To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed.