Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin

References

• Ruzek D, Avšič Županc T, Borde J, et al. Tick-borne encephalitis in Europe and Russia: review of pathogenesis, clinical features, therapy, and vaccines. Antiviral Res. 2019;164:23–51.
   PubMed Web of Science ®Google Scholar
• Goryashchenko AS, Uvarova VI, Osolodkin DI, et al. Discovery of small molecule antivirals targeting tick-borne encephalitis virus. Annu Rep Med Chem. 2022;58:1–54. doi:10.1016/bs.armc.2022.08.007
   Google Scholar
• Postler TS, Beer M, Blitvich BJ, et al. Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae. Arch Virol. 2023;168:224.
   PubMed Web of Science ®Google Scholar
• Füzik T, Formanová P, Růžek D, et al. Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody. Nat Commun. 2018;9:436.
   PubMed Web of Science ®Google Scholar
• Pulkkinen LIA, Barrass SV, Domanska A, et al. Molecular organisation of tick-borne encephalitis virus. Viruses. 2022;14:792.
   PubMed Web of Science ®Google Scholar
• Hardy JM, Newton ND, Modhiran N, et al. A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses. Nat Commun. 2021;12:3266.
   PubMed Web of Science ®Google Scholar
• Sirohi D, Chen Z, Sun L, et al. The 3.8 Å resolution cryo-EM structure of Zika virus. Science. 2016;352:467–470.
   PubMed Web of Science ®Google Scholar
• Zhang X, Ge P, Yu X, et al. Cryo-EM structure of the mature dengue virus at 3.5-Å resolution. Nat Struct Mol Biol. 2013;20:105–110.
   PubMed Web of Science ®Google Scholar
• Li T, Zhao Q, Yang X, et al. Structural insight into the Zika virus capsid encapsulating the viral genome. Cell Res. 2018;28:497–499.
   PubMed Web of Science ®Google Scholar
• Tan TY, Fibriansah G, Kostyuchenko VA, et al. Capsid protein structure in Zika virus reveals the flavivirus assembly process. Nat Commun. 2020;11:895.
   PubMed Web of Science ®Google Scholar
• Therkelsen MD, Klose T, Vago F, et al. Flaviviruses have imperfect icosahedral symmetry. Proc Natl Acad Sci USA. 2018;115:11608–11612.
   PubMed Web of Science ®Google Scholar
• Agudelo M, Palus M, Keeffe JR, et al. Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease. J Exp Med. 2021;218:e20210236.
   PubMed Web of Science ®Google Scholar
• Yang X, Qi J, Peng R, et al. Molecular basis of a protective/neutralizing monoclonal antibody targeting envelope proteins of both tick-borne encephalitis virus and louping Ill virus. J Virol. 2019;93:e02132-18.
   PubMed Web of Science ®Google Scholar
• Chernokhaeva LL, Rogova YV, Kozlovskaya LI, et al. Experimental evaluation of the protective efficacy of tick-borne encephalitis (TBE) vaccines based on European and Far-eastern TBEV strains in mice and in vitro. Front Microbiol. 2018;9:1487.
   PubMed Web of Science ®Google Scholar
• Delrue I, Verzele D, Madder A, et al. Inactivated virus vaccines from chemistry to prophylaxis: merits, risks and challenges. Expert Rev Vaccines. 2012;11:695–719.
   PubMed Web of Science ®Google Scholar
• Pichkur EB, Vorovitch MF, Ivanova AL, et al. The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution. Emerg Microb. Infect. 2024;13:2313849.
   Google Scholar
• Vorovitch MF, Kozlovskaya LI, Romanova LIU, et al. Genetic description of a tick-borne encephalitis virus strain Sofjin with the longest history as a vaccine strain. SpringerPlus. 2015;4:761.
   PubMedGoogle Scholar
• Vorovitch MF, Samygina VR, Pichkur E, et al. Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL. Acta Cryst. 2024;D80:44–59.
   Google Scholar
• Moiseenko AV, Bagrov DV, Vorovitch MF, et al. Size distribution of inactivated tick-borne encephalitis virus particles revealed by a comprehensive physicochemical approach. Biomedicines. 2022;10:2478.
   PubMed Web of Science ®Google Scholar
• Punjani A, Rubinstein JL, Fleet DJ, et al. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017;14:290–296.
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–1612.
   PubMed Web of Science ®Google Scholar
• Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crysta. 2004;D60:2126–2132.
   Google Scholar
• Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crysta. 2018;D74:519–530.
   Google Scholar
• Afonine PV, Poon BK, Read RJ, et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crysta. 2018;D74:531–544.
   Google Scholar
• Dueva EV, Tuchynskaya KK, Kozlovskaya LI, et al. Spectrum of antiviral activity of 4-aminopyrimidine N-oxides against a broad panel of tick-borne encephalitis virus strains. Antivir Chem Chemother. 2020;28:204020662094346.
   PubMedGoogle Scholar
• Tuchynskaya KK, Fomina AD, Nikitin NA, et al. Effect of immature tick-borne encephalitis virus particles on antiviral activity of 5-aminoisoxazole-3-carboxylic acid adamantylmethyl esters. J Gen Virol. 2021;102:001658.
   Web of Science ®Google Scholar
• Goetschius DJ, Lee H, Hafenstein S. CryoEM reconstruction approaches to resolve asymmetric features. Adv Virus Res. 2019;105:73–91.
   PubMed Web of Science ®Google Scholar
• Punjani A, Zhang H, Fleet DJ. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat Methods. 2020;17:1214–1221.
   PubMed Web of Science ®Google Scholar
• Punjani A, Fleet DJ. 3D variability analysis: resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J Struct Biol. 2021;213:107702.
   PubMed Web of Science ®Google Scholar
• Zhang W, Kaufmann B, Chipman PR, et al. Membrane curvature in flaviviruses. J Struct Biol. 2013;183:86–94.
   PubMed Web of Science ®Google Scholar
• Svoboda P, Haviernik J, Bednar P, et al. A combination of two resistance mechanisms is critical for tick-borne encephalitis virus escape from a broadly neutralizing human antibody. Cell Rep. 2023;42:113149.
   PubMed Web of Science ®Google Scholar
• DiNunno NM, Goetschius DJ, Narayanan A, et al. Identification of a pocket factor that is critical to Zika virus assembly. Nat Commun. 2020;11:4953.
   PubMed Web of Science ®Google Scholar
• Newton ND, Hardy JM, Modhiran N, et al. The structure of an infectious immature flavivirus redefines viral architecture and maturation. Sci Adv. 2021;7:eabe4507.
   PubMed Web of Science ®Google Scholar
• Renner M, Dejnirattisai W, Carrique L, et al. Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins. Nat Commun. 2021;12:1238.
   PubMed Web of Science ®Google Scholar
• Metz B, Kersten GFA, Baart GJE, et al. Identification of formaldehyde-induced modifications in proteins: reactions with insulin. Bioconjugate Chem. 2006;17:815–822.
   PubMed Web of Science ®Google Scholar