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This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program.COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database.From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country.The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness.

IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as an aetiology agent of clustered cases of pneumonia in Wuhan, China and the disease is called Coronavirus Disease (COVID-19). The COVID-19 outbreak in Malaysia is categorized according to clusters. However, information on the genomic nature and diversity of the circulating strains is sparsely available. Hence, the study was aimed to characterize the virus and identify mutations. MethodologySARS-CoV-2 viral RNA was extracted from isolates and original specimen and subjected to next generation sequencing on Illumina NextSeq 500 platform. Full genome sequences were obtained by assembling against reference genomes using BBDuk and MEGAHIT softwares. Phylogenetic tree was constructed using Neigbour-joining & Tamura-Nei model and mutations were identified via MEGA X alignment. Results and Discussion[Refer to Poster]. ConclusionGenomic diversity of the Malaysian SARS-CoV-2 is apparent through the circulating type and unique mutations. Comparison of early outbreak and current strains have shown a shift from type B to C. Unique mutations identified exclusively among Malaysian SARS-CoV2 is indicative of rapidly evolving virus. This could pose a challenge in vaccine development. Characterization of the SARS-CoV-2 virus by molecular epidemiology carries significant information for preventive measures, diagnosis, and therapy of infectious diseases.Genomic diversity of the Malaysian SARS-CoV-2 is apparent through the circulating type and unique mutations. Comparison of early outbreak and current strains have shown a shift from type B to C. Unique mutations identified exclusively among Malaysian SARS-CoV2 is indicative of rapidly evolving virus. This could pose a challenge in vaccine development. Characterization of the SARS-CoV-2 virus by molecular epidemiology carries significant information for preventive measures, diagnosis, and therapy of infectious diseases.