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. 2020 Sep;6(9):e04658.
doi: 10.1016/j.heliyon.2020.e04658. Epub 2020 Aug 20.

Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies

Rahila Sardar  1   2 , Deepshikha Satish  1 , Shweta Birla  1 , Dinesh Gupta  1
Affiliations

Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies

Rahila Sardar et al. Heliyon. 2020 Sep.

Abstract

We have performed an integrative analysis of SARS-CoV-2 genome sequences from different countries. Apart from mutational analysis, we have predicted host antiviral miRNAs targeting virus genes, PTMs in the virus proteins and antiviral peptides. A comparison of the analyses with other coronavirus genomes has been performed, wherever possible. Our analysis confirms unique features in the SARS-CoV-2 genomes absent in other evolutionarily related coronavirus family genomes, which presumably confer unique infection, transmission and virulence capabilities to the virus. For understanding the crucial factors involved in host-virus interactions, we have performed Bioinformatics aided analysis integrated with experimental data related to other corona viruses. We have identified 42 conserved miRNAs that can potentially target SARS-CoV-2 genomes. Interestingly, out of these, 3 are previously reported to exhibit antiviral activity against other respiratory viruses. Gene expression analysis of known host antiviral factors reveals significant over-expression of IFITM3 and down regulation of cathepsins during SARS-CoV-2 infection, suggesting its active role in pathogenesis and delayed immune response. We also predicted antiviral peptides which can be used in designing peptide based drugs against SARS-CoV-2. Our analysis explores the functional impact of the virus mutations on its proteins and interaction of its genes with host antiviral mechanisms.

Keywords: Antiviral miRNA; Antiviral peptides; Bioinformatics; Coronavirus; Genetics; Infectious disease; Virology.

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Figures

Figure 1
Figure 1
Schematic domain representation of spike glycoprotein A. Spike glycoprotein mutations B. PTMs identified in the Spike glycoproteins.
Figure 2
Figure 2
miRNA target identification A. Venn diagram showing host-miRNA targets identified in the 3 genomes. B. host-miRNA target network in SARS-CoV-2 protein showing maximum number of miRNAs targeting ORF1ab, followed by spike glycoprotein and nucleocapsid protein.
See this image and copyright information in PMC

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