{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T19:24:30Z","timestamp":1764962670641,"version":"3.46.0"},"reference-count":129,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01AI151807"],"award-info":[{"award-number":["U01AI151807"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32 AI007526-24"],"award-info":[{"award-number":["T32 AI007526-24"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2022\/03645-1"],"award-info":[{"award-number":["2022\/03645-1"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2023\/14670-0"],"award-info":[{"award-number":["2023\/14670-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"crossref","award":["4057586\/2022-0"],"award-info":[{"award-number":["4057586\/2022-0"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>\n                    Bussuquara virus (BSQV), an orthoflavivirus discovered in Brazil in 1956, has been detected throughout the Americas in diverse mosquito and vertebrate species, including humans. Critical gaps in BSQV knowledge include its capacity for urban transmission and clinical pathogenesis outcomes, with insufficient historical experimentation to draw genomic or phenotypic comparisons to related orthoflavivirus species. The objective of this study was to conduct morphologic, genomic, phylogenetic, and\n                    <jats:italic>in vitro<\/jats:italic>\n                    viral fitness characterization of BSQV using the four available historical strains. We used next generation sequencing and rapid amplification of cDNA ends to construct consensus genomes, followed by phylogenetic analysis and genome annotation to evaluate orthoflavivirus evolutionary relationships and genome characteristics. Infected mosquito (C6\/36) and non-human primate (Vero CCL81) cells were imaged with transmission electron microscopy. Viral replication kinetics were quantified across seventeen cell lines of mosquito, mammal, rodent, avian, non-human primate, and human origin. BSQV morphologic (virion diameter, cytopathic effect) and genomic (size, organization, architecture, sequence motifs) results were in line with canonical orthoflavivirus characteristics. One of the four strains (CoAr 41922) shared greater sequence homology to the Naranjal orthoflavivirus than other BSQV strains and was thus excluded from infection phenotype experiments. All three confirmed BSQV strains replicated robustly in most mosquito and all vertebrate cell lines, causing either minimal (mosquito) or moderate to extreme (vertebrate) cytopathic effects. We conclude that BSQV is a generalist orthoflavivirus with a broad range of susceptible vertebrate and mosquito vectors. Our data build a foundation for pathogenesis and vector competence studies to determine the potential of BSQV to emerge into epizootic and urban transmission cycles.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0013774","type":"journal-article","created":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T18:54:01Z","timestamp":1764960841000},"page":"e0013774","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Hiding in plain sight: Genomic and phenotypic characterization of mosquito-borne Bussuquara virus"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-4160-0325","authenticated-orcid":true,"given":"Madeline R.","family":"Steck","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cec\u00edlia A.","family":"Banho","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vsevolod L.","family":"Popov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiping","family":"Hao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathryn A.","family":"Hanley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mauricio L.","family":"Nogueira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0708-3289","authenticated-orcid":true,"given":"Nikos","family":"Vasilakis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,12,5]]},"reference":[{"issue":"2","key":"pntd.0013774.ref001","doi-asserted-by":"crossref","first-page":"275","DOI":"10.3181\/00379727-101-24909","article-title":"Bussuquara, a new arthropod-borne virus","volume":"101","author":"G Gomes","year":"1959","journal-title":"Proc Soc Exp Biol Med"},{"issue":"2","key":"pntd.0013774.ref002","doi-asserted-by":"crossref","first-page":"183","DOI":"10.3390\/v17020183","article-title":"Bussuquara Virus: A Neglected Orthoflavivirus with Broad Distribution Across Central and South America and the Caribbean","volume":"17","author":"MR Steck","year":"2025","journal-title":"Viruses"},{"issue":"4","key":"pntd.0013774.ref003","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/0035-9203(71)90179-9","article-title":"The first isolation of bussuquara virus from man","volume":"65","author":"S Srihongse","year":"1971","journal-title":"Trans R Soc Trop Med Hyg"},{"issue":"4","key":"pntd.0013774.ref004","first-page":"170","article-title":"Prevalence of Flavivirus antibodies in young voluntary recruits to military service in the province of Formosa, Argentina","volume":"30","author":"G Glowacki","year":"1998","journal-title":"Rev Argent Microbiol"},{"key":"pntd.0013774.ref005","first-page":"35","article-title":"Immunofluorescence in pathogenesis of group A, B, and C arbovirus in the hamster","volume":"15","author":"D de Paola","year":"1968","journal-title":"An Microbiol (Rio J)"},{"issue":"6283","key":"pntd.0013774.ref006","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1126\/science.aaf5036","article-title":"Zika virus in the Americas: Early epidemiological and genetic findings","volume":"352","author":"NR Faria","year":"2016","journal-title":"Science"},{"key":"pntd.0013774.ref007","doi-asserted-by":"crossref","first-page":"107192","DOI":"10.1016\/j.ijid.2024.107192","article-title":"Dengue outbreaks in Brazil and Latin America: the new and continuing challenges","volume":"147","year":"2024","journal-title":"Int J Infect Dis"},{"key":"pntd.0013774.ref008","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/B978-0-323-82501-6.00010-4","article-title":"Chapter 8 - Other Neglected Mosquito-Borne Flaviviruses: Ilh\u00e9us, Bussuquara, Rocio, Kokobera, Stratford, and Wesselsbron Viruses.","volume-title":"Zika and Other Neglected and Emerging Flaviviruses [Internet]","author":"LA. Beltz","year":"2021"},{"issue":"1","key":"pntd.0013774.ref009","doi-asserted-by":"crossref","first-page":"92","DOI":"10.3390\/v15010092","article-title":"Clinical Landscape and Rate of Exposure to Ilheus Virus: Insights from Systematic Review and Meta-Analysis","volume":"15","author":"VG da Costa","year":"2022","journal-title":"Viruses"},{"issue":"3","key":"pntd.0013774.ref010","doi-asserted-by":"crossref","first-page":"372","DOI":"10.3390\/vaccines10030372","article-title":"Yellow Fever: Origin, Epidemiology, Preventive Strategies and Future Prospects","volume":"10","author":"E Gianchecchi","year":"2022","journal-title":"Vaccines"},{"issue":"11","key":"pntd.0013774.ref011","doi-asserted-by":"crossref","first-page":"2293","DOI":"10.3390\/v13112293","article-title":"Rocio Virus: An Updated View on an Elusive Flavivirus","volume":"13","author":"MV Saivish","year":"2021","journal-title":"Viruses"},{"issue":"3","key":"pntd.0013774.ref012","doi-asserted-by":"crossref","first-page":"650","DOI":"10.3390\/microorganisms13030650","article-title":"(Re)Emerging Arboviruses of Public Health Significance in the Brazilian Amazon","volume":"13","author":"KC Dye-Braumuller","year":"2025","journal-title":"Microorganisms"},{"issue":"6","key":"pntd.0013774.ref013","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41564-020-0714-0","article-title":"The continued threat of emerging flaviviruses","volume":"5","author":"TC Pierson","year":"2020","journal-title":"Nat Microbiol"},{"issue":"12","key":"pntd.0013774.ref014","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1002\/jmv.25717","article-title":"A lesson learnt from the emergence of Zika virus: What flaviviruses can trigger Guillain-Barr\u00e9 syndrome?","volume":"92","author":"C Leung","year":"2020","journal-title":"J Med Virol"},{"key":"pntd.0013774.ref015","author":"MS Cunha","year":"2020"},{"issue":"6","key":"pntd.0013774.ref016","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1051\/vetres\/2010039","article-title":"West Nile virus and its emergence in the United States of America","volume":"41","author":"KO Murray","year":"2010","journal-title":"Vet Res"},{"key":"pntd.0013774.ref017"},{"issue":"1","key":"pntd.0013774.ref018","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/jme\/tjac155","article-title":"Establishment of a Culex tarsalis (Diptera: Culicidae) cell line and its permissiveness to arbovirus infection","volume":"60","author":"EE Schirtzinger","year":"2022","journal-title":"J Med Entomol"},{"issue":"6","key":"pntd.0013774.ref019","article-title":"Purification of RNA using TRIzol (TRI reagent)","volume":"2010","author":"DC Rio","year":"2010","journal-title":"Cold Spring Harb Protoc"},{"issue":"15","key":"pntd.0013774.ref020","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"13","key":"pntd.0013774.ref021","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"W Li","year":"2006","journal-title":"Bioinformatics"},{"key":"pntd.0013774.ref022"},{"key":"pntd.0013774.ref023"},{"issue":"5","key":"pntd.0013774.ref024","doi-asserted-by":"crossref","first-page":"593","DOI":"10.2217\/fvl.10.39","article-title":"Structural and functional parameters of the flaviviral protease: a promising antiviral drug target","volume":"5","author":"SA Shiryaev","year":"2010","journal-title":"Future Virol"},{"key":"pntd.0013774.ref025","article-title":"Running with scissors: evolutionary conflicts between viral proteases and the host immune system","volume":"12","author":"BV Tsu","year":"2021","journal-title":"Front Immunol"},{"issue":"6","key":"pntd.0013774.ref026","doi-asserted-by":"crossref","first-page":"956","DOI":"10.3390\/v13060956","article-title":"Molecular Insights into the Flavivirus Replication Complex","volume":"13","author":"K van den Elsen","year":"2021","journal-title":"Viruses"},{"issue":"11","key":"pntd.0013774.ref027","article-title":"Compartmentalized replication organelle of flavivirus at the ER and the factors involved","volume":"78","author":"Y Ci","year":"2021","journal-title":"Cell Mol Life Sci"},{"issue":"1","key":"pntd.0013774.ref028","doi-asserted-by":"crossref","first-page":"44","DOI":"10.3390\/v14010044","article-title":"Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review","volume":"14","author":"A Wahaab","year":"2021","journal-title":"Viruses"},{"issue":"3","key":"pntd.0013774.ref029","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3390\/pathogens8030148","article-title":"Role of Endoplasmic Reticulum-Associated Proteins in Flavivirus Replication and Assembly Complexes","volume":"8","author":"HA Rothan","year":"2019","journal-title":"Pathogens"},{"issue":"1","key":"pntd.0013774.ref030","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s44298-024-00031-7","article-title":"The endoplasmic reticulum (ER): a crucial cellular hub in flavivirus infection and potential target site for antiviral interventions","volume":"2","author":"M Verhaegen","year":"2024","journal-title":"Npj Viruses"},{"issue":"14","key":"pntd.0013774.ref031","doi-asserted-by":"crossref","first-page":"6365","DOI":"10.1128\/JVI.00447-16","article-title":"Membrane anchors of the structural flavivirus proteins and their role in virus assembly","volume":"90","author":"J Blazevic","year":"2016","journal-title":"J Virol"},{"issue":"12","key":"pntd.0013774.ref032","doi-asserted-by":"crossref","first-page":"5735","DOI":"10.1128\/JVI.00340-16","article-title":"Transmembrane Domains of NS2B Contribute to both Viral RNA Replication and Particle Formation in Japanese Encephalitis Virus","volume":"90","author":"XD Li","year":"2016","journal-title":"J Virol"},{"issue":"12","key":"pntd.0013774.ref033","doi-asserted-by":"crossref","first-page":"8873","DOI":"10.1074\/jbc.M609919200","article-title":"The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner","volume":"282","author":"S Miller","year":"2007","journal-title":"J Biol Chem"},{"issue":"22","key":"pntd.0013774.ref034","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01174-18","article-title":"Role of Capsid Anchor in the Morphogenesis of Zika Virus","volume":"92","author":"J Rana","year":"2018","journal-title":"J Virol"},{"issue":"4","key":"pntd.0013774.ref035","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1002\/rmv.1835","article-title":"Flaviviral NS4b, chameleon and jack-in-the-box roles in viral replication and pathogenesis, and a molecular target for antiviral intervention","volume":"25","author":"J Zmurko","year":"2015","journal-title":"Rev Med Virol"},{"issue":"2","key":"pntd.0013774.ref036","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1128\/JVI.02882-14","article-title":"Two distinct sets of NS2A molecules are responsible for dengue virus RNA synthesis and virion assembly","volume":"89","author":"X Xie","year":"2014","journal-title":"J Virol"},{"issue":"8","key":"pntd.0013774.ref037","doi-asserted-by":"crossref","first-page":"4609","DOI":"10.1128\/JVI.02424-12","article-title":"Membrane topology and function of dengue virus NS2A protein","volume":"87","author":"X Xie","year":"2013","journal-title":"J Virol"},{"issue":"1","key":"pntd.0013774.ref038","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.virol.2011.11.022","article-title":"Mutational analysis of the West Nile virus NS4B protein","volume":"426","author":"JA Wicker","year":"2012","journal-title":"Virology"},{"issue":"1","key":"pntd.0013774.ref039","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/0042-6822(87)90443-0","article-title":"Analysis of disulfides present in the membrane proteins of the West Nile flavivirus","volume":"156","author":"T Nowak","year":"1987","journal-title":"Virology"},{"issue":"9","key":"pntd.0013774.ref040","doi-asserted-by":"crossref","first-page":"2251","DOI":"10.1099\/0022-1317-82-9-2251","article-title":"Determination of the intramolecular disulfide bond arrangement and biochemical identification of the glycosylation sites of the nonstructural protein NS1 of Murray Valley encephalitis virus","volume":"82","author":"BJ Blitvich","year":"2001","journal-title":"J Gen Virol"},{"issue":"13","key":"pntd.0013774.ref041","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"M Zuker","year":"2003","journal-title":"Nucl Acids Res"},{"issue":"5","key":"pntd.0013774.ref042","article-title":"Different degrees of 5\u2019-to-3\u2019 DAR interactions modulate Zika virus genome cyclization and host-specific replication","volume":"94","author":"XD Li","year":"2020","journal-title":"J Virol"},{"issue":"11","key":"pntd.0013774.ref043","doi-asserted-by":"crossref","first-page":"6631","DOI":"10.1128\/JVI.79.11.6631-6643.2005","article-title":"Long-range RNA-RNA interactions circularize the dengue virus genome","volume":"79","author":"DE Alvarez","year":"2005","journal-title":"J Virol"},{"issue":"1","key":"pntd.0013774.ref044","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0022-2836(87)90455-4","article-title":"Conserved elements in the 3\u2032 untranslated region of flavivirus RNAs and potential cyclization sequences","volume":"198","author":"CS Hahn","year":"1987","journal-title":"J Mol Biol"},{"issue":"1","key":"pntd.0013774.ref045","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2008.01.016","article-title":"West Nile virus genome cyclization and RNA replication require two pairs of long-distance RNA interactions","volume":"373","author":"B Zhang","year":"2008","journal-title":"Virology"},{"issue":"9","key":"pntd.0013774.ref046","doi-asserted-by":"crossref","first-page":"4588","DOI":"10.1093\/nar\/gkad223","article-title":"Investigating RNA-RNA interactions through computational and biophysical analysis","volume":"51","author":"T Mrozowich","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"pntd.0013774.ref047","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.virusres.2008.07.016","article-title":"Genome cyclization as strategy for flavivirus RNA replication","volume":"139","author":"SM Villordo","year":"2009","journal-title":"Virus Res"},{"issue":"14","key":"pntd.0013774.ref048","doi-asserted-by":"crossref","first-page":"6719","DOI":"10.1128\/JVI.75.14.6719-6728.2001","article-title":"Essential role of cyclization sequences in flavivirus RNA replication","volume":"75","author":"AA Khromykh","year":"2001","journal-title":"J Virol"},{"issue":"19","key":"pntd.0013774.ref049","doi-asserted-by":"crossref","first-page":"10623","DOI":"10.1128\/JVI.77.19.10623-10629.2003","article-title":"Significance in replication of the terminal nucleotides of the flavivirus genome","volume":"77","author":"AA Khromykh","year":"2003","journal-title":"J Virol"},{"issue":"4","key":"pntd.0013774.ref050","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1128\/JVI.02037-10","article-title":"The 5\u2019 and 3\u2019 downstream AUG region elements are required for mosquito-borne flavivirus RNA replication","volume":"85","author":"P Friebe","year":"2011","journal-title":"J Virol"},{"key":"pntd.0013774.ref051","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/bs.aivir.2016.10.001","article-title":"Insect-Specific Viruses: A Historical Overview and Recent Developments","volume":"98","author":"CM Roundy","year":"2017","journal-title":"Adv Virus Res"},{"issue":"4","key":"pntd.0013774.ref052","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.3390\/v7041927","article-title":"Insect-specific flaviviruses: a systematic review of their discovery, host range, mode of transmission, superinfection exclusion potential and genomic organization","volume":"7","author":"BJ Blitvich","year":"2015","journal-title":"Viruses"},{"issue":"6","key":"pntd.0013774.ref053","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.4269\/ajtmh.2010.10-0280","article-title":"Isolation and characterization of sylvatic mosquito-borne viruses in Trinidad: enzootic transmission and a new potential vector of mucambo virus","volume":"83","author":"AJ Auguste","year":"2010","journal-title":"Am J Trop Med Hyg"},{"issue":"2","key":"pntd.0013774.ref054","doi-asserted-by":"crossref","first-page":"410","DOI":"10.4269\/ajtmh.17-0350","article-title":"Characterization of Three New Insect-Specific Flaviviruses: Their Relationship to the Mosquito-Borne Flavivirus Pathogens","volume":"98","author":"H Guzman","year":"2018","journal-title":"Am J Trop Med Hyg"},{"issue":"4","key":"pntd.0013774.ref055","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1590\/0037-8682-0485-2016","article-title":"Cacipacore virus as an emergent mosquito-borne Flavivirus","volume":"50","author":"MLG de Figueiredo","year":"2017","journal-title":"Rev Soc Bras Med Trop"},{"issue":"5","key":"pntd.0013774.ref056","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.4269\/ajtmh.15-0117","article-title":"Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama","volume":"93","author":"J-P Carrera","year":"2015","journal-title":"Am J Trop Med Hyg"},{"issue":"4","key":"pntd.0013774.ref057","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"5","key":"pntd.0013774.ref058","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"6","key":"pntd.0013774.ref059","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"issue":"2","key":"pntd.0013774.ref060","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"DT Hoang","year":"2018","journal-title":"Mol Biol Evol"},{"issue":"3","key":"pntd.0013774.ref061","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"S Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"pntd.0013774.ref062"},{"issue":"6","key":"pntd.0013774.ref063","doi-asserted-by":"crossref","first-page":"137","DOI":"10.3390\/v9060137","article-title":"The 5\u2019 and 3\u2019 Untranslated Regions of the Flaviviral Genome","volume":"9","author":"WC Ng","year":"2017","journal-title":"Viruses"},{"issue":"9","key":"pntd.0013774.ref064","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.3390\/v3091739","article-title":"Functional RNA elements in the dengue virus genome","volume":"3","author":"LG Gebhard","year":"2011","journal-title":"Viruses"},{"issue":"1","key":"pntd.0013774.ref065","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1007\/s12560-021-09502-z","article-title":"The RNA Secondary Structure Analysis Reveals Potential for Emergence of Pathogenic Flaviviruses","volume":"14","author":"B Mishra","year":"2022","journal-title":"Food Environ Virol"},{"key":"pntd.0013774.ref066","doi-asserted-by":"crossref","first-page":"546","DOI":"10.3389\/fmicb.2017.00546","article-title":"Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes","volume":"8","author":"A Fern\u00e1ndez-Sanl\u00e9s","year":"2017","journal-title":"Front Microbiol"},{"issue":"7","key":"pntd.0013774.ref067","doi-asserted-by":"crossref","first-page":"3738","DOI":"10.3390\/ijms22073738","article-title":"Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence","volume":"22","author":"S Ramos-Lorente","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"3","key":"pntd.0013774.ref068","doi-asserted-by":"crossref","first-page":"642","DOI":"10.3390\/cells10030642","article-title":"The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization","volume":"10","author":"L De Falco","year":"2021","journal-title":"Cells"},{"key":"pntd.0013774.ref069","author":"M Zeng","year":"2020"},{"issue":"1","key":"pntd.0013774.ref070","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004604","article-title":"Dengue virus RNA structure specialization facilitates host adaptation","volume":"11","author":"SM Villordo","year":"2015","journal-title":"PLoS Pathog"},{"issue":"11","key":"pntd.0013774.ref071","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1080\/15476286.2015.1094599","article-title":"New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation","volume":"12","author":"JS Kieft","year":"2015","journal-title":"RNA Biol"},{"issue":"1","key":"pntd.0013774.ref072","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1038\/s41467-022-28977-3","article-title":"Structural analysis of 3\u2019UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution","volume":"13","author":"A Slonchak","year":"2022","journal-title":"Nat Commun"},{"key":"pntd.0013774.ref073","first-page":"203","volume-title":"Origin and Evolution of 3\u2032Utr of Flaviviruses: Long Direct Repeats as A Basis for the Formation of Secondary Structures and Their Significance for Virus Transmission. In: Advances in Virus Research [Internet]","author":"TS Gritsun","year":"2006"},{"issue":"11","key":"pntd.0013774.ref074","doi-asserted-by":"crossref","first-page":"3297","DOI":"10.1099\/vir.0.82235-0","article-title":"Direct repeats in the 3\u2019 untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission","volume":"87","author":"TS Gritsun","year":"2006","journal-title":"J Gen Virol"},{"issue":"2","key":"pntd.0013774.ref075","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.virol.2006.09.033","article-title":"Direct repeats in the flavivirus 3\u2032 untranslated region; a strategy for survival in the environment?","volume":"358","year":"2007","journal-title":"Virology"},{"issue":"6","key":"pntd.0013774.ref076","article-title":"Short Direct Repeats in the 3\u2019 Untranslated Region Are Involved in Subgenomic Flaviviral RNA Production","volume":"94","author":"Q-Y Zhang","year":"2020","journal-title":"J Virol"},{"issue":"2","key":"pntd.0013774.ref077","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3390\/v16020242","article-title":"The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses","volume":"16","author":"X Zhang","year":"2024","journal-title":"Viruses"},{"issue":"16","key":"pntd.0013774.ref078","doi-asserted-by":"crossref","first-page":"9365","DOI":"10.1128\/JVI.00567-13","article-title":"Differential RNA sequence requirement for dengue virus replication in mosquito and mammalian cells","volume":"87","author":"SM Villordo","year":"2013","journal-title":"J Virol"},{"key":"pntd.0013774.ref079","doi-asserted-by":"crossref","first-page":"595","DOI":"10.3389\/fgene.2018.00595","article-title":"The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis","volume":"9","author":"C Mazeaud","year":"2018","journal-title":"Front Genet"},{"issue":"6","key":"pntd.0013774.ref080","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1099\/vir.0.82811-0","article-title":"Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3\u2019 stem-loop structure is not required for replication","volume":"88","author":"PAGC Silva","year":"2007","journal-title":"J Gen Virol"},{"issue":"2","key":"pntd.0013774.ref081","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.virol.2004.11.008","article-title":"The majority of the nucleotides in the top loop of the genomic 3\u2019 terminal stem loop structure are cis-acting in a West Nile virus infectious clone","volume":"331","author":"S Elghonemy","year":"2005","journal-title":"Virology"},{"issue":"2","key":"pntd.0013774.ref082","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.virol.2004.07.022","article-title":"The flavivirus-conserved penta-nucleotide in the 3\u2032 stem-loop of the West Nile virus genome requires a specific sequence and structure for RNA synthesis, but not for viral translation","volume":"331","author":"M Tilgner","year":"2005","journal-title":"Virology"},{"issue":"1","key":"pntd.0013774.ref083","doi-asserted-by":"crossref","first-page":"195","DOI":"10.3390\/v15010195","article-title":"Morphologic and Genetic Characterization of Ilheus Virus, a Potential Emergent Flavivirus in the Americas","volume":"15","author":"JA Plante","year":"2023","journal-title":"Viruses"},{"issue":"2","key":"pntd.0013774.ref084","doi-asserted-by":"crossref","first-page":"120","DOI":"10.3390\/pathogens13020120","article-title":"The Dynamic Landscape of Capsid Proteins and Viral RNA Interactions in Flavivirus Genome Packaging and Virus Assembly","volume":"13","author":"A Jablunovsky","year":"2024","journal-title":"Pathogens"},{"issue":"1","key":"pntd.0013774.ref085","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrmicro1067","article-title":"A structural perspective of the flavivirus life cycle","volume":"3","author":"S Mukhopadhyay","year":"2005","journal-title":"Nat Rev Microbiol"},{"issue":"18","key":"pntd.0013774.ref086","doi-asserted-by":"crossref","first-page":"11813","DOI":"10.1128\/JVI.79.18.11813-11823.2005","article-title":"Resuscitating mutations in a furin cleavage-deficient mutant of the flavivirus tick-borne encephalitis virus","volume":"79","author":"S Elshuber","year":"2005","journal-title":"J Virol"},{"issue":"11","key":"pntd.0013774.ref087","doi-asserted-by":"crossref","first-page":"338","DOI":"10.3390\/v9110338","article-title":"Structures and Functions of the Envelope Glycoprotein in Flavivirus Infections","volume":"9","author":"X Zhang","year":"2017","journal-title":"Viruses"},{"issue":"1","key":"pntd.0013774.ref088","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/s12985-021-01611-2","article-title":"The key amino acids of E protein involved in early flavivirus infection: viral entry","volume":"18","author":"T Hu","year":"2021","journal-title":"Virol J"},{"issue":"5","key":"pntd.0013774.ref089","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1128\/JVI.78.5.2648-2652.2004","article-title":"Contribution of disulfide bridging to epitope expression of the dengue type 2 virus envelope glycoprotein","volume":"78","author":"JT Roehrig","year":"2004","journal-title":"J Virol"},{"issue":"11","key":"pntd.0013774.ref090","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00104-20","article-title":"Flavivirus envelope protein glycosylation: impacts on viral infection and pathogenesis","volume":"94","author":"DL Carbaugh","year":"2020","journal-title":"J Virol"},{"issue":"10","key":"pntd.0013774.ref091","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011681","article-title":"N-linked glycosylation of flavivirus E protein contributes to viral particle formation","volume":"19","author":"K Ishida","year":"2023","journal-title":"PLoS Pathog"},{"key":"pntd.0013774.ref092","doi-asserted-by":"crossref","first-page":"1205002","DOI":"10.3389\/fimmu.2023.1205002","article-title":"Secretory pathways and multiple functions of nonstructural protein 1 in flavivirus infection","volume":"14","author":"S Zhang","year":"2023","journal-title":"Front Immunol"},{"key":"pntd.0013774.ref093","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/s12985-016-0590-7","article-title":"Flavivirus NS1: a multifaceted enigmatic viral protein","volume":"13","author":"M Rastogi","year":"2016","journal-title":"Virol J"},{"issue":"6173","key":"pntd.0013774.ref094","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1126\/science.1247749","article-title":"Flavivirus NS1 crystal structures reveal a surface for membrane association and regions of interaction with the immune system","volume":"343","author":"DL Akey","year":"2014","journal-title":"Science"},{"issue":"1","key":"pntd.0013774.ref095","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1021\/acsinfecdis.3c00566","article-title":"Roles of NS1 Protein in Flavivirus Pathogenesis","volume":"10","author":"DR Perera","year":"2024","journal-title":"ACS Infect Dis"},{"issue":"1","key":"pntd.0013774.ref096","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s12929-024-01048-z","article-title":"The glycosylation deficiency of flavivirus NS1 attenuates virus replication through interfering with the formation of viral replication compartments","volume":"31","author":"S Huang","year":"2024","journal-title":"J Biomed Sci"},{"issue":"5","key":"pntd.0013774.ref097","doi-asserted-by":"crossref","first-page":"959","DOI":"10.3390\/vaccines11050959","article-title":"NS1 Protein N-Linked Glycosylation Site Affects the Virulence and Pathogenesis of Dengue Virus","volume":"11","author":"E Fang","year":"2023","journal-title":"Vaccines (Basel)"},{"issue":"7","key":"pntd.0013774.ref098","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.3390\/v13071393","article-title":"Potential phosphorylation of viral nonstructural protein 1 in dengue virus infection","volume":"13","author":"T Dechtawewat","year":"2021","journal-title":"Viruses"},{"issue":"1","key":"pntd.0013774.ref099","doi-asserted-by":"crossref","first-page":"9578","DOI":"10.1038\/s41467-024-54010-w","article-title":"AMFR-mediated Flavivirus NS2A ubiquitination subverts ER-phagy to augment viral pathogenicity","volume":"15","author":"L Zhang","year":"2024","journal-title":"Nat Commun"},{"issue":"3","key":"pntd.0013774.ref100","article-title":"Zika-virus-encoded NS2A disrupts mammalian cortical neurogenesis by degrading adherens junction proteins","volume":"21","author":"KJ Yoon","year":"2017","journal-title":"Cell Stem Cell"},{"issue":"12","key":"pntd.0013774.ref101","article-title":"Mutagenesis of Dengue Virus Protein NS2A Revealed a Novel Domain Responsible for Virus-Induced Cytopathic Effect and Interactions between NS2A and NS2B Transmembrane Segments","volume":"91","author":"R-H Wu","year":"2017","journal-title":"J Virol"},{"issue":"5","key":"pntd.0013774.ref102","doi-asserted-by":"crossref","first-page":"2396","DOI":"10.1128\/JVI.80.5.2396-2404.2006","article-title":"A single amino acid substitution in the West Nile virus nonstructural protein NS2A disables its ability to inhibit alpha\/beta interferon induction and attenuates virus virulence in mice","volume":"80","author":"WJ Liu","year":"2006","journal-title":"J Virol"},{"issue":"5","key":"pntd.0013774.ref103","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02375-19","article-title":"Zika Virus NS2A-Mediated Virion Assembly","volume":"10","author":"X Zhang","year":"2019","journal-title":"mBio"},{"issue":"5","key":"pntd.0013774.ref104","article-title":"Dengue NS2A Protein Orchestrates Virus Assembly","volume":"26","author":"X Xie","year":"2019","journal-title":"Cell Host Microbe"},{"key":"pntd.0013774.ref105","doi-asserted-by":"crossref","first-page":"17037","DOI":"10.1038\/nmicrobiol.2017.37","article-title":"Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection","volume":"2","author":"S Aguirre","year":"2017","journal-title":"Nat Microbiol"},{"issue":"32","key":"pntd.0013774.ref106","doi-asserted-by":"crossref","first-page":"19100","DOI":"10.1074\/jbc.270.32.19100","article-title":"Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5 *","volume":"270","author":"M Kapoor","year":"1995","journal-title":"J Biol Chem"},{"issue":"24","key":"pntd.0013774.ref107","doi-asserted-by":"crossref","first-page":"12895","DOI":"10.1128\/JVI.00942-09","article-title":"Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication","volume":"83","author":"R Assenberg","year":"2009","journal-title":"J Virol"},{"issue":"10","key":"pntd.0013774.ref108","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.3390\/v13102077","article-title":"Roles of Non-Structural Protein 4A in Flavivirus Infection","volume":"13","author":"P Klaitong","year":"2021","journal-title":"Viruses"},{"issue":"5","key":"pntd.0013774.ref109","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007736","article-title":"A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle","volume":"15","author":"A P\u0142aszczyca","year":"2019","journal-title":"PLoS Pathog"},{"issue":"25","key":"pntd.0013774.ref110","doi-asserted-by":"crossref","first-page":"22147","DOI":"10.1074\/jbc.M110.192500","article-title":"Flavivirus NS4A-induced autophagy protects cells against death and enhances virus replication","volume":"286","author":"JE McLean","year":"2011","journal-title":"J Biol Chem"},{"issue":"6","key":"pntd.0013774.ref111","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.3390\/v13061060","article-title":"Membrane-associated flavivirus replication complex\u2014its organization and regulation","volume":"13","author":"E Morita","year":"2021","journal-title":"Viruses"},{"key":"pntd.0013774.ref112","article-title":"The flavivirus protein NS4B recruits the cis-Golgi protein ACBD3 to modify ER-Golgi trafficking for virion release [Internet]","author":"WL Yau","year":"2024","journal-title":"bioRxiv"},{"issue":"8","key":"pntd.0013774.ref113","doi-asserted-by":"crossref","first-page":"865","DOI":"10.3390\/vaccines12080865","article-title":"The Flavivirus Non-Structural Protein 5 (NS5): Structure, Functions, and Targeting for Development of Vaccines and Therapeutics","volume":"12","author":"JZH Goh","year":"2024","journal-title":"Vaccines (Basel)"},{"issue":"2","key":"pntd.0013774.ref114","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.virol.2008.07.013","article-title":"Phosphorylation of Yellow Fever Virus NS5 Alters Methyltransferase Activity","volume":"380","author":"D Bhattacharya","year":"2008","journal-title":"Virology"},{"issue":"10","key":"pntd.0013774.ref115","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0000856","article-title":"C6\/36 Aedes albopictus cells have a dysfunctional antiviral RNA interference response","volume":"4","author":"DE Brackney","year":"2010","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0013774.ref116","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002470","article-title":"Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma","volume":"8","author":"EM Morazzani","year":"2012","journal-title":"PLoS Pathog"},{"issue":"10","key":"pntd.0013774.ref117","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0000848","article-title":"Comparison of dengue virus type 2-specific small RNAs from RNA interference-competent and -incompetent mosquito cells","volume":"4","author":"JC Scott","year":"2010","journal-title":"PLoS Negl Trop Dis"},{"issue":"3","key":"pntd.0013774.ref118","doi-asserted-by":"crossref","first-page":"271","DOI":"10.3390\/v11030271","article-title":"Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells","volume":"11","author":"GP G\u00f6ertz","year":"2019","journal-title":"Viruses"},{"issue":"2","key":"pntd.0013774.ref119","doi-asserted-by":"crossref","first-page":"436","DOI":"10.3390\/v15020436","article-title":"Antiviral RNAi Response in Culex quinquefasciatus-Derived HSU Cells","volume":"15","author":"M Altinli","year":"2023","journal-title":"Viruses"},{"key":"pntd.0013774.ref120","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ibmb.2019.04.008","article-title":"Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection","volume":"109","author":"C R\u00fcckert","year":"2019","journal-title":"Insect Biochem Mol Biol"},{"issue":"1","key":"pntd.0013774.ref121","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-025-07617-8","article-title":"Prolonged exposure to heat enhances mosquito tolerance to viral infection","volume":"8","author":"HD Perdomo","year":"2025","journal-title":"Commun Biol"},{"key":"pntd.0013774.ref122","doi-asserted-by":"crossref","first-page":"103514","DOI":"10.1016\/j.dci.2019.103514","article-title":"How are arbovirus vectors able to tolerate infection?","volume":"103","author":"JH Oliveira","year":"2020","journal-title":"Dev Comp Immunol"},{"key":"pntd.0013774.ref123","doi-asserted-by":"crossref","first-page":"12410","DOI":"10.1038\/ncomms12410","article-title":"Virus-derived DNA drives mosquito vector tolerance to arboviral infection","volume":"7","author":"B Goic","year":"2016","journal-title":"Nat Commun"},{"issue":"4","key":"pntd.0013774.ref124","article-title":"Matrix metalloproteinase 9 facilitates Zika virus invasion of the testis by modulating the integrity of the blood-testis barrier","volume":"16","author":"L Hui","year":"2020","journal-title":"PLoS Pathog"},{"key":"pntd.0013774.ref125","doi-asserted-by":"crossref","first-page":"2158","DOI":"10.3389\/fmicb.2019.02158","article-title":"Selective disruption of the blood\u2013brain barrier by Zika virus","volume":"10","author":"AR Leda","year":"2019","journal-title":"Frontiers in Microbiology"},{"issue":"2","key":"pntd.0013774.ref126","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0117849","article-title":"New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences","volume":"10","author":"G Moureau","year":"2015","journal-title":"PLoS One"},{"key":"pntd.0013774.ref127","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.micron.2013.12.006","article-title":"Microscopy techniques in flavivirus research","volume":"59","author":"MK Chong","year":"2014","journal-title":"Micron"},{"issue":"2","key":"pntd.0013774.ref128","doi-asserted-by":"crossref","first-page":"287","DOI":"10.3390\/v17020287","article-title":"Towards a Universal Translator: Decoding the PTMs That Regulate Orthoflavivirus Infection","volume":"17","author":"HM Schmidt","year":"2025","journal-title":"Viruses"},{"issue":"9","key":"pntd.0013774.ref129","doi-asserted-by":"crossref","first-page":"957","DOI":"10.3390\/v12090957","article-title":"Fatal Outcome of Ilheus Virus in the Cerebrospinal Fluid of a Patient Diagnosed with Encephalitis","volume":"12","author":"BHGA Milhim","year":"2020","journal-title":"Viruses"}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0013774","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T18:54:19Z","timestamp":1764960859000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0013774"}},"subtitle":[],"editor":[{"given":"Luis Adri\u00e1n","family":"Diaz","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,5]]},"references-count":129,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0013774","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,5]]}}}