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.

Autor: Suharsono H; Biochemistry Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia., Mahardika BK; The Animal Biomedical and Molecular Biology Laboratory, Udayana University, Jl. Sesetan-Markisa 6A, Denpasar, 80223, Bali, Indonesia., Sudipa PH; Veterinary Bacteriology and Mycology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia., Sari TK; Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia., Suardana IBK; Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia., Mahardika GN; The Animal Biomedical and Molecular Biology Laboratory, Udayana University, Jl. Sesetan-Markisa 6A, Denpasar, 80223, Bali, Indonesia. gnmahardika@unud.ac.id.; Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia. gnmahardika@unud.ac.id.
Jazyk: angličtina
Zdroj: Archives of virology [Arch Virol] 2023 May 08; Vol. 168 (6), pp. 156. Date of Electronic Publication: 2023 May 08.
DOI: 10.1007/s00705-023-05787-6
Abstrakt: 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.
(© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)
Databáze: MEDLINE
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