Grubaugh et al, 2019
These include what is the virus, is it novel, or does it represent the re-emergence of a known pathogen; what is its mode of transmission; where does the emerging virus come from (in particular, what is its reservoir host and/or geographic source); what ecological factors underpin its emergence; how many introductions into humans have there been; what is the timing of these introduction events, and was there a period of undetected transmission before the first reported case; during flare-ups and future outbreaks, how are they connected to previous events; and what is the nature of virus evolution and is there evidence for local adaptation?
Grubaugh et al (2019) is a Nature Microbiology review article that describes "how many of the key questions in infectious disease epidemiology, from the initial detection and characterization of outbreak viruses, to transmission chain tracking and outbreak mapping, can now be much more accurately addressed using recent advances in virus sequencing and phylogenetics." The authors then highlight the utility of this approach with a hypothetical outbreak and how genomics could be used at each of its stages. The paper also outlines the requirements and challenges for the implementation of this system.