From 9bb8661d167c38b2f5c79fd151f7af00d233f527 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Mon, 8 Jan 2024 09:40:40 -0800 Subject: [PATCH] Withdraw lineage KD.5 -- an indel artefact caused the false appearance of S:L244F as explained in #2405. The deleted range is now masked in XBC in the usher tree so there is no longer a branch for this lineage. --- lineage_notes.txt | 2 +- lineages.csv | 55 ----------------------------------------------- 2 files changed, 1 insertion(+), 56 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 1b402c75..6b925964 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -3642,7 +3642,6 @@ KD.1 Alias of XBC.1.3.1.1, S:R346S, Australia, from sars-cov-2-variants/lineage- KD.2 Alias of XBC.1.3.1.2, ORF1a:M3661L, ORF1a:M3934I, Australia/New Zealand KD.3 Alias of XBC.1.3.1.3, C10519T, C19524T, New Zealand KD.4 Alias of XBC.1.3.1.4, ORF1a:K394R, ORF1a:L730F, ORF1a:T965I, Australia/Japan -KD.5 Alias of XBC.1.3.1.5, S:L244F, Australia XBC.1.4 Australia, S:G184S, from #1622 XBC.1.5 Philippines/South Korea/Japan, ORF1a:T708I after A10042C, from #1671 XBC.1.6 S:346S, S:M452R, found in Australia, from #1755 @@ -4030,4 +4029,5 @@ XDK Recombinant lineage of XBB.1.16.11 (likely) and JN.1.1.1 (breakpoint between *HK.1.1 Withdrawn as smaller than thought (only 6 sequences have 257V and G22927T): Alias of XBB.1.9.2.5.1.1.1.1, S:455F (G22927T), China *HK.10 Withdrawn unless lineage grows: Alias of XBB.1.9.2.5.1.1.10, S:L455F, on C19983T branch, China *HK.3.11 Withdrawn, as part of 14988C sublineage of EG.5.1.1, not HK.3: Alias of XBB.1.9.2.5.1.1.3.11, S:A475V, Finland/Denmark/Sweden +*KD.5 Withdrawn: Alias of XBC.1.3.1.5, S:L244F, Australia, indel artefact caused false S:L244F (#2405) diff --git a/lineages.csv b/lineages.csv index c4d64cb1..ca77d1d1 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2500308,61 +2500308,6 @@ Japan/PG-554438/2023,KD.4 Japan/PG-568650/2023,KD.4 Japan/PG-574069/2023,KD.4 Japan/PG-574068/2023,KD.4 -Australia/WA12911/2023,KD.5 -Australia/WA12682/2023,KD.5 -Australia/WA14290/2023,KD.5 -Australia/WA13772/2023,KD.5 -Australia/WA13979/2023,KD.5 -Australia/WA13130/2023,KD.5 -Australia/WA13751/2023,KD.5 -Australia/WA13562/2023,KD.5 -Australia/WA13674/2023,KD.5 -Australia/WA14359/2023,KD.5 -Australia/WA14477/2023,KD.5 -Australia/WA14272/2023,KD.5 -Australia/WA13904/2023,KD.5 -Australia/WA14229/2023,KD.5 -Australia/WA14228/2023,KD.5 -Australia/WA14387/2023,KD.5 -Australia/WA15055/2023,KD.5 -Australia/WA15006/2023,KD.5 -Australia/WA15327/2023,KD.5 -Australia/WA15373/2023,KD.5 -Australia/WA15362/2023,KD.5 -Australia/WA15434/2023,KD.5 -Australia/WA15467/2023,KD.5 -Australia/WA14998/2023,KD.5 -Australia/WA14982/2023,KD.5 -Australia/WA13149/2023,KD.5 -Australia/WA13151/2023,KD.5 -Australia/WA12280/2023,KD.5 -Australia/WA15269/2023,KD.5 -Australia/WA14942/2023,KD.5 -Australia/WA14166/2023,KD.5 -Australia/WA14573/2023,KD.5 -Australia/WA13781/2023,KD.5 -Australia/WA13484/2023,KD.5 -Australia/WA15080/2023,KD.5 -Australia/WA14498/2023,KD.5 -Indonesia/JI-ITD-61055NT/2023,KD.5 -Australia/NSW-ICPMR-45298/2023,KD.5 -Australia/WA13545/2023,KD.5 -Australia/WA13197/2023,KD.5 -Australia/WA13996/2023,KD.5 -Australia/WA13973/2023,KD.5 -Australia/WA14542/2023,KD.5 -Australia/WA13969/2023,KD.5 -Australia/WA14156/2023,KD.5 -Australia/WA13923/2023,KD.5 -Australia/WA13206/2023,KD.5 -Australia/WA15319/2023,KD.5 -Australia/WA15017/2023,KD.5 -Australia/WA15291/2023,KD.5 -Australia/WA15205/2023,KD.5 -Singapore/R58MR96/2023,KD.5 -Singapore/R57MR70/2023,KD.5 -Australia/QLD0x0137BB/2023,KD.5 -Australia/WA15342/2023,KD.5 SouthAfrica/NICD-R10771/2023,JP.1.1 SouthAfrica/NICD-R10786/2023,JP.1.1 SouthAfrica/NICD-R10465/2023,JP.1.1