Do I need to go through all the reasons the H1N1 paper is wrong? Okay.
- They used virulence and codons bias as proxies for fitness; neither is appropriate. (I feel like this one was designed specifically to annoy me.)
- They never directly measured viral replication rate, the actual way to evaluate viral fitness.
- In using the 2009 pandemic strain as the reference genome, they attributed to single-base substitutions (substitution in the genetic rather than phylogenetic sense) differences that were actually due to reassortment (a form of recombination, for anyone who doesn’t know the term).
- They claimed a viral lineage went extinct despite the fact that it was still circulating.
I mean come on. I’m supposed to take this stuff seriously?
And in addition to that, they’ve made excuses for the continued existence of HIV despite it not crossing over into humans since the early 20th century. Each HIV-1 lineage (M, N, and O) jumped one time and one time only and persists since that initial crossover.