Silmäys BA.2.75 PANGO-linjaan

 GITHUB asia "773. Mitä siitä kerrotaan)

28 päivää sitten oli tällainen otsikko asiasta: Silcn  ehdottaa tälle alalinjalle  designaatiota.

BA.2 sublineage with S:K147E, W152R, F157L, I210V, G257S, D339H, G446S, N460K, R493Q (73 seq as of 2022-06-29, mainly India) #773

Proposal for a sublineage of BA.2
Earliest sequence: 2022-06-02 (India)
Countries detected: India (5 seq, from 3 states)

Defining mutations:
S:K147E, W152R, F157L, I210V, G257S, D339H (mutated from G339D), G446S, N460K, R493Q (reversion)
ORF1a:S1221L, P1640S, N4060S
ORF1b:G662S
E:T11A

Don't think much needs to be said to explain why I'm proposing this. Very recent, long branch with 9 new spike mutations, detection in multiple states that aren't all close together (Maharashtra, Karnataka, Jammu and Kashmir). I expect quite a few people have been monitoring it :)

Usher tree is a bit messy because of some poor quality sequences, particularly the one from Jammu and Kashmir which has multiple artefactual reversions. As a result this lineage is placed on a branch with a couple of Indian sequences with reversions at S:954 (also probably erroneous - apparent reversions at this site seem to crop up a lot in Indian sequences). Despite what the tree shows, the evidence is currently consistent with all 9 S mutations having appeared on the same long branch. As usual, the 2nt mutation at S:339 is mislabelled.

https://user-images.githubusercontent.com/42699509/174730395-ed6a3244-118f-47d0-907c-a3f6ab27b054.png

(11 asiantuntijatiedemiestä osallistuu tähän asiankäsitelyyn ja kommentaatioihin) .

 (Ryhisner kommentoi  27 päivää sitten) :

 Man, we must be on the same wavelength, Silcn, because I noticed one sequence of this yesterday. I wasn't quite sure what to make of it—whether it was real or not, coming from India, as I don't really have the expertise to judge such things. Excellent spot, mate.

 

( Silcn vastaa 27 päivää sitten:)

Now found in Germany: EPI_ISL_13378378, EPI_ISL_13378924
And also in Canada: EPI_ISL_13392500
EPI_ISL_13389935 is another Indian sequence, with NNNs covering the locations of all the S mutations but it shares all the non-S mutations.

 

(Agamedilab pistää väliin tiedon toisesta kytevästä supermutantista 26 päivää sitten):

 

 BA.1.1 sublineage with 12 aa substitutions including 5 spike mutations (S:S494P, S:V1128A, S:F59S, S:D420N, S:Y449N, 12 seq., Slovenia) #778

 

(Silcn kommentoi 26 päivää sitten Intiasta tulleen lisää näytteitä:)

 

 More Indian sequences: EPI_ISL_13409385, EPI_ISL_13409444, EPI_ISL_13409465

 

 (Thomaspeacock kommentoi 25 päivää sitten:)

 

Although this is still fairly limited in absolute sequence number, the divergent mutation profile, the wide geographical spread, and the rapidness that new sequences have emerged makes me think this should get designated pretty soon to faciliate its monitoring.

 

(Silcn antaa lisätietoja  sekvensseistä:)

 Most of these sequences have T5386G, and 2 of them also have A11537G though. I mean those brought up by FedeGueli.

 (Sitten havaitaankin pikainen designaatio viivytyksittä:)

InfrPopGen      self-assigned this 24 days ago

 

InfrPopGen added this to the BA.2.75 mile 24 days ago  ( Tarkistukseni tehty 18.7. 2022)

 

Tässä vaiheessa ilmeni BA 2.75 PANGO-luetteloon , ja sen monitorointi on käynnissä, kuitenkaan siitä ei vielä ole niin paljon  näyrteitä, jotta  olisi saatavilla käyrää tai muita taulukoita Cov.lineages-lähteen puolella. Taitaa vielä olla vain GITHUB-puolella  suurin  saatavilla oleva tietomäärä Nyt tulvii maailmaalta tietoa tästä  variantista, että sitä sanotaan mediassa  Centaurus-nimiseksi ja sitä  alkaa olla ueassa muussakin maassa. 

Intiassa monitoroituja nyt:

https://docs.google.com/spreadsheets/d/1zKF3PKaosF3OCcW54gWkyV7Spz8uWrCsYef9IHbj7FA/edit#gid=0

 

(Tämä tiedemiesten  nettikeskustelu jatkuu  designaation jälkeen ja viimeinen maininta on 3 päivää sitten seuraava:

 

Shay: Two cases were spotted in Israel (I'll update after it's uploaded to GISAID); they are returning from France without known contact with someone from India. They are clustering with a sample previously collected in the Netherlands.
This is evidence for BA.2.75 already transmitting in Europe, not in relation to India.