New rules for genomics-informed COVID-19 responses–Lessons learned from the first waves of the Omicron variant in Australia

• DOI: 10.1371/journal.pgen.1010415
• Publication Date: 2022-10-13T17:26:02Z
• Authors: Ashleigh F. Porter; Norelle Sherry; Patiyan Andersson; Sandra A. Johnson; Sebastian Duchene; Benjamin P. Howden
• Keywords: Pandemic; Viral phylodynamics; Population genomics; 2019-20 coronavirus outbreak

During the COVID-19 pandemic, phylodynamics and phylogeography have been launched into spotlight as tools to model spread of SARS-CoV-2 virus.In Australia, we relied on genomic epidemiology (and associated derived parameters such viral growth rate, reproductive number, estimated sampling proportion) inform public health policy changes [1].This was possible due high proportion cases sequenced in Australia throughout 2020 2021, where maintained low burdens both deaths.The recent Omicron 'waves' experienced globally, combined with relaxation restrictions, has seen a significant jump Australia's case numbers, rising top 10 globally newly reported deaths August September 2022 (https://covid19.who.int/table).With around 10-fold more per day compared previous year, our sequencing strategy had adapt along virus.Here, emphasise how 'COVID-normal' future, way sequence during high-case load settings can optimise application phylogenomic methods sufficiently pandemic response. The rise variantDuring first stage (January November 2021), comprehensive genomics-informed response numbers COVID-19.The also enabled one highest genome rates (up 80% Victorian "second wave" 2020, Fig 1) [1].However, introduction variant late coinciding lifting led an exponential increase (Fig 1).We anticipate there number undiagnosed (e.g.PCR tests underestimating true transmission [3]), peak wave, overwhelming demand for testing, which inundated established diagnostic PCR testing systems created shortage rapid antigen tests.Furthermore, half were being counted from positive 1), not able be sequenced.The ongoing wave local global impacts, underlining necessity prepare future variants, including subvariants other emerging variants concern (VOCs) that are manageable by current control methods.