BA.2.12.1 saltation, USA (California, 3 counties, 3 seqs)

[ryhisner]

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

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.

Genomes

Genomes

EPI_ISL_19142916, EPI_ISL_19164072, EPI_ISL_19223353

[HynnSpylor]

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

[xz-keg]

No further seqs