TMPRSS2 variants and their susceptibility to COVID-19: focus in East Asian and European populations

  1. Ney Pereira Carneiro dos Santos
  2. André Salim Khayat
  3. Juliana Carla Gomes Rodrigues
  4. Pablo Pinto
  5. Gilderlanio Santana de Araújo
  6. Lucas Favacho Pastana
  7. Jéssyca Amanda Gomes Medeiros
  8. Marianne Rodrigues Fernandes
  9. Arthur Ribeiro-dos-Santos
  10. Bruna Claudia Meireles Khayat
  11. Fabiano Cordeiro Moreira
  12. André Maurício Ribeiro-dos-Santos
  13. Paula Baraúna de Assumpção
  14. Ândrea Ribeiro-dos-Santos
  15. Paulo Pimentel de Assumpção
  16. Sidney Santos

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Abstract

The manifestation of the COVID-19 varies from absence of symptoms to Severe Acute Respiratory Syndrome. The epidemiological data indicate that infection and mortality rates are greater in European populations in comparison with eastern Asians. To test if epidemiological patterns may be partly determined by human genetic variation, we investigated, by exomic and databank analyses, the variability found in the TMPRSS2 gene in populations from different continents, since this gene is fundamental to virus access into human cells. The functional variants revealed low diversity. The analyses of the variation in the modifiers of gene expression indicate that the European populations may have much higher levels of pulmonary expression of the TMPRSS2 gene and would be more vulnerable to infection by SARS-CoV-2. By contrast, the pulmonary expression of the TMPRSS2 may be reduced in the populations from East Asia, which implies that they are less susceptible to the virus infection and, these genetic features might also favor their better outcomes. The presented data, if confirmed, indicates a potential genetic contribution of TMPRSS2 to individual susceptibility to viral infection, and might also influence COVID-19 outcome.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.09.20126680: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics committee approvals: The present study was approved by the Brazilian National Committee for Ethics in Research (CONEP) and the Research Ethics Committee of the UFPA Tropical Medicine Center, under CAAE number 20654313.6.0000.5172.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    We compared our results with those of the populations included in the phase 3 release of the 1,000 Genomes Project (available at http://www.1000genomes.org) [32].
    http://www.1000genomes.org
    suggested: (1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828)
    Data on the genomic variants in Brazilian populations were also obtained from the Online Archive of Brazilian Mutations (ABraOM), freely available at http://abraom.ib.usp.br [31]. 4.2.
    Online Archive
    suggested: None
    Bioinformatic analysis: The quality of the FASTQ reads was analyzed (FastQC v.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    0.13 - http://hannonlab.cshl.edu/fastx_toolkit/).
    http://hannonlab.cshl.edu/fastx_toolkit/
    suggested: (FASTX-Toolkit, RRID:SCR_005534)
    The sequences were mapped and aligned with the reference genome (GRCh37) using the BWA v.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    0.7 tool (http://bio-bwa.sourceforge.net/), and the file was then indexed and sorted (SAMtools v.
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    1.129 - http://broadinstitute.github.io/picard/), mapping quality recalibration, and local realignment (GATK v.
    http://broadinstitute.github.io/picard/
    suggested: (Picard, RRID:SCR_006525)
    GATK
    suggested: (GATK, RRID:SCR_001876)

    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.
    • 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

    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 10.1101/2020.06.09.20126680v1 on medRxiv