Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages.
Arch Virol
; 168(6): 156, 2023 May 08.
Article
in English
| MEDLINE | ID: covidwho-2319620
ABSTRACT
The currently dominant Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swiftly diverged into clades. To predict the probable impact of these clades, the consensus insertions/deletions (indels) and amino acid substitutions of the whole genome of clades were compared with the original SARS-CoV-2 strain. The evolutionary history of representatives of clades and lineages was inferred using the maximum-likelihood method and tested using the bootstrap method. The indels and polymorphic amino acids were found to be either clade-specific or shared among clades. The 21K clade has unique indels and substitutions, which probably represent reverted indels/substitutions. Three variations that appear to be associated with SARS-CoV-2 attenuation in the Omicron clades included a deletion in the nucleocapsid gene, a deletion in the 3'untranslated region, and a truncation in open reading frame 8. Phylogenetic analysis showed that the Omicron clades and lineages form three separate clusters.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
COVID-19
/
Amino Acids
Type of study:
Observational study
/
Prognostic study
/
Randomized controlled trials
Topics:
Variants
Limits:
Humans
Language:
English
Journal:
Arch Virol
Year:
2023
Document Type:
Article
Affiliation country:
S00705-023-05787-6
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