| Author | Scarpa, Fabio | |
| Author | Azzena, Ilenia | |
| Author | Ciccozzi, Alessandra | |
| Author | Giovanetti, Marta | |
| Author | Locci, Chiara | |
| Author | Casu, Marco | |
| Author | Fiori, Pier Luigi | |
| Author | Borsetti, Alessandra | |
| Author | Cella, Eleonora | |
| Author | Quaranta, Miriana | |
| Author | Pascarella, Stefano | |
| Author | Sanna, Daria | |
| Author | Ciccozzi, Massimo | |
| Access date | 2023-11-21T12:24:10Z | |
| Available date | 2023-11-21T12:24:10Z | |
| Document date | 2023 | |
| Citation | SCARPA, Fabio et al. Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant. Int. j. mol. sci. v. 24, n. 17, 2023. Doi https://dx.doi.org/10.3390/ijms241713573. | en_US |
| ISSN | 1422-0067 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/61382 | |
| Language | eng | en_US |
| Publisher | MDPI | en_US |
| Rights | open access | en_US |
| Title | Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant | en_US |
| Type | Article | en_US |
| Abstract | The XBB.1.16 SARS-CoV-2 variant, also known as Arcturus, is a recent descendant lineage of the recombinant XBB (nicknamed Gryphon). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the immune response compared to other circulating lineages. In this context, we conducted a comprehensive genome-based survey to gain a detailed understanding of the evolution and potential dangers of the XBB.1.16 variant, which became dominant in late June. Genetic data indicates that the XBB.1.16 variant exhibits an evolutionary background with limited diversification, unlike dangerous lineages known for rapid changes. The evolutionary rate of XBB.1.16, which amounts to 3.95 × 10-4 subs/site/year, is slightly slower than that of its direct progenitors, XBB and XBB.1.5, which have been circulating for several months. A Bayesian Skyline Plot reconstruction suggests that the peak of genetic variability was reached in early May 2023, and currently, it is in a plateau phase with a viral population size similar to the levels observed in early March. Structural analyses indicate that, overall, the XBB.1.16 variant does not possess structural characteristics markedly different from those of the parent lineages, and the theoretical affinity for ACE2 does not seem to change among the compared variants. In conclusion, the genetic and structural analyses of SARS-CoV-2 XBB.1.16 do not provide evidence of its exceptional danger or high expansion capability. Detected differences with previous lineages are probably due to genetic drift, which allows the virus constant adaptability to the host, but they are not necessarily connected to a greater danger. Nevertheless, continuous genome-based monitoring is essential for a better understanding of its descendants and other lineages. | en_US |
| Affilliation | Department of Biomedical Sciences. University of Sassari. Sassari, Italy | en_US |
| Affilliation | Department of Biomedical Sciences. University of Sassari. Sassari, Italy/Department of Veterinary Medicine. University of Sassari. Sassari, Italy. | en_US |
| Affilliation | Unit of Medical Statistics and Molecular Epidemiology. Università Campus Bio-Medico di Roma. Rome, Italy. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Rene Rachou. Belo Horizonte, MG, Brazil/Sciences and Technologies for Sustainable Development and One Health. Università Campus Bio-Medico di Roma. Rome, Italy. | en_US |
| Affilliation | Department of Biomedical Sciences. University of Sassari. Sassari, Italy/Department of Veterinary Medicine. University of Sassari. Sassari, Italy. | en_US |
| Affilliation | Department of Veterinary Medicine. University of Sassari. Sassari, Italy. | en_US |
| Affilliation | Department of Biomedical Sciences. University of Sassari. Sassari, Italy/Azienza Ospedaliera Universitaria. Sassari. Sassari, Italy. | en_US |
| Affilliation | National HIV/AIDS Research Center. National Institute of Health.Rome, Italy. | en_US |
| Affilliation | Burnett School of Biomedical Sciences. University of Central Florida. Orlando, FL, USA. | en_US |
| Affilliation | Department of Biochemical Sciences "A. Rossi Fanelli".Sapienza Università di Roma. Rome, Italy. | en_US |
| Affilliation | Department of Biochemical Sciences "A. Rossi Fanelli".Sapienza Università di Roma. Rome, Italy. | en_US |
| Affilliation | Department of Biomedical Sciences. University of Sassari. Sassari, Italy. | en_US |
| Affilliation | Unit of Medical Statistics and Molecular Epidemiology. Università Campus Bio-Medico di Roma. Rome, Italy. | en_US |
| Subject | XBB.1.16 | en_US |
| Subject | epidemiology | en_US |
| Subject | genetics | en_US |
| Subject | genome-based survey | en_US |
| Subject | molecular evolution | en_US |
| Subject | phylodynamics | en_US |
