On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal

  1. Vítor Borges
  2. Joana Isidro
  3. Helena Cortes-Martins
  4. Sílvia Duarte
  5. Luís Vieira
  6. Ricardo Leite
  7. Isabel Gordo
  8. Constantino P. Caetano
  9. Baltazar Nunes
  10. Regina Sá
  11. Ana Oliveira
  12. Raquel Guiomar
  13. João Paulo Gomes
  14. Portuguese network for SARS-CoV-2 genomics

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Abstract

Mutations in the Spike motif predicted to correspond to the fusion peptide are considered of interest as this domain is a potential target for anti-viral drug development that plays a pivotal role in inserting SARS-CoV-2 into human cell membranes. We tracked the temporal and geographical spread of a SARS-CoV-2 variant with the Spike D839Y mutation in the fusion peptide, which was detected early during the COVID-19 epidemic in Portugal. We show that this variant was most likely imported from Italy in mid-late February 2020, becoming prevalent in the Northern and Central regions of Portugal, where represented 22% and 59% of the sampled genomes, respectively, until the end of April 2020. Based on our high sequencing sampling during the early epidemics [15,5% (1275/8251) and 6,0% (1500/24987) of all confirmed cases until the end of March and April, respectively)], we estimate that, between March 14 th and April 9 th (covering the exponential phase of the epidemic), the relative frequency of Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) at every three days, being potentially associated with one in each four (20.8-29.7%, CI 95%) COVID-19 cases in Portugal during the same period. This observation places the Spike Y839 variant in the origin of the largest SARS-CoV-2 transmission chain during the first month of the COVID-19 epidemic in Portugal. We hypothesize that population/epidemiological effects (founder effects) and enhanced selective advantage might have concomitantly contributed to the increasing frequency trajectory of the Spike Y839 variant. Screening of the D839Y mutation globally confirmed its detection in 12 additional countries, even though the huge differences in genome sampling between countries hampers any accurate estimate of D839Y global frequency. In summary, our data points out that SARS-CoV-2 Spike Y839 variants, namely the descendent variant of the globally spread G614 variant detected in Portugal, need continuous and close surveillance.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.10.20171884: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical Approval: This study was approved by the Ethical Committee (“Comissao de Etica para a Saúde”) of the Portuguese National Institute of Health.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Pooling, denaturation and dilution of bead-based normalized libraries was performed according to the manufacturer’s instructions for the MiSeq or NextSeq 550 systems (Illumina).
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Briefly, the core bioinformatics steps (documented in Borges et al, 2018 and https://insaflu.readthedocs.io/) involved: i) raw NGS reads quality analysis and improvement using FastQC; (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic), respectively (read’s ends were cropped 30bp for primer clipping); ii) draft de novo assembly using SPAdes (http://cab.spbu.ru/software/spades/) followed by classification and contigs assignment of Human Betacoronavirus; and, iii) reference-based mapping, consensus generation and variant detection using the multisoftware tool Snippy (https://github.com/tseemann/snippy), using the Wuhan-Hu-1/2019 genome sequence (https://www.ncbi.nlm.nih.gov/nuccore/MN908947) as reference.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    SPAdes
    suggested: (SPAdes, RRID:SCR_000131)
    Phylogenetic analysis and real-time data sharing on SARS-CoV-2 genetic diversity and geotemporal spread in Portugal: A total of 1516 SARS-CoV-2 genome sequences were analyzed in this study (corresponding to INSA’s collection as of July 23rd, 2020; Table S1) using the SARS-CoV-2 Nextstrain pipeline (Hadfield et al, 2018) version from March 23, 2020 (https://github.com/nextstrain/ncov), with slight modifications.
    Portugal
    suggested: None
    In brief, sequences were aligned against the reference Wuhan-Hu-1/2019 genome of SARS-CoV-2 (GenBank accession MN908947) using MAFFT (Kaoth et al, 2002), the alignment was visually inspected, manually curated and further used to build a maximum likelihood phylogenetic tree based on the GTR model using IQ-TREE (Nguyen et al, 2015) following the Nextstrain implementation (the first 130bp and last 50 bp, as well as a few bases within the alignment, were masked as likely sequencing artifacts).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    Results from OddPub: Thank you for sharing your code.

    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

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  2. Version published to 10.1101/2020.08.10.20171884v1 on medRxiv
  3. Version published to 10.1080/22221751.2020.1844552