Omicron emerged as the fifth variant of concern of SARS-CoV-2
coronavirus pandemic in late 2021 and rapidly overtook the previously
predominant Delta variants with a significantly faster transmission rate
and unique mutations on the spike gene. Hence, the ability to identify
viral variants rapidly and affordably in large number of patients, which
facilitates the monitoring of the transmission and clinical impact of
new variants, is needed to obtain information for updating the public
health policy. In this study, we evaluated the capability of two RT-PCR
and mass spectrometry-based SARS-CoV-2 variant classification platforms
to distinguish Delta, Omicron BA.1, and Omicron BA.2 variants in 618
COVID-19-positive samples from patients in Bangkok collected during
November 2011-March 2022. Analysis of the time-evolution pattern of
SARS-CoV-2 variant profiles indicated that the BA.1 and BA.2 possess up
to 2-3 times higher transmission rates than the Delta variant. Our study
showcases a cost-effective virus surveillance that enables a
quantitative estimation of variant-specific public health impact.