GITHUB uutisia 8.6. 2024 sars-2 koronaviruksen varianttien kehityksestä

Asia #2646 tullut eilen  särmille:  Siitä muutama kopiokuva tähän: Linkki  esittää

 3prim UTR  rakenteen, mutta sitä en saa kopioitua tähän.  UTR muutokset lienevät   avaintekijää SARS-2 viruksen  tässä valtavassa  rönsyilyssä. 

KP.3.1 + ∆29728-29776 (bigger s2m deletion) [47 seq, 4 continents, June 7] #2646

Open

ryhisner opened this issue Jun 7, 2024 · 0 comments 

Earliest sequence: 2024-4-15, Australia, Victoria — EPI_ISL_19084514
Most recent sequence: 2024-5-6, Spain, Madrid — EPI_ISL_19144199
Continents circulating: Oceania (7), Asia (2), Europe (2)
Countries circulating: Australia (5), New Zealand (2), Spain (2), China (1), Singapore (1)
Number of Sequences: 11
GISAID Nucleotide Query: A1620G, G15372T, -G29734
CovSpectrum Query: Nextcladepangolineage:KP.3* & [2-of: A1620G, G15372T] & [1-of: 29729-, !29735-]
Substitutions/Deletions on top of KP.3:
ORF1a: E452G (NSP2_E282G)
Nucleotide: G15372T, A19722G, A1620G, ∆29728-29733 + ∆29760-29776

Phylogenetic Order of Mutations: G15372T, A19722G → A1620G (ORF1a:E452G), ∆29728-29733 + ∆ 29760-29776

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3_29728-29776.json?c=gt-ORF1ab_452&gmax=21555&gmin=266&label=id:node_2371524

 Evidence
BA.2 was the first global variant to feature a deletion in s2m, a 3' UTR stem-loop that is highly conserved in sarbecoviruses. All Omicron since BA.1 have had ∆29734-29759. This sublineage adds 23 nucleotides to the standard Omicron s2m deletion with ∆29728-29776. When the s2m deletion is enlarged, this is the most common pattern. s2m's function is unknown, and the reason for its deletion in BA.2/4/5 is also a mystery.