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Art Poon
@art_poon
Hepatitis C virus (left) is my teaching example of a consensus nomenclature based on sequence variation. It benefits from a deep evolutionary history leading to visually distinct clades (confusingly termed "genotypes").
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Art Poon
@art_poon
Thanks to a global sequencing and data sharing effort, we have an unprecedented picture of the evolution of #SARSCoV2 — but the compressed time scale and direct sampling of ancestors means a lack of gaps we can use to define categories.
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Art Poon
@art_poon
I used IQTREE in both cases, with protein sequences for the LANL-curated HCV reference genomes (to get better estimates of internal branch lengths), and nucleotide sequences for SC2. So the scale comparison is VERY crude!
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Art Poon
@art_poon
In my experience, the virus-specific database (which has been around for months, if we're talking about the same thing) does not contain all available records in the general NCBI database - perhaps because it is manually curated.
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Phil Grayson
@phil_d_grayson
Would building trees from data collected within a window of time help, or reduce the data too substantially? If one of the problems is sampling ancestors, could that solve the issue for some trees?
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Art Poon
@art_poon
Interesting take on the problem. I think with time scale of pandemic, many ancestral variants still relevant clinically and epidemiologically. Also have to deal with genomes from old samples with delayed release.
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