LF.3.1 (FLiRT+ S:V445P) with S:P>L1143F (42)

[FedeGueli]

Very early to propose but there could be a trend toward 445P in lineages with S:F456L, caught first by @DoropFan,

LF.3 [Jn.1.16.1> C5581A, C7594T, Orf1a:A4285V (C13119T) ]> S:V>H445P ( T>A22896C)
[alternative placement JN.1.42 (C5581A) >> FLirt >> S:445) analysed by @aviczhl2 ]
Query:C13119T,C5581A, C7594T,T22896C
Samples: 4 (California) (3 on Gisaid)
First collected on 2024-05-01
IDs:
EPI_ISL_19101707, EPI_ISL_19101709, EPI_ISL_19135408, USA/2024CV0744/2024|PP747627.1

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5f6c9_31e760.json?c=userOrOld&label=id:node_7124795

This very new lineage has been already splitted in two branches that both carry spike mutations:

Branch 1 with S:P>L1143F Designated LF.3.1.1
Jn.1.16.1> C5581A, C7594T, Orf1a:A4285V (C13119T) > S:V>H445P ( T>A22896C) > C13860T > C10894T, C18888T, C20628T, S:P>L1143F ( C24989T)
Query: C10894T, C18888T,T3565C

Branch 2 with S:D745A now proposed in cov-lineages/pango-designation#2697

Jn.1.16.1> C5581A, C7594T, Orf1a:A4285V (C13119T) > S:V>H445P ( T>A22896C) > S:D745A (A23796C)
Query: T22896C,A23796C,T3565C
Samples: 20
Countries : 6 (Peru', Colombia Ecuador)

Note: This was formerly placed not under JN.1.16.1 and it has been tracked as Branch 124 in #1089

[xz-keg]

This shall be sub-branch of JN.1.42, or recomb involving JN.1.42, due to C5581A.

[FedeGueli]

Thx added that placement as hypothesis as of today, we will se if more will pop up. i m curious to see where JN.1.42 emerged first, it seems coming from South America, it could make sense that it managed to fly under the radar and appearing heavily mutated and evolved

[FedeGueli]

5

[FedeGueli]

parental lineage designated LF.3

[FedeGueli]

DESIGNATED LF.3.1 VIA cov-lineages/pango-designation@33233d8

[Memorablea]

Hello, I found it here due to observing many S: V445P sequences. May I ask, what role does S: V445P exhibit in the sequence? How should we view a mutation that has been observed in a previous sequence but has no growth advantage?

[FedeGueli]

Hello, I found it here due to observing many S: V445P sequences. May I ask, what role does S: V445P exhibit in the sequence? How should we view a mutation that has been observed in a previous sequence but has no growth advantage?

445P was in all XBB so for sure not bad. JN.1.50 with it is one of the fastest lineage. Most of sequences with it at the start of Jn.1 wave were artifacts likely. and likely it works well with 456L with some Epistatic effect.

[FedeGueli]

proposed now:; cov-lineages/pango-designation#2669

[FedeGueli]

Designated LF.3.1.1 via cov-lineages/pango-designation@b0a4a61

[xz-keg]

The S:D745A branch is designated LF.3.1.2 via cov-lineages/pango-designation@d247018#commitcomment-148151048