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

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.

Fig 1. Phylogenetic tree of 115 SARS-CoV-2 whole genome sequences from Malaysia.

Sequences from our study are shown in blue and the 7 sequences with known links to the Tablighi Jamaat gathering are denoted with red circles. The tree is rooted on the branch separating lineages A and B. The key single nucleotide variants in lineage B.6 are highlighted.

Fig 2

(A) Epidemic curve of COVID-19 in Malaysia and time course of reported total cases, Tablighi-associated cases, and lineages based on 115 Malaysian sequences, from the first reported case on 25 January to 20 September 2020. The Tablighi Jamaat gathering in Kuala Lumpur is labelled as “mass gathering, KL”. The different phases of lockdown are shown, comprising the movement control order (MCO), conditional movement control order (CMCO) and recovery movement control order (RMCO). (B) Time course of global reported lineage B.6 SARS-CoV-2 sequences available in the GISAID database (as of 20 September 2020). The timescale of the horizontal axis is the same as (A). Countries with fewer than 5 lineage B.6 sequences are included in “others”, comprising Brazil (1), China (3), France (1), Gambia (1), Guam (3), Hong Kong (1), Iceland (1), Jamaica (1), Japan (4), Kenya (1), Myanmar (1), New Zealand (3), Oman (4), Portugal (2), Saudi Arabia (2), Senegal (1), Sierra Leone (1), South Africa (4), South Korea (2), Slovenia (1) and Turkey (1). (C) The percentage rates of lineage B.6 sequences over total available complete sequences (in brackets) from each country available at GISAID as of 20 September 2020. Asia Pacific countries are colored grey.

Fig 3. Phylogenetic tree of 1,122 high-quality B.6 lineage SARS-CoV-2 sequences with > 29,000 bp, < 1% Ns and < 0.05% unique amino acid mutations available from the GISAID database as of 20 September 2020.

Sequences linked to the Tablighi Jamaat gathering are labelled in blue and denoted with red circles.