Collection of BQ.1(.1). diversity to watch

[corneliusroemer]

BQ.1 appears to be fast growing. Some Spike mutations are showing up repeatedly, but it's too early to designate sublineages other than BQ.1.1 for them at this point. I think it reduces noise to track them in one issue for now.

• [x] S:E619Q 6 times, 3x US, 1x CAN, 2x Austria (once in representative surveillance), the Austrians have S:549I as well Spike_E619Q,Spike_N460K,Spike_L452R designated as BQ.1.3
• [x] S:I666V 8 times, 2x US, 3x CAN, 1x IL, 1x DK, 1x GER Spike_I666V,Spike_N460K,Spike_L452R designated as BQ.1.2
• [x] S:144- https://github.com/cov-lineages/pango-designation/issues/1202
• [x] S:346T with G8075A, G20469A, 4x US
• [x] S:190T, 3x in DK, 2x also with S:556K Spike_R190T,Spike_N460K,Spike_L452R
• [x] S:L54F, 5x US, 3x FR Spike_L54F,Spike_N460K,Spike_L452R
• [x] S:146L https://github.com/cov-lineages/pango-designation/issues/1189
• [x] S:144- with C26455T (maybe 8 to date) as BQ.1.18
• [ ] S:S151N, 3x AUS, Spike_S151N,Spike_N460K,Spike_L452R
• [ ] S:152L 2x in CAN, it's defining in BA.2.75 Spike_W152L,Spike_N460K,Spike_L452R
• [ ] S:A348S, 2x US, 1x FR
• [ ] S:260V https://github.com/cov-lineages/pango-designation/issues/1180

Furthermore:

• [ ] BQ.1.1 has picked up S:822F in 8 uploads from England Spike_L822F,Spike_R346T,Spike_N460K,Spike_L452R
• [ ] BQ.1.1 with S:147E, singlet NY, Spike_K147E,Spike_R346T,Spike_N460K,Spike_L452R
• [ ] BQ.1.1 with S:262S, singlet England Spike_A262S,Spike_N460K,Spike_K444T,Spike_R346T,Nsp13_N268S
• [x] S:253G (2x England) convergent with XBB and others #1209
• [ ] S:261D (1x Japan)
• [ ] S:251L
• [ ] S:352S (1x Congo) predicted to be fitter than BQ.1 alone
• [ ] S:494P (1x Denmark, 1x France, homoplasic)
• [ ] BQ.1.1 S:S490I (homoplasic, Italy England 1 each)
• [ ] BQ.1.1 S:V445A (England 1x)
• [ ] BQ.1.1 S:V445F (France 1x)
• [ ] BQ.1.1 S:G446S (England 1x) Spike_G446S,Spike_N460K,Spike_K444T,Spike_R346T,Nsp13_N268S If you find interesting small things in BQ.1.(.1) that you think are not ready yet for an issue - feel free to add it as a comment here to this issue.

[corneliusroemer]

S:E619Q (now BQ.1.3) is very common in random surveillance in Austria - these can't be used for designations as they are spike only but they show growth.

[corneliusroemer]

I also saw the 147E but it seems to still be a singlet. I'll add it to the list as this may well end up growing.

[corneliusroemer]

@FedeGueli your comments get a bit overwhelming, can you edit previous comments and structure them somehow rather than adding one comment after another? That'd be very helpful! Which ones are the most notable ones in your view, that sort of stuff would be very useful. But just adding comment after comment is making it confusing. Thanks for your work!

[FedeGueli]

BQ.1 query : NSP12_Y273H,Spike_K444T,Spike_N460K

Growing or Fast

• [ ] Spike_S98F 43 seqs multiple continents BQ.1. (not monophyletic apparently see usher)
• [ ] Spike_H1101Y 3 seqs multiple countries very recent bq.1.1
• [ ] Spike S255F - 33 seqs BQ.1 Non Monophyletic
• [ ] Spike_S254F - 15 sequences (Uk)
• [ ] Spike_N603S - 50 sequences in BQ.1.19 and 27 with Spike_D614S (proposed) FAST
• [x] Spike_Q607H 11 seqs (BQ.1.1) NOW BQ.1.1.16**
• [ ] Spike_D253Y - 22 sequence
• [ ] Spike_P251L 33 seq. not monophyletic
• [ ] Spike_D215H - 8 sequences
• [ ] Spike_F157L 19 seq (BQ.1.1) fast
• [ ] Spike_A688V 22 seqsBQ.1.1 (not BQ.1.8) FAST
• [ ] Spike_W152L 25 seqs BQ.1.11 see main post
• [ ] Spike_C1243F 23 seqs BQ.1.2
• [ ] Spike_T307I 12 seqs BQ.1.8
• [ ] Spike_H245Y 32 seqs BQ.1 FAST
• [ ] Spike_N360K 7 seq BQ.1
• [ ] Spike_T470I 7 ses BQ.1.3
• [ ] Spike_Y248D 5 seqs BQ.1.1
• [ ] Spike_L176F 39 seqs BQ.1.1 (Nigerian sublineage)
• [ ] Spike_K182I 20 seqs USA BQ.1.1 FAST
• [ ] Spike_T323I 31 seqs BQ.1.1
• [ ] Spike_K147E 27 seqs see main post growing
• [ ] Spike_P251S - 10 sequences (Uk,Fra,Bel)
• [ ] Spike_P251H 19 seq (orf3a:t151I in france)
• [ ] Spike_T29I 10 seqs BQ.1.1
• [ ] Spike_T299I 10 seqs BQ.1.1
• [ ] SPike_S221L 9 seqs BQ.1.1
• [ ] Spike_Y145H - 13 sequences bq.1.1

• [ ] Spike_K182Q - 20 seqs Canada

  Not Growing or slow

• [ ] Spike_D389H 2 seqs BQ.1.1 Spain
• [ ] SPike_N164T - 10 sequences
• [ ] Spike_G252D 4 seqs bq.1.1
• [ ] SPike_A688S 2 seqs bq.1.1
• [ ] Spike_S256A 3 seqs bq.1.1
• [ ] Spike_A411S - 5 seq *BQ.1.1
• [ ] Spike_D1139Y 12 seqs BQ.1.3
• [ ] Spike_M1237I 13 seqs BQ.1.1.7
• [ ] Spike_D936H 10 seqs BQ.1.18
• [ ] Spike_A222V - 4 seqs Australia BQ.1
• [ ] Spike_R346I - 5 seqs Aus Ita BQ.1
• [ ] SPike_S689I. 9 seqs (BQ.1)
• [x] Spike_S151I - 9 viruses
• [ ] Spike_P1162L - 9 sequences
• [ ] Spike_R346S - 13 sequences non monophyletic
• [ ] Spike_Y170H - 5 sequences
• [ ] Spike_D1260Y - 5 sequences
• [ ] Spike_A264V - 4 sequences BQ.1.1
• [ ] Spike_F186L - 4 sequence ( 1 with S:145-146 del)
• [ ] Spike_A292V - 3 sequences
• [ ] Spike_A1020S - 2 sequences
• [ ] Spike_A352S - 1 sequence from Congo Brazzaville
• [ ] Spike_P499S + Spike_N641del + Spike_V642I ((BQ.1.1 MONITOR)) singlet from uk
• [x] Spike_T240I + S:346T 9 sequences South Africa , proposed in #1240
• [ ] Spike_P322S 1 seq BQ.1
• [ ] Spike_Q271E 1 seq BQ.1
• [ ] Spike_A262S 7 seqs BQ.1
• [ ] SPike_S162I 3 seqs BQ.1.14
• [ ] Spike_Y473S EPI_ISL_15497060 1 from Nigeria
• [ ] Spike_T430I 1 (BQ.1.1)
• [ ] Spike_A653V 2 seqs France
• [ ] Spike_S50A 2 seqs BQ.1.11
• [ ] Spike_D1146H 5 seqs BQ.1.8
• [ ] Spike_S940F 11 seqs BQ.1.8
• [ ] Spike_P621S 2 seqs
• [ ] Spike_M177L,SPike_H1101Y,Spike_P1143S 1 seq france bq.1.1
• [ ] Spike_E309Q 1 seqs
• [ ] SPike_D428Y 1 seq france bq.1.1
• [ ] SPike_Y145H,Spike_K356N 1 seq UK BQ.1
• [ ] Spike_Y279F
• [ ] Spike_G257D
• [ ] Spike_M153T,Spike_i358V,Spike_L922F
• [ ] Spike_R190S 2seqs
• [ ] Spike_D178N 3 seqs
• [ ] Spike_L216F 3 seqs BQ.1
• [ ] Spike_C1248Y 2 seqs BQ.1.1
• [ ] Spike_E224Q 3 seqs BQ.1.1
• [ ] Spike_T259I 2 seqs BQ.1.1 Uk
• [ ] Spike_H146Y 4 seq Uk
• [ ] Spike_Q675H 2 seq
• [ ] Spike_Q52K, 1 seq
• [ ] Spike_T274I 1seq
• [ ] Spike_M153I 2 seq BQ.1.1
• [ ] Spike_I203L 1seq
• [ ] Spike_W152R 2 seq
• [ ] Spike_G476S 3 seq BQ.1.1 england within S:T307I bigger lineage
• [ ] Spike_T678I 2 seq
• [ ] Spike_S247I 2 seq
• [ ] Spike_G184S 6 seqs BQ.1.13
• [ ] Spike_C1236S 10 seqs
• [ ] Spike_A1070V 6 Seqs BQ.1.5
• [ ] Spike_D215Y 2 seq BQ.1.8
• [ ] Spike_E465D 1 seq
• [ ] Spike_Q321H 1 seq
• [ ] Spike_Y248C 1 seq

From Netherlands : EPI_ISL_15581345 Spike_P479R + Spike_G485S From Australia i spotted heavily mutated BQ.1.1 EPI_ISL_15578381: Spike_S12P,Spike_T20I,Spike_N137S,Spike_D339N,SPike_P479L, Spike_T604I, Spike_A831T

[Sinickle]

S:484V on the S:666V branch, now in 8 sequence, 6 uploaded in the last 10 days.

S:484V seems to come up often but not be advantageous, so not expecting much from it though.

[FedeGueli]

@corneliusroemer i have split the fast and slow spike mutated lineages in the post above.

last update 29/10

[RajLABN]

BQ.1.1* with S:D1199G - from Spain & UK | EPI_ISL_15495043, EPI_ISL_15505617

(another BQ.1* with S:D1199B from NY | EPI_ISL_15577876 )

[ryhisner]

Seven BQ.1.1.3 + A688V from New York City today. A few others from NYC today:

• BQ.1 + V445A • BQ.1.1 + E471Q • BQ.1.1 + K202R • BQ.1.1.4 + W152R • BQ.1.2 + K278R • BQ.1.6 + K147R • BQ.1.14 + T478I

There are lots more, but I'm too tired to log any more.

[RajLABN]

Two more BQ.1.1* with D1199N from NY - EPI_ISL_15669230, EPI_ISL_15669316

[FedeGueli]

Two more BQ.1.1* with D1199N from NY - EPI_ISL_15669230, EPI_ISL_15669316

please propose it @RajLABN this issue s going too big. it will be helpful to check numbers but i dot think Cornelius can designate from such a long list!

[FedeGueli]

Seven BQ.1.1.3 + A688V from New York City today. A few others from NYC today:

• BQ.1 + V445A • BQ.1.1 + E471Q • BQ.1.1 + K202R • BQ.1.1.4 + W152R • BQ.1.2 + K278R • BQ.1.6 + K147R • BQ.1.14 + T478I

There are lots more, but I'm too tired to log any more.

Thanks a lot @ryhisner ! i noticed that S:A688V that is fast in BQ.1.8 popped up in BQ.1.1 too so i think it is in some way beneficial cc @thomaspeacock maybe interested in this.

[ryhisner]

@RajLABN & @FedeGueli — those BQ.1.1* + D1199N are both recombinants. EPI_ISL_15669316 is that crazy CA.1/BQ.1.1 recombinant that took the worst/best mutations of both and added S:F490S.

The other—EPI_ISL_15669230—also has to be a recombinant—it took K147E, W152R, and F157L from BA.2.75.2*.

[ryhisner]

BQ.1.1 + S221L looks like it's up to 12 sequences—only eight have R346T, but the other four have no coverage there, and they all share ORF1b:N1191S, which isn't found in the other two BQ.1* that have S221L (both of which are BQ.1.3).

One of the BQ.1.1 uploaded today (missing coverage at S:346) also has G482D, which I believe is a first for a BQ.1*. EPI_ISL_15677319

[corneliusroemer]

I'll close this - I've gone pretty systematically through BQ.1 and BQ.1.1 designating any interesting Spike lineages.