Detection and characterization of SARS-CoV-2 variants in Thailand from 2020-2023 using next-generation sequencing
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Abstract
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.
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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Personal views expressed by the contributors in their articles are not necessarily those of the Journal of Associated Medical Sciences, Faculty of Associated Medical Sciences, Chiang Mai University.
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