Data for publications related genomic epidemiology for the Victorian SARS-CoV-2 response from The Peter Doherty Institute for Infection and Immunity and the Victorian Department of Health and Human Services in Australia.

Raw genome sequence reads have been deposited at NCBI SRA within PRJNA613958. Every isolate was sequenced with Illumina paired-end 150bp reads. Some isolates have additional Nanopore data.

Early versions of consensus genomes were deposited in GISAID, but some were rejected due to "frame shifts". NCBI also rejected them for the same reason. Investigation is ongoing to confirm if these are genuine indels or sequencing artifacts.

Download a multi-FASTA file VIC.ffn of all genomes.

Download the aligned-FASTA file VIC.afa

Download Newick file VIC.nwk

If you use any of the data in this repository or PRJNA613958 please cite:

T Seemann, CR Lane, NL Sherry, S Duchene, AG da Silva, L Caly, ML Sait, SA Ballard, K Horan, MB Schultz, T Hoang, M Easton, S Dougall, TP Stinear, J Druce, M Catton, B Sutton, A van Diemen, C Alpren, DA Williamson, BP Howden. Tracking the COVID-19 pandemic in Australia using genomics BioRxiv, May 2020.