Iota variant12/16/2023 The latest major variants, Delta and Kappa, sharing two mutations E484Q (glutamic acid E substituted by glutamine Q) and L452R (leucine L altered by arginine R) were identified in India’s second COVID-19 wave. The Beta variant has E484K, while the Gamma variant has the E484K and the K417T mutations. Both Beta and Gamma variants have more substitutions other than N501Y. An emerging variant derived from B.1.1.7 also carries E484K mutation-glutamic acid E replaced with lysine K. The Alpha variant has an N501Y mutation: at the 501 residue, N asparagine has been replaced with Y tyrosine, as well as K417N-lysine K replaced with asparagine N. We will focus our discussion here on the VOCs that have major global health impacts since the 4 th quarter of the year 2020, including Alpha variant (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Kappa and Delta (B.1.617.1 and B.1.617.2) (Table 1). The spike gene mutations account for most of the clinically influential VOCs while the ORF1a frame of the genome serves as a key region for NSP mutations. Although by the beginning of May 2021, there has been reported more than 1.4 million sequences and among them 3913 major representative variants genomes that have been identified and included in the global SARS-CoV-2 sequence database operated by Global Initiative on Sharing Avian Influenza Data (GISAID), not all genetic mutations lead to variation in major proteins and/or alter virus infectivity. These genes are encoded in several groups, namely ORF1a (NSP1-11), ORF1b (NSP12-16), ORF3a, ORF6, ORF7a, ORF7b, ORF8 and ORF10.Ī variant can be as simply as a virus bearing a deviant mutation or complicated combinations of deviations leading to significant phenotypical alteration from original genome. NSPs are mostly enzymes or functional proteins that play a role in viral replication and methylation and may induce host responses to infection. SPs are encoded by 4 genes, including E (envelop), M (membrane), S (spike) and N (nucleocapsid) genes. The architecture of SARS-CoV-2 is made of two groups of proteins: structural proteins (SP) and non-structural proteins (NSP). SARS-CoV-2 is a positive-sense single-stranded RNA virus whose genome is of a low stability thus is more prone for mutation accumulation, with approximately 9.8 × 10 −4 substitutions/site yearly.
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