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Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

Shuvam Banerjee, Shrinjana Dhar, Sandip Bhattacharjee, Pritha Bhattacharjee
doi: https://doi.org/10.1101/2020.04.06.027854
Shuvam Banerjee
1Environmental Epigenomics Lab, Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata – 700019
2UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector 3, LB-8, Bidhan Nagar, Kolkata – 700098
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Shrinjana Dhar
1Environmental Epigenomics Lab, Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata – 700019
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Sandip Bhattacharjee
3Health-Management in Occupational Health, Siemens, Gurgaon, India
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Pritha Bhattacharjee
1Environmental Epigenomics Lab, Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata – 700019
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  • For correspondence: 777.pritha@gmail.com
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Abstract

Background COVID-19 is a disease with global public health emergency that have shook the world since its’ first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known.

Methods Available data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination.

Findings All the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body.

Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. The molecular divergence, evolved from the ancestral strain (S) lead to extremely lethal (E), lethal(L) and non lethal (N) strains with the involvement of an Intermediate strain(I).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 09, 2020.
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Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence
Shuvam Banerjee, Shrinjana Dhar, Sandip Bhattacharjee, Pritha Bhattacharjee
bioRxiv 2020.04.06.027854; doi: https://doi.org/10.1101/2020.04.06.027854
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Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence
Shuvam Banerjee, Shrinjana Dhar, Sandip Bhattacharjee, Pritha Bhattacharjee
bioRxiv 2020.04.06.027854; doi: https://doi.org/10.1101/2020.04.06.027854

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