nextstrain / WNV

the repository used to build West Nile Virus for nextstrain
https://nextstrain.org/WNV/NA
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Ingest: annotate EF631122 and EF631123 as unknown collection date #41

Closed j23414 closed 1 week ago

j23414 commented 1 week ago

Description of proposed changes

NCBI GenBank records EF631122 and EF631123 have collection date annotations of "05-Aug-1931" in location "USA: Illinois, Cook County". This is inconsistent with known history of West Nile Virus (WNV) in the USA, as the first sequenced case should be around or after 1999.

Searching the literature of the submitters:

EF631123 shows up in a phylogenetic tree in Figure 1 within the WN02 clade which would be consistent with a post-2002 collection date, and as far as I can tell, the paper doesn't mention a pre-1999 sample in the USA:

I also tried searching earlier publications:

And concluded to set their collection dates as unknown or "XXXX-XX-XX" rather than potentially skewing downstream analysis with a set 1931 date.

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