Genomic sequencing has proven vital in detecting the source and variants of COVID-19, improving contact tracing, reducing disease transmission and ensuring health security for Australia.
But genomic sequencing isn’t new and researchers from the NHMRC Centre of Digital Health (CRE) have been investigating it’s use in cases from public surveillance of Salmonella Typhimurium, predicting antibiotic resistance for Mycobacterium tuberculosis and more recently in examining the spread of COVID-19.
So, how can near real-time genome sequencing of SARS-CoV-2 which causes COVID-19 compare to a computational agent-based model (ABM)? Based on analysis of infected patients in Australia in the first 10 weeks of the pandemic in Australia, Professor Vitali Sintchenko and his team of researchers found:
“The prospective sequencing of SARS-CoV-2 clarified the probable source of infection in cases where epidemiological links could not be determined, significantly decreased the proportion of COVID-19 cases with contentious links, documented genomically similar cases associated with concurrent transmission in several institutions and identified previously unsuspected links. Only a quarter of sequenced cases appeared to be locally acquired and were concordant with predictions from the ABM. These high-resolution genomic data are crucial to track cases with locally acquired COVID-19 and for timely recognition of independent importations once border restrictions are lifted and trade and travel resume.”
You can read the full report in Nature Medicine here: Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
“Countries which have had a coordinated and national approach to managing the COVID-19 pandemic have fared better than others. And researchers have been able to show just how effective the application of genomic sequencing has been for the pandemic management. The globalisation of COVID-19 and the ongoing threat of antimicrobial-resistant organisms however, continues to be problematic,” said Professor Vitali Sintchenko, CRE Chief Investigator and Director of the Centre for Infectious Disease and Microbiology – Public Health at Westmead Hospital and NSW Health Pathology in Sydney.