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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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BA.2.12.1 saltation, USA (California, 3 counties, 3 seqs) #1658

Closed ryhisner closed 2 months ago

ryhisner commented 3 months ago

Description

Sub-lineage of: BA.2.12.1 Earliest sequence: 2024-3-9 Most recent sequence: 2024-5-6 Continents circulating: North America (3) Countries circulating: USA (3) Number of Sequences: 3 GISAID Nucleotide Query: G5180A, C7420T, C13356T CovSpectrum Query: Nextcladepangolineage:BA.2.12.1* & [6-of: C16608T, C18312T, G22132T, A22206G, G22770A, A22881G, T22896C, G22899T, A22995T] Substitutions/Deletions on top of BA.2.12.1 on Shared Branch #1: Spike: ∆Y144, R190S, R214H, D215G, K440R, V445A, G446V, N460K, K478I ORF1a: D1639N, L3829F, T4364I ORF1b: H1087Y E: V62F Nucleotide: C3874T, A5371G, G5180A, C7420T, C11750T, C13356T, C16608T, C16726T, T16776C, C18312T, ∆21992-21994, G22132T, G22203A, A22206G, A22881G, T22896C, G22899T, A22995T, T22942A, C23683T, G26428T

Substitutions/Deletions on top of BA.2.12.1 on Branch #2: Spike: P9L, F157S, E340K, R346T, N417T, G482R, ∆A484, E554Q, A570V, K679R, T859S, V1177I N: P279S Nucleotide: A11600G, A16512G, C21588T, T22032C, C22033A, G22580A, G22599C, A22812C, G23006C, ∆23012-23014, G23222C, C23271T, A23598G, A24137T, G25091A, A25512T, G28001A, T28297C, C29108T

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/chronic_multiples/main/BA.2.12.1_USA_CA__2024.json?label=id:node_4659742

image

Evidence I think these sequences are all likely from the same patient, but because they were collected in three different counties in California, I suppose there is a small chance that these are three different patients, which is why I put this post together. Two of the counties border each other on the west coast of California while the third is on the eastern border of the state.

There is dropout in all three sequences, so there is some uncertainty about the full mutational profile. Below is an approximation of the mutations in the most recent sequence, which was uploaded today but collected on May 6.

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Genomes

Genomes EPI_ISL_19142916, EPI_ISL_19164072, EPI_ISL_19223353
HynnSpylor commented 3 months ago

Great Catch! Different counties are slightly worried, but the detail information is unknown. I wonder if we could confirm them.

aviczhl2 commented 2 months ago

No further seqs