Designate clade 26B (XFG.3.4.1)#1206
Open
trvrb wants to merge 1 commit into
Open
Conversation
Elevate lineage XFG.3.4.1 to clade 26B, descending from clade 25C (XFG). Defining Spike mutation S:S680P (nuc 23600), plus five synonymous/non-Spike nucleotide markers (10615, 13608, 15762, 18885, 28822) included so the clade demarcates exactly at XFG.3.4.1 rather than a higher node. XFG.3.4.1 has risen to a clear majority in South America (~76%, one-sided 95% Wilson lower bound 59% in a 50-sequence window around January 2026), first detected ~October 2025. Demarcated at XFG.3.4.1 rather than its descendant QF.2: QF.2 adds only the single substitution C27812T, which is synonymous, so it carries no expected fitness change beyond XFG.3.4.1. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This was referenced Jun 26, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
With this PR we designate clade 26B (lineage XFG.3.4.1), which descends from clade 25C (XFG).
Demarcation:
We demarcate at XFG.3.4.1 rather than its descendant QF.2. QF.2 adds only a single substitution beyond XFG.3.4.1, C27812T, which is synonymous — so QF.2 carries no expected fitness change on top of XFG.3.4.1, and the broader XFG.3.4.1 cut is the right clade boundary.
Spike mutations vs parent clade (1): S680P
Frequency (windowed fixed-N tip counts, one-sided 95% Wilson lower bound):
PR output on Nextstrain:
Closes #1182