Genomic epidemiology of SARS-CoV-2 in Mauritius reveals a new wave of infections dominated by the B.1.1.318, a variant under investigation

  1. Houriiyah Tegally
  2. Magalutcheemee Ramuth
  3. Daniel Amoaka
  4. Cathrine Scheepers
  5. Eduan Wilkinson
  6. Marta Giovanetti
  7. Richard J Lessells
  8. Jennifer Giandhari
  9. Arshad Ismail
  10. Darren Martin
  11. Emmanuel James San
  12. Margaret Crawford
  13. Rodney S Daniels
  14. Ruth Harvey
  15. Somduthsingh Bahadoor
  16. Janaki Sonoo
  17. Myriam Timol
  18. Lovena Veerapa-Mangroo
  19. Anne von Gottberg
  20. Jinal N. Bhiman
  21. Tulio de Oliveira
  22. Shyam Manraj

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Abstract

Mauritius, a small island in the Indian Ocean, has had a unique experience of the SARS-CoV-2 pandemic. In March 2020, Mauritius endured a small first wave and quickly implemented control measures which allowed elimination of local transmission of SARS-CoV-2. When borders to the island reopened, it was accompanied by mandatory quarantine and testing of incoming passengers to avoid reintroduction of the virus into the community. As variants of concern (VOCs) emerged elsewhere in the world, Mauritius began using genomic surveillance to keep track of quarantined cases of these variants. In March 2021, another local outbreak occurred, and sequencing was used to investigate this new wave of local infections. Here, we analyze 154 SARS-CoV-2 viral genomes from Mauritius, which represent 12% of all the infections seem in Mauritius, these were both from specimens of incoming passengers before March 2021 and those of cases during the second wave. Our findings indicate that despite the presence of known VOCs Beta (B.1.351) and Alpha (B.1.1.7) among quarantined passengers, the second wave of local SARS-CoV-2 infections in Mauritius was caused by a single introduction and dominant circulation of the B.1.1.318 virus. The B.1.1.318 variant is characterized by fourteen non-synonymous mutations in the S-gene, with five encoded amino acid substitutions (T95I, E484K, D614G, P681H, D796H) and one deletion (Y144del) in the Spike glycoprotein. This variant seems to be increasing in prevalence and it is now present in 34 countries. This study highlights that despite having stopped the introduction of more transmissible VOCs by travel quarantines, a single undetected introduction of a B.1.1.318 lineage virus was enough to initiate a large local outbreak in Mauritius and demonstrated the need for continuous genomic surveillance to fully inform public health decisions.

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    SciScore for 10.1101/2021.06.16.21259017: (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
    These were used for SARS-CoV-2 Whole Genome Sequencing (WGS).
    WGS
    suggested: None
    Raw reads coming from Illumina sequencing were assembled using Exatype (https://sars-cov-2.exatype.com/), Galaxy ARTIC pipeline (2. https://covid19.galaxyproject.org/artic/), Genome Detective 1.126 (https://www.genomedetective.com/) and the Coronavirus Typing Tool (26,27).
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    The pipeline contains several python scripts that manage the analysis workflow.
    python
    suggested: (IPython, RRID:SCR_001658)
    In short it allows for the filtering of genotypes, the alignment of genotypes in MAFFT (31), phylogenetic tree inference in IQ-Tree(32), tree dating and ancestral state construction and annotation.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The BLAST function in GISAID (7) was also used to find sequences most similar to the Mauritius dataset and infer belonging to the B.1.1.318 lineage.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Selection analysis: To identify which, if any, of the observed mutations in the Spike protein was most likely to increase viral fitness, we used the natural selection analysis of SARS-CoV-2 pipeline (https://observablehq.com/@spond/revised-sars-cov-2-analytics-page) (36,37).
    SARS-CoV-2
    suggested: (BioLegend Cat# 944703, RRID:AB_2890874)
    ML trees from this data subset was inspected in TempEst v1.5.3 (39) for the presence of a temporal (i.e. molecular clock) signal.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    MCMC chains were run for >100 million generations and sampled every 10000th step, with convergence assessed using Tracer v1.7 (40).
    Tracer
    suggested: (Tracer, RRID:SCR_019121)

    Results from OddPub: Thank you for sharing your code and data.

    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.

    Results from scite Reference Check: We found no unreliable references.

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