Molecular evolution and structural analyses of spike protein COVID-19 variants in Negeri Sembilan of peninsular Malaysia

The sharing of COVID-19 sequences worldwide has allowed for comprehensive and real-time analyses of COVID-19 genomic diversity at regional levels. Temporal distribution of COVID-19 variants and lineages enables better infection control, surveillance, and facilitates policy making for public health. 417 sequences extracted from all COVID-19 cases in Negeri Sembilan of peninsular Malaysia from July 2021 until May 2022 were used for this study. Phylogenomics revealed a total of 20 circulating lineages, of which seven are still circulating. The majority (60.4%) of viruses in Negeri Sembilan are of GRA lineage with strong representation from the Malaysian lineage BA.1.1 (24.7%). A time series analysis showed a change in the dominating circulating lineage from AY.79 to BA.1.1, which correlated to the relaxing of lockdowns implemented by the Malaysian government. Several Malaysian sub-lineages (BA.2.40.1, BA.2.57 and BA.2.9) have emerged from April 2022 onwards. Evolutionary mutations of the sub-lineages also gave rise to novel single nucleotide polymorphisms (SNPs) in the spike proteins. Out of the 70 SNPs isolated from all samples, in silico prediction revealed five novel SNPs that could cause functional defects to the spike protein, which are S221L, L226S, V826L, C1240F and C1243F. Structural modelling of the V826L showed that the L826 possibly confers an increase in protein flexibility within the S2 region of S protein, which supports our in-silico predictions.