Rapid RNA sequencing of coronavirus for public health surveillance and transmission

There is an ongoing worldwide outbreak of the COVID-19 coronavirus. As of February 18 2020, nearly 73,500 cases have been identified and 1,875 deaths reported. To prevent further spread and to understand how the COVID-19 virus is spreading, where it came from, and when it likely jumped from animal to humans, the genome sequences of these viruses have been instrumental in providing insights. So far, Canada has reported 8 cases of COVID-19 (5 in BC; 3 in ON). However, no Canadian genomes have been made publicly available. In contrast, over 102 genomes have been released from several other countries including China, Taiwan, Japan, Australia and the United States. Here, the Public Health Laboratory in Alberta, Edmonton and Calgary and the National Microbiology Laboratory in Winnipeg have teamed up with genomics, bioinformatics, microbiology and infectious disease experts to address this challenge. We are verifying a direct RNA sequencing method capable of accelerated inexpensive sequencing of COVID-19 virus genomes. We aim to roll out this rapid method into Canada's frontline operations, along with direct analysis to promote global sharing and uptake of needed genome information. The lab methodology and data analysis will be openly available to help the global response in combating this disease.