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Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant
Fabio Scarpa1, Ilenia Azzena1,2, Alessandra Ciccozzi3
1Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.
International Journal of Molecular Sciences
|September 9, 2023
Summary
The SARS-CoV-2 XBB.1.16 (Arcturus) variant shows limited diversification and a slower evolutionary rate. Genetic and structural analyses suggest it is not exceptionally dangerous or highly expansive compared to other lineages.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- The SARS-CoV-2 XBB.1.16 variant (Arcturus) emerged as a descendant of XBB.
- XBB.1.16 possesses unique spike mutations potentially impacting immune evasion.
- Understanding its evolutionary trajectory and potential risks is crucial.
Purpose of the Study:
- To conduct a comprehensive genome-based survey of the SARS-CoV-2 XBB.1.16 variant.
- To analyze the evolution, genetic diversification, and structural characteristics of XBB.1.16.
- To assess the potential dangers and expansion capabilities of XBB.1.16.
Main Methods:
- Genome-based evolutionary analysis.
- Bayesian Skyline Plot reconstruction for genetic variability.
- Structural analysis of spike proteins and ACE2 affinity.
Main Results:
- XBB.1.16 exhibits limited genetic diversification and a slightly slower evolutionary rate (3.95 × 10^-4 subs/site/year) than its progenitors.
- Peak genetic variability occurred in early May 2023, followed by a plateau phase.
- Structural analyses reveal no significant differences from parent lineages, with unchanged theoretical ACE2 affinity.
Conclusions:
- Genetic and structural data do not indicate exceptional danger or high expansion capability for XBB.1.16.
- Observed genetic differences are likely due to genetic drift, facilitating viral adaptability rather than increased threat.
- Continuous genome-based monitoring of SARS-CoV-2 variants remains essential.
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