Deltavarianttien "driving mutations" -linkki ja XT-omikronvariantin tutkinnasta: (S: G75V)

 Seuraan tiedemiesten kirjeenvaihtoa , joka johti sitten   tämän uuden  rekombinantin  (XT)  linjan määrittelyyn.

XT

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Recombinant lineage of BA.1 and BA.2, South Africa lineage, from pango-designation issue #478

 

 

Tiedemies, jonka  nimimerkki on cornelius, antaa tässä yhteydessä  linkin  AY.s  driving-mutation- kohdista vastauksena erääseen  kysymykseen.  Otan talteen linkin.  Tämä linkki on siitä  keskustelusta, jota tiedemiehet kävivät  XT- rekombinantin suhteen, sillä siinä on  osanen, aminohappomuutos,   joka on joissain   deltavartiantin sekvensseissa ja lambdassa nimittäin   S:G75V, siis spike-proteiinissa glysiini  (G75)   on vaihtunut valiiniksi (V) .  Vertailemalla  erilaisia AY-deltavirusvariantteja joissa  on esiintynyt tuo aminohappomuutos sellaisiin, joissa sitä ei esiintynyt, havaittiin, että virus saa kasvuetua tuosta mutaatiosta. 

SITAATTI  koskien  mutaatiota S: G75V. :

( look at this one:
https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
here there are mutations driving to each of the AY.s lineages

If i understood well what you were asking for )

 

 XT-omikron variantista on seuraava alkukuvaus:

 SITAATTI

South African BA.2/BA.1* Recombinant with S:75V and breakpoint at ORF3a/M Protein (11 Seqs as of 2022-04-10) #478

Recombinant between: BA.2 & BA.1*
Earliest sequence: 2021/12/13 (South Africa)
Most recent sequence: 2022/2/21 (South Africa)
Countries circulating: South Africa (Gauteng, Limpopo and North-West)
Likely breakpoint: between 26062 and 26528 (from ORF3a to M protein).
Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1* side): 

 Cov-spectrum query: ORF1a:G1307S, ORF1a:S135R, ORF1a:T842I, S:G75V, M:D3G

(Chrisruis kysyy)  can you have a look at this one? It's from South Africa, which means there are probably many more of this recombinant than 9.

It's interesting for a couple of reasons:

• Very early recombinant, earliest sample from early December
• Sustained circulation into March
• BA.1 breakpoint after BA.2 spike
• It has S:G75V which was part of Lambda
• Recombinant from South Africa
• Common throughout South Africa
• Seems to be growing, now at almost 1%?

(Corneliusroeamer vastaa)  I noticed S:75V also increased in proportion in Delta. It seems to have provided a 1%/day growth advantage, which is not insignificant.

(Deltan avulla on katsottu  S:G75V-mutaation  merkitystä   viruksen kasvuun. Se on edullinen viruksen kasvulle).

 https://cov-spectrum.org/explore/United%20Kingdom/AllSamples/Y2021/variants?pangoLineage=B.1.617.2*&aaMutations1=S%3A75V&pangoLineage1=B.1.617.2*&analysisMode=CompareToBaseline&

(Corneliusroemar  noteeraa):  I agree that the circulation across multiple regions of South Africa over several months supports designation in this case. We've added this as XT,