Identification of SARS-CoV-2 variants using Next Generation Sequencing at Bamrasnaradura Infectious Diseases Institute
Keywords:
COVID-19, SARS-CoV-2, NGS, variant, ThailandAbstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome analysis using next-generation sequencing (NGS) is an important tool to study epidemiology and vaccine efficacy evaluations. According to WHO recommendations in 2021, this technique can be used for SARS-CoV-2 variants monitoring. This study aims to identify SARS-CoV-2 variants by using NGS techniques from nasopharyngeal/throat swab specimen of COVID-19 patients in routine service at Bamrasnaradura Infectious Diseases Institute, Thailand during June 2021 to March 2022. A total of 135 specimens were extracted for total nucleic acid extraction with an automated machine. Library preparation and genome sequencing were done by using Ion AmpliSeqTM and the Ion torrent GeneStudioTM S5 system. SARS-CoV-2 Insight Research Plug-in Package and SARS-CoV-2 lineage Plug-in for Torrent Suite Software were used for data analysis. The samples consisted of 50 males and 85 females with a median age of 33 years (range from 6 months to 86 years). The results of the SARS-CoV-2 variants showed the Omicron, Delta, and Alpha strain in 89 (65.93%), 40 (29.63%), and 6 (4.44%) samples. The most prevalence of SARS-CoV-2 strains detected from January to March 2022 was Omicron BA.1 and BA.2, which began to spread in Thailand. The results of this study can provide information on the epidemiology of COVID-19 and monitor the virus evolution, for further implement in evaluation of vaccines effectiveness and therapeutic medicine.
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