Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention

Salma Jamal
,
Jasdeep Singh
,
Javaid Ahmad Sheikh
,
Hina Singh
,
Mohd Khubaib
,
Sunil Kohli
,
Ulrich Dobrindt
ORCID logo ,
Syed Asad Rahman
,
Nasreen Zafar Ehtesham
,
Seyed Ehtesham Hasnain
*
Version 1 : Received: 20 March 2020 / Approved: 23 March 2020 / Online: 23 March 2020 (00:42:35 CET)

How to cite: Jamal, S.; Singh, J.; Sheikh, J.A.; Singh, H.; Khubaib, M.; Kohli, S.; Dobrindt, U.; Rahman, S.A.; Ehtesham, N.Z.; Hasnain, S.E. Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention. Preprints 2020, 2020030320. https://doi.org/10.20944/preprints202003.0320.v1 Jamal, S.; Singh, J.; Sheikh, J.A.; Singh, H.; Khubaib, M.; Kohli, S.; Dobrindt, U.; Rahman, S.A.; Ehtesham, N.Z.; Hasnain, S.E. Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention. Preprints 2020, 2020030320. https://doi.org/10.20944/preprints202003.0320.v1

Abstract

We are witnessing the severe third outbreak mediated by coronaviruses affecting global public health with unprecedented economic consequences. A better understanding of its phylogenetics, exploration of sequence features and mutational changes could unveil its genealogy to gain insights into the mechanism of transmission and development of possible interventions. Our comparative genomic analyses of >160 isolates of SARS-CoV-2 reveal phylogenetic kinship with other coronaviruses and emergence of evolutionary divergence in clinical isolates. t-SNE-based clustering revealed different clades but no continent specific clusters. Amino acid substitutions at RBD of spike protein provide possible reasons for rapid transmission. Few proteins specific to SARS-CoV-2 were identified which could have implications as therapeutic targets and diagnostic biomarkers. Virtual screening identified repurposed drugs, known nutraceuticals, for specific interventions. These phylogenetic observations reveal the ancestry and computational studies reveal the emergency measures to interject this emerging pathogen that pose threat to whole of mankind.

Keywords

envelope protein; furin cleavage site; hydrophobic aggregation and rapid transmission; immediate ancestor; pangolins coronaviruses; SARS-CoV-2; spike protein

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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