XBB.1.5 spike diversity - multiple lineages issue to track easily if any spike mutation appears (and circulates) within XBB.1.5 lineage - Last update 12/03/2023

[FedeGueli]

@corneliusroemer , happy new year first!, then here the new XBB.1.5 Spike Diversity Issue: (last update 12/03/23)

XBB.1.5 query : T17124C,T23018C +

Legenda: N or n= not growing = zero new sequences blank = growing little but different from 0seqs y= growing around 15% since last update yy = growing more than 20% since last update yyy = growing more than 50% since last update (Designated lineages are out of the game , no updates for them) Lineages with less than 10 sequences now will not be updated.

Mutation	W Sequences	Growing (Y>+20%,YY>+30%/W)	RBD	Notes
Spike_V952I	XBB.1.5.6
Spike_K1181I	XBB.1.5.5
Spike_T883I	XBB.1.5.4
Spike_A411S	XBB.1.5.3
S:T284I+S:K147I	XBB.1.5.2
Spike_T323I	XBB.1.5.12			predicted as advantageous by Bloomcalc.
Spike_F456L	XBB.1.5.10
Spike_A411T	Spike_R646H	N
Spike_R214L	EM.1
Spike_Q675H	EL.1			#1631
Spike_T259I	EK.2
Spike_K417S	EK.1			#1638
Spike_T573I	XBB.1.5.1
Spike_T678P		n
Spike_N148T	424	YY
Spike_G1219V	293
Spike_N978S	279	Yy		#1699
Spike_P621S	274	yy		non monoph.
Spike_T478R	199	YY	Yes
Spike_K1045R	194	YY
Spike_A348T	186	YY	Yes	#1660 #1661
Spike_K97T	181	YY		#1643
Spike_V36I	173	y
Spike_L176F	160	YY
Spike_I666V	142	y		non monophyl.
Spike_E583D	138	YY
Spike_A852S	132	YY
Spike_P521S	129	YYY		#1688
Spike_i410V+Spike_p521S	127	YYY		#1688
Spike_I197V	124	Y		#1745
Spike_P1162L	120	YY
Spike_S494P	118	Y	Yes	#1610
Spike_t547I	118	Y
Spike_M177I	113	YYY
Spike_N703S	105	YY		https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f220_332430.json?label=id:node_8090637
Spike_S221L	105	Y		non monophyl.
Spike_S640F	99	Y
Spike_A688V	94	YY
Spike_F59L	94	YY
Spike_T51I	87	YYY
Spike_H245Y	86	YY
Spike_H245Y	86	y
Spike_H49Y	81	YY
Spike_P251S	78	YY		#1684
Spike_T299I	75
Spike_R346I	74	y	Yes
Spike_h1058Y	73	Y
Spike_I410V	71	YYY	y
Spike_K304Q	70	YYY
Spike_T1117R	67
Spike_W64R	67	Y		https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_e957_331fa0.json?c=country&label=id:node_8073903
Spike_P1162S	66	YY
Spike_A348S	65		Yes	#1595
Spike_G1099D	64
Spike_N540K	64	YYY		#1710
Spike_S689T	61
Spike_T307I	60	y
Spike_P521T	58	YY
Spike_S514F	57	y		down binding
Spike_H69Y	56
Spike_Q675K	56	Y
Spike_A352V	55		y
Spike_V1122M	55	YYY
Spike_Q1201K	54	Y
Spike_Q52H	54	yy
Spike_A1078S	53	Y
Spike_V1122L	53	YY
Spike_F157L	52	YY
Spike_S256L	51
Spike_T478I	51	y
Spike_D198G	48
Spike_E1144Q	48	Y
Spike_E619K	48	Y
Spike_Q677H	47	y		Iceland
Spike_A1020V	46	1
Spike_G257S	46	YY
Spike_P463S	46	Y	Y	Non monophyl.
Spike_S31F	46	Y
Spike_S254F	44	YY
Spike_t588I	44	YYY
Spike_T588I	44	yy
Spike_K558N	43
Spike_E324K	42
Spike_S939F	42	Y
Spike_V772I	42	yy
Spike_N137S	41	YYY		fast
Spike_P479L	41		yes	australia
Spike_A352S	40		Yes
Spike_G476S	38		y
Spike_N481S	38
Spike_L922F, Spike_t747I	37
Spike_Q836R	37	YY
Spike_L335F	36	y
Spike_T430I	36		y
Spike_T941S	36
Spike_V130I	36
Spike_A288T	35
Spike_C1243F	34	Y
Spike_D1146Y	34
Spike_D936H	34
Spike_R190S	34
Spike_D215G	33	Y
Spike_E406Q	33	y
Spike_p812S	33	y
Spike_W152R	33	Y
Spike_E340Q	32
Spike_G485S	32		Yes
SPike_N354K	32	Y	Y
Spike_S255F	32	y
Spike_T478E	32	y
Spike_R78M	31	y
Spike_A288S	30
Spike_I834V	30	Y
Spike_T240I	30	Y
Spike_A475V	29		Yes
Spike_A1078T	28
Spike_A222S	28	YY
Spike_T470I	28	Y	y
Spike_T859N	28	Y
Spike_V445S	28	Y
Spike_A222V	27
Spike_F490P	27	YY	y
Spike_S750N	27	Y
Spike_T553I	27
Spike_Y145K,Spike_H146K	27			It makes 145-147KKK
Spike_G268S	25
Spike_K182R	25	Y
Spike_L513F	25	Y
Spike_M153I	25
Spike_N99S	25	Y
Spike_t385I	25	y	y
SPike_I1114V	24
Spike_V483F	24		y
Spike_E661D	23
Spike_N1023S	23
Spike_K444T,Spike_L452R	22		Yes
Spike_E1202Q	22	Y
Spike_T676I	22	N
Spike_t961M	22	Y
Spike_A67T	20	Y
Spike_D215Y	20	y
Spike_G485D	20		y
Spike_K77N	20	Y
Spike_S71F	20
Spike_t323R	20	YY
Spike_L858I	20	y
Spike_P1112S	19	YY
Spike_P681R	19	Y
Spike_E554Q	18
Spike_K444R	18	Y	y
Spike_T768N	18	N
Spike_K182E	18	yy
Spike_A435T	17	Y
Spike_A694V	17	y
Spike_D138G	17	y
Spike_I210del	17
Spike_L84I	17	N
Spike_P1143S	17	N
Spike_R1185H	17
Spike_S255P	17
Spike_T523A	17	yy
Spike_v289L	17	YY
Spike_V70F	17	Y
Spike_R237K	17	yyy
Spike_A522P	16	N
Spike_K356T	16	y	Y
Spike_R408G	16	YY
Spike_S591T	16	yy
Spike_V308L	16	Y
Spike_D1199N/H/E	15	N
Spike_i128V	15	Y
Spike_P631S	15	N
Spike_Q493L	15	Y	Y
Spike_S937T	15	N
Spike_V642G	15	y
Spike_i997V	15	y
Spike_E471Q	14		Y
Spike_K304Q,Spike_A411S	14	y
Spike_L518V	14	Y
Spike_M177T	14	y
Spike_P1162Q	14
Spike_Q474K	14	y
Spike_S691P	14	Y
Spike_T549A	14	yy
Spike_T791I	14	N
Spike_T859I	14	y
Spike_A846S	13	y
Spike_A93S	13
Spike_D1146N	13	Y
Spike_D427Y	13	y	Y
Spike_E619A	13	Y
Spike_I1216T	13	Y
Spike_K150N	13	Y
Spike_K462E	13	N	y	#
SPike_P479H	13	n
Spike_S929T	13
Spike_T547K	13	Y
Spike_i1221V	13
Spike_T618I	13	y
Spike_V159I	13	y
Spike_A522V	12	N
Spike_A684P	12	N
Spike_A845S	12	y
Spike_D574Y	12	n
Spike_g257D	12	y
Spike_G446I	12	n	Y
Spike_I670V	12
Spike_N148K	12	Y
Spike_N658K	12
Spike_N74D	12
Spike_Q52R	12
Spike_N481T	12	y
Spike_E1150D	11	N
Spike_e516Q,Spike_t883I,Spike_D1168H	11
Spike_H519L	11	N	Y
Spike_k129R	11	N
SPike_Y200C	11	n
Spike_E554V	11
Spike_I68T	11
Spike_P272S	11
Spike_M740T	11
Spike_g1124S	11	y
Spike_H1101R	11	y
Spike_I418V	11	y
Spike_A701S	10
Spike_D215H	10	N
Spike_D53E	10	N
Spike_E281D	10
Spike_H1159R	10
SPike_N679R	10	Y
Spike_P337S	10	N
Spike_V227L	10	N
Spike_V510L	10	N
Spike_I233V	10	y
Spike_R1014K	10
Spike_r765C	10	y
Spike_R403K	10
Spike_V483I	10	y	Y
Spike_D843N	9	N
Spike_E583D,Spike_L858I	9	yy
Spike_G339Q	9	Y
Spike_Y636F	9	N
Spike_E96D	9
Spike_Y396H	9	n	Y
Spike_D808N	9
Spike_E154D	9
Spike_G339R	9	y
Spike_G482S	9		y
Spike_N149Y	9	y
Spike_Q218R	9	y
Spike_N481Y	9
Spike_V367I	9
Spike_L242F	8
Spike_N185S	8	n
Spike_V1122L,Spike_p1162S	8
Spike_V83P	8
Spike_V433I	8		Y
Spike_G184S	8
Spike_N481S,Spike_G482del	8
Spike_T500A	8		y
Spike_V610I	8
Spike_V622A	8
Spike_A264V	8
Spike_g75S	8
Spike_S325F	8
Spike_K97R	8	y
Spike_N540Y	8	y
Spike_N234D	7	n
Spike_R646H	7	y
Spike_T208A	7
Spike_W64L	7	Y
Spike_A372V	7	n
Spike_g219S	7
Spike_P82L	7	n
Spike_V267L	7
Spike_v511I	7			b
Spike_L455F	7		Yes
Spike_N282S	7	y
Spike_N354S	7
Spike_D53N	6
Spike_E465D	6
Spike_K182Q	6
Spike_p174R	6	n
Spike_V722D	6	Y
Spike_T236S	6
Spike_G261C	6
Spike_A260T	5	n
Spike_D1184Y	5	n
Spike_D88H	5	n
Spike_I1225V	5	n
Spike_i598V	5
Spike_k182Q	5
Spike_K444N	5	n
Spike_L1012S	5
Spike_L242F	5	y
Spike_N925Y	5	n
Spike_P174S	5	y
Spike_P330L	5
Spike_R190T	5	N
Spike_R567I	5
Spike_R646L	5
Spike_V1068I	5
Spike_D420N	5	n
Spike_D88G	5	n
Spike_D936E	5	n
Spike_G381R	5
Spike_E154Q,	4
Spike_G485V	4	n	Y
Spike_G932C	4	n
Spike_G946R	4	n
Spike_k1086R	4
Spike_K356E	4	n	Yes
Spike_L179S	4
Spike_N450D	4
Spike_N532Y	4
Spike_N658S	4
Spike_Q580L	4
Spike_S1021A	4	N
Spike_S477K	4	n
Spike_T284I, Spike_R403K, Spike_L513F	4	n
Spike_V407I	4	n
Spike_Y351H	4			NOT UPDATED
Spike_G482V	4	n	y
Spike_N606K	4	n
Spike_N751Y	4	n
Spike_P621H	4	N
Spike_S937L	4	n
Spike_Y660F	4
Spike_G838S	3	N		NOT UPDATED
Spike_A163V	3	n		NOT UPDATED
Spike_A348P	3	N	Y
Spike_A647V	3	n		NOT UPDATED
Spike_D1127G	3	n		NOT UPDATED
Spike_G75R	3	n
Spike_L452M	3		Y
Spike_L517P	3	Y
Spike_N658Y	3	n
Spike_p499L	3
Spike_Q218H	3	N
Spike_Q607R	3
Spike_R357I	3	N	y
Spike_S686R	3	Y
Spike_T415I	3	N	y
Spike_t470N	3	n	y
Spike_Y200H	3
Spike_Y451H	3	N
Spike_A1016V	2	N		NOT UPDATED
Spike_A871V	2	n		NOT UPDATED
Spike_D1118Y	2	n		NOT UPDATED
Spike_D1165Y	2	N		NOT UPDATED
Spike_D428G	2	N		NOT UPDATED
Spike_D627H	2	N		NOT UPDATED
Spike_E1188V	2	n		NOT UPDATED
Spike_E132Q	2	n		NOT UPDATED
Spike_E406Q,Spike_G482S	2
Spike_E654V	2			NOT UPDATED
Spike_I402V	2			NOT UPDATED
Spike_K356N	2	N	y	NOT UPDATED
Spike_K529R	2	N		NOT UPDATED
Spike_K537R	2	n		NOT UPDATED
Spike_K947T	2	N		NOT UPDATED
Spike_N360S	2	n		NOT UPDATED
Spike_N536S	2	n		NOT UPDATED
Spike_N61K	2	n		NOT UPDATED
Spike_P272T	2	n		NOT UPDATED
Spike_Q271L	2	N		NOT UPDATED
Spike_Q787H	2	N		NOT UPDATED
Spike_R102I	2	n		NOT UPDATED
Spike_R273M	2	N		NOT UPDATED
Spike_S162I	2	n		NOT UPDATED
Spike_S596I	2	n		NOT UPDATED
Spike_T645I	2	n		NOT UPDATED
Spike_W152S	2	n		NOT UPDATED
Spike_y160F	2	N		NOT UPDATED
Spike_Y248H	2	N		NOT UPDATED
Spike_Y248S	2	N		NOT UPDATED
SPike_Y453F	2	N		NOT UPDATED
Spike_A1016S	1	N		NOT UPDATED
Spike_A243S, Spike_A263P	1	n		NOT UPDATED
Spike_A262T	1	N		NOT UPDATED
Spike_A397S	1	n		NOT UPDATED
Spike_A845D	1	n
Spike_D1199G	1	N		NOT UPDATED
Spike_d614S	1	N		NOT UPDATED
Spike_D867G	1	n		NOT UPDATED
Spike_E154Q,Spike_G72R	1	n
Spike_E156A	1	n
Spike_E484K (from ryan)	1	n	YY	NOT UPDATED
Spike_E96G	1	N		NOT UPDATED
Spike_F168V	1	N		NOT UPDATED
Spike_F392Y	1	N		NOT UPDATED
Spike_G446N	1	N	Y	NOT UPDATED
Spike_G545S	1	N		NOT UPDATED
Spike_H146R	1	N		NOT UPDATED
Spike_I233T	1	N		NOT UPDATED
Spike_I472V	1	N		NOT UPDATED
Spike_i770V	1	N		NOT UPDATED
Spike_K1073T	1	N		NOT UPDATED
Spike_K182N	1	N		NOT UPDATED
Spike_K790R	1	N		NOT UPDATED
Spike_L1024H	1	n		NOT UPDATED
Spike_L241S	1	N		NOT UPDATED
Spike_M153T	1	N		NOT UPDATED
Spike_N122S	1	N		NOT UPDATED
Spike_N282K,Spike_A222T	1	N
Spike_N282Y	1	N		NOT UPDATED
Spike_N450K	1	N	Yes	NOT UPDATED
Spike_P1162L,Spike_D1163Y	1	N
Spike_P499S	1	N	Yes	NOT UPDATED
Spike_p812R	1	N		NOT UPDATED
Spike_Q1201k,Spike_E1202Q	1	N		NOT UPDATED
Spike_Q787K	1	N		NOT UPDATED
Spike_S359I	1	N		NOT UPDATED
Spike_T124S	1	N		NOT UPDATED
Spike_T430I,Spike_p521S	1	n
Spike_T696I	1	n		NOT UPDATED
Spike_t73A	1	n		NOT UPDATED
Spike_T998S	1	N		NOT UPDATED
Spike_V483A	1	N	Y	NOT UPDATED
Spike_V503F	1	N		NOT UPDATED
Spike_W258S	1	n		NOT UPDATED
Spike_D1084E	0
Spike_G669S	0
Spike_N417I	0
Spike_T835I	0

[aviczhl2]

Spike_K356E--1 sequence from USA, making it level-8.

[BorisUitham]

Spike_S494P as well 1 sequence. Mild immune escape peak in bloomlab calculator

[Sinickle]

I think the S:485S mutation might be important. This mutation is also on two CJ.1 sequences. S:485S has appeared 154 times since Jan 1 2022. So, 7/154 times it has been accompanied with S:486P and S:490S. There have been 7000 sequences submitted with S:486P and 6.6 million submitted without it, since 2022.

So it's been ~43x more common on this background. Given their adjacency, it might be adaptive.
Notably, S:485D seems to be granting an advantage to BA.2.3.20 which has S:484R.

[olias120676]

Spike_R214L, 2 sequences in GISAID 1 USA, 1 UK. However I can see there are another 3 in the UK in the past week not on GISAID yet.

Also 1 P479H in the UK.

[oobb45729]

I checked. Yes, G485S may assist ACE2 binding in the F486P background. G485 may form a hydrogen bond with C488, which may be undesirable for ACE2 binding in variants with F486, which mainly interacts with M82 and Y83 of ACE2. However, P486 mainly interacts with L79 and M82 of ACE2. The G485-C488 hydrogen bond would likely assist the interactions.

[oobb45729]

What is special about K356T is that it leads to a new N-glycan site at N354. So K356X variants other than K356T or K356S probably won't have the K356T type immune escape.

[plomano]

A348V: EPI_ISL_16308285 L455F: EPI_ISL_16272184 T883I: EPI_ISL_16294118, EPI_ISL_16343692 A475V: EPI_ISL_16343595, EPI_ISL_16343338, EPI_ISL_16343409 Y453H: EPI_ISL_16330495 L858I: EPI_ISL_16272402

I made a CoV-Spectrum collection that contains a bunch of common muts for XBB.1.5 to make it easier for me to track. https://cov-spectrum.org/collections/130

[thomasppeacock]

Keep up the good work folks!

With the high ACE2 binding XBB.1.5 is showing (and its widespread and rapid growth) I think its likely, similar to BA.2.75, this generates quite a lot of successful antigenically distinct sublineages. Important to monitor in the next few weeks.

[Sinickle]

Spike_A411S is in 3 different Northeastern US states, 5 seqs. One of them is the S:L455F sequence @plomano notes.

[plomano]

A352V: EPI_ISL_16343645

352 is notably evasive, but also has horribly negative ACE2 and RBD expression effects, so I'm not sure if it will take off, but I felt prudent to post it.

[RajLABN]

XBB.1.5 + S:K1181I - 16 sequences (NY, FL, PA - USA)

[RajLABN]

XBB.1.5 + S:D1199N/H/E (NY, MA) XBB.1.5 +S:A1078S/T - 10 Sequences (Cov-Spectrum finds 20) XBB.1.5 +S:N1023S - 3 sequences (Singapore (local case), NJ) XBB.1.5 +S:L1012S - 4 sequences (South Carolina, New York)

[RajLABN]

Thankyou @FedeGueli - your list makes tracking issues lot easier

[plomano]

A348T: EPI_ISL_16381444, EPI_ISL_16344978, EPI_ISL_16388964 N450K: EPI_ISL_16398246

[aviczhl2]

1 more sequence for S:K356E EPI_ISL_16388978

[RajLABN]

XBB.1.5 with S:C1243F (1 seq from NY)

[plomano]

F157L: EPI_ISL_16420377 W152R: EPI_ISL_16417574, EPI_ISL_16420377, EPI_ISL_16070584, EPI_ISL_16343266, EPI_ISL_16137835

[BorisUitham]

There are 2 sequences of a XBB.1.5 with both 444T and 452R. One in US and one in Sweden. EPI_ISL_16268936 EPI_ISL_16439461 https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=s%3A444t%2Cs%3A452r&nextcladePangoLineage=xbb.1.5*&

edit: the one in the united states has 486v and 252g so its might just wrongly assigned be nextclade. the one in sweden does seem to be xbb.1.5 though, perhaps a recombinant with ch.1.1 or bq.1.1 so ill look into that today and maybe make an issue

[Sinickle]

@BorisUitham I saw the Sweden one before but am expecting it's not real. It has 4 breakpoints in the spike alone! As you said, it looks unrelated to the US one. Good to track though for if more cases do come up!

[BorisUitham]

XBB.1.5 with P681R EPI_ISL_16491509

edit:pangolin calls it xbb.1.5 but position 486 has not been sequenced. it does contain g252v so it is at least xbb.1*

[plomano]

A348S: EPI_ISL_16456183

[ciscorucinski]

@FedeGueli I think creating a markdown table would be highly beneficial and much easier to read. Something like the following...

?	Mutation	Sequences	Growing	RBD	Notes
[]	Spike_A348T	4
[]	Spike_N450K	1		Yes
[_]	Spike_G1219V	70	Yes
[_]	Spike_T573I	29	Yes
[]	XBB.1.5*+Spike_D1199N/H/E				Location: NY, MA
[]	Spike_A1078S/T	10			Cov-Spectrum finds 20 sequences

I have the whole list from above converted to a markdown table in a gist. This can be copy-pasted into Google Sheets (split into columns via | ) or the visual table can be automatically copy-pasted into Google Sheets with no additional work Gist: https://gist.github.com/ciscorucinski/7fbd8723a3f4f180780aa0bab14d5d0e

I don't know what the checkboxes represent and if the spacing matters. Also, you could add a column for date updated

Note: GitHub will automatically create a markdown table from Google Sheets data. Just copy-paste the data as a comment, You can delete the metadata that is copied. See below code

<google-sheets-html-origin><style type="text/css"><!--td {border: 1px solid #cccccc;}br {mso-data-placement:same-cell;}--></style>

[FedeGueli]

Thank you very much @ciscorucinski , done!

[Mike-Honey]

N148T: EPI_ISL_15921566 70+, mostly in US, Moldova. Some recent (2023-01).

[Sinickle]

@Mike-Honey I think the large majority of those are an artifact. They seem to usually have S_H146K, Spike_ins152k, and no 144 deletion. That being said, I think some of them are legitimate.

[Mike-Honey]

Thanks for looking into that @Sinickle. I don't want to waste anyone's time and I clearly lack context for this. Here's the interactive page I was using, now filtering to require Y144del. I hope it's useful in this task - perhaps to monitor for new muts appearing like I666V, before you dig in with your usual tools for a proper assessment.

https://github.com/Mike-Honey/sars-cov-2-genomes#gisaid-mutation-frequency

Let me know any feedback or issues. I update the data once or twice a week.

[plomano]

K444R: EPI_ISL_16527441 G485D: EPI_ISL_16483134 V483F: EPI_ISL_16527381, EPI_ISL_16527203, EPI_ISL_16527215, EPI_ISL_16527277 K356N: EPI_ISL_16478530 A352V: EPI_ISL_16343645 A348V: EPI_ISL_16308285 T430I: EPI_ISL_16572823, EPI_ISL_16572816 R357I: EPI_ISL_16560723

[Mike-Honey]

K147I: EPI_ISL_16478361 15 samples submitted 2023-01-20 - all US, mostly North Dakota, Minnesota and Texas. The samples from North Dakota look like around 40% of their recent submissions (all lineages), although sample sizes from ND are small.

[Mike-Honey]

I666V: EPI_ISL_16617564 18 samples, including 8 from Vienna Austria (around 8% of the Austrian XBB.1.5 samples), collected from 2021-01-09 onwards.

[BorisUitham]

@Mike-Honey could I666V increase TMPRSS2 usage? BQ.1.2 has higher TMPRSS2 usage than bq.1.1 and the difference in spike is that bq.1.2 has I666V (the other spike difference is that bq.1.1 has 346T, which is also in xbb.1.5). https://www.medrxiv.org/content/10.1101/2022.12.06.22283000v3 figure 5F. if this holds true to xbb* base this might lead to differing tropism and increase cell entry so this could be a mutation to watch

[corneliusroemer]

I've designated: XBB.1.5.1: S:T573I XBB.1.5.2: S:T284I and S:K147I XBB.1.5.3: S:A411S

S:T883I is obvious candidate but looks very homoplasic/messy, so better wait a bit more. Things will become clearer over the next few weeks.

[oobb45729]

E583D: 10 (8 with G23311T and 2 with G23311C) (5 of them also has P1162L)

It was in a successful sublineage of Mu and it is predicted to escape an SD1-targeting antibody. https://dms-vep.github.io/SARS-CoV-2_Omicron_BA.1_spike_DMS_C68.59/C68.59_escape_plot.html

[oobb45729]

P1162L: 18 P1162S: 3 P1162Q: 3 Q1201K: 5 (related to a potential TRS sequence) T859N: 2

[oobb45729]

Also SD1-targeting antibody escaping: K558N: 4 E554V: 2 E554Q: 1

S2-targeting antibody escaping: D1153H: 3 https://dms-vep.github.io/SARS-CoV-2_Omicron_BA.1_spike_DMS_mAbs/CC67.105_escape_plot.html https://dms-vep.github.io/SARS-CoV-2_Omicron_BA.1_spike_DMS_mAbs/CC9.104_escape_plot.html

[Mike-Honey]

@FedeGueli Spike_I666V please go ahead and propose it if you think it is deserving. I can't really tell from my end.

[FedeGueli]

Possible sublineage of interest with saltation appeared in XBB.1.5: def.: C1190T, G22770A, C23099T, A24430C, C25484T, C26198T,C22413T ORF1a:P309S S:R403K, S:L513F S::T284I ORF3a:A31V, orf3a:T269M

tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_2e636_191290.json?label=id:node_9560114

Gisaid query: NS3_A31V,NS3_T269M,spike_R403K seq: 2 @corneliusroemer @thomasppeacock @InfrPopGen

[BorisUitham]

another one that might be interesting is XBB.1.5 with Spike_Q675H because of its position. It is currently at 39 sequences, but the geographic spread throughout europe is already wide: austria, canary islands, croatia, france, germany, ireland, italy, poland, spain, switzerland, ukraine. also present in usa: california, new york, maryland and new jersey

edit: actually its at 41.

[ryhisner]

Three sequences from USA, Massachusetts were recently uploaded that have S:A348P. This was a mutation convergent in chronic BA.2 sequences but has largely disappeared over the last 4-6 months. EPI_ISL_16852008, EPI_ISL_16852026, EPI_ISL_16852035

Also, the first XBB.1.5 with S:P812R showed up in Connecticut, USA, yesterday. EPI_ISL_16851953 See Issue #1627 for more details on S:P812R, which creates a new cleavage site.

[ryhisner]

An XBB.1.5 with K356T from USA, Pennsylvania: EPI_ISL_16851287

There is also one from Australia with K356T. I think it's probably real, but some missing coverage and the alleged reversion S:I368L make its reality a bit uncertain to me. EPI_ISL_16826045

[aviczhl2]

S:K97T appears to be in almost 30% of the South African XBB.1.5 sequences.

Interestingly, given its high prevalence in South African XBB.1.5, this mutation haven't found in anywhere else, only appears in South Africa.

[plomano]

L452M: EPI_ISL_16700525 G446N: EPI_ISL_16816554 V483I: EPI_ISL_16810656, EPI_ISL_16699887 V483A: EPI_ISL_16816506

[plomano]

446I: EPI_ISL_16835007, EPI_ISL_16763024, EPI_ISL_16863255, EPI_ISL_16779891, EPI_ISL_16742476, EPI_ISL_16753647, EPI_ISL_16533790

354K: EPI_ISL_16823724, EPI_ISL_16735375, EPI_ISL_16612672, EPI_ISL_16824768, EPI_ISL_16824857, EPI_ISL_16654888, EPI_ISL_16850535, EPI_ISL_16824783, EPI_ISL_16824793, EPI_ISL_16810615, EPI_ISL_16753495, EPI_ISL_16824714, EPI_ISL_16633591, EPI_ISL_16654889, EPI_ISL_16742098

485V: EPI_ISL_16783482

[ryhisner]

XBB.1.5 with S:A484K—a 2-nuc mutation—and S:N556K showed up in California. EPI_ISL_16936101 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41525_ea4630.json?c=gt-S_484&f_userOrOld=uploaded%20sample

[rquiroga7]

@FedeGueli I have proposed two S:A348T lineages in issues #1660 and #1661 . This mutation is predicted as negatively affecting RBD expression and ACE2 binding but increasing antigenic evasion.

[Outpfmance]

XBB.1.5 with S:N679R (10 sequences) https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=s%3A679r&nextcladePangoLineage=XBB.1.5

N679R is also in the recent CH.1.1 mutant sequence. And they've been growing relatively fast lately.

[ryhisner]

Spike-only singlet from Austria today with S:L461V— EPI_ISL_17010459. That's a C->G nuc change and a mutation that's only been seen in six other sequences in the entire pandemic.

[ryhisner]

Others from Austria, mostly spike-only sequences today: • H66Q • N137S (4) • K182Q • I210del • R246S • A260T • V445A (P445A) • E465D (2) • M740T (4) • N751Y (2) • P812A

[ryhisner]

There are now four sequences in the S:T284I, S:R403K, S:L513F lineage described above by @FedeGueli, three from Illinois (USA) and one from Ohio (USA). Both of these states are in the US Midwest, but they do not border one another. I actually live in Indiana, the state that lies between Ohio and Illinois. EPI_ISL_16681042, EPI_ISL_16835959, EPI_ISL_17023204, EPI_ISL_17023295

[ryhisner]

There have also been six XBB.1.5 with S:S408N (along with four XBF, six CH.1.1, and seven BQ.1*). Mutations at S:408 have been extremely rare, but perhaps that is beginning to change. With the new breed of variants, previously deleterious mutations could become beneficial due to unpredictable epistasis. The overall numbers are still extremely small (52 sequences in the past two months), but there's been a visible increase in S:R408G/N recently.

[oobb45729]

Speaking of rare mutations on mutated sites of BA.2, there is one with S:K764Q recently.