Genomic sequencing is the process of analysing microbial genomes on microbiological samples taken from a patient and comparing them with other cases. This provides extremely detailed, high resolution information about the characteristics of a pathogen, whether that be a parasite, virus, fungus or bacteria. Professor Vitali Sintchenko is a public health microbiologist and informatician with the NSW Health Pathology and the University of Sydney and conducts translational research on biosurveillance of communicable diseases. He explains how genomic sequencing has emerged as an important tool to contain COVID-19.

“Genomic sequencing as a technique has evolved over decades. Academic pathologists have been critical in implementing and translating it into practice in large reference facilities in Australia, as well as in New Zealand. Prior to COVID-19, genomic sequencing was used in Australia to trace the source of food-borne bacteria outbreaks and other infections with epidemic potential, such as tuberculosis. What this pandemic has shown is that genomics can be really powerful in providing high-resolution characterisation of pathogens for public health disease control in real-time.

“We first started sequencing coronavirus directly from clinical samples in January/February 2020, at the very beginning of the pandemic. Initially this was done to verify results from polymerase chain reaction tests, however, the additional value of genomics was quickly recognised. By using sequencing technology, health authorities have been able to monitor outbreaks, look for clustering of cases, recognise transmission pathways within the community and understand the evolution of the virus,” said Prof Sintchenko.

In Australia, when a throat and nose swab returns a COVID-positive result, it is sent to a genome sequencing laboratory. Due to the country’s relatively low number of COVID-19 cases, it has been possible to do this to almost every positive result. By sequencing locally acquired cases, authorities are able to detect when certain clusters have stopped. By sequencing returned travellers in quarantine, it is possible to detect variants of concern early and ensure they are not transmitted to the local population.

“What has been absolutely fascinating is the international effort in sequencing and the readiness to share sequencing data. Many countries with the capacity to do so, rapidly invested in sequencing the virus and shared their data using international databases such as GISAID. Thanks to these efforts, we now have data from hundreds of thousands of genomes across different continents. This has helped us to understand not only the spread and evolution of the virus, but also to track variants of concern such as UK and South African strains, plus many others that are emerging.

“As you can see, genomics helps to answer important questions which have implications for both individual patient management and for the public health response, such as informing guidelines, policies, testing protocols,” said Prof Sintchenko.