XP omikronrekombinantti, jossa akseptori on BA.1.1 ja donori BA.2.

Tämän variantin XP  s-piikin ( spike) mutaatiokirjoon  BA.1.1  varianttityyppinen ja mutatoituneita aminohappoja S-proteiinissa  on  ainakin 31 tyypillisine   BA.1.1 linjan mukaan.  Siinä merkitään   linjan deletiokohdat  substituutiomalleina Y145D, L212I. Orf1a ja Orf 1b ovat linjatyypilliset. Samoin  Orf3a. M-proteiinissa on  tavallisten  linjaan kuuluvien mutaatioiden lisäksi L120I.  Sitten esiintyy Orf9b mutaatio   P10S ja N on BA.2 tyyppiä eli  siinä on lisänä S413R, jota nähdään BA.2 ja BA.3 - linjoissa.  Nukleotiditasossa on jokin pieni   muutos , kaksi nukleotidimuutosa, joita ilmenee myös  gammassa (P.1) ja C37.1- linjassa ( C37 on lambda). Skotlannissa tätä varianttia on ilmennyt 57 sekvenssiä 27.3. 2022 mennessä.  Linjan selvitelyjen jälkeen lisättiin tämä  rekombinantti nimellä XP uutena linjana tietueisiin ja sen asian käsitelly on  PANGO.linjoissa # 481 numerolla.

Potential BA.1.1/BA.2 Recombinant with Likely Breakpoint at ORF6/N Protein (57 Seqs in UK-Scotland as of 2022-03-27) #481

Description

Recombinant between: BA.1.1 & BA.2
Earliest sequence: 2022/2/26 (UK-Scotland)
Most recent sequence: 2022/3/14 (UK-Scotland)
Countries circulating: UK
Likely breakpoint: between 27385 and 29509 (from ORF6 to N).

 Sitaatti tiedemiesten keskustelusta

" Also, big thanks to     ( name)  for conforming the S2M deletion as an evidence that this cluster is more likely a potential recombinant than BA.1.1 convergently gaining an additional A29510C (N:S413R) mutation."

" That is an interesting little branch. Scotland/QEUH-3880993/2022 has A28877T and G28878C which apparently got that little branch (with A29510C and private mutations A24190C and C26880A) placed on a very large branch with those two mutations in BA.1.1. But then all the rest of the sequences do not have A28877T and G28878C, so UShER placed those on a little branch with two back-mutations/reversions. Here is a view of the proposed recombinants with Scotland/QEUH-3880993/2022 all by itself and all other sequences after reversions on 28877 and 28878:"

"Could that imply a different breakpoint for Scotland/QEUH-3880993/2022 (after 28878) vs. the rest of the sequences (before 28877)?"

"Also, very nice to have that deletion as a confirmation that this wasn't just a chance mutation at 29510"

"There might be 2 recombination events where the breakpoint for most of above sequences are before 28877."

"I've also noticed this just now. That's why (nimi)  thinks some BA.1 in Greece/Russia are recombinants with Gamma :D

 24 päivää sitten:

"(Nimi)   changed the title Potential BA.1.1/BA.2 Recombinant with Likely Breakpoint at ORF6/N Protein (48 Seqs in UK-Scotland as of 2022-03-22) Potential BA.1.1/BA.2 Recombinant with Likely Breakpoint at ORF6/N Protein (57 Seqs in UK-Scotland as of 2022-03-27)"

(Nimi)    19 päivää sitten:

Added new lineage XP from #481 with 54 new sequence designations