CONTINUOUS INTRODUCTION, DISPERSAL, AND REPLACEMENT OF SARSCOV-2 VARIANTS IN KEDAH, MALAYSIA

Abstract

Intro: A national SARS-CoV-2 genome sequencing consortium was established in Aug 2021 to help monitor the emergence of the COVID-19 variants. Tropical Infectious Diseases Research and Education Centre (TIDREC) received samples from the states of Kedah, Kelantan, Perak, and Terengganu between Aug 2021 and March 2022 and samples from Kedah and Perlis from 1 Apr 2022. In the current study, we sequenced and analyzed the SARS-CoV-2 strains received from Kedah between July 2021 to June 2022. Methods: The RNA was extracted and screened for the presence of SARS-CoV-2 RNA using qRT-PCR. Samples with a Ct value less than 32 were selected for sequencing. The genome libraries were prepared using Ion AmpliSeq™ SARSCoV-2 Research Panel and sequenced using the Ion GeneStudio™ S5 Prime System. The genome sequences were assembled, and SARS-CoV-2 lineages were assigned using PANGOLIN COVID-19 Lineage Assigner. Findings: A total of 310 samples were sequenced and analyzed. Results showed that all 310 samples belonged to two groups of Variants of Concern (VOC), Delta and Omicron. Our results revealed that between Aug 2022 and mid-December, the Delta variant was the only circulating VOC in Kedah, with AY.59 as the dominant circulating lineage. The Omicron, BA.1.1, was first detected on 21 Dec 2022 in our collection. The Delta and Omicron variants were co-circulated in Kedah between Jan and Feb 2022. After that, the Omicron BA.2 lineage was reported in Feb 2022, and it replaced the BA.1 and its descendent lineages as the dominant lineage starting in March 2022. The Omicron BA.5 lineage was first detected in samples collected on 26 May 2022, suggesting the emergence of BA.5 in Kedah. Conclusion: We reported the continuous introduction, dispersal, and replacement of SARS-CoV-2 variants in Kedah, Malaysia. Continuous monitoring of the circulating SARS-CoV-2 is vital to detect the emergence of newer SARSCoV-2 variants.