SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights.

Swapnil B Kadam,Anupama A Pable,Vitthal T Barvkar,Geetika S Sukhramani,Pratibha Bishnoi

doi:10.1002/jobm.202000537

Swapnil B Kadam, Anupama A Pable + Show 3 more

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https://doi.org/10.1002/jobm.202000537

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Abstract

The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID‐19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS‐CoV‐2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor‐binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS‐CoV‐2 is likely to have originated from bat‐derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS‐CoV‐2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS‐CoV‐2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS‐CoV‐2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS‐CoV‐2 including secondary structures in the genome and protein–protein interactions which can be useful to understand the aggressive spread of the SARS‐CoV‐2. The mutations and the haplotypes reported in the SARS‐CoV‐2 genome are summarized to understand the virus evolution.

Highlights

Corona viruses (CoVs) are the positive stranded RNA viruses which taxonomically come under family Coronaviridae and subfamily Coronavirinae
In 2002, 55 SARS-CoV was emerged in China and infected 8422 persons leading to the death of 916 56 individuals
On the basis of highest conserved protein encoding open reading frame 73 (ORF) 1a/1b sequence, the new virus clustered with SARS-CoV under genus beta coronavirus

Summary

INTRODUCTION

Corona viruses (CoVs) are the positive stranded RNA viruses which taxonomically come under family Coronaviridae and subfamily Coronavirinae. On the basis of highest conserved protein encoding open reading frame (ORF) 1a/1b sequence, the new virus clustered with SARS-CoV under genus beta coronavirus. The sequences are submitted to GISAID with accession number: EPI_ISL_402119; EPI_ISL_402120; EPI_ISL_402121; EPI_ISL_402124 and EPI_ISL_402127-402130 [4,6] After these initial submissions of SARS-CoV2 genome sequences, multiple entries from different parts of world were appeared in GISAID. The SARS-CoV2 contains a positive sense single stranded RNA genome covered by an enveloped structure. SARS-CoV2 genomic RNA consists of 5′-cap and 3′-poly-A tail structure. This positive sense RNA is used as template for translation in host. The examinations of the amino acid doi:10.20944/preprints202005.0519.v1 substitutions in different proteins could enlighten how these differences affect the virulence and 114 pathogenesis of SARS-CoV2 [11]. The various components of viral genome are discussed below 115 in detail

Accessory proteins

CONCLUSION