Case study: Whole genome sequencing to track COVID-19

The COVID-19 pandemic required high-resolution tracking of importations and virus spread in the community and high-risk settings.

The Public Health Microbial Genomics Unit at Westmead Hospital was established as a collaboration between the Centre for Infectious Diseases and Microbiology-Public Health, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, and the Sydney Infectious Diseases Institute at the University of Sydney. The team of clinicians and researchers developed, evaluated and implemented prospective, near-real-time public health genomic surveillance of SARS-CoV-2 in NSW to provide timely recognition of multiple independent importations of COVID-19 into NSW, as well as clusters of local transmission. These activities were supported by the NSW Health Prevention Research Support Program and a COVID-19 Priority Research Grant.

This research determined the sensitivity and specificity of different methodologies to generate SARS-CoV-2 whole genome sequences. The most sensitive and reliable workflow was implemented into laboratory testing in late 2020, increasing the ability to generate complete genomes from 13% to 40% of all COVID-19 cases in NSW at that time.

The Public Health Pathogen Genomics Team sequenced the first genome responsible for the first case of COVID-19 in NSW in January 2020. They have sequenced over 30,000 genomes since, reporting new variants, clusters and transmission links to NSW Health.

Funding from NSW Health provided next-generation sequencing equipment and, with it, capacity to explore diseases of public health concern such as COVID-19, building capability vital to NSW and Australia’s pandemic response. The grant funded translational research into new testing methods that boosted the numbers of samples that could be successfully sequenced. The strong integration of genomic surveillance into the public health response for COVID-19 in NSW has been proven to deliver the best value for the community.