Tapparel, C., Siegrist, F., Petty, T. J. & Kaiser, L. Picornavirus and enterovirus diversity with associated human diseases. Infect. Genet. Evol. 14, 282–293 (2013).
Rhoades, R. E., Tabor-Godwin, J. M., Tsueng, G. & Feuer, R. Enterovirus infections of the central nervous system. Virology 411, 288–305 (2011).
Hughes, L. E. & Ryan, M. D. in Encyclopedia of Virology (Third Edition) (eds Mahy, B. W. J. & Van Regenmortel, M. H. V.) (Academic Press, 2008).
Bian, L. et al. Coxsackievirus A6: a new emerging pathogen causing hand, foot and mouth disease outbreaks worldwide. Expert Rev. Anti Infect. Ther. 13, 1061–1071 (2015).
Ang, L. W. et al. Seroepidemiology of coxsackievirus A6, coxsackievirus A16, and enterovirus 71 infections among children and adolescents in Singapore, 2008-2010. PLoS ONE 10, e0127999 (2015).
Österback, R. et al. Coxsackievirus A6 and hand, foot, and mouth disease, Finland. Emerg. Infect. Dis. 15, 1485–1488 (2009).
Fujimoto, T. et al. Hand, foot, and mouth disease caused by coxsackievirus A6, Japan, 2011. Emerg. Infect. Dis. 18, 337–339 (2012).
Fujimoto, T. [Hand-foot-and-mouth disease, aseptic meningitis, and encephalitis caused by enterovirus]. Brain Nerve 70, 121–131 (2018).
Li, Y. et al. Emerging enteroviruses causing hand, foot and mouth disease, China, 2010-2016. Emerg. Infect. Dis. 24, 1902–1906 (2018).
Gao, L. et al. Spectrum of enterovirus serotypes causing uncomplicated hand, foot, and mouth disease and enteroviral diagnostic yield of different clinical samples. Clin. Infect. Dis. 67, 1729–1735 (2018).
He, S. et al. An emerging and expanding clade accounts for the persistent outbreak of coxsackievirus A6-associated hand, foot, and mouth disease in China since 2013. Virology 518, 328–334 (2018).
Anh, N. T. et al. Emerging coxsackievirus A6 causing hand, foot and mouth disease, Vietnam. Emerg. Infect. Dis. 24, 654–662 (2018).
Puenpa, J. et al. Hand, foot and mouth disease caused by coxsackievirus A6, Thailand, 2012. Emerg. Infect. Dis. 19, 641–643 (2013).
Wu, Y. et al. The largest outbreak of hand; foot and mouth disease in Singapore in 2008: the role of enterovirus 71 and coxsackievirus A strains. Int. J. Infect. Dis. 14, e1076–e1081 (2010).
Feder, H. M., Bennett, N. & Modlin, J. F. Atypical hand, foot, and mouth disease: a vesiculobullous eruption caused by Coxsackie virus A6. Lancet Infect. Dis. 14, 83–A86 (2014).
Lott, J. P. et al. Atypical hand-foot-and-mouth disease associated with coxsackievirus A6 infection. J. Am. Acad. Dermatol. 69, 736–741 (2013).
Montes, M. et al. Hand, foot, and mouth disease outbreak and coxsackievirus A6, northern Spain, 2011. Emerg. Infect. Dis. 19, 676–678 (2013).
Sinclair, C. et al. Atypical hand, foot, and mouth disease associated with coxsackievirus A6 infection, Edinburgh, United Kingdom, January to February 2014. Euro Surveill. 19, 20745 (2014).
Drago, F., Ciccarese, G., Broccolo, F., Rebora, A. & Parodi, A. Atypical hand, foot, and mouth disease in adults. J. Am. Acad. Dermatol. 77, e51–e56 (2017).
Yang, X. et al. Clinical features and phylogenetic analysis of severe hand-foot-and-mouth disease caused by Coxsackievirus A6. Infect. Genet. Evol. 77, 104054 (2020).
Blomqvist, S. et al. Co-circulation of coxsackieviruses A6 and A10 in hand, foot and mouth disease outbreak in Finland. J. Clin. Virol. 48, 49–54 (2010).
Broccolo, F. et al. Severe atypical hand-foot-and-mouth disease in adults due to coxsackievirus A6: Clinical presentation and phylogenesis of CV-A6 strains. J. Clin. Virol. 110, 1–6 (2019).
Jiang, P., Liu, Y., Ma, H.-C., Paul, A. V. & Wimmer, E. Picornavirus morphogenesis. Microbiol. Mol. Biol. Rev. 78, 418–437 (2014).
Hogle, J. M. Poliovirus cell entry: common structural themes in viral cell entry pathways. Annu. Rev. Microbiol. 56, 677–702 (2002).
Harutyunyan, S. et al. Viral uncoating is directional: exit of the genomic RNA in a common cold virus starts with the poly-(A) tail at the 3′-end. PLoS Pathog. 9, e1003270 (2013).
Buchta, D. et al. Enterovirus particles expel capsid pentamers to enable genome release. Nat. Commun. 10, 1138 (2019).
Korant, B. D., Lonberg-Holm, K., Noble, J. & Stasny, J. T. Naturally occurring and artificially produced components of three rhinoviruses. Virology 48, 71–86 (1972).
Fricks, C. E. & Hogle, J. M. Cell-induced conformational change in poliovirus: externalization of the amino terminus of VP1 is responsible for liposome binding. J. Virol. 64, 1934–1945 (1990).
Plevka, P., Perera, R., Cardosa, J., Kuhn, R. J. & Rossmann, M. G. Crystal structure of human enterovirus 71. Science 336, 1274 (2012).
Wang, X. et al. A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat. Struct. Mol. Biol. 19, 424 (2012).
Ren, J. et al. Structures of coxsackievirus A16 capsids with native antigenicity: implications for particle expansion, receptor binding, and immunogenicity. J. Virol. 89, 10500–10511 (2015).
Xu, L. et al. Atomic structures of coxsackievirus A6 and its complex with a neutralizing antibody. Nat. Commun. 8, 505 (2017).
Chen, J. et al. A 3.0-angstrom resolution cryo-electron microscopy structure and antigenic sites of coxsackievirus A6-like particles. J. Virol. 92, e01257–01217 (2018).
Lee, H. et al. The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs. Sci. Adv. 2, e1501929 (2016).
Belnap, D. M. et al. Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus. J. Virol. 74, 1342–1354 (2000).
Oberste, M. S., Penaranda, S., Maher, K. & Pallansch, M. A. Complete genome sequences of all members of the species Human enterovirus A. J. Gen. Virol. 85, 1597–1607 (2004).
Chapman, M. S. & Liljas, L. in Advances in Protein Chemistry (Academic Press, 2003).
Krupovic, M. & Koonin, E. V. Multiple origins of viral capsid proteins from cellular ancestors. Proc. Natl Acad. Sci. USA 114, E2401–E2410 (2017).
Wien, M. W., Curry, S., Filman, D. J. & Hogle, J. M. Structural studies of poliovirus mutants that overcome receptor defects. Nat. Struct. Biol. 4, 666–674 (1997).
Smyth, M., Pettitt, T., Symonds, A. & Martin, J. Identification of the pocket factors in a picornavirus. Arch. Virol. 148, 1225–1233 (2003).
Lewis, J. K., Bothner, B., Smith Thomas, J. & Siuzdak, G. Antiviral agent blocks breathing of the common cold virus. Proc. Natl Acad. Sci. USA 95, 6774–6778 (1998).
Oliveira, M. A. et al. The structure of human rhinovirus 16. Structure 1, 51–68 (1993).
Chow, M. et al. Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature 327, 482–486 (1987).
Moscufo, N., Simons, J. & Chow, M. Myristoylation is important at multiple stages in poliovirus assembly. J. Virol. 65, 2372–2380 (1991).
Scouras, A. D. & Daggett, V. The dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Sci. 20, 341–352 (2011).
Zhu, R. et al. Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10. Sci. Adv. 4, eaat7459 (2018).
Chen, J. et al. Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses. Cell Discov. 5, 4 (2019).
Foo, D. G. W. et al. Identification of neutralizing linear epitopes from the VP1 capsid protein of Enterovirus 71 using synthetic peptides. Virus Res. 125, 61–68 (2007).
Gao, F. et al. Enterovirus 71 viral capsid protein linear epitopes: identification and characterization. Virol. J. 9, 26 (2012).
Borley, D. W. et al. Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus. PLoS ONE 8, e61122 (2013).
Wang, L. et al. Bioinformatics-based prediction of conformational epitopes for Enterovirus A71 and Coxsackievirus A16. Sci. Rep. 11, 5701 (2021).
Hadfield, A. T. et al. The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle. Structure 5, 427–441 (1997).
Chandler-Bostock, R. et al. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog. 16, e1009146 (2020).
Wilson, K. A., Holland, D. J. & Wetmore, S. D. Topology of RNA-protein nucleobase-amino acid pi-pi interactions and comparison to analogous DNA-protein pi-pi contacts. RNA 22, 696–708 (2016).
Lentz, K. N. et al. Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of the three poliovirus serotypes. Structure 5, 961–978 (1997).
Jeong, E., Kim, H., Lee, S.-W. & Han, K. Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Mol. Cells 16, 161–167 (2003).
Schmidt, N. J., Ho, H. H. & Lennette, E. H. Propagation and isolation of group A coxsackieviruses in RD cells. J. Clin. Microbiol. 2, 183–185 (1975).
Rueckert, R. R. in Comparative Virology (eds Maramorosch, K. & Kurstak, E.) (Academic Press, 1971).
Flint, S. J., Enquist, L. W., Racaniello, V. R. & Skalka, A. M. Principles of Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses 2nd edn (ASM Press, 2004).
Harland, J. & Brown, S. M. HSV growth, preparation, and assay. Methods Mol. Med. 10, 1–8 (1998).
Watson, D. H., Russell, W. C. & Wildy, P. Electron microscopic particle counts on herpes virus using the phosphotungstate negative staining technique. Virology 19, 250–260 (1963).
Carpenter, J. E., Henderson, E. P. & Grose, C. Enumeration of an extremely high particle-to-PFU ratio for Varicella-zoster virus. J. Virol. 83, 6917–6921 (2009).
Klasse, P. J. Molecular determinants of the ratio of inert to infectious virus particles. Prog. Mol. Biol. Transl. Sci. 129, 285–326 (2015).
Liu, Y. et al. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science 347, 71–74 (2015).
Smith, T. J. et al. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233, 1286–1293 (1986).
Curry, S., Chow, M. & Hogle, J. M. The poliovirus 135S particle is infectious. J. Virol. 70, 7125–7131 (1996).
Zhao, Y. et al. Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10. Nat. Commun. 11, 38 (2020).
Xu, L. et al. Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating. Cell Host Microbe 29, 448–462.e5 (2021).
Hrebik, D. et al. ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. Proc. Natl Acad. Sci. USA 118, e2024251118 (2021).
R Core Team. R: a language and environment for statistical computing. (Vienna, Austria, 2018).
Kärber, G. Beitrag zur kollektiven Behandlung pharmakologischer Reihenversuche. Naunyn-Schmiedebergs Arch. f.ür. experimentelle Pathologie und Pharmakologie 162, 480–483 (1931).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Vilas, J. L. et al. MonoRes: automatic and accurate estimation of local resolution for electron microscopy maps. Structure 26, 337–344.e334 (2018).
Ramírez-Aportela, E. et al. Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics 36, 765–772 (2020).
de la Rosa-Trevín, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013).
de la Rosa-Trevín, J. M. et al. Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 195, 93–99 (2016).
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D. 67, 235–242 (2011).
Pettersen, E. F. et al. UCSF chimera – a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D. 66, 486–501 (2010).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. D. 75, 861–877 (2019).
Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. Sect. D. 67, 355–367 (2011).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. Sect. D. 66, 12–21 (2010).
Wiederstein, M., Gruber, M., Frank, K., Melo, F. & Sippl, M. J. Structure-based characterization of multiprotein complexes. Structure 22, 1063–1070 (2014).
Wiederstein, M. & Sippl, M. J. TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. Nucleic Acids Res. 48, W31–W35 (2020).
Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A 32, 922–923 (1976).
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evolution 30, 772–780 (2013).
Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999).
Crameri, F. Scientific colour maps. Zenodo (2018).
Brewer, C. A. Colorbrewer colour maps. https://colorbrewer2.org/ (2020).
Pettersen, E. F. et al. UCSF chimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D. Struct. Biol. 74, 519–530 (2018).