SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

  1. Yoong Min Chong
  2. I-Ching Sam
  3. Jennifer Chong
  4. Maria Kahar Bador
  5. Sasheela Ponnampalavanar
  6. Sharifah Faridah Syed Omar
  7. Adeeba Kamarulzaman
  8. Vijayan Munusamy
  9. Chee Kuan Wong
  10. Fadhil Hadi Jamaluddin
  11. Yoke Fun Chan

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Abstract

Malaysia had 10,219 confirmed cases of COVID-19 as of September 20, 2020. About 33% were associated with a Tablighi Jamaat religious mass gathering held in Kuala Lumpur between February 27 and March 3, 2020, which drove community transmission during Malaysia’s second wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to better understand the molecular epidemiology and spread. We obtained 58 SARS-CoV-2 whole genome sequences from patients in Kuala Lumpur and performed phylogenetic analyses on these and a further 57 Malaysian sequences available in the GISAID database. Nine different SARS-CoV-2 lineages (A, B, B.1, B.1.1, B.1.1.1, B.1.36, B.2, B.3 and B.6) were detected in Malaysia. The B.6 lineage was first reported a week after the Tablighi mass gathering and became predominant (65.2%) despite being relatively rare (1.4%) globally. Direct epidemiological links between lineage B.6 viruses and the mass gathering were identified. Increases in reported total cases, Tablighi-associated cases, and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly travel-associated and showed limited onward transmission. There were also temporally correlated increases in B.6 sequences in other Southeast Asian countries, India and Australia, linked to participants returning from this event. Over 95% of global B.6 sequences originated from Asia Pacific. We also report a nsp3-C6310A substitution found in 47.3% of global B.6 sequences which was associated with reduced sensitivity using a commercial diagnostic real-time PCR assay. Lineage B.6 became the predominant cause of community transmission in Malaysia after likely introduction during a religious mass gathering. This event also contributed to spikes of lineage B.6 in other countries in the Asia-Pacific. Mass gatherings can be significant causes of local and global spread of COVID-19. Shared genomic surveillance can be used to identify SARS-CoV-2 transmission chains to aid prevention and control, and to monitor diagnostic molecular assays.

Clinical Trial Registration : COVID-19 paper.

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  1. Version published to 10.1371/journal.pntd.0008744
  2. ScreenIT

    SciScore for 10.1101/2020.08.27.269738: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the University Malaya Medical Centre ethics committee (no. 2020730-8928).
    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 using MAFFT with default parameters [7].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Phylogenetic analysis was conducted with RAxML 8.2.11 implemented in Geneious with default parameters (generalized time-reversal (GTR) + gamma substitution model and bootstrapped 1000 times) using sequenced samples and 50 other Malaysian genome sequences available at GISAID (www.gisaid.org) as of July 17 2020 [8].
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    The alignment was then subjected to maximum-likelihood (ML) phylogenetic analyses using IQTREE v1.6.12 [11], using the GTR+F+I+G4 nucleotide substitution model and assessing branch support by the Shimodaira-Hasegawa-like approximate likelihood ratio test with 1,000 replicates.
    IQTREE
    suggested: None
    The ML tree was visualized using FigTree v1.4.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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: We detected the following sentences addressing limitations in the study:
    A caveat is that the number of whole genome sequences reported from developing countries in Asia is relatively low and likely underreports the true incidence of B.6. It is notable that this lineage is a very minor contributor in developed countries with greater sequencing volumes (Fig 3C). Whole genome sequencing of SARS-CoV-2 in our centre not only allowed important insights into local epidemiology, but was also used to track networks within a healthcare-associated cluster, which will be reported elsewhere. Furthermore, public sharing of sequences contributed to identification of the C6310A (nsp3-S1197R) mutation affecting the sensitivity of a commercial PCR assay, leading to updated primers/probes. This mutation is present in only 0.8% of global sequences, but as many as 393 (40.5%) of 970 available lineage B.6 sequences, and within our centre we estimate that the reduced sensitivity of the original assay impacted 10% of positive samples. With many diagnostic kits now on the market and the continued evolution of the virus, this shows the importance of choosing reputable manufacturers who diligently monitor new circulating sequences for potential primer/probe mismatches [27]. There were 40 (37.0%) non-B.6 lineage sequences reported from Malaysia. At least 28 (70%) reported recent international travel (including 3 of the earliest cases from lineage A, imported from China), compared to 2/42 (4.8%) of our B.6 cases. Our sequenced cases with lineages B.1.1, B.2 and B.3 had trave...

    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

    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.

  3. Version published to 10.1101/2020.08.27.269738v1 on bioRxiv