Rapid diagnosis and genome sequencing to follow CoV-2019 outbreak

Rapid diagnosis of SARS-CoV-2 is critical for slowing the spread of the virus. Here we propose developing streamlined protocols for virus detection and genome sequencing. We will develop protocols that allow viral detection using qRT-PCR from patient samples using field kits for rapid RNA isolation. We will implement this protocol on the portable Ubiquitome Liberty16 qPCR platform. We will develop protocols to detect virus in pooled samples to increase assay throughput. We will also perform genome sequencing using the inexpensive, real-time Oxford Nanopore Flongle DNA sequencing platform. Finally, we will integrate the genomic sequence data from the New Zealand samples into the context of samples worldwide by leveraging the NextStrain nCoV-2019 database. We aim to be able to enable a single person to screen more than 500 samples per day and obtain up to 24 whole genome sequences per day.