Addressing unknowns of COVID-19 transmission and infection combining pathogen genomics and epidemiology to inform public health interventions

There is a growing pressure to understand the transmission patterns of COVID-19. As a new, emergent virus we have important gaps in the epidemiology of its infection. Those gaps translate also to limited understanding on who is infectious and for how long and how is connected to clinical outcome. Here we propose several objectives that involve combining viral genome data to epidemiological, clinical information to address those gaps. We will obtain viral complete genome sequences and epidemiological data and combine to (1) inform public health measures by revealing highways of transmission; (2) identify when an individual is infectious; (3) identify early warnings of local spread; (4) viral diversity connected to immune, drug and diagnostic; (5) complement current diagnostic approaches, and (6) identify the connection to adverse clinical outcomes. To this end, we have put together a nation-wide group of infectious disease, genomics, bioinformaticians and clinical researchers from more than 30 institutions.