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 #1510
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FedeGueli
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FedeGueli
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Spike_K356E--1 sequence from USA, making it level-8. |
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Spike_S494P as well 1 sequence. Mild immune escape peak in bloomlab calculator |
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I think the S:485S mutation might be important. So it's been ~43x more common on this background. Given their adjacency, it might be adaptive. |
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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. |
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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. |
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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. |
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A348V: EPI_ISL_16308285 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
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help wanted
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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. |
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Spike_A411S is in 3 different Northeastern US states, 5 seqs. One of them is the S:L455F sequence @plomano notes. |
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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. |
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XBB.1.5 + S:K1181I - 16 sequences (NY, FL, PA - USA) |
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XBB.1.5* + S:D1199N/H/E (NY, MA) |
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Thankyou @FedeGueli - your list makes tracking issues lot easier |
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A348T: EPI_ISL_16381444, EPI_ISL_16344978, EPI_ISL_16388964 |
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1 more sequence for S:K356E |
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XBB.1.5 with S:C1243F (1 seq from NY) |
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F157L: EPI_ISL_16420377 |
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There are 2 sequences of a XBB.1.5 with both 444T and 452R. One in US and one in Sweden. 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 |
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@BorisUitham I saw the Sweden one before but am expecting it's not real. It has 4 breakpoints in the spike alone! |
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XBB.1.5 with P681R 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* |
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A348S: EPI_ISL_16456183 |
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@FedeGueli I think creating a markdown table would be highly beneficial and much easier to read. Something like the following...
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 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 |
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Thank you very much @ciscorucinski , done! |
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N148T: EPI_ISL_15921566 |
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@FedeGueli Thanks to reply! I try to propose an issue for discussion in #1704 |
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Just raised: XBB.1.5 cases in China #1717 |
FedeGueli
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Yes, that's the 5th one from the US Midwest. with T284I, R403K, L513F, ORF3a:A31V, ORF3a:T269M, and ORF1a:P309S. I've got a proposal mostly written for that one, and if another sequence shows up, I'll probably post it. |
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I don't think I've ever seen this S2 deletion before: S:∆859-860. It's in an XBB.1.5 from Georgia, USA, which also has another very rare S2 mutation with S:C1236Y, which has only ever been in ~160 sequences worldwide. EPI_ISL_17128969 |
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XBB.1.5 w/ Spike_V83P [ 5 California & 1 Mexico] : A 2-Nuc change |
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Two cases of XBB.1.5 were reported today in Guangdong, China. The serial numbers are EPI_ISL_17170853 and EPI _ISL _17170852 |
The pedigree of 17170852 was identified as EM.1, a descendant of XBB.1.5.7. In Zhanjiang, Guangdong, China. |
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Yesterday's two came from Yichang, Hubei, serial numbers 17182661 and 17182662. |
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This last update has been very time expending. I m not sure if this could be kept updated anymore. Please write down here if you spot any lineage rising. i suggest @corneliusroemer to take a look at lineages growing with YYY, likely they are the most fit. |
FedeGueli
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XBB.1.5 in Haikou, Hainan, China, available at 17175998.It has S: S254F |
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@Mike-Honey just proposed one with S:I666V |
thomasppeacock
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XBB.1.5
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S:T478I got designated XBB.1.5.40 |
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XBB.1.5 seems to get outcompeted by a number of parallel XBB lineages - there's already a lot of sublineages due to early spread in high-sampling-geographies (US, Europe) so I think we can slow down here. |
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Closed indeed |
@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.
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