From cd150097b2b808d67d8928b6f7e6601e99c3dd14 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Mon, 10 Jun 2024 11:49:25 -0700
Subject: [PATCH] Fixup: Add date annotations for rare genotypes

Six of the samples that are force-included in the Nextclade dataset tree have empty collection date fields in the metadata output from NCBI Datasets. This results in the samples being removed downstream by the TreeTime clock filter. This commit adds collection dates (which were manually extracted from the strain names in the NCBI metadata) for these samples so that they will be included in the Nextclade dataset tree.
---
 ingest/defaults/annotations.tsv | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/ingest/defaults/annotations.tsv b/ingest/defaults/annotations.tsv
index 386122a..a951ca9 100644
--- a/ingest/defaults/annotations.tsv
+++ b/ingest/defaults/annotations.tsv
@@ -146,3 +146,13 @@ U64582	date	1988-XX-XX
 X84865	date	1994-XX-XX
 X84872	date	1990-XX-XX
 X84879	date	1971-XX-XX
+#
+# Strains with rare genotypes
+# Dates are retrieved from epi-weeks reported within strain names on NCBI
+# These are force-included in the nextclade tree to boost representation of rare genotypes
+AF410989	date	1987-03-09 # genotype E
+AY037009	date	2000-06-12 # genotype G2 
+AY037043	date	2000-04-17 # genotype H2
+AY037026	date	1997-03-24 # genotype H2
+AY037028	date	2000-03-13 # genotype D2
+FJ668380	date	2003-02-10 # genotype D10