Having spent much of the last 15 years trying to improve molecular phylogenetics, I had formed the fairly firm view that my research was very interesting (of course!!!) but rather useless in the short term. Turns out I was wrong. Phylogenetic analyses are crucial to understanding the evolution and spread of SARS-CoV-2, that much is obvious. What was less obvious is just how hard it would be to estimate good phylogenies of SARS-CoV-2. There are lots of challenges: the sheer volume of data is staggering and ever-increasing (currently ~60K genomes); the virus evolves very slowly so we have very little information to work with; human bodies and virus sampling kits both degrade the virus RNA very quickly meaning there's a lot of non-phylogenetic information; certain labs seem to repeatedly make the same sequencing errors; the list goes on. The result is a global effort of phylogenetics and molecular evolution labs pulling together to jointly solve these problems, and to estimate good and reliable phylogenies with well-characterised uncertainty. The result is a continuously-updated phylogeny and protocol for estimating it, where all the research is done reproducibly and in the open. This has facilitated new collaborations with academia and industry, a better understanding of the history and evolution of the virus, and the issues associated with sequencing it.
Rob is an associate professor in the Division of Ecology and Evolution in the Research School of Biology at the ANU.