ABSTRACT
BackgroundAs 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 Malaysias main wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to understand the molecular epidemiology. MethodsWe 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. ResultsNine 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. ConclusionLineage 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 SummaryThe 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.
Subject(s)
COVID-19ABSTRACT
IntroductionHealthcare workers (HCW) are presumed to be at increased risk of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection due to occupational exposure to infected patients. We aim to determine the prevalence of anti-SARS-CoV-2 antibodies among asymptomatic HCW.MethodsWe prospectively recruited HCW from the National Public Health Laboratory and two COVID-19 designated public hospitals in Klang Valley, Malaysia between April 13th and May 12th, 2020. Quota sampling was applied to ensure adequate representation of the HCW involved in provision of care for patients directly and indirectly. All participants had worked in the respective healthcare facility for at least 30 days prior study enrollment. HCW who were previously confirmed with COVID-19 infection or listed as “patient under investigation” were excluded. A self-administered questionnaire was used to capture sociodemographic information, history of contact with COVID-19 cases within the past month, clinical signs and symptoms and adherence to universal precautions. Blood samples were taken to test for anti-SARS-CoV-2 antibodies by surrogate virus neutralization test.ResultsA total of 400 HCW were recruited, comprising 154 (38.5%) nurses, 103 (25.8%) medical doctors, 47 (11.8%) laboratory technologists and others (23.9%). The mean age was 35±7.8 years, with females predominant (74%). A majority (68.9%) reported direct contact with COVID-19 patients, body fluids of COVID-19 patients and/or contaminated objects and surfaces in the past month within their respective workplaces. Nearly all claimed to adhere to personal protection equipment (PPE) guidelines (97%-100% adherence) and hand hygiene practice (91%-96% adherence). None (95% CI: 0, 0.0095) of the participants had anti-SARS-CoV-2 antibodies detected, despite 135 (33.8%) reporting respiratory symptoms one month prior to study recruitment. One hundred and fifteen (29%) participants claimed to have contact with known COVID-19 persons outside of the workplace.ConclusionOur finding of zero seroprevalence among asymptomatic HCW suggests a low risk of asymptomatic COVID-19 infection in our healthcare setting; which is at expected levels for a country with an incidence of 26 per 100,000. The adequacy of PPE equipment and strict adherence to infection prevention and control measures offers considerable protection during contact with COVID-19 cases and should be ensured to prevent future nosocomial transmission.