Closed FedeGueli closed 1 year ago
Spike_K356E--1 sequence from USA, making it level-8.
Spike_S494P as well 1 sequence. Mild immune escape peak in bloomlab calculator
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.
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.
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.
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.
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
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.
Spike_A411S is in 3 different Northeastern US states, 5 seqs. One of them is the S:L455F sequence @plomano notes.
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.
XBB.1.5 + S:K1181I - 16 sequences (NY, FL, PA - USA)
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)
Thankyou @FedeGueli - your list makes tracking issues lot easier
A348T: EPI_ISL_16381444, EPI_ISL_16344978, EPI_ISL_16388964 N450K: EPI_ISL_16398246
1 more sequence for S:K356E EPI_ISL_16388978
XBB.1.5 with S:C1243F (1 seq from NY)
F157L: EPI_ISL_16420377 W152R: EPI_ISL_16417574, EPI_ISL_16420377, EPI_ISL_16070584, EPI_ISL_16343266, EPI_ISL_16137835
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
@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!
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*
A348S: EPI_ISL_16456183
@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>
Thank you very much @ciscorucinski , done!
N148T: EPI_ISL_15921566 70+, mostly in US, Moldova. Some recent (2023-01).
@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.
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.
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
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.
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.
@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
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.
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
P1162L: 18 P1162S: 3 P1162Q: 3 Q1201K: 5 (related to a potential TRS sequence) T859N: 2
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
@FedeGueli Spike_I666V please go ahead and propose it if you think it is deserving. I can't really tell from my end.
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
Gisaid query: NS3_A31V,NS3_T269M,spike_R403K seq: 2 @corneliusroemer @thomasppeacock @InfrPopGen
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.
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.
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
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.
L452M: EPI_ISL_16700525 G446N: EPI_ISL_16816554 V483I: EPI_ISL_16810656, EPI_ISL_16699887 V483A: EPI_ISL_16816506
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
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
@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.
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.
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.
Others from Austria, mostly spike-only sequences today: • H66Q • N137S (4) • K182Q • I210del • R246S • A260T • V445A (P445A) • E465D (2) • M740T (4) • N751Y (2) • P812A
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
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.
Speaking of rare mutations on mutated sites of BA.2, there is one with S:K764Q recently.
@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.