Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations

  1. Hsin-Chou Yang
  2. Chun-houh Chen
  3. Jen-Hung Wang
  4. Hsiao-Chi Liao
  5. Chih-Ting Yang
  6. Chia-Wei Chen
  7. Yin-Chun Lin
  8. Chiun-How Kao
  9. Mei-Yeh Jade Lu
  10. James C. Liao

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

In this study, we discovered that the genome of SARS-CoV-2 to date can be classified in six major types characterized by 14 signature single nucleotide variations (SNVs). In particular, type VI, that was first reported in China and spread to different countries, has become the major type (more than 95% among data collected after mid-May 2020). The signature SNVs for this strain type, C241T (5′UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (S protein D614G), exhibit high pairwise allelic associations, and the haplotype 241T-3037T-14408T-23403G has the highest frequency. Understanding nucleotide variations in the SARS-CoV-2 genome will provide useful insight for the developmental history of the pandemic, and even the disease management, if the biological significance is understood.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.04.22.055863: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Multiple sequence alignment was performed by using MUSCLE (4).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    Mutation frequencies in gene regions were illustrated and coefficient of LD (R2) between pairs of nucleotides was calculated by using PLINK (6).
    PLINK
    suggested: (PLINK, RRID:SCR_001757)
    Phylogenetic tree analysis was performed by using MEGA X (7).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1073/pnas.2007840117
  3. ScreenIT

    SciScore for 10.1101/2020.04.22.055863: (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
    Multiple sequence alignment was performed by using MUSCLE (4).
    MUSCLE
    suggested: (MUSCLE, SCR_011812)
    Mutation frequencies in gene regions were illustrated and coefficient of LD (R2) between pairs of nucleotides was calculated by using PLINK (6).
    PLINK
    suggested: (PLINK, SCR_001757)
    analysis was performed by using MEGA X (7).
    MEGA
    suggested: (Mega BLAST, SCR_011920)

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

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.04.22.055863 on bioRxiv