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FL.2 with S:N641K emerged likely in Eastern Africa and shows a lot of Spike diversity: three branches 259S / 809T / 471Q (79 seqs, 14 countries) #2180
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Continuing the discussion from the previous page, it seems like a HAT cleavage site at S:R667 may have played an important role in SARS-CoV-1, at least according to this paper. https://journals.physiology.org/doi/full/10.1152/ajplung.00509.2016 |
It appears that a HAT cleavage site promotes cell-cell fusion, something we haven't seen a great deal of since Delta. https://journals.asm.org/doi/10.1128/jvi.05300-11 |
Now i am extending a bit too much ( also Sars1 not having the FCS could have an impact) but S:I666V in BQ.1.2 was the only mutation found experimentally in cell lines to bring back fusogenictity to pre omicron era. Wondering if linked. c @thomaspeacock |
The emergence in Eastern Africa is deduced by two early (march-april) samples from airport surveillance from Kenya and Somalia cc @corneliusroemer see original issue for more info. |
Hello Fredrico,
I use the software tool "Peptide Cutter".
https://web.expasy.org/peptide_cutter/
When given the test sequence ...GS*N*VF.... (and the "Trypsin" optimized
analysis is enabled) this is the result:
[image: Peptide cutter result for "GSNVF" sequence.png]
*No cleavage *(from Trypsin or any other enzyme supported by Peptide
Cutter).
But the sequence ...S*K*V... produces:
[image: Peptide cutter result for "GSKVF" sequence.png]
*100% cleavage* (if the enzyme has access to the ...GS*K*VF... sequence).
Interestingly, TMPRSS2 (another trypsin-like protease) is membrane bound.
The spile only becomes available to this enzyme after it has become bound
to ACE2 at the cellular membrane.
Conversely, the HAT enzyme is soluble, so the spike is continuously
available to this enzyme prior to binding to ACE2.
Therefore, the spike that antibodies "see" prior to ACE2 binding can have
this site already cleaved, and therefore not be recognized by the antibody.
*IMPORTANT*
Tissues other than the human airway will not have this site cleaved by HAT,
and therefore antibodies that target this site on the spike should still
function in the rest of the body.
- thiolist
(Michael Ott)
…On Sun, Aug 13, 2023 at 5:35 AM Federico Gueli ***@***.***> wrote:
The emergence in Eastern Africa is deduced by two early (march-april)
samples from airport surveillance from Kenya and Somalia
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Thank you @th |
Tracking updates: 08-18, 2 seqs from USA
08-22, 4 seqs from USAhttps://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11928_4bf8d0.json?f_userOrOld=uploaded%20sample&label=id:node_6965878
08-30, 3 seqs from USA
|
both w 259S |
Transferred from sars-cov-2-variants/lineage-proposals#520
Defining Mutations:
FL.2
>C25521T
>T23485A(S:N641K), A29683T
Query:
T23485A, C25521T
Earliest seq: 2023-03-15 (
EPI_ISL_17363241
, England, UK)Latest seq: 2023-08-03 (
EPI_ISL_18089995
, Sweden)Sampled Countries: USA (23; California/16, Arizona/4, New York/2, Texas/1), Sweden (21), Canada (9, Ontario), UK (6, England/5, Scotland/1), France (2), Austria (1), China (1, Shanghai), Germany (1), India (1), Ireland (1), Israel (1), Italy (1), Japan (1), Spain (1)
Genomes:
EPI_ISL_17363241, EPI_ISL_17395881, EPI_ISL_17400810, EPI_ISL_17448553, EPI_ISL_17488308, EPI_ISL_17488334, EPI_ISL_17511907, EPI_ISL_17514054, EPI_ISL_17537803, EPI_ISL_17537913, EPI_ISL_17549297, EPI_ISL_17553672, EPI_ISL_17555869, EPI_ISL_17558172, EPI_ISL_17590487, EPI_ISL_17630281, EPI_ISL_17630455, EPI_ISL_17630478, EPI_ISL_17664440, EPI_ISL_17668930, EPI_ISL_17668978, EPI_ISL_17668999, EPI_ISL_17690272, EPI_ISL_17713615, EPI_ISL_17721736, EPI_ISL_17722643-17722644, EPI_ISL_17722718, EPI_ISL_17731144, EPI_ISL_17731521, EPI_ISL_17732731, EPI_ISL_17732763, EPI_ISL_17732771, EPI_ISL_17732773, EPI_ISL_17732812, EPI_ISL_17732815, EPI_ISL_17732819, EPI_ISL_17764343, EPI_ISL_17764728, EPI_ISL_17767911, EPI_ISL_17768311, EPI_ISL_17769714, EPI_ISL_17781527, EPI_ISL_17791659, EPI_ISL_17797041, EPI_ISL_17809292, EPI_ISL_17809729, EPI_ISL_17838302, EPI_ISL_17838841, EPI_ISL_17854148, EPI_ISL_17855011, EPI_ISL_17950471, EPI_ISL_17950512, EPI_ISL_17951643, EPI_ISL_17981065, EPI_ISL_18005336, EPI_ISL_18010050, EPI_ISL_18045881, EPI_ISL_18046161, EPI_ISL_18046249, EPI_ISL_18046277, EPI_ISL_18055042, EPI_ISL_18057063, EPI_ISL_18069764, EPI_ISL_18069768, EPI_ISL_18069925, EPI_ISL_18089985, EPI_ISL_18089987, EPI_ISL_18089990, EPI_ISL_18089995
UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_432ef_8c6650.json?f_userOrOld=uploaded%20sample
Trivia:
S:N641K
only sampled 170 times during the whole pandemic, about 1/3 is from this branch. It may be associated with novel cleavage site of HAT (see comment by @thiolist ), related study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9167920/S:259S, E554A
andK356N
, but there are also mutations likeS:P809T
,E471Q
from other branches, all forms some kind of long branches:The text was updated successfully, but these errors were encountered: