Flagging collection dates for `PP_000JSDD.3` and `PP_000JSEB.3`

[j23414]

Describe the possible issue

NCBI GenBank records EF631122 and EF631123 (corresponding to PP_000JSDD.3 and PP_000JSEB.3) 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.

Evidence of the problem

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:

• Amore, G., Bertolotti, L., Hamer, G.L., Kitron, U.D., Walker, E.D., Ruiz, M.O., Brawn, J.D. and Goldberg, T.L., 2010. Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005–2007. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1548), pp.1871-1878.

I also tried searching earlier publications:

• Bertolotti, L., Kitron, U.D., Walker, E.D., Ruiz, M.O., Brawn, J.D., Loss, S.R., Hamer, G.L. and Goldberg, T.L., 2008. Fine-scale genetic variation and evolution of West Nile Virus in a transmission “hot spot” in suburban Chicago, USA. Virology, 374(2), pp.381-389.
• Bertolotti, L., Kitron, U. and Goldberg, T.L., 2007. Diversity and evolution of West Nile virus in Illinois and the United States, 2002–2005. Virology, 360(1), pp.143-149.

Suggested change

I was going to manually annotate these to unknown date "XXXX-XX-XX" to avoid potentially skewing downstream analysis. My best guess is these sequences should be between 2002-2007.

Full list of affected sequences

• https://pathoplexus.org/seq/PP_000JSDD.3
• https://pathoplexus.org/seq/PP_000JSEB.3

[emily-smith1]

Thanks for flagging this. Have there been any attempts to contact the corresponding author yet?

[j23414]

Not yet! I usually email NCBI helpdesk for fixing genbank annotations, and I'll probably try that next. Although I have a few other fixes to submit: date, geoloc, and host fixes from annotations.tsv

I imagine pathoplexus is still designing how to propagate community curated fixes back up to their NCBI records

[m-a-martin]

I agree with Jennifer and Emily that these collection dates are almost certainly spurious and that the correct collection dates are currently unknown. I do not think Pathoplexus currently supports annotating unknown collection dates as XXX-XX-XX. I believe Collection Date is currently a required field, so maybe these sequences should be removed from the database?