Real-time phylogeography of SARS-CoV-2 directly from patient samples

Aims Sequence 200 SARS-CoV-2 whole-genomes from Eastern/Southern/Metropolitan Sydney using both Oxford Nanopore and Illumina platforms, in order to compare the accuracy, reproducibility and practicality of these methods for SARS-CoV-2 rapid surveillance Profile SARS-CoV-2 clusters in real time, determining phylogeographic relationships Determine the extended respiratory virome of SARS-CoV-2 infected patients using viral capture sequencing, in order to assess the incidence of co-infections and correlate this upper respiratory tract (URT) viral load and presence of other viral infections with disease severity and patient outcomes in the clinical setting Outcomes Contribution of Australian data in real-time Application of phylogeography to inform community transmission in the region with the highest rate in NSW Development of models of higher clinical risk (transmission, co-infection, viral factors including mutations, viral load, duration of virus shedding, correlation with virus culture) Application of these models to inform testing strategies (multiplex virus detection, virus load, WGS) as aids to patient prognosis and follow-up