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Repository for suggesting new lineages that should be added to the current scheme
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FE.1.1.1+Orf8:A55V+S:V622I in Puerto Rico and Canada (173 seqs, 4 countries) #2067

Closed aviczhl2 closed 1 year ago

aviczhl2 commented 1 year ago

from https://github.com/sars-cov-2-variants/lineage-proposals/issues/155 FE.1.1.1+C15180T+T9445C+C28057T(orf8:A55V)+G23426A(S:V622L)

GISAID query: G23426A,C28057T,T23018C No of seqs: 110( Puerto Rico 75 Canada 31 USA-FL 1 USA-OH 2 USA-TX 1) First:EPI_ISL_17537601 2023-2-12, Canada Latest:EPI_ISL_17831578,2023-5-30,Puerto Rico

usher

Screenshot 2023-06-24 at 23 30 25
aviczhl2 commented 1 year ago

133, Germany

arodzh-sudo commented 1 year ago

An update on this, now 169 seqs as of 07/10/2023. Latest: EPI_ISL_17851506, EPI_ISL_17950296, EPI_ISL_17952483 from NY and Massachusetts 2023-06-17

A possible additional sublineage with ORF1a:V710I/G2393A (NSP2:V530I) with 97 seqs all from Puerto Rico.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c102_d96550.json

Screenshot 2023-07-11 at 13-51-51 Nextstrain _ fetch _ genome ucsc edu _ trash _ ct _ subtreeAuspice1_genome_1c102_d96550 json

aviczhl2 commented 1 year ago

now 169 seqs as of 07/10/2023

I only find 135 on GISAID. Are some of them masked on G23426A,C28057T or T9445C? Do you have an updated query?

Note that some seqs are uploaded both to GISAID and other platforms like GenBank. On usher you need to be careful that non-GISAID seqs may have a GISAID back-up.

arodzh-sudo commented 1 year ago

The number of sequences (169) is based on the cov-spectrum query FE.1.1.1* (Nextclade) + ORF8:A55V, S:V622I (World) using GISAID as source. Some of these sequences do not exhibit T9445C and C15180T or do not have sequencing coverage on those regions.

I only find 135 on GISAID. Are some of them masked on G23426A,C28057T or T9445C? Do you have an updated query?

Based on this and using only G23426A,C28057T as the Nucl Mutations query in GISAID, the total number of seqs are 173 (excluding two B.1.1 seqs from 2021) which all are FE.1.1.1 and exhibit the main mutations Orf8:A55V+S:V622I.

aviczhl2 commented 1 year ago

The number of sequences (169) is based on the cov-spectrum query FE.1.1.1* (Nextclade) + ORF8:A55V, S:V622I (World) using GISAID as source. Some of these sequences do not exhibit T9445C and C15180T or do not have sequencing coverage on those regions.

I only find 135 on GISAID. Are some of them masked on G23426A,C28057T or T9445C? Do you have an updated query?

Based on this and using only G23426A,C28057T as the Nucl Mutations query in GISAID, the total number of seqs are 173 (excluding two B.1.1 seqs from 2021) which all are FE.1.1.1 and exhibit the main mutations Orf8:A55V+S:V622I.

Yes you're right. I edited the query. Use G23426A,C28057T,T23018C you'll get all seqs and excludes the B.1.1 ones, now there's 173 seqs.

aviczhl2 commented 1 year ago

It is designated as HE.1