Second branch of XEC with Orf1a:I1367L (167, >20 places)

[FedeGueli]

From sars-cov-2-variants/lineage-proposals#1908

XEC has three main branches one defined by Orf1a:A599T the other defined by Orf1a:I1367L that is convergent with Kp.3.3.4
@ryhisner already analyzed that Orf1a:I1367L is one of most frequent mutation in chronically infected patients ( at least of the ones sampled)

Defining mutations: XEC > Orf1a:I1367L (A4364C)
Query: C19716T, C25006T,A4364C
Samples: 41
First collected on 2024-07-08 in Germany
Countries: 11 (main ones: Germany, Canada, Italy)
Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_25849_dbb1f0.json?f_userOrOld=uploaded%20sample&label=id:node_7076039

IDs:
EPI_ISL_19283843, EPI_ISL_19299882, EPI_ISL_19326349,
EPI_ISL_19338698, EPI_ISL_19338888, EPI_ISL_19338902,
EPI_ISL_19338943, EPI_ISL_19341036, EPI_ISL_19343732,
EPI_ISL_19343943, EPI_ISL_19343958, EPI_ISL_19357917,
EPI_ISL_19357960, EPI_ISL_19358107, EPI_ISL_19358118,
EPI_ISL_19358189-19358190, EPI_ISL_19358340-19358341, EPI_ISL_19363463,
EPI_ISL_19363781, EPI_ISL_19363785, EPI_ISL_19364201,
EPI_ISL_19369749, EPI_ISL_19370079, EPI_ISL_19372197,
EPI_ISL_19373234, EPI_ISL_19373237, EPI_ISL_19378379,
EPI_ISL_19378382, EPI_ISL_19379598, EPI_ISL_19381037,
EPI_ISL_19381214, EPI_ISL_19383780, EPI_ISL_19384099,
EPI_ISL_19384101, EPI_ISL_19385479, EPI_ISL_19385566,
EPI_ISL_19385761, EPI_ISL_19386322, EPI_ISL_19386493,

[FedeGueli]

Evidences for it to be faster tha main branches are weak: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nucMutations=C18657T%2CC19716T%2CC25006T%2C4364A&nucMutations1=C19716T%2CC25006T%2CA4364C&analysisMode=CompareToBaseline&

But the trend when compared to XEC w/o Orf1a:I1367L to me is real.

[FedeGueli]

45 , Portugal Norway

Ping @corneliusroemer i would designate this because while RBD is short of mutations (beside flirt 493E 445X 478X and new 435S) it seems mutations outside spike are gaining relevance as happenend in the old Delta times. (my view)

[FedeGueli]

57 Slovenia

[FedeGueli]

75 Spain

[DailyCovidCases]

Tree now:
usher

@corneliusroemer This branch should be designated since it's growing rapidly

[FedeGueli]

98

[FedeGueli]

107 Australia

[Fearuncle]

Designated as XEC.2

[FedeGueli]

Designated XEC.2 via ba3711a

[corneliusroemer]

I was thinking for a long time whether this is actually a recombinant but in the end didn't go for it because it's unclear. The following is what I found: this lineage has the ORF1a from KP.3.3.4, the most common KP.3.3 in Germany where this recombinant was likely born. So in some sense, this might well have been the original XEC, with a double breakpoint. If that was the case, then XEC could either be due to an independent recombination event or one of the two is a recombinant of the other. It's very muddy what the sequence of events is here, so better keep it simpler also to keep it memorable and call similar things by similar names. There's a small chance that the XEC cluster is actually 3 recombinants, maybe from a single chronic infectee? We likely won't ever know for sure.

…

On Sat, Sep 28, 2024, 21:46 Federico Gueli ***@***.***> wrote: Designated XEC.2 via ba3711a <ba3711a> — Reply to this email directly, view it on GitHub <#2768 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF77AQOGTK2722V6WJLV52TZY4BRZAVCNFSM6AAAAABN3B67SCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBQHA3TOMZUGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[FedeGueli]

I was thinking for a long time whether this is actually a recombinant but in the end didn't go for it because it's unclear. The following is what I found: this lineage has the ORF1a from KP.3.3.4, the most common KP.3.3 in Germany where this recombinant was likely born. So in some sense, this might well have been the original XEC, with a double breakpoint. If that was the case, then XEC could either be due to an independent recombination event or one of the two is a recombinant of the other. It's very muddy what the sequence of events is here, so better keep it simpler also to keep it memorable and call similar things by similar names. There's a small chance that the XEC cluster is actually 3 recombinants, maybe from a single chronic infectee? We likely won't ever know for sure.
…
On Sat, Sep 28, 2024, 21:46 Federico Gueli @.> wrote: Designated XEC.2 via ba3711a <ba3711a> — Reply to this email directly, view it on GitHub <#2768 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF77AQOGTK2722V6WJLV52TZY4BRZAVCNFSM6AAAAABN3B67SCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBQHA3TOMZUGA . You are receiving this because you were mentioned.Message ID: @.>

Agree 100% Thx