SARS-CoV-2 Spike Protein XBB.1.5 Mutations Altered Four Conserved Antigenic Determinants

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dc.contributor.authorAkbulut, Ekrem
dc.contributor.authorYildirim, Meltem
dc.contributor.authorKahraman, Huseyin
dc.date.accessioned2026-04-04T13:31:05Z
dc.date.available2026-04-04T13:31:05Z
dc.date.issued2026
dc.departmentİnönü Üniversitesi
dc.description.abstractThe continuous evolution of SARS-CoV-2 affects its infectivity and ability to evade the immune system. The XBB.1.5 subvariant carries numerous mutations compared to previous Omicron variants and exhibits significant evasion of polyclonal neutralizing antibodies. In this study, the mechanistic effects of mutations in the XBB.1.5 spike protein on structural stability, antigenic markers, and antibody epitopes were analyzed using homology modeling, epitope prediction, protein stability analysis, coarse-grained dynamic simulations, and chain-specific interface mapping. Thirty-eight amino acid substitutions were identified relative to Wuhan-Hu-1, including 22 in the receptor-binding region. The prefusion trimeric fold was conserved, with localized rearrangements in the N-terminal domain, receptor-binding domain, and S1/S2 region. Linear B-cell epitope prediction yielded similar epitope counts and length distributions in wild-type and XBB.1.5, but only moderate residue-level overlap (Jaccard approximate to 0.40-0.62), indicating epitope turnover and alteration of four conserved antigenic determinants. Functional screening suggested that similar to 45% of substitutions could affect protein function. Chain-specific interface analysis of the A-B protomer interface indicated preserved inter-protomer coupling with modest repacking of the polar/directional contacts. Overall, XBB.1.5 appears to maintain ACE2 engagement while redistributing antibody targets, underscoring the need for updated vaccine formulations and therapeutic antibodies.
dc.description.sponsorshipInonu University Scientific Research Projects Unit [FCD-2023-3227]
dc.description.sponsorshipThis research was funded by Inonu University Scientific Research Projects Unit, grant number FCD-2023-3227.
dc.identifier.doi10.3390/ijms27041940
dc.identifier.issn1661-6596
dc.identifier.issn1422-0067
dc.identifier.issue4
dc.identifier.orcid0000-0002-7526-9835
dc.identifier.pmid41752076
dc.identifier.scopus2-s2.0-105031506676
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.3390/ijms27041940
dc.identifier.urihttps://hdl.handle.net/11616/108574
dc.identifier.volume27
dc.identifier.wosWOS:001701103800001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherMdpi
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_WOS_20250329
dc.subjectSARS-CoV-2
dc.subjectCOVID-19
dc.subjectspike
dc.subjectXBB.1.5
dc.subjectepitope
dc.subjectimmune escape
dc.titleSARS-CoV-2 Spike Protein XBB.1.5 Mutations Altered Four Conserved Antigenic Determinants
dc.typeArticle

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