Grove, J. & Marsh, M. The cell biology of receptor-mediated virus entry. J. Cell Biol. 195, 1071â1082 (2011).
Simmonds, P. et al. ICTV virus taxonomy profile: Flaviviridae. J. Gen. Virol. 98, 2â3 (2017).
Rey, F. A. & Lok, S.-M. Common features of enveloped viruses and implications for immunogen design for next-generation vaccines. Cell 172, 1319â1334 (2018).
Hubálek, Z. & Halouzka, J. West Nile feverâa reemerging mosquito-borne viral disease in Europe. Emerg. Infect. Dis. 5, 643â650 (1999).
Wang, Z.-D. et al. A new segmented virus associated with human febrile illness in China. N. Engl. J. Med. 380, 2116â2125 (2019).
Kartashov, M. Y. et al. Novel Flavi-like virus in ixodid ticks and patients in Russia. Ticks Tick Borne Dis. 14, 102101 (2023).
Postler, T. S. et al. Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae. Arch. Virol 168, 224 (2023).
Qin, X.-C. et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc. Natl Acad. Sci. USA 111, 6744â6749 (2014).
Ladner, J. T. et al. A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe 20, 357â367 (2016).
Paraskevopoulou, S. et al. Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol. 7, veab030 (2021).
Kobayashi, K. et al. Gentian Kobu-sho-associated virus: a tentative, novel double-stranded RNA virus that is relevant to gentian Kobu-sho syndrome. J. Gen. Plant Pathol. 79, 56â63 (2013).
Debat, H. & Bejerman, N. Two novel flavi-like viruses shed light on the plant-infecting koshoviruses. Arch. Virol 168, 184 (2023).
Petrone, M. E. et al. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proc. Natl Acad. Sci. USA 121, e2403805121 (2024).
Ferron, F., Sama, B., Decroly, E. & Canard, B. The enzymes for genome size increase and maintenance of large (+)RNA viruses. Trends Biochem. Sci 46, 866â877 (2021).
Shi, M. et al. Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. J. Virol. 90, 659â669 (2016).
Garry, C. E. & Garry, R. F. Proteomics computational analyses suggest that the envelope glycoproteins of segmented Jingmen Flavi-like viruses are class II viral fusion proteins (b-penetrenes) with mucin-like domains. Viruses 12, 260 (2020).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583â589 (2021).
Lin, Z. et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379, 1123â1130 (2023).
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679â682 (2022).
Lee, S. et al. Petascale Homology Search for Structure Prediction. Preprint at bioRxiv https://doi.org/10.1101/2023.07.10.548308 (2023).
Blitvich, B. J. & Firth, A. E. A review of Flaviviruses that have no known arthropod vector. Viruses 9, 154 (2017).
Kielian, M. & Rey, F. A. Virus membrane-fusion proteins: more than one way to make a hairpin. Nat. Rev. Microbiol. 4, 67â76 (2006).
Rey, F. A., Heinz, F. X., Mandl, C., Kunz, C. & Harrison, S. C. The envelope glycoprotein from tick-borne encephalitis virus at 2âà resolution. Nature 375, 291â298 (1995).
Dessau, M. & Modis, Y. Crystal structure of glycoprotein C from Rift Valley fever virus. Proc. Natl Acad. Sci. USA 110, 1696â1701 (2013).
Fédry, J. et al. The ancient gamete fusogen HAP2 is a eukaryotic class II fusion protein. Cell 168, 904â915.e10 (2017).
Guardado-Calvo, P. & Rey, F. A. The viral class II membrane fusion machinery: divergent evolution from an ancestral heterodimer. Viruses 13, 2368 (2021).
Li, L. et al. The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science 319, 1830â1834 (2008).
El Omari, K., Iourin, O., Harlos, K., Grimes, J. M. & Stuart, D. I. Structure of a Pestivirus envelope glycoprotein E2 clarifies its role in cell entry. Cell Rep. 3, 30â35 (2013).
Li, Y., Wang, J., Kanai, R. & Modis, Y. Crystal structure of glycoprotein E2 from bovine viral diarrhea virus. Proc. Natl Acad. Sci. USA 110, 6805â6810 (2013).
Kong, L. et al. Hepatitis C virus E2 envelope glycoprotein core structure. Science 342, 1090â1094 (2013).
Khan, A. G. et al. Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2. Nature 509, 381â384 (2014).
Aitkenhead, H. et al. Structural comparison of typical and atypical E2 Pestivirus glycoproteins. Structure 32, 273â281 (2024).
Torrents de la Peña, A. et al. Structure of the hepatitis C virus E1E2 glycoprotein complex. Science 378, 263â269 (2022).
Metcalf, M. C. et al. Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies. Nat. Commun. 14, 3980 (2023).
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243â246 (2024).
Oliver, M. R. et al. Structures of the hepaci-, pegi-, and pestiviruses envelope proteins suggest a novel membrane fusion mechanism. PLoS Biol. 21, e3002174 (2023).
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366â368 (2021).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236â1240 (2014).
Urayama, S.-I., Takaki, Y. & Nunoura, T. FLDS: a comprehensive dsRNA sequencing method for intracellular RNA virus surveillance. Microbes Environ. 31, 33â40 (2016).
Hou, X. et al. Artificial intelligence redefines RNA virus discovery. Preprint at bioRxiv https://doi.org/10.1101/2023.04.18.537342 (2023).
Chen, Y.-M. et al. RNA viromes from terrestrial sites across China expand environmental viral diversity. Nat. Microbiol. 7, 1312â1323 (2022).
Arhab, Y., Bulakhov, A. G., Pestova, T. V. & Hellen, C. U. T. Dissemination of internal ribosomal entry sites (IRES) between viruses by horizontal gene transfer. Viruses 12, 612 (2020).
Modis, Y., Ogata, S., Clements, D. & Harrison, S. C. Structure of the dengue virus envelope protein after membrane fusion. Nature 427, 313â319 (2004).
MacIntosh, G. C. in Ribonucleases (ed. Nicholson, A. W.) 89â114 (Springer, 2011).
Puente-Lelievre, C. et al. Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone. Preprint at bioRxiv https://doi.org/10.1101/2023.12.12.571181 (2024).
Vaney, M.-C. et al. Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery. Nat. Commun. 13, 3718 (2022).
Bamford, C. G. G., de Souza, W. M., Parry, R. & Gifford, R. J. Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol. 8, veac085 (2022).
Mushegian, A. Methyltransferases of Riboviria. Biomolecules 12, 1247 (2022).
Li, Z., Jaroszewski, L., Iyer, M., Sedova, M. & Godzik, A. FATCAT 2.0: towards a better understanding of the structural diversity of proteins. Nucleic Acids Res. 48, 60â64 (2020).
Mifsud, J. C. O. et al. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evol. 9, veac124 (2022).
Kong, Y. et al. Metatranscriptomics reveals the diversity of the tick virome in northwest China. Microbiol. Spectr. 10, e0111522 (2022).
Costa, V. A. et al. Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evol. 9, vead011 (2023).
Perveen, N. et al. Virome diversity of Hyalomma dromedarii ticks collected from camels in the United Arab Emirates. Vet World 16, 439â448 (2023).
Guo, G. et al. Virome analysis provides an insight into the viral community of Chinese mitten crab Eriocheir sinensis. Microbiol. Spectr. 11, e0143923 (2023).
Dunay, E. et al. Viruses in sanctuary chimpanzees across Africa. Am. J. Primatol. 85, e23452 (2023).
Elbadry, M. A. et al. Diversity and genetic reassortment of keystone virus in mosquito populations in Florida. Am. J. Trop. Med. Hyg. 108, 1256â1263 (2023).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150â3152 (2012).
Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647â1649 (2012).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772â780 (2013).
Edgar, R. C. et al. Petabase-scale sequence alignment catalyses viral discovery. Nature 602, 142â147 (2022).
Mifsud, J. C. O. BatchArtemisSRAMiner: v1.0.0. Zenodo https://doi.org/10.5281/zenodo.8417951 (2023).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114â2120 (2014).
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674â1676 (2015).
Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023â1025 (2022).
Edgar, R. C. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nat. Commun. 13, 6968 (2022).
Mifsud, J. C. O. et al. Underlying data for âMapping glycoprotein structure reveals Flaviviridae evolutionary historyâ. Zenodo https://doi.org/10.5281/zenodo.11092288 (2024).
Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, 293â296 (2021).
Renner, M. et al. Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins. Nat. Commun. 12, 1238 (2021).
Egloff, M.-P., Benarroch, D., Selisko, B., Romette, J.-L., & Canard, B. An RNA cap (nucleoside-2â²-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 21, 2757â2768 (2002).
Noble, C. G. et al. A conserved pocket in the dengue virus polymerase identified through fragment-based screening. J. Biol. Chem. 291, 8541â8548 (2016).
Jia, H., Zhong, Y., Peng, C. & Gong, P. Crystal structures of flavivirus NS5 guanylyltransferase reveal a GMP-arginine adduct. J. Virol. 96, e0041822 (2022).
Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281â292 (2020).
Krey, T. et al. Crystal structure of the Pestivirus envelope glycoprotein E(rns) and mechanistic analysis of its ribonuclease activity. Structure 20, 862â873 (2012).
Dong, X. et al. A novel virus of Flaviviridae associated with sexual precocity in Macrobrachium rosenbergii. mSystems 6, e0000321 (2021).
Sievers, F. et al. Fast, scalable generation of highâquality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Capella-Gutiérrez, S., Silla-MartÃnez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972â1973 (2009).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530â1534 (2020).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587â589 (2017).
Le, T. K. & Vinh, L. S. FLAVI: an amino acid substitution model for flaviviruses. J. Mol. Evol. 88, 445â452 (2020).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307â321 (2010).
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518â522 (2017).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526â528 (2018).
Revell, L. J. phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12, e16505 (2024).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28â36 (2017).
Hackl, T., Ankenbrand, M. & van Adrichem, B. gggenomes: A grammar of graphics for comparative genomics. Github https://github.com/thackl/gggenomes (2024).
Winter, D. J. Rentrez: an R package for the NCBI eUtils API. R J. 9, 520â526 (2017).
Chamberlain, S. A. & Szöcs, E. taxize: taxonomic search and retrieval in R. F1000Res. 2, 191 (2013).
Rambaut, A. & Drummond, A. J. FigTree: Tree figure drawing tool, version 1.4.0. http://tree.bio.ed.ac.uk/software/figtree/ (2012).
Jombart, T., Kendall, M., AlmagroâGarcia, J. & Colijn, C. treespace: Statistical exploration of landscapes of phylogenetic trees. Mol. Ecol. Resour. 17, 1385â1392 (2017).
Kendall, M. & Colijn, C. Mapping phylogenetic trees to reveal distinct patterns of evolution. Mol. Biol. Evol. 33, 2735â2743 (2016).
Legendre, P. & Legendre, L. Numerical Ecology (Elsevier, 2012).
Saberi, A., Gulyaeva, A. A., Brubacher, J. L., Newmark, P. A. & Gorbalenya, A. E. A planarian nidovirus expands the limits of RNA genome size. PLoS Pathog. 14, e1007314 (2018).
Rolland, C., La Scola, B. & Levasseur, A. How Tupanvirus degrades the ribosomal RNA of its amoebal host? The ribonuclease T2 track. Front. Microbiol. 11, 1691 (2020).
Barrio-Hernandez, I. et al. Clustering predicted structures at the scale of the known protein universe. Nature 622, 637â645 (2023).
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026â1028 (2017).
Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, 200â204 (2018).
Gabler, F. et al. Protein sequence analysis using the MPI bioinformatics toolkit. Curr. Protoc. Bioinformatics 72, e108 (2020).
Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237â2243 (2018).
Mirdita, M. et al. Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Res. 45, 170â176 (2017).
Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).
Buchfink, B., Ashkenazy, H., Reuter, K., Kennedy, J. A. & Drost, H.-G. Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust. Preprint at bioRxiv https://doi.org/10.1101/2023.01.24.525373 (2023).
Deorowicz, S., Debudaj-Grabysz, A. & GudyÅ, A. FAMSA: fast and accurate multiple sequence alignment of huge protein families. Sci. Rep. 6, 33964 (2016).
Chernomor, O., von Haeseler, A. & Minh, B. Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65, 997â1008 (2016).
Moi, D. et al. Structural phylogenetics unravels the evolutionary diversification of communication systems in Gram-positive bacteria and their viruses. Preprint at bioRxiv https://doi.org/10.1101/2023.09.19.558401 (2023).
