Workplace transmission of SARS-CoV-2 among health-care workers in Malaysia

COVID19 genomic surveillance is instrumental to better understand transmission dynamics in a setting, detect emergence of new variants and monitor spread of variants at the national, regional and global levels. Complete viral genome sequences are powerful enough to approximate epidemiology and enable informed public health response policies and determine their success. Between 24th November to 9th December 2020, a workplace COVID-19 outbreak, assigned as the Hilir cluster, occurred among healthcare workers (HCWs) in a northeast Malaysian university teaching hospital that was not designated for COVID-19 treatment. Mass screening of 1,292 individuals based on case interviews, contact tracings and nucleic acid testing detected 17 cases from various hospital wards and units. To investigate how COVID19 transmission occurred we whole genome sequenced 14 samples collected from healthcare workers and 5 samples from the concurrent community outbreaks. The genomes of these samples were compared with closely-related publically available genomes from GISAID to gain insights into COVID19 transmission in the hospital and at the local and global scale. The 14 viral sequences obtained from the Hilir cluster were assigned to Pango lineages B.1.524 (7 samples) and B.1.36.16 (7 samples) whereas the community samples were assigned as either B.1.524 and B.1. Phylogenetics revealed multiple introduction of B.1.524 into the workplace, while close relatedness of all B.1.36.16 samples suggested that the introduction of these lineages into the workplace likely stemmed from a single introduction. These lines of genomic evidences contradicted with the proposed transmission route, underlining the central role of genomics in COVID-19 or any future pandemics surveillance. The study also highlight the difficulty in enforcing and maintaining isolation methods in a hospital setting.