Tracking lineages with S:L455F+S:F456L+S:A475V (non-EG.5)

[oobb45729]

### Tasks
- [x] GK.3.1
- [x] JD.1.1 (former cluster 1)
- [x] GW.5.1.1 (former cluster 5 and singlet 2): https://github.com/cov-lineages/pango-designation/issues/2277
- [x] GK.4 (former cluster 3): https://github.com/cov-lineages/pango-designation/issues/2276
- [x] XCP (former cluster 8): https://github.com/sars-cov-2-variants/lineage-proposals/issues/772
- [x] FL.15.1.1 (former cluster 10): https://github.com/sars-cov-2-variants/lineage-proposals/issues/646
- [x] GW.5.3.1 (former cluster 12 and singlet 10): https://github.com/cov-lineages/pango-designation/issues/2298
- [x] GK.8.1 (former cluster 16 and singlet 17): https://github.com/sars-cov-2-variants/lineage-proposals/issues/909
- [x] GK.1.6.1 (former cluster 9 and singlet 6): https://github.com/cov-lineages/pango-designation/issues/2304
- [x] GK.1.2.1 (former cluster 13): https://github.com/cov-lineages/pango-designation/issues/2314
- [x] GK.1.8 (former cluster 7): https://github.com/cov-lineages/pango-designation/issues/2313
- [x] XCY (former cluster 15 and singlet 20): https://github.com/sars-cov-2-variants/lineage-proposals/issues/887
- [x] GY.1.1.1 (former cluster 28): https://github.com/cov-lineages/pango-designation/issues/2337
- [x] JF.1.1.1 (former cluster 21): https://github.com/cov-lineages/pango-designation/issues/2361
- [x] GK.1.11 (former cluster 2 and singlet 1): https://github.com/cov-lineages/pango-designation/issues/2315
- [x] XDM (former cluster 42): https://github.com/sars-cov-2-variants/lineage-proposals/issues/1163
- [x] GK.1.10.1 (former cluster 29): https://github.com/cov-lineages/pango-designation/issues/2479
- [ ] Cluster 4 (former singlet 5): a GK.1.2 subbranch with ORF1a:A260V, ORF1a:G1030D, S:A475V (3 seq. USA, Denmark)
- [ ] Cluster 14 (former singlet 7): a GK.1 subbranch with ORF1a:D1323N and S:A475V (2 seq. Brazil)
- [ ] Cluster 17 (former singlet 9): an EG.5.1.1+ORF1a:L590F+ORF1a:T3775I recombinant with XBB.1.5.70 (+S:A475V and S:E1150A) https://github.com/sars-cov-2-variants/lineage-proposals/issues/898
- [ ] Cluster 19 (former singlet 19): a GK.1+nuc:C13551T subbranch with ORF1a:A138D, ORF1a:M1014T, ORF1a:M3695T, ORF1b:I2568M then ORF3a:T34M, ORF9b:S10F then ORF1a:H1545Y, ORF1b:I1690V, S:A475V, ORF3a:Y107C (2 seq. USA)
- [ ] Cluster 23: a GK.1+ORF1a:T3287I then nuc:C11956T subbranch with S:A475V (41 seq. Brazil, USA)
- [ ] Cluster 24 (former singlet 30): a GK.1.1+ORF1b:I1862V then ORF3a:D27H subbranch with S:A475V (7 seq. UK)
- [ ] Cluster 25 (former singlet 33): a GK.1.10+ORF1a:Y2262H subbranch with ORF1a:T2432I, S:A475V (29 seq. Denmark, Belgium, Austria, Netherlands, Brazil, USA, UK)
- [ ] Cluster 26 (former singlet 25): a GK.1.1+ORF1b:I1862V subbranch with S:A475V, nuc:G26217A (2 seq. Spain)
- [ ] Cluster 27 (former singlet 14): a GK.1+ORF1a:G112D+ORF1a:G1073R+ORF1a:T3555A+S:A475V+S:T732I+ORF7a:T120I subbranch with S:A475V (9 seq. Austria)
- [ ] Cluster 30 (former singlet 16): an XBB.1.5.70+ORF1a:F3604L subbranch with S:A475V (11 seq. Brazil, France, Ireland)
- [ ] Cluster 31 (former singlet 39): an XCH.1+ORF1a:T4265I then N:A119T then S:A262S+ORF8:I10S subbranch with S:A475V (12 seq. Ireland)
- [ ] Cluster 32 (former singlet 44): a XBB.1.5.70+ORF1a:V988I+ORF1a:L3919F+ORF1b:G977A+ORF3a:Q57H subbranch with S:F157L, S:A475V, ORF3a:Y107C (3 seq. Italy)
- [ ] Cluster 33 (former singlet 35): a GK.1.1.1+nuc:C28603T then nuc:C4832T+nuc:C28163T then nuc:C17172A subbranch with S:A475V (2 seq. USA)
- [ ] Cluster 34: a JF.1.1+nuc:A2521G subbranch with S:A475V (7 seq. Canada)
- [ ] Cluster 35: a GK.1+nuc:C25944T subbranch with S:A475V (3 seq. Brazil)
- [ ] Cluster 36: a GW.5.1+ORF1a:K3353R+ORF1b:A37S then ORF1b:K2557R subbranch with ORF1b:V2233I, S:N185D, S:A475V (5 seq. Greece)
- [ ] Cluster 37 (former singlet 48): a GK.1.5+nuc:T931C then ORF10:P10S subbranch with S:A475V (3 seq. Brazil, Japan, Chile)
- [ ] Cluster 38: a GK.1 subbranch with ORF1a:S1733G, ORF1a:M3655I, ORF1a:L3829F, ORF1b:V464I, S:A475V, S:E554K, S:H1101Y (2 seq. Finland)
- [ ] Cluster 39 (former singlet 37): an XCH+ORF3a:T175K subbranch with ORF1b:L2349S, S:A475V (2 seq. USA)
- [ ] Cluster 40 (former singlet 51): a JF.1.1+ORF3a:D222N then ORF1a:N557S subbranch with S:A475V, ORF8:Q91* (8 seq. France, UK, Switzerland, Italy)
- [ ] Cluster 41 (former singlet 52): a JD.1.2.2+ORF1a:I2790V subbranch with S:A475V, ORF7a:G70D (2 seq. Brazil)
- [ ] Cluster 43: an XDE/XBB.1.16 recombinant with S:A475V (5 seq. USA)
- [ ] Cluster 44: a GK.1.10+ORF1a:D2060N then ORF1a:T2007I subbranch with ORF1a:A1397V, ORF1b:T2432I, ORF1b:K2557R, S:A475V (7 seq. UK)
- [ ] Cluster 45 (former singlet 64): a GK.1+ORF1a:P2055S+S:E619K subbranch with ORF1a:M85-, ORF1a:S4153F, ORF1b:T1655I, S:A475V, S:N556K, E:A41V, ORF7a:P34L, ORF7a:*122L, ORF7b:M1I, ORF9b:P3L (5 seq. Brazil)
- [ ] Cluster 46 (former singlet 56): a JF.1.1 subbranch with ORF1a:G2258D, S:A475V (5 seq. USA, Canada)
- [ ] Cluster 47: a GK.1.1.1+ORF1b:H2388Y subbranch with ORF1a:S2360I, ORF1a:Q4015R, S:A475V, S:E554K, ORF6:Y31H, N:Q389H (6 seq. Chile)
- [ ] Cluster 48 (former singlet 70): a GK.1.1+ORF7b:A15S then ORF1b:V464I then nuc:C14937T subbranch with S:A475V (3 seq. Canada)
- [ ] Cluster 49: a GK.10 subbranch with S:K356T, S:A475V (37 seq. Brazil) https://github.com/sars-cov-2-variants/lineage-proposals/issues/1344
- [ ] Cluster 50 (former singlet 59): a GN.1.3 subbranch with ORF1a:T1538I, S:A475V, ORF3a:T268M, ORF10:Q29* (2 seq. Italy)
- [ ] Singlet 3: an XBB.1.5.70 singlet with ORF1a:G493S, ORF1a:A520V, S:A475V, and ORF6:V5I
- [ ] Singlet 4: a GK.1+ORF1b:A2222V? singlet with S:A475V
- [ ] Singlet 8: a GK.1+nuc:T11695C singlet with S:A475V and ORF3a:Q57H
- [ ] Singlet 11: a GK.1.1.1+ORF1b:H2388Y singlet with ORF1a:C689Y, ORF1b:V1685A, S:A475V
- [ ] Singlet 15: a GK.2.1.1 (https://github.com/sars-cov-2-variants/lineage-proposals/issues/716) singlet with ORF1a:T904I, ORF1a:T1721I, ORF1b:V2178F, S:A475V, ORF7a:L5F
- [ ] Singlet 18: a DV.7.1+ORF1a:K3353R singlet with S:A475V, ORF3a:Q185H, M:L29F
- [ ] Singlet 21: https://github.com/sars-cov-2-variants/lineage-proposals/issues/888
- [ ] Singlet 22: a GK.1+ORF1a:E328A singlet with ORF7a:P68S then ORF8:F120V, ORF8:I121L then S:A475V
- [ ] Singlet 23: a GK.1+nuc:T11695C singlet with ORF1a:S1510F then S:A475V and ORF3a:M125I
- [ ] Singlet 26: a GK.2.1 singlet with S:A475V and ORF6:N28D
- [ ] Singlet 29: a JF.1+nuc:T26729C then nuc:G14202A+nuc:C25614T singlet with S:A475V
- [ ] Singlet 31: a GK.1.1.1+ORF8:E110Q then ORF1a:KSF141-143del then nuc:T8341C singlet with S:A475V
- [ ] Singlet 32: a GK.1.10 singlet with S:D142Y, S:A475V, ORF3a:W128C (may belong to cluster 29)
- [ ] Singlet 34: a GK.1+ORF1b:A2222V then nuc:A25336F singlet with ORF1a:R398C, ORF1a:H1610Y, ORF1a:K3353R, ORF1a:A3620V, S:A222S, S:A475V
- [ ] Singlet 36: a GK.1.1+nuc:A23014G then ORF1b:P959S singlet with S:A475V
- [ ] Singlet 38: a GK.2.1 singlet with S:A475V
- [ ] Singlet 40: a GK.1.1.1+ORF1a:V3718I singlet with S:L5F, S:A475V, S:E918A, M:I76F
- [ ] Singlet 41: an XCH+ORF1b:V596I then ORF1a:S2132G+S:E619K singlet with S:A475V
- [ ] Singlet 42: a JD.1.2+ORF1a:G2959D then ORF1b:D1973N singlet with ORF1b:D1465N, S:A475V
- [ ] Singlet 43: a JD.1.2+N:P365L singlet with ORF1a:Y97H, ORF1a:P309S, ORF1a:T1168I, ORF1a:K2029N, ORF1a:A2994V, S:L54F, S:A475V, ORF8:Y31C
- [ ] Singlet 45: a GK.1+ORF1a:T3287I singlet with ORF1b:R1518K, S:I19L, S:A475V, N:R191H, ORF10:A28V
- [ ] Singlet 46: a GK.2+nuc:T4885C singlet with S:A475V, N:T271I
- [ ] Singlet 47: a GK.1.1+nuc:G12442A then ORF1a:E37D, ORF8:R52I then ORF1a:G519S then S:K356T singlet with ORF1a:P959S, ORF1b:H604Y, S:A475V, S:K478R
- [ ] Singlet 49: a GK.1+nuc:C25731T then ORF1a:T2093I singlet with ORF1a:S443F, ORF1a:S1307N, ORF1a:L3060F, S:A475V, ORF3a:P274S
- [ ] Singlet 50: a JF.1.1+nuc:T12751A singlet with S:A475V
- [ ] Singlet 53: a JD.1.2+nuc:T15309C then nuc:G17334C singlet with ORF1a:T329I, ORF1a:T2532I, ORF1b:T2488M, S:A475V, ORF7a:H47N, ORF8:S67F
- [ ] Singlet 54: a JF.1.1+ORF1b:H1550Y then ORF1a:S901G then ORF1b:G1568C then ORF1a:D1639N+N:L139F singlet with S:A475V
- [ ] Singlet 55: a JF.1.1+N:A119S singlet with ORF1a:N1995H, S:A475V
- [ ] Singlet 57: a GK.2.1+S:P1162S singlet with ORF1a:L46F, S:A475V
- [ ] Singlet 58: a GK.1.1.1+nuc:C28603T then nuc:C4832T+nuc:C28163T then nuc:C17172T+S:S255F then ORF1a:G1101S singlet with ORF1a:L2240I, S:A475V
- [ ] Singlet 60: a GK.2+nuc:G16236A then nuc:C10456T then nuc:C28432T then ORF1a:V3653A then ORF1a:I3140T singlet with ORF1a:S2891F, ORF1b:I1822V, S:A475V, ORF8:C90F
- [ ] Singlet 61: a GK.1.1+ORF1a:P1220L then ORF1a:S2900F+S:L335F singlet with ORF1a:I1714V, ORF1b:N2124S, S:G184V, S:R190S, S:A475V
- [ ] Singlet 62: a GK.1+nuc:G11029A+nuc:C26028T then ORF1a:V3748I then ORF1a:G519S then nuc:G29473A then nuc:T10357C singlet with S:A262S, S:A475V
- [ ] Singlet 63: a GK.1+nuc:T11695C then ORF1a:I693T then ORF1a:L552F+S:T874I singlet with S:A475V, ORF3a:I63T, ORF7a:T11K
- [ ] Singlet 65: a GK.1.1.1+ORF3a:T34M singlet with ORF1a:F31S, ORF1a:D223G, S:A475V, ORF8:H17Q
- [ ] Singlet 66: a GK.1+ORF1a:T3287I then ORF1b:I1598V then ORF1a:G1073R+ORF1a:V2149A singlet with S:A475V, ORF8:Y31C
- [ ] Singlet 67: a GK.2+N:R195K then nuc:C10969T then ORF1a:82-86del+ORF1a:L1523I+S:E1111Q+ORF7a:100-103del singlet with S:A475V
- [ ] Singlet 68: a GK.1.10+ORF1a:G2091D+ORF1b:K1400R+S:L441R+E:C44Y singlet with ORF1b:S2338L+S:A475V
- [ ] Singlet 69: a GK.1.1+nuc:C29730T then ORF8:Q18* then S:N481K then N:A376V singlet with S:A475V, ORF7a:A13S
- [ ] Singlet 71: a GK.1.10+S:K182E then nuc:C10228T singlet with S:A475V
- [ ] Singlet 72: a JF.1.1+ORF1a:V3718I then nuc:T21291C singlet with ORF1b:V605I, S:A475V, S:V622A
- [ ] Singlet 73: a HV.1/GK.1.8 recombinant with ORF1a:V690I, N:P151L
- [ ] Singlet 74: a JF.1.1+nuc:C9943T then nuc:C28909T then ORF1a:S2103F+nuc:T9040G singlet with S:A475V
- [ ] Singlet 75: a GK.1.1+ORF1a:R3662C then ORF1a:S944L then ORF1a:A405V singlet with ORF1a:G519S, S:K77N, S:A475V

[oobb45729]

The GK.1 subbranch (former singlet 1): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1*%26ORF1a%3AP309L%26S%3AA475V&

[oobb45729]

Cluster 5 (former singlet 2) (2 seq. UK, Italy): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGW.5*%26S%3AA475V&

[ryhisner]

Great idea for a tracking issue, @oobb45729.

There are only four singlets so far, but I wonder if we'll eventually have to create an issue like this for S:S446I + FLip. The fact that this unusual combo has already appeared in EG.5.1.1, the XBB.1.5 branch with S:A475V mentioned above, DV.7.1 (CH.1.1.1.7.1), and GK.1 is pretty remarkable. Perhaps FLip somehow makes a hydrophobic residue at 446 advantageous? I still don't know how to use those handy spike-structure-viewing programs, so I don't have any way of looking more closely to see if there are any structural reasons to think this might be the case. EPI_ISL_18012368, EPI_ISL_18072823, EPI_ISL_18078439, EPI_ISL_18113536 (Collection dates July 8, July 25, August 3, and August 9)

[oobb45729]

Singlet 3: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26ORF6%3AV5I%26S%3AA475V&

[xz-keg]

There are 23 seqs for branch 2 now.

[oobb45729]

Cluster 3: Maybe GK.3 should be broaden to XBB.1.5.70+nuc:C12469T. https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26S%3AL455F%26S%3AF456L%26S%3AA475V%26ORF1a%3AT2859I& https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29541_7b3e20.json?c=gt-S_475&label=id:node_7211617

[oobb45729]

Singlet 4: A low-quality sequence with ORF1b:A2222V, S:A475V, S:S704L on the top of XBB.1.5.70. https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26S%3AL455F%26S%3AF456L%26S%3AA475V%26S%3AS704L%26ORF1b%3AA2222V& There's a GK.1 subbranch with ORF1b:A2222V. Maybe singlet 4 belongs to it. https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26S%3AL455F%26S%3AF456L%26S%3AS704L%26ORF1b%3AA2222V&

[FedeGueli]

@oobb45729 please propose in the main page CLuster 3 when it will reach 10 seqs

[oobb45729]

Cluster 4 (former Singlet 5) (3 seq. USA, Denmark): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=ORF1a%3AA260V%26ORF1a%3AG1030D%26S%3AA475V& https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10393_38c610.json?c=gt-S_475&label=id:node_7229849

[FedeGueli]

Sixth sequence of Cluster 3 detected in the US in a traveller from Spain

[oobb45729]

Singlet 6: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1*%26ORF3a%3AV50I%26S%3AA475V&

[ryhisner]

That latest one is a pooled sample, which Gingko, unaccountably, is still uploading. And I've yet to see a single high-quality sequence from Ginkgo.

Maybe they will find a way to use their latest Chat-GPT-like AI technology to solve the mystery of how to produce a decent genetic sequence. And maybe this advanced AI gizmo will learn to speak English and tell the Ginkgo people to stop uploading pooled samples.

[FedeGueli]

Cluster 3 went to 9 sequences today 2 France , 1 Spain i think it could be moved to main page when it reaches 10. cc @oobb45729

[krosa1910]

This is a very interesting combination that I have missed for a while. Just today I scrubbed through some past twitters and discovered a conversation between two brilliant DMS researchers about immune escape for covid.

So I could consider this version as somewhat "Flip+", as S:475V seemed to be dependent on Flip for sustained growth among XBB*. We aren't that deep into an age of flip itself, yet it already led great refocusing among this community. Would be interesting to see if it could outgrow its Flip parents, which itself had somewhat outgrown their S:456L parents. Preliminary datas are pointing toward "yes".

[FedeGueli]

Added #763 to the tasklist

[oobb45729]

Cluster 7: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_306d9_a271c0.json?label=id:node_7242518

[oobb45729]

Cluster 14 (former singlet 7): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70.1*%26ORF1a%3AD1323N%26S%3AA475V&

[oobb45729]

Singlet 8:

[oobb45729]

Cluster 20 (former singlet 9): The EG.5.1.1 donor: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AEG.5.1.1*%26ORF1a%3AL590F&

[plomano]

https://www.frontiersin.org/articles/10.3389/fimmu.2023.1219546/full

I stumbled on this paper on 475V that seemed to go under the radar. Some interesting observations in there.

[oobb45729]

Cluster 12 (former singlet 10): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGW.5*%26ORF1a%3AI694V%26S%3AA475V&

[oobb45729]

Singlet 11: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1.1*%26S%3AA475V%26ORF1a%3AC689Y&

[oobb45729]

Cluster 11 (former singlet 12): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AHK.3*%26S%3AA475V%26ORF1a%3AM902I&

[oobb45729]

Singlet 13: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AHK.3*%26S%3AA475V%26S%3AT747I&

[FedeGueli]

Cluster 3 > GK.4

[oobb45729]

Cluster 27 (former singlet 14): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1*%26S%3AA475V%26S%3AT732I&

[oobb45729]

Singlet 15: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.2*%26S%3AA475V%26S%3AP1162S&

[oobb45729]

Cluster 30 (former singlet 16): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26S%3AA475V%26ORF1a%3AF3604L&

[oobb45729]

Cluster 16 (former singlet 17): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70*%26S%3AA475V%26ORF6%3AE55Q&

[oobb45729]

Singlet 18: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3ADV.7.1*%26S%3AA475V&

[oobb45729]

Cluster 19 (former singlet 19): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70.1*%26S%3AA475V%26ORF3a%3AY107C&

[oobb45729]

Cluster 13: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70.1*%26S%3AN185D%26S%3AA475V%26ORF1a%3AT4175I&

[oobb45729]

Cluster 15 (former singlet 20) https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=ORF1a%3AR542C%26S%3AA475V%26ORF8%3AP38S&

[oobb45729]

Singlet 22:

[oobb45729]

Singlet 23: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5.70.1*%26S%3AA475V%26ORF1a%3AS1510F&

[oobb45729]

I just realized that GK.3 and GK.4 with nuc:C12469T and nuc:G12467T(ORF1a:A4068S) have a new TRS-like sequence TCTAAAC. @ryhisner

[krosa1910]

Ah, a nasty one uploaded today. EPI_ISL_18343279 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2dff7_dd6700.json?f_userOrOld=uploaded%20sample This one is weird, because it has C16342T as the typical XBB.2.3 reversion, plus C1884T that is very very abundant in XBB.2.3 population among Europe. Yet it has S:G252V instead of S:D253G. @oobb45729 you could decide to include it or leave it as I don't really like environmental sequences.

[oobb45729]

Singlet 24: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AHK*%26ORF1b%3AI570T%26S%3AA475V&

[oobb45729]

Cluster 26 (former singlet 25): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1.1*%26S%3AA475V%26ORF1b%3AI1862V%26G26217A&

[oobb45729]

Ah, a nasty one uploaded today. EPI_ISL_18343279 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2dff7_dd6700.json?f_userOrOld=uploaded%20sample This one is weird, because it has C16342T as the typical XBB.2.3 reversion, plus C1884T that is very very abundant in XBB.2.3 population among Europe. Yet it has S:G252V instead of S:D253G. @oobb45729 you could decide to include it or leave it as I don't really like environmental sequences.

It could be some sort of recombination or contamination. I would not include it for now.

[oobb45729]

Singlet 26: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.2.1*%26ORF6%3AN28D%26S%3AA475V&

[oobb45729]

Cluster 20 (former singlet 27): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AHK.3*%26S%3AP809S%26S%3AA475V&

[FedeGueli]

Thank you @oobb45729 for your tracking great job this one and # 527 is filling up the high range of the chart with some more recomb and other convergent lineages.

[oobb45729]

Cluster 21: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AJF.1*%26ORF1a%3AP2005S%26S%3AA475V&

[oobb45729]

Cluster 22: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AEG.5.1.1*%26S%3AA475V%26N%3AT166R&

[oobb45729]

Singlet 27: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AEG.5.1.1*%26S%3AA475V%26C13620T%26C23248T&

[oobb45729]

Singlet 28: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AEG.5.1.1*%26S%3AA475V%26S%3AT716I&

[oobb45729]

S:A475V is appearing in multiple lineages of EG.5.1+S:L455F. As I'm not very familiar with the EG.5.1 tree, maybe it's time to split the issue. I think that a new issue (maybe more than one) tracking EG.5+S:L455F+S:A475V lineages could be created, and this issue will only track non-EG.5 ones. Who wants to do this? @NkRMnZr @FedeGueli @BorisUitham @aviczhl2 @Over-There-Is @krosa1910

[FedeGueli]

Thank you @oobb45729 for this great work. I prefer one only issue but up to you what is more comfortable for you!

[krosa1910]

S:A475V is appearing in multiple lineages of EG.5.1+S:L455F. As I'm not very familiar with the EG.5.1 tree, maybe it's time to split the issue. I think that a new issue (maybe more than one) tracking EG.5+S:L455F+S:A475V lineages could be created, and this issue will only track non-EG.5 ones. Who wants to do this? @NkRMnZr @FedeGueli @BorisUitham @aviczhl2 @Over-There-Is @krosa1910

Mr NK have taken the job for EG.5+S:A475V, so I think you could continue doing it for non-EG.5.