The ability to generate pathogen genomes in near real time has revolutionised infectious disease diagnostics and public health surveillance. To date, SARS-CoV-2 genomes have been used as a highly sensitive early warning signal, initially to identify and control importations of SARS-CoV-2 into the Australian community. As the pandemic progressed, genomic data has identify and traced the spread of variants of concern (VOCs). These VOCs, defined by constellations of mutations, have increased transmissibility and the ability to evade vaccine and naturally induced immunity. As we move towards COVID normal, genomics continues to be used to identify new variants and highlight punctuated evolution, in addition to guiding the use of antiviral treatment in cases at risk of progression to severe disease.
A key example is the international spread of the SARS-CoV-2 Omicron VOC which rapidly became dominant in Australia. Omicron is characterized by over 30 non-synonymous mutations in the spike protein many of which are within key epitopes that provide SARS-CoV-2 an advantage over vaccine-induced immunity and reduce the effectiveness of antiviral treatments. The rapid identification of Omicron cases in NSW enabled in vitro neutralisation assays to be conducted within 17 days of the first case of Omicron in Australia. These assays confirmed in silico predictions of immune evasion and demonstrated the reduced ability of post-two and three dose vaccination sera to neutralize Omicron, however neutralisation was improved following vaccine boosters.
This work described the important partnership between genomics and traditional virology and outlines how functional genomics provides evidence to quantify the public health impact of new SARS-CoV-2 variants.