New rules for genomics-informed COVID-19 responses–Lessons learned from the first waves of the Omicron variant in Australia
Ashleigh F. Porter, Norelle L. Sherry, Patiyan Andersson, Sandra Johnson, Sebastián Duchêne, Benjamin P. Howden
Abstract
During the COVID-19 pandemic, phylodynamics and phylogeography have been launched into the spotlight as tools to model the spread of the SARS-CoV-2 virus. In Australia, we have relied on genomic epidemiology (and associated derived parameters such as viral growth rate, reproductive number, and estimated sampling proportion) to inform public health policy changes This was possible due to the high proportion of SARS-CoV-2 cases sequenced in Australia throughout 2020 and 2021, where we maintained low burdens of both cases and deaths. The recent Omicron 'waves' experienced in Australia and globally, combined with the relaxation of public health restrictions, has seen a significant jump in Australia's case numbers, rising to the top 10 globally in newly reported cases and deaths in August and September 2022 (https://covid19.who.int/table). With around 10-fold more cases per day in 2022 compared to the previous year, our sequencing strategy has had to adapt along with the virus. Here, we emphasise how in the 'COVID-normal' future, the way we sequence during high-case load settings can optimise our application of phylogenomic methods to sufficiently inform the COVID-19 pandemic response.