SIMPLOT, IQ-tree, Fylogeniapuu... REKOMBINANTTI BA.2/BA.1 kyseessä. Asia pohdittavana. Koska teksti oli mielestäni erittäin insiktiä antava ja valaiseva ,joten otan siitä kuvia talteen ja sitaattia tähän:
Kaiketi tätä varianttia ei ole levinnyt ja se onkin vain mainittu rekombinaatioitten joukossa yleisnimellä " RECOMBINANT". Asia on edelleen "open" GITHUB#514.
Description
Recombinant between: BA.1 and BA.2
Earliest sequence: 2022-02-01
Most recent sequence: 2022-02-01
Countries circulating: Uncertain (travellers arrived in Hong Kong from Germany via the Netherlands)
Breakpoint: 20055-21618
We detected a recombinant between Omicron subvariants BA.1 and BA.2. It was detected in early Feb from two epidemiologically linked cases. This recombinant has a breakpoint at around the 5' end of spike (20055-21618).
Evidence
Figure 1. Detection of a BA.1/BA.2 recombinant. A) Mapping of BA.1- and BA.2- specific SNPs with respect to the reference sequence (Genbank: MN908947.3). BA.1- and BA.2- specific SNPs found in Patients 1 and 2 samples are shown in red and blue boxes, respectively. The corresponding amino acid changes of these SNPs are also indicated. The putative breaking point is indicated by an arrow. B) Phylogeny of viral RNA sequences 5’ and 3’ to the putative breaking point. The Maximum likelihood tree was generated using IQ-TREE employing the TIM+F+I nucleotide substitution model with Wuhan-Hu-1 (GenBank: MN908947.3) as the outgroup. References sequences, together with their accession numbers in GISAID or Genbank, are shown as indicated. The red node points show strongly supported branches by SH-aLRT and ultrafast bootstrap values. Scale bar indicates estimated genetic distance.
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