Analysing only Spike gene sequences from SARS-CoV-2

Hi everyone, is it possible to look at the phylogenetic relationship of only the spike, or other individual SARS-CoV-2 genes on the platform, like it is possible for influenza (i.e. to look at only the Haemagglutinin gene/protein or Neuraminidase gene/protein)?


Hello @KLaurie!

When you asked the question there wasn’t a spike only build yet, but now there is!

If I understand your request correctly, this should be exactly what you were looking for: auspice

The reason that we didn’t have spike only builds in contrast to separate HA/NA builds for flu is that the flu genome is naturally subdivided into 8 segments that reassort frequently. So it doesn’t make much sense (without accounting for reassortment) to make a single “whole genome” flu build, in the same sense one can make a whole-genome SARS-CoV-2 build [caveat: SARS-CoV-2 does recombine but recombination is rare enough to not entirely make a whole genome tree pointless, at least on short time scales. The fact that it does causes some issues, as recombination violates the assumptions that go into tree building].

I hope this helps!