12.2 Nextstrain
We’ll be visualizing the evolutionary history of SARS-CoV-2 with a web application called Nextstrain, developed by Trevor Bedford and colleagues at the Fred Hutch Cancer Center.
Reading a phylogenetic tree
Nextstrain provides a guide on how to interpret their phylogenetic trees.
The figure below shows a “transmission tree” of viruses, where every dot is individual who was infected. Some of these individuals infect others, and some are dead ends (no transmission). After a mutation (diamonds) occurs on a branch, any sample to the right of the mutation will also carry it.
Fig. 1. The “true” tree of virus transmission through a population (source).