Canada’s northern communities are particularly vulnerable to infectious disease because of social determinants of health plus their widespread harvesting of wildlife. The current COVID-19 pandemic is of particular concern to northern peoples and governments since their food security and livelihood needs are often directly dependent on the human-animal interface, at which COVID-19 can transmit in both directions. Although response planning and preparations are well underway by those governments, the challenges they face will be severe and compounded by all the normal challenges of providing services in the north. In collaboration with academic researchers, territorial governments, and private companies in multiple sectors we aim to address critical gaps in our understanding of the COVID-19 pandemic by generating genome sequences of all human and potential zoonotic coronaviruses, especially in the prairies and Northern Canada. This will provide critical information to fill current gaps in the north’s evolving strategy to address the spread of COVID-19, including development of appropriate risk communication, contact tracing, and rapid, locally based diagnostics.