The large numbers of mutations seen in the BA.1, BA.2 and BA.3 lineage sequences may have accrued at an accelerated pace under the influence of positive selection. To test for evidence of this, we applied a selection analysis pipeline to all of the available sequences designated as BA.1, BA.2 and BA.3 in GISAID as of 20 December 2021. We ran selection screens individually on BA.1, BA.2 and BA.3 sequences, according to a previously described procedure34. We downsampled alignments of individual protein-encoding regions to obtain a median of 110 genetically unique BA.1 sequences, 3 BA.2 sequences, 2.5 BA.3 sequences and around 100 other unique sequences for each gene/open reading frame (ORF) from a representative collection of other SARS-CoV-2 lineages (used as background sequences to contextualize evolution within the Omicron subclade).
A) Amino-acid mutations on the spike gene of the BA.2 B) Amino-acid mutations on the spike gene of the BA.3 C) Raw maximum likelihood phylogeny of 13,462 SARS-CoV-2 genomes, including 148 BA.2 and 19 BA.3. The newly identified SARS-CoV-2 Omicron variant is shown in colour versus grey for all other lineages. D) A zoomed-in view of the Omicron clade showing the evolutionary relationship between BA.1, BA.2 and BA.3.
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