SARS-CoV-2 has observably higher propensity to accept uracil as nucleotide substitution: Prevalence of amino acid substitutions and their predicted functional implications in circulating SARS-CoV-2 in India up to July, 2020

Abstract

SARS-CoV-2 has emerged as pandemic all over the world since late 2019. In this study, we investigated the diversity of the virus in the context of SARS-CoV-2 spread in India. Full-length SARS-CoV-2 genome sequences of the circulating viruses from all over India were collected from GISAID, an open data repository, until 25thJuly, 2020. We have focused on the non-synonymous changes across the genome that resulted in amino acid substitutions. Analysis of the genomic signatures of the non-synonymous mutations demonstrated a strong association between the time of sample collection and the accumulation of genetic diversity. Most of these isolates from India belonged to the A2a clade (63.4%) which has overcome the selective pressure and is spreading rapidly across several continents. Interestingly a new clade I/A3i has emerged as the second-highest prevalent type among the Indian isolates, comprising 25.5% of the Indian sequences. Emergence of new mutations in the S protein was observed. Major SARS-CoV-2 clades in India have defining mutations in the RdRp. Maximum accumulation of mutations was observed in ORF1a.Other than the clade-defining mutations, few representative non-synonymous mutations were checked against the available crystal structures of the SARS-CoV-2 proteins in the DynaMut server to assess their thermodynamic stability. We have observed that SARS-CoV-2 genomes contain more uracil than any other nucleotide. Furthermore, substitution of nucleotides to uracil was highest among the non-synonymous mutations observed. The A+U content in SARS-CoV-2 genome is much higher compared to other RNA viruses, suggesting that the virus RdRp has a propensity towards uracil incorporation in the genome. This implies that thymidine analogues may have a better chance to competitively inhibit SARS-CoV-2 RNA replication than other nucleotide analogues.

Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys)

“…The ORF1a/b residue 2103 lies in nonstructural protein 3 (nsp3), which is the largest protein in the SARS-CoV-2 proteome and localizes with other viral proteins to the cell membrane [27,28]. The S2103F mutation in this protein has been detected at low frequency in human samples, including in India [29], but is not restricted to a particular clade and, through the course of the pandemic, has never been detected in greater than 1% of all sequenced isolates (nextstrain.org accessed on 29 November 2021 [30,31]).…”

Intra-host SARS-CoV-2 evolution in the gut of mucosally-infected Chlorocebus aethiops (African green monkeys)

“…The ORF1a/b residue 2103 lies in nonstructural protein 3 (nsp3), which is the largest protein in the SARS-CoV-2 proteome and localizes with other viral proteins to the cell membrane [20,21]. The S2103F mutation in this protein has been detected at low frequency in human samples including in India [22], but is not restricted to a particular clade and through the course of the pandemic has never been detected in greater than 1% of all sequenced isolates (nextstrain.org [23,24]).…”