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Genomic surveillance reveals COVID-19 outbreak clusters in a tertiary center in Malaysia: A cross-sectional study
Norazimah Tajudin1, Seok Mui Wang2,3,4, Mariam Mohamad5
1Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
Background:
Genomic surveillance activity is a useful tool in epidemiologic investigations and monitoring of virus evolution. This study aimed to describe the COVID-19 outbreaks through SARS-CoV-2 virus genomic surveillance by whole genome sequencing.
Methods:
A cross-sectional study was conducted using archived clinical samples of confirmed laboratory-positive COVID-19 from June 2021 to June 2022 from a tertiary center in Malaysia. The samples were subjected to whole genome sequencing. A phylogenetic tree was constructed using the maximum likelihood method in MEGA 11 software. The clinical data were obtained through paper, electronic, and hospital information systems.
Results:
A total of 86 clinical samples were successfully sequenced. The phylogenetic tree revealed seven clusters, consisting of 24 cases. Three clusters were associated with health care workers and health care-associated individuals. The SARS-CoV-2 Delta variants were observed in the first three clusters and subsequently replaced with the Omicron variants.
Conclusions:
Whole genome sequencing is robust and reliable, enhancing epidemiologic investigations, leading to the identification of clusters and preventing the spreading of COVID-19 among health care workers. Monitoring of the SARS-CoV-2 variants is necessary to study the viral dynamics and maintain the effectiveness of public health interventions.
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