SARS-CoV-2 and COVID-19

There are quite a few topics in phylogenetics and evolution that are “hot” in the context of the current pandemic. One is whether or not the “lineages” or clades with mutations that are accumulating in the virus as it spreads out around the world can justify terms such as “strains”. Another is attempting to keep track of recombinations between lineages, which can be facilitated by crowding in hospital wards. Another is how to efficiently keep track of phylogeny/nomenclature when we have over 40,000 genome sequences with very low levels of diversity between them.