Abstract
The novel coronavirus 2 (nCoV2) outbreaks took place in December 2019 in Wuhan City, Hubei Province, China. It continued to spread worldwide in an unprecedented manner, bringing the whole world to a lockdown and causing severe loss of life and economic stability. The coronavirus disease 2019 (COVID-19) pandemic has also affected India, infecting more than 10 million till 31st December 2020 and resulting in more than a hundred thousand deaths. In the absence of an effective vaccine, it is imperative to understand the phenotypic outcome of the genetic variants and subsequently the mode of action of its proteins with respect to human proteins and other bio-molecules. Availability of a large number of genomic and mutational data extracted from the nCoV2 virus infecting Indian patients in a public repository provided an opportunity to understand and analyze the specific variations of the virus in India and their impact in broader perspectives. Non-structural proteins (NSPs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus play a major role in its survival as well as virulence power. Here, we provide a detailed overview of the SARS-CoV2 NSPs including primary and secondary structural information, mutational frequency of the Indian and Wuhan variants, phylogenetic profiles, three-dimensional (3D) structural perspectives using homology modeling and molecular dynamics analyses for wild-type and selected variants, host-interactome analysis and viral–host protein complexes, and in silico drug screening with known antivirals and other drugs against the SARS-CoV2 NSPs isolated from the variants found within Indian patients across various regions of the country. All this information is categorized in the form of a database named, Database of NSPs of India specific Novel Coronavirus (DbNSP InC), which is freely available at http://www.hpppi.iicb.res.in/covid19/index.php.
Highlights
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is responsible for the global pandemic of coronavirus disease 2019 (COVID-19) (Gorbalenya et al, 2020)
We have focused on the sequences of non-structural proteins (NSPs) of SARS-CoV2 extracted from Indian patients and created a database, Database of NSPs of India specific Novel Coronavirus (DbNSP InC)
We observed in NSP12 that the RNA-directed RNA polymerase (RdRp) has the most observed mutations at site 323, having a mutation frequency of 78.44% and that the mutation is from amino acid proline (P) to leucine (L)
Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is responsible for the global pandemic of coronavirus disease 2019 (COVID-19) (Gorbalenya et al, 2020). The SARS-CoV2 is an enveloped non-segmented positive sense single-stranded RNA virus. It belongs to the Nidovirales order and Coronaviridae family (Fehr and Perlman, 2015). One major characteristic feature of SARS-CoV2 genome is that almost twothirds of the genome (∼20 kb) corresponds to the replicase gene (ORF1ab), which expresses a polyprotein. The remaining part of the genome ∼10 kb encodes other structural and accessory proteins. The replicase gene is followed by the ORF2 spike glycoprotein (S), ORF3a, ORF4 envelope (E) gene, ORF5 membrane (M) gene, ORF6, ORF7a, ORF7b, ORF8, ORF9 nucleocapsid phosphoprotein (N), and ORF10 (Wu et al, 2020; Yoshimoto, 2020). Spike, envelope, membrane, and nucleocapsid proteins are the structural proteins, while the rest are accessory proteins. The ORF1ab polyprotein is composed of 16 non-structural proteins (NSPs)
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