ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. Identification of virus lineages is key to tracking the chains of transmission and for monitoring variants of interest as well as variants of concern. This study aimed to develop and validate a cost-effective method to determine SARS-CoV-2 lineages of virus samples from the first wave of the pandemic in Thailand (January -May 2020). A lineage-specific single nucleotide polymorphism (SNP) genotyping panel of SARS-CoV-2 was designed based on genomic surveillance data generated in the first wave. Viral RNA specimens obtained from the Department of Pathology, Faculty of Medicine Ramathibodi Hospital were analyzed by a MassARRAY (R) platform in comparison to a next generation sequencing of the virus genome. The MassARRAY (R) system was able to identify the SARS-CoV-2 lineages with high accuracy supporting its application as a rapid and cost-effective method for identification of circulating COVID-1 9 variants in the country, and has the ability to accommodate new SARS-CoV-2 variants by simple modifications of the assay protocol.
ABSTRACT
Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented in March of 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.