, and supporting pandemic control efforts in Thailand and Southeast Asia.