Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India

Abstract

India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on GISAID, a global initiative for sharing avian flu data. In this study, we have analysed the spike protein sequences from all five isolates and also compared their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and another at 1124 in the S2 domain of spike protein of the isolates from West Bengal only. There was one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of the mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.

A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics

“…The substituted branched-chain amino acids were shown to interfere with the folding rate, shape, or conformation of a protein, which agreed to the previous studies [ 28 , 30 , 67 ]; Liji, 2020; [ 29 ]. We observed altered drug specificity in the spike protein of Surat isolates when glycine was replaced with valine similar to West Bengal isolates [ 68 ]. G14S mutation can influence the catalytic activity and folding rate of PLPro worldwide [ 69 ].…”

Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states

“…A number of studies from India have described the presence of various mutations across the SAR-CoV-2 genome with hints of selection and in silico predictions of alterations in protein functions [16][17][18] so far. In this study an attempt has been made to understand the pattern of evolution within human hosts, to infer the ancestries of the viral isolates using the phylogenetic network approach which had been used earlier to build SARS-CoV-2 infection paths [19] and make an effort at correlating it with morbidity.…”

Identification of Genotypic Variants and its Proteomic mutations of Brazilian SARS-CoV-2 Isolates

“…Our findings show that most of the proteins are involved in the cellular and metabolic process and none identified from information molecules. The mutant (P323L) identified in RdRp of BRA/CD1739-P4/2020 (G14) transmits its biological function from cellular process to virulence mechanism (Table 2 ) and resulted in the destabilization of its structure (Begum et al, 2020). Similarly, the change of Pro to Leu in helicase protein resulted in the enhanced flexibility of the secondary structure.…”