SARS-CoV-2 lineage B.6 is the major contributor to 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

Reviewed by

Read the full article

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

Background

As of June 30, 2020, Malaysia had confirmed 8,639 cases of COVID-19. About 39% of these were associated with a religious mass gathering event held in Kuala Lumpur between February 27 and March 1, 2020, which drove community transmission during Malaysia’s main wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to understand the molecular epidemiology.

Methods

We obtained whole genome sequences of SARS-CoV-2 from 58 COVID-19 patients in Kuala Lumpur, Malaysia, and performed phylogenetic analyses on these and a further 50 Malaysian sequences available in the GISAID database. Malaysian lineage B.6 sequences were further analysed with all available worldwide lineage B.6 sequences.

Results

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 mass gathering and became predominant (63%) despite being relatively rare (1.4%) among available global sequences. Increases in reported cases and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly associated with travel 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. We also report the presence of a nsp3-C6310A substitution found in 40.5% of global B.6 sequences which has associated with reduced sensitivity in a commercial assay.

Conclusion

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 region.

Author Summary

The COVID-19 pandemic in Malaysia was driven mainly by transmission following a religious mass gathering held in Kuala Lumpur at the end of February. To study the genetic epidemiology of SARS-CoV-2 in Malaysia, we analysed 50 available and 58 newly-generated Malaysian whole genome virus sequences. We found that lineage B.6, rare (1.4%) globally, first appeared after the mass gathering and became the most predominant (62.9%) in Malaysia. Increases in COVID-19 cases and locally-acquired B.6 strains were temporally linked. Non-B.6 viruses were mainly associated with travel and showed limited spread. Increases in B.6 viruses in Southeast Asian countries, India and Australia were linked to participants returning from this mass gathering. Altogether, 95.3% of global B.6 sequences originated in Asia or Australia. We also report a mutation in the virus nsP3 gene found in 40.5% of global B.6 sequences and associated with reduced detection by a commercial diagnostic test. In conclusion, the religious mass gathering in Kuala Lumpur was associated with the main wave of COVID-19 cases of predominantly B.6 lineage in Malaysia, and subsequent spread of B.6 viruses regionally. Genome sequence data provides valuable insight into virus spread and is important for monitoring continued accuracy of diagnostic kits.

Article activity feed

  1. 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.

  2. Version published to 10.1101/2020.08.27.269738 on bioRxiv