Emergence of RBD and D614G Mutations in Spike Protein: An Insight from Indian SARS-CoV-2 Genome Analysis

Abstract

Currently, entire world is crumbled due to COVID-19 caused by novel SARS-CoV-2. Globally, over 5 million people are infected by SARS-CoV-2 with 6% fatality rate. The surface spike (S) protein plays a key role in the pathogenesis of SARS-CoV-2 by mediating viral entry through human angiotensin converting enzyme 2 (hACE2) receptors on the host cell and there is a big global race to find viral neutralizing antibodies and vaccine against S protein of SARS-CoV-2. Since SARS-CoV-2 evolved into 10 different clades in a very short span, a study on sipke protein mutation is essential to have effective vaccine coverage globally. Based on the mutation analysis of S protein from 166 Indian SARS-CoV-2 genome, a total of 40 different SNPs comprising of 14 synonymous and 26 non-synonymous mutations were observed, and notably, Indian S protein diverged into two major clusters, D614 and G614, with 11 different types. Majority of Indian strains fall in A2a and O clusters. Alarmingly, we have observed six SNPs at RBD and notably two of them at RBM (S438F and S494P). S494P SNP, similar to Bat–SARS like-CoV, may indicate a low ACE2 binding affinity. Interestingly 38% of Indian strains harbor a characteristic D614G SNP which was found predominantly in A2a cluster, mostly comprising USA and European strains with high disease severity. The association of disease severity with D614G SNP is well-correlated in states with high death rate except Maharashtra. Notably, more than 50% of D614G mutation were observed in Northern part of India and 14% in Southern part but not in Kerala and Tamil Nadu strains. Highly conserved motif, D614 (608-VAVLYQDVNCT-618) in upstream and also few downstream, of S1/S2 furin cleavage site may indicate specific key role in efficient interaction with host proteases in pathogenesis. Further studies are warranted to clarify the impact of SD614G SNP association to disease severity . Interestingly, C2367T (Y789Y) synonymous SNP is observed in 37% of Indian strains and notably similar SNPs with degeneracy bases were observed which is a key indication for the possibility of misdiagnosis by Real-Time PCR and revised strategies are needed for the precise diagnosis. Circulation of high number of signature SNPs [D614G and C2367T (Y789Y)] in certain states may be an early indication of emergence of community transmission in India. Further large genome sequence data from India will aid in deep understanding on the diversity of circulating SASR-Cov-2 and its impact on disease severity, origin of imported cases to India, community spread, effect on diagnosis and vaccine coverage.

Identification of novel mutations in SARS-COV-2 isolates from Turkey

“…1b). The alanine-to-valine substitution as residue 771 was previously seen in one Belgian strain [12].…”

“…Among the synonymous SNPs in the S protein, the C23929T (Y789Y) mutation was observed in only one Turkish sequence (EPI_ISL_455719) in the S gene. It was reported previously with high prevalence in Indian strains (39.13%) and in one US strain (EPI_ISL_436,898) [7,12], but not in any other European strains so far. C22444T (S protein) and C28854T substitution (N protein) were observed to be uncommon co-occurring mutations in viral isolates from Turkey (8 samples) and Saudi Arabia (9 samples) (Table S2), which may provide evidence for a travel-associated origin of these mutations.…”

“…An SNP with "T" at position 28,144 encoding leucine was classified as L type, while "C" at this position encoding serine is referred as S type. It has been suggested that the L type is more aggressive and contagious than the S type [12]. Thus, it appears that the L type is predominant in the Turkish population.…”

Identification of novel mutations in SARS-COV-2 isolates from Turkey

“…within community [21,22]. The present study also revealed C22444T (S protein) along with C28854T substitution (N protein) as un-common co-evolved mutation both in viral isolates from Turkey (8 samples) and Saudi Arabia (9 samples) (Table S1), which may provide an evidence for travel-associated origin of these mutations to Turkey from Saudi Arabia.…”

“…Notably, seven novel mutations were identi ed in spike (S) protein at different positions which include two synonymous mutations (22444C>T and 23929C>T) and four substitutional mutations (I468V, A771V, T1238I, G1251V) ( Table 2). Among synonymous SNPs, C23929T (Y789Y) mutant was observed in only one Turkish sequence (EPI_ISL_455719) of S protein, which was previously reported with high prevalence in Indian strain (39.13%) and one in USA strain (EPI ISL 436898) [12,21], but not in any other European strain so far. Although, no change in amino acid (Y789Y) at this site, but it was established as a signature SNP in Indian strains, therefore it can be used to trace and monitor the transmission of SARS-CoV-2…”