From b3097febbdbea2e88a5dc69ec4845cbd9d90d1b2 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 13 Nov 2024 09:57:41 -0800 Subject: [PATCH] Ingest: annotate EF631122 and EF631123 as unknown collection date MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit EF631122 and EF631123 have collection date annotations of "05-Aug-1931" and "05-Aug-1931" in location "USA: Illinois, Cook County". However, the first initial case of WNV sequenced in USA should be after 1999. Searching the literature of the submitters: EF631123 shows up in a phylogenetic tree within the WN02 grouping, and 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 searched 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. And concluded to set their collection dates as unknown or "XXXX-XX-XX" rather than potentially skew downstream analysis with a 1931 date. --- ingest/defaults/annotations.tsv | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ingest/defaults/annotations.tsv b/ingest/defaults/annotations.tsv index a5f7a2a..b2a5f25 100644 --- a/ingest/defaults/annotations.tsv +++ b/ingest/defaults/annotations.tsv @@ -303,4 +303,6 @@ AY765264 region Europe DQ318020 date 1972-XX-XX DQ318020 host Culex tigripes D00246 country Australia -D00246 date 1960-XX-XX \ No newline at end of file +D00246 date 1960-XX-XX +EF631122 date XXXX-XX-XX +EF631123 date XXXX-XX-XX