Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis

  1. Rahila Sardar
  2. Deepshikha Satish
  3. Shweta Birla
  4. Dinesh Gupta

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Abstract

The ongoing pandemic of the coronavirus disease 2019 (COVID - 19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes

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    SciScore for 10.1101/2020.03.21.001586: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Coronavirus subtyping and Mutation Analysis: All assembled query genomes in FASTA format were analyzed using Genome Detective Coronavirus Typing Tool (version 1.1.3)(5) which allows quick identification and characterization of novel coronavirus genomes.
    Mutation Analysis
    suggested: None
    MSA was performed using online CLUSTAL-OMEGA software.
    CLUSTAL-OMEGA
    suggested: None
    Neighbor joining method with bootstrap value of 1000 replicates was used for the construction of consensus tree using MEGA software(6) (10.1.7 version).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    (Figure 1(b)) To identify potential host microRNA target sites in the virus genome sequences, we have used miRanda (3.3 a version)(12, 13) software, with an energy threshold of −20 kcal/mol.
    miRanda
    suggested: (miRanda, RRID:SCR_017496)
    We also used psRNATarget server to compare the predicted targets by the two methods(14).
    psRNATarget
    suggested: (psRNATarget, RRID:SCR_013321)
    Immunogenic properties analysis: All the genes and protein sequences for SARS-CoV2 were retrieved from ViPR database.
    ViPR
    suggested: (vipR, RRID:SCR_010685)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.03.21.001586 on bioRxiv