Swap out reference for a more recent virus

[trvrb]

@cassiawag @miparedes ---

I'm using reference virus genome A/Beijing/32/1992 to root each cluster phylogeny. It would work to use augur refine to generate a timetree and root things this will, but this is pretty slow. In order to increase the accuracy of this method we should be using a more recent reference virus. If you look at https://nextstrain.org/flu/seasonal/h3n2/ha/12y you'll see that everything circulating finds a common ancestor after A/Perth/16/2009. This should make a good choice.

You'll want to find matching Genbank files via FluDB (https://www.fludb.org/brc/vaccineRecommend.spg?decorator=influenza) and use these to replace config/reference_h3n2_ha.gb, etc... These need to have CDS and gene for each segment. Not all Genbank files do.

This is not blocking things, but should improve accuracy of rooting.

[cassiawag]

The genbank references that I'm looking have a different length segments than the current genbank references: https://www.fludb.org/brc/fluStrainDetails.spg?strainName=A/Perth/16/2009(H3N2)&decorator=influenza

I don't think this should be a problem. In HA, for example, it's just an extra 8 nucleotides prior to the start of the coding region. I think the alignment should eliminate any length differences in our sequences . Does that sound correct to you @trvrb?

[trvrb]

This is fine, you should see that the CDS annotation shifts appropriately however: https://www.ncbi.nlm.nih.gov/nuccore/GQ293081?%3Fdb=nucleotide

[trvrb]

See note here #13 (comment). This will require modifying a few other config files and can wait a bit.