XBB.1.5.15 sublineage with ORF1a:G519S and S:Q146K (mainly USA, >800 seq)

[oobb45729]

Defining mutations:

XBB.1.5.15(with G15957T) then ORF1a:G519S(G1820A)+S:Q146K(C21998A)

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=10204c%2615957t%261820a%2621998a&
ORF1a:G519S is a frequently occurring mutation and it seems that S:Q146K happened multiple times in XBB.1.5.

[corneliusroemer]

That tree is too narrow, you should make one that encompasses as many nearest neighbours as possible (with 5000 context samples) like this:

When something appears to occur multiple times we also need to be careful. Have a look at the way issues from others like Ryan Hisner are written and try to emulate their style.

[oobb45729]

[emily-smith1]

Hopefully this can help!

Description

Sub-lineage of: XBB.1.5
Earliest sequence: 2022-12-07 (USA-CA)
Most recent sequence: 2023-01-19 (USA-CA)
Countries circulating: USA, Canada
Number of sequences: 129
GISAID query: G1820A,G15957T,C21998A,C22000A,T23018C,T23019C,T22882G
Substitutions on top of XBB.1.5: S:H146K and ORF1a:G519S after G15957T

This one is tricky. There appears to be another XBB.1.5 cluster (n=7) that has S:H146K and ORF1a:G519S following G15957T as well if you zoom way out on the tree, but those have some reversions or frameshift in Spike that are likely sequencing artifacts. I was able to filter out by adding S:N440K (T22882G) to the GISAID query.

Evidence

UShER tree (zoomed in to the proposed lineage): https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_218e8_daae40.json?f_userOrOld=uploaded%20sample&label=id:node_3883100

UShER tree (zoomed out to include all 5000 on subtree): https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_218e8_daae40.json?c=gt-ORF1ab_519&label=id:node_3877569

This proposed lineage currently has a 61% growth advantage worldwide since Dec 1 (using same combo of mutations listed above):

[corneliusroemer]

Thanks @emily-smith1! What's this growth advantage with respect to, and for which region? Should be against XBB.1.5 and US - maybe that is already the case :)

[emily-smith1]

You're welcome! The previous one was worldwide, without a baseline. Agreed that since this is mostly US, something more specific would make sense.

Here is one specifically for the US, last 3 months, relative to XBB.1.5:

[corneliusroemer]

Thanks! And here we see... mostly noise ;) I'll take a systematic look at XBB.1.5 this week

[corneliusroemer]

S:146K appears to be rising in XBB.1.5, but it seems very inconsistently sequenced. Bit tricky to designate that way.

[ryhisner]

ORF1a:G519S is also rising in prevalence lately, mostly in the US. Intriguingly, ORF1a:G519S also rose as a percentage of Delta over many months—though again, primarily in the US. The pattern is somewhat similar to what has been seen in ORF1a:82-86del and (as I recently noticed) A27000G, where the prevalence seems to gradually rise with ~3-7% growth advantage within a given variant but then falls back to very low levels with the emergence of a new variant.

[oobb45729]

ORF1a:G519S is one of the most frequent ORF1ab mutations along with ORF1a:K3353R, ORF1a:L3606F, ORF1b:K2557R, etc.

[AnonymousUserUse]

Note: the lineage proposed in this issue has been designated as FD.2 (=XBB.1.5.15.2) and monitored by US CDC.