HV.1 Spike Diversity Collection (UPDATED 2024-02-21)

[krosa1910]

HV.1* is a mystery to me, so I would like to create this colleciton of its Spike Diversity to see if there is an underlying reason behind its success in North America.

Standardized way of this search: C5835T,T22917G,T22930A for HV.1* parent.

Dead/Small/Proposed Observations

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1. S:S12F Query(small,30 total):C21597T+Base neutral
2. dead S:K41E 7 seqs, Query: C12513T,A21683G Canada, Ontario
3. S:S94F 22 small (=4+2+1seqs Query1 Also with S:T284I): C21843T,C5835T,C22413T US,CT Dead Query2:C21843T,C5835T,C22413T US and Iceland
4. S:M177I 35small=9(A)+20(C)+6(T)seqs, complicated because any of G22093X (X=A,T,C) appear as S:M177I Query:G22093A,C5835T,G27915T/G22093C,C5835T,G27915T/G22093T,C5835T,G27915T. US,NY/ US and Canada/US,CA unworthy
5. Small S:G181V 24 seqs , Query: T22917G,C12513T,G22104T,G22895C US,CA+Utah
6. Small? S:N185S 44 seqs Query: A22116G,C5835T,T22917G US and Canada Revived?
7. Dead S:P217H 17 seqs Query: C5835T,C22212A US,DC
8. Designated HV.1.7 S:S221L 47 (non monoph.)seqs Query1: C22224T,C5835T,T22917G,G701T Canada,AB Query2:C22224T,C5835T,T22917G,G1820A US,NY/MD plus one US,CA singlet
9. Designated S:K444T 31seqs, Query: C5835T,C12513T,A22893C Multiple Countries designated HV.1.1
10. Small? S:T470I 48seqs Query: T22917G,C3369T,C22971T US,CA and 1 US,FL singlet
11. HV.1.3 S:Q493L 93 seqs Query: C5835T,A23040T,T22917G Multiple Countries
12. S:S514F 162 seqs, Query: C12513T,C23103T US, Canada and Australia designated HV.1.2
13. Small S:E554Q 24 seqs Query: G23222C,G19735T,G22895C US,NY+OH
14. Small S:P561S 5 seqs Query: T22917G,C5835T,C23243T US,IA
15. Small S:G/D614S 31 seqs Query: G23402A,C5835T,G27915T Spain proposed in HV.1 (EG.5.1.6.1) sublineage with S:G614S (25 seqs in 7 countries) #1061
16. Small S:P621S 33 seqs Query: C5835T,C23423T,G27915T US,CA/CT/NY unworthy
17. Designated HV.1.6.1 S:S704L 145 seqs Query: C23673T,C5835T,T22917G,G27915T US, Canada and France
18. Small S:A879T 19 seqs Query: G24197A,C5835T US and Canada unworthy
19. Small S:L938F 28 seqs Query: C24374T,T6673C US,HI/AZ unworthy
20. Small S:V963I 3 seqs Query: T712C,G24449A,G27915T US,MD/NY/VA
21. Designated HV.1.4 S:A1078S 163 seqs Query: G24794T,C27945T,C22033A Multiple Countries 236
22. Designated HV.1.5 S:L1265F 168 seqs Query: C25355T,T22917G,C5835T,T28297C US, Canada and Australia.
23. Designated HV.1.8S:T208M Query(142): C1093T, C1302T, C22185T growing
24. Designated HV.1.9 S:N211I,T1117IQuery(65):C24912T,C22624T,A22194T,C14119T growing

Past Watches (I JUST DELETED THE STILL WATCHING ONES)

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1. Small? S:V16F Query(49): G21608T,T24829C descending
2. S:S31F Query(36):C29284T,C21654T,C5835T descending
3. S:H49Y Query(69):C21145T,C21707T,C5835T neutral
4. S:T95I Query(small,35 total):C21846T+Base growing
5. S:W152R Query (66): C18713T, T22016A,C5835T neutral
6. S:M153I Query(small,46 total):G22021T+Base growing
7. S:N185S Query(40):A24742G,A22116G descending
8. S:A222S Query(small,36 total):G22226T+Base neutral
9. S:V227I Query(103):C13378T,G22241A,G2494T growing
10. S:R357K Query(small,47 total):G22632A+Base growing
11. S:L/R452W Query(48,121 total):C15720T,C22916T,C5835T growing
12. S:T470I Query(small,40 total):C22971T+Base growing
13. (S:A1078S=HV.1.4*),S:F/S490P Query(31):T23030C,G24794T,C27945T neutral
14. S:T553I Query(small,32 total):C23220T+Base growing
15. S:T572I Query(small, 30total):C23277T+Base neutral
16. S:V642G Query(small,32 total):T23487G+Base neutral
17. S:V656I Query(64):A28877T,G28878C,G23528A,C5835T neutral
18. S:Q836L Query(82):C29364T,A24069T growing
19. S:G1124S Query(43): C2695T, G24932A, C25433T neutral
20. S:P1162L Query(small,80 total): C25047T+Base neutral
21. S:Q1208H Query(small,38 total): G25186T+Base neutral
22. S:K1245R Query(41):A25296G,T12574C growing

Trees of current stuff

Now Watching Trees

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1. S:S98F Polytomy- Query:C21855T+HV.1*=C5835T,T22917G,T22930A Count:(15;84)
2. S:K147I,E619Q Single Branch- Query: A22002T,G23417C,-G26529A Count:(8;56)
3. S:N148T Polytomy- Query: A22005C,T22930A,C5835T,T22917G Count: (18; 181) Main Branch Query:C10189T, A22005C,C10125T Count: (6;62)
4. S:G184V Polytomy- Query: G22113T,T22930A,C5835T,T22917G Count: (20;101) Main Branch Query: G22113T,C23185T, A23539T Count: (12;68)
5. S:G184S Polytomy- Query:G22112A,T22930A,C5835T,T22917G Count: (10;19)
6. S:S221L outside HV.1.7* Polytomy- Query:C22224T,T22930A,C5835T,T22917G,-T23198C Count: (6;62)
7. S:D253E Single Branch- Query: T22321G,T22930A,C5835T,T22917G Count: (7;114)
8. S:T307I Polytomy- Query:C22482T,T22930A,C5835T,T22917G Count: (5;84)
9. S:I410V,S:H1101Q- Single Branch Query:A22790G,C24865G,T22917G Count: (7;72)
10. S:L455F Polytomy- Single Branch Query: G22927T,T22917G,C5835T,T22930A Count: (12;100) Main Branch Query: G22927T,T23198C,T22917G Count: (7;54)
11. S:G482S Polytomy (mostly one branch)- Query:G23006A,T22917G,T22930A,C5835T Count: (31;66)) Main Branch Query:C13665T,G23006A,T22930A Count: (29;52)
12. S:T573I Polytomy (mostly two branches)- Query:C23280T,T22917G,C5835T,T22930A Count: (17;108) Main Branch Query 1: C23280T,T1834A,G18826A Count: (8;60)(Main Branch Query 2: C18713T, C23280T,T22930A,T22917G Count: (7;34)
13. S:P681R Polytomy (seemingly three branches)- Query:-C21711T,C23604G,T22930A,C5835T,T22917G,-A22629C Count: (16;174) Main Branch Query 1: C23604G,T22930A,C22185T Count: (10;146) Main Branch Query 2: G12806A,C23604G,T22930A Count: (1;16) Main Branch Query 3: C23604G, C26456T,T22930A Count: (5;12)
14. S:S939F Polytomy(mostly one branch)- Query: Count:-G22870A,C24378T,T22930A,C5835T,G22317T,T22917G (6,likely 7 with one wrong date; 75) Main Branch Query: C24337T, C24378T, C25075T,T22930A Count: (4,likely 5; 50)
15. S:H1101Y Polytomy Query: C24863T,T22930A,C5835T,T22917G Count: (24;145) Main Branch Query: C24863T,T22930A,C5835T,T22917G,C23673T Count: (19; 85) Oh, it was already designated as KL.1.1
16. S:Q1201K Polytomy Query: C25163A,T22930A,C5835T,T22917G Count: (7;95)
17. S:V1264L Polytomy Query: G25352T,T22930A,C5835T,T22917G Count: (10;240) Main Branch Query: G25352T,T22930A,C5835T,T22917G,A16140G Count: (4;206)

S:98F tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_17854_596060.json?f_userOrOld=uploaded%20sample&label=id:node_1022987

S:K147I+S:E619Q tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_93d8_5992c0.json?f_userOrOld=uploaded%20sample

S:N148 tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_b9a1_599cb0.json?f_userOrOld=uploaded%20sample

S:G184V tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1390a_59b6d0.json?f_userOrOld=uploaded%20sample&label=id:node_1035383

S:G184S tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3d18f_59c540.json?f_userOrOld=uploaded%20sample&label=id:node_1025408

S:S221L tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_42cf9_59d7a0.json?f_userOrOld=uploaded%20sample&label=id:node_1025408

S:D253E tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_20f8_59e350.json?f_userOrOld=uploaded%20sample&label=id:node_1025409

S:T307I tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_a558_59f860.json?f_userOrOld=uploaded%20sample

S:I410V+S:H1101Q tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_114a2_5a0b00.json?f_userOrOld=uploaded%20sample

S:L455F tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_12c20_5a11b0.json?f_userOrOld=uploaded%20sample

S:G482R tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_300bc_5a1450.json?f_userOrOld=uploaded%20sample&label=id:node_1025408

S:T573I tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2530c_5a4ae0.json?f_userOrOld=uploaded%20sample&label=id:node_1027082

S:P681R tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1ba0_5ab050.json?f_userOrOld=uploaded%20sample&gt=nuc.22930A,S.356K&label=id:node_1022987

S:S939F tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_4c0f_5b47f0.json?f_userOrOld=uploaded%20sample&gt=S.252V

S:H1101Y tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_cf1_5b8850.json?f_userOrOld=uploaded%20sample

S:Q1201K tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_d481_5bb670.json?f_userOrOld=uploaded%20sample&label=id:node_1025408

S:V1264L tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_e352_5bbdb0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Thank you great work.

[krosa1910]

K41E 4 to 6
S704L 21 to 26
V1264L 23 (22+1( to 37 (34+2+1)
V16F 9(8+1) to 11(10+1)
S94F 5(3+2) to 6 (4+2)
N148T 5 to 6
W152R 3 to 5
N185S 13 to 14
S221L 8(6+1+1) to 9(6+2+1)
I410V 9 to 10
L938F 3 to 4
L1265F 17 to 23
I would say S704L and S1265F is worthing a proposal, maybe also V1264L(with caution about Canadian cluster) and N185S

[FedeGueli]

Lets wait they hit 40 sequences before proposing them (704L, 1264L 1265F) . Great work @krosa1910

[RajLABN]

HV.1 has picked S:494P too
5 sequences (NY, CA USA)
EPI_ISL_18316940, EPI_ISL_18379501, EPI_ISL_18404330,
EPI_ISL_18410315-18410316

[krosa1910]

Yeah, I would update that sometime this week, also L452W is deserving tracking.

[FedeGueli]

@krosa1910 please propose the S:704L branch and the S:514F branch and the S:V1264L branch

[FedeGueli]

Please propose also the S:L1265F and the S:A1078S. while keeping 493L and 1162S monitored. thank you.

[FedeGueli]

You can also on Pango a multiple issue saying these are the spike mutated branches of HV.1 if any of them has interest to be diesignated and etc etc

[FedeGueli]

ping @corneliusroemer please take a look there is some interesting spike diversity in HV.1 that grew over the 100 seqs.

[FedeGueli]

S:S514F has been designated HV.1.2 via cov-lineages/pango-designation@471889e

[FedeGueli]

@corneliusroemer the author cannot connect in this moment to internet so i updatted the issue flagging the ones you may want to evaluate for designation.
S:704L S:1078S S:493L and S:1265F are already big enough to be designated. please when u save a minute to look at these ones.

[FedeGueli]

S:L1265F designated HV.1.5 via cov-lineages/pango-designation@4813e2f

[FedeGueli]

S:S704L designated HV.1.6.1 via cov-lineages/pango-designation@ffdf027

[FedeGueli]

S:S221L designated HV.1.7 via cov-lineages/pango-designation@57891f2

[NkRMnZr]

S:S1265F designated HV.1.5 via cov-lineages/pango-designation@4813e2f

Should be L1265F not S

[FedeGueli]

S:S1265F designated HV.1.5 via cov-lineages/pango-designation@4813e2f

Should be L1265F not S

Thank you edited everywhere now.

[FedeGueli]

@corneliusroemer S:Q493L maybe deserves a designation. around 100 sequences and widespread

[FedeGueli]

@corneliusroemer S:Q493L maybe deserves a designation. around 100 sequences and widespread

it has already been designated #924

Thank you missed that was the same here.

[krosa1910]

Will try to update this issue, as I think HV.1* is still not over yet.

[krosa1910]

HV.1* now is very big, at over 28k on Gisaid, yet it is starting to lose momentum, so something at levels of 3 seq seems less interesting now. Thus I decided to find some newer branches and replace old ones.
Basically, any old branch under 30 sequences/ about 0.1% total samples are shut, while I would open some new ones at 30+ seqs.
So in total, I am watching Q1208H, V16F, S98F, W152R, I410V/H1101Q, G1124S, P1162L, Q1201K and I think V1264L，N148T and T208M could be proposed. Others are shut down as they doesn't seem to show dominance over parent given time like two months.
I will now consider the following candidates (after bogging down some valid trees that is)
H49Y,T95I,M153I,G184V,V227I,D253E,L455F,T470I,T573I,E619Q,V642G,P/H681R(under T208M),Q836L,S939F, H1101Y, K1245R, S12F S31F(N148Q,K150V,E154V seemed to be related to deletions or frameshift in S protein and not very good qualities, which I am not familiar with and profound of, so I ignore those but encourage others to look at those), N185S,N211I+T1117I,A222S,T307I,R357K,L/R452W,F/S490P(under A1078S=HV.1.4*),T553I,T572I,V656I
Also 478 and 554 are weird, while H245Y and N450D seems to rise recently despite not reaching 30 yet, people could start investigating it if they want.

[FedeGueli]

HV.1* now is very big, at over 28k on Gisaid, yet it is starting to lose momentum, so something at levels of 3 seq seems less interesting now. Thus I decided to find some newer branches and replace old ones. Basically, any old branch under 30 sequences/ about 0.1% total samples are shut, while I would open some new ones at 30+ seqs. So in total, I am watching Q1208H, V16F, S98F, W152R, I410V/H1101Q, G1124S, P1162L, Q1201K and I think V1264L and T208M could be proposed. Others are shut down as they doesn't seem to show dominance over parent given time like two months. I will now consider the following candidates (after bogging down some valid trees that is) Y49H, T95I, M153I,M153K G184V, V227I, D253E , L455F,T470I , T573I, E619Q, V642G, P681R, Q836L, S939F, H1101Y, Q1208H, K1245R, S12F S31F, N148Q, K150V, E154V, N185S, N211I, Also 478 and 554 are weird, and people could start investigating it if they want. While N450D and L455F seems to rise recently.

Thank you great update! please track 148T too!

[FedeGueli]

Thanks @krosa1910 greeat work.
Please propose S:N148T and the S:t208M+681R one. thank you.

[FedeGueli]

S:L452W already proposed in #1044

[krosa1910]

Thanks @krosa1910 greeat work. Please propose S:N148T and the S:t208M+681R one. thank you.

N148T seems too sparse and can be only proposed in the multiple trees manner, T208M+681R seems good enough though.

[FedeGueli]

Thanks @krosa1910 greeat work. Please propose S:N148T and the S:t208M+681R one. thank you.

N148T seems too sparse and can be only proposed in the multiple trees manner, T208M+681R seems good enough though.

Thx if not monophyletic better wait! Thx

[FedeGueli]

S:N211I, S:T1117I, New Zealand>

this has been designated HV.1.9 via cov-lineages/pango-designation@f6e4c4f

[FedeGueli]

S:T573I https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_d962_fe34d0.json?f_userOrOld=uploaded%20sample

This one with the query : C3924T, C12295A,C23280T counts 53, please propose it.

[krosa1910]

Sorry for my laptop crashing that inhibited this update, i will "reupdate" today.
Thinking about the JN.1* boom, I would consider a new rule now. Some HV.1* can have like a cluster of 70 seqs but if it does not show up lately I still consider it to lose the race ultimately, while for some "newer" faces can be at 30 seqs does not limit their potential.
Thus the new rule now would consider two parts, part 1 is for mutations that gains presence within the last 30 days (sequencing since 12-25) with some decent size (30+ seqs) while part 2 is for mutations that are large enough (50+ mono tree) despite not in the recent samples.

[FedeGueli]

Thanks @krosa1910

[FedeGueli]

Yesterday i proposed #1338 335S 403K in Aus.

[krosa1910]

(Range:140-146)del is really weird. I have asked people things about it months ago yet I don't get a definitive answer so I would ignore them.

[FedeGueli]

(Range:140-146)del is really weird. I have asked people things about it months ago yet I don't get a definitive answer so I would ignore them.

yes it is. the 144del makes a mess in reading the sequence in that part. For a long while i suspected that also S:N148T was affected by something similar.

[krosa1910]

A lot of E554X+HV.1*, maybe deserving a new issue (if not for the fact that HV.1* is now falling considerably, yet it is still like twice as large as BA.2.86* without L455S or thrice as large as JD.1.1*/JG.3*) If some more experienced individuals like @NkRMnZr NK can help me then probably I could sort it out.

[FedeGueli]

A lot of E554X+HV.1*, maybe deserving a new issue (if not for the fact that HV.1* is now falling considerably, yet it is still like twice as large as BA.2.86* without L455S or thrice as large as JD.1.1*/JG.3*) If some more experienced individuals like @NkRMnZr NK can help me then probably I could sort it out.

good idea lets wait next week to see how it goes in January

[FedeGueli]

i ve checked growing lineages, it seems to me very hard times for all of them in January.

[FedeGueli]

There is a HV.1 Flip lineage not listed here that managed to criculate in January:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1bc88_fdd4c0.json?c=userOrOld&label=id:node_3597976

Defining mutations:
HV.1 > C10279T > Orf1a:A3688V (C11328T) > Orf1a:I1203T (T3873C), S:L455F (G22927T),N:G214S (G28913A)
Query: T3873C,G28913A
Samples: 13 as of 16/02/2024
Countries:

[krosa1910]

Yep, I think I give up this mega lineage collection now. JN.1* sweep everything now, whileHV.1* is not even outcompeting EG.5.1* now( JG.3.2* and GE.1.2.1* seem to lead the last stand of XBB*). This would really be the last update if not for something not miraculous.
New Standard
A. >10seq from 01-01-2024, a arbitrary but self-explainatary threshold I chose for JN.1* total dominance
B. >5 seq from 01-01-2024 and >50seq overall
Things omitted: anything from 140-146del plus anything with Y144 and Y145, S5F, H/Q146K, mutations that seems to be more likely contaminated instead of true (such as V127F, F/L157S, R158G because of JN.1* contamination)

[FedeGueli]

Agree thanks great work by now

[krosa1910]

There are 17 final candidates chosen here, I would update on their queries (a general query or a specific one if a main tree fits), T/K478X AND E554X ARE OMITTED BECAUSE THEY ARE TOO MESSY YET STILL HAVING SOME NUMBERS SO I WOULD PROBABLY OPEN TWO NEW ISSUES FOR THEM. I heard L/R452w is also complex due to polytomy plus pollution, maybe also one for it.

[FedeGueli]

Thank you for your work here i m closing it now

[krosa1910]

Thank you for your work here i m closing it now

Yeah, by a crude search XBB* total is only 893/27503, EG.5.1* is 513 and HV.1* is a mere 143, even lower than FLirt being 264. So I don't think this issue is very valuable now, I would turn my effort toward the Flirt one.