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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Delta sublineage with S:222V and S:250S (mostly in South Africa) #229

Closed corneliusroemer closed 3 years ago

corneliusroemer commented 3 years ago

New lineage proposal by @CorneliusRoemer

Description Sub-lineage of: B.1.617 (sister lineage of #228 as it shares a synonymous mutation C2509T) Earliest sequence: US 2021-12 (just 1 single sequence), then South Africa 2021-19 where it reached 15-20% relative overall share Most recent sequence: Current Countries circulating: Mostly South Africa, but also around the world

Significant mutations (amongst others): ORF1b:765C, s:250S Country Total Variant Sequences First seq. found at Last seq. found at  
Australia 15 2021-25 2021-29  
Austria 1 2021-23 2021-23  
Belgium 3 2021-24 2021-34  
Brazil 3 2021-31 2021-31  
Canada 4 2021-22 2021-27  
Croatia 3 2021-25 2021-25  
Denmark 4 2021-27 2021-33  
Eswatini 7 2021-25 2021-27  
Finland 2 2021-31 2021-31  
France 8 2021-25 2021-29  
Germany 40 2021-22 2021-37  
Greece 12 2021-29 2021-32  
Ireland 3 2021-29 2021-32  
Israel 1 2021-31 2021-31  
Italy 6 2021-27 2021-32  
Japan 1 2021-31 2021-31  
Luxembourg 3 2021-25 2021-27  
Mauritius 1 2021-24 2021-24  
Netherlands 11 2021-23 2021-26  
New Zealand 1 2021-28 2021-28  
Norway 2 2021-32 2021-33  
Poland 1 2021-35 2021-35  
South Africa 738 2021-19 2021-35  
South Korea 1 2021-26 2021-26  
Spain 2 2021-25 2021-31  
Sweden 146 2021-24 2021-36  
Switzerland 4 2021-25 2021-33  
United Kingdom 18 2021-20 2021-35  
United States 38 2021-12 2021-35  
Zimbabwe 1 2021-27 2021-27

image https://cov-spectrum.ethz.ch/explore/South%20Africa/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22name%22%3A%22B.1.617.2*%22%2C%22mutations%22%3A[%22s%3A250s%22%2C%22s%3A222v%22%2C%22orf1b%3A765c%22]%7D%2C%22matchPercentage%22%3A1%7D

Genomes (~ 1000) sa.txt

Evidence image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_5835b_f70100.json?c=country&label=nuc%20mutations:C2509T,G15760T,A22310T,G29212T,T29742G

Proposed lineage name AY.x

chrisruis commented 3 years ago

Thanks @corneliusroemer We've added this as lineage AY.38 in v1.2.80 with 924 sequence designations. We've started the lineage on a branch with C2509T (synonymous) which seems to coincide with the introduction(s) into South Africa. S:T250S therefore occurs several branches downstream of where we've started AY.38

ryhisner commented 7 months ago

I just noticed that this lineage has a very large s2m deletion: ∆29717-29772. At 56 nucleotides, that makes it more than twice as large as the 26-nucleotide BA.2/4/5 s2m deletion of ∆29734-29759. I'm not aware of any other Delta lineages that have an s2m deletion, though I haven't done an exhaustive search or anything.

Also interesting: about 10% of AY.38 have ORF9b:I5T.

FedeGueli commented 7 months ago

I just noticed that this lineage has a very large s2m deletion: ∆29717-29772. At 56 nucleotides, that makes it more than twice as large as the 26-nucleotide BA.2/4/5 s2m deletion of ∆29734-29759. I'm not aware of any other Delta lineages that have an s2m deletion, though I haven't done an exhaustive search or anything.

Also interesting: about 10% of AY.38 have ORF9b:I5T.

Thx Ryan!!