{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:49:16Z","timestamp":1785408556043,"version":"3.56.0"},"reference-count":31,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T00:00:00Z","timestamp":1778803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21 AI 156059"],"award-info":[{"award-number":["R21 AI 156059"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"award":["R21 AI 156059"],"award-info":[{"award-number":["R21 AI 156059"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Yellow fever virus (YFV) is divided into seven genotypes, including West Africa II (WAII) and South America I (SAI). The first wild-type YFVs isolated, Asibi (Ghana\/1927) and French Viscerotropic virus ([FVV] Senegal\/1927), are members of WAII. The first YFV strain isolated in South America, JSS (Brazil\/1935), was associated with the last outbreak of urban YF in Brazil and has been insufficiently studied. We utilized Next Generation Sequencing to compare JSS with Asibi, FVV, and other South American YFV strains. SAI strains, including JSS, had higher genetic diversity than WAII strains. Phylogenetic and phylogeographic studies of YFV in South America have revealed the circulation of five lineages within Brazil, termed 1A-1E. JSS was found to be distinct from the five genetic lineages currently recognized in Brazil, and so we termed JSS as the currently sole member of Brazilian linage 1F. a comparison of JSS with all other Brazilian genomes of YFV suggests that lineage 1F appears to have become extinct.<\/jats:p>","DOI":"10.3390\/v18050564","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T16:07:26Z","timestamp":1779206846000},"page":"564","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Characterization of Yellow Fever Virus Strain JSS, the Original South American Strain"],"prefix":"10.3390","volume":"18","author":[{"given":"Madison E.","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4841-2456","authenticated-orcid":false,"given":"Clairissa A.","family":"Hansen","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-5354-4393","authenticated-orcid":false,"given":"Jill K.","family":"Thompson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8826-1568","authenticated-orcid":false,"given":"Haiping","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nigel","family":"Bourne","sequence":"additional","affiliation":[{"name":"Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA"},{"name":"Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3740-7448","authenticated-orcid":false,"given":"Alan D. T.","family":"Barrett","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA"},{"name":"Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,15]]},"reference":[{"key":"ref_1","unstructured":"Simon, L.V., Hashmi, M.F., and Torp, K.D. (2024). Yellow Fever. StatPearls, StatPearls Publishing."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Gianchecchi, E., Cianchi, V., Torelli, A., and Montomoli, E. (2022). Yellow Fever: Origin, Epidemiology, Preventive Strategies and Future Prospects. Vaccines, 10.","DOI":"10.3390\/vaccines10030372"},{"key":"ref_3","unstructured":"Fields, B.N., Knipe, D.M., and Howley, P.M. (2007). Fields\u2019 Virology, Wolters Kluwer Health\/Lippincott Williams & Wilkins."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Domingo, E., Garc\u00eda-Crespo, C., Lobo-Vega, R., and Perales, C. (2021). Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics. Viruses, 13.","DOI":"10.3390\/v13091882"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Beck, A., Guzman, H., Li, L., Ellis, B., Tesh, R.B., and Barrett, A.D.T. (2013). Phylogeographic reconstruction of African yellow fever virus isolates indicates recent simultaneous dispersal into east and west Africa. PLoS Negl. Trop. Dis., 7.","DOI":"10.1371\/journal.pntd.0001910"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/S0928-8244(03)00238-4","article-title":"Comparative phylogenies of yellow fever isolates from Peru and Brazil","volume":"39","author":"Bryant","year":"2003","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bryant, J.E., Holmes, E.C., and Barrett, A.D. (2007). Out of Africa: A molecular perspective on the introduction of yellow fever virus into the Americas. PLoS Pathog., 3.","DOI":"10.1371\/journal.ppat.0030075"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"6999","DOI":"10.1128\/JVI.75.15.6999-7008.2001","article-title":"Phylogenetic and evolutionary relationships among yellow fever virus isolates in Africa","volume":"75","author":"Mutebi","year":"2001","journal-title":"J. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"851","DOI":"10.3201\/eid3104.240108","article-title":"Yellow Fever Virus in Mosquitoes from Rainforest Bordering Manaus, Brazil, 2022","volume":"31","author":"Bernardi","year":"2025","journal-title":"Emerg. Infect. Dis. J."},{"key":"ref_10","unstructured":"Strode, G.K. (1951). Chapter 2: The virus. Yellow Fever, McGraw-Hill Book Co. Inc."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1099\/0022-1317-46-1-1","article-title":"The In Vivo Differentiation of Strains of Yellow Fever Virus in Mice","volume":"46","author":"Fitzgeorge","year":"1980","journal-title":"J. General. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Meier, K.C., Gardner, C.L., Khoretonenko, M.V., Klimstra, W.B., and Ryman, K.D. (2009). A mouse model for studying viscerotropic disease caused by yellow fever virus infection. PLoS Pathog., 5.","DOI":"10.1371\/journal.ppat.1000614"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1084\/jem.111.1.21","article-title":"Antigenic analysis of certain group B arthropod-borne viruses by antibody absorption","volume":"111","author":"Clarke","year":"1960","journal-title":"J. Exp. Med."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1099\/vir.0.81236-0","article-title":"Genome analysis and phylogenetic relationships between east, central and west African isolates of Yellow fever virus","volume":"87","author":"Aroner","year":"2006","journal-title":"J. Gen. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Strother, A.E., Thompson, J.K., Widen, S.G., and Barrett, A.D.T. (2022). Genetic Diversity Does Not Contribute to Attenuation of HeLa Passaged Wild-Type Yellow Fever Virus Strain French Viscerotropic Virus. Viruses, 14.","DOI":"10.3390\/v14030527"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Delatorre, E., de Abreu, F.V.S., Ribeiro, I.P., G\u00f3mez, M.M., dos Santos, A.A.C., Ferreira-De-Brito, A., Neves, M.S.A.S., Bonelly, I., de Miranda, R.M., and Furtado, N.D. (2019). Distinct YFV Lineages Co-circulated in the Central-Western and Southeastern Brazilian Regions From 2015 to 2018. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01079"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Lee, M.E., Hansen, C.A., Thompson, J.K., Hao, H., Bourne, N., and Barrett, A.D. (2026). Differences in genetic diversity between early isolates of yellow fever virus genotypes. Emerg. Microbes Infect., in press.","DOI":"10.1080\/22221751.2025.2601371"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1016\/j.str.2024.04.020","article-title":"Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase","volume":"32","author":"Hansen","year":"2024","journal-title":"Structure"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Lu, G., and Gong, P. (2013). Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface. PLoS Pathog., 9.","DOI":"10.2210\/pdb4k6m\/pdb"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1128\/JVI.02704-06","article-title":"Structure and function of flavivirus NS5 methyltransferase","volume":"81","author":"Zhou","year":"2007","journal-title":"J. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.3201\/eid1009.040197","article-title":"Genetic divergence and dispersal of yellow fever virus, Brazil","volume":"10","author":"Vasconcelos","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"ref_22","first-page":"1","article-title":"Urgent call for action: Avoiding spread and re-urbanisation of yellow fever in Brazil","volume":"113","author":"Possas","year":"2018","journal-title":"Mem. Do Inst. Oswaldo Cruz"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Nederlof, R.A., Virgilio, T., Stemkens, H.J.J., da Silva, L.C.C.P., Montagna, D.R., Abdussamad, A.M., Chipangura, J., and Bakker, J. (2025). Yellow Fever in Non-Human Primates: A Veterinary Guide from a One Health Perspective. Vet. Sci., 12.","DOI":"10.3390\/vetsci12040339"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.virol.2011.01.030","article-title":"Amino acid changes within the E protein hinge region that affect dengue virus type 2 infectivity and fusion","volume":"413","author":"Butrapet","year":"2011","journal-title":"Virology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1099\/vir.0.034793-0","article-title":"Determinants of attenuation in the envelope protein of the flavivirus Alfuy","volume":"92","author":"Prow","year":"2011","journal-title":"J. Gen. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/0042-6822(91)90471-M","article-title":"Nucleotide changes responsible for loss of neuroinvasiveness in Japanese encephalitis virus neutralization-resistant mutants","volume":"181","author":"Cecilia","year":"1991","journal-title":"Virology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1128\/JVI.76.4.1932-1943.2002","article-title":"Single mutation in the flavivirus envelope protein hinge region increases neurovirulence for mice and monkeys but decreases viscerotropism for monkeys: Relevance to development and safety testing of live, attenuated vaccines","volume":"76","author":"Monath","year":"2002","journal-title":"J. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"7692","DOI":"10.1128\/JVI.75.16.7692-7702.2001","article-title":"Attenuation of Murray Valley Encephalitis Virus by Site-Directed Mutagenesis of the Hinge and Putative Receptor-Binding Regions of the Envelope Protein","volume":"75","year":"2001","journal-title":"J. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1006\/viro.1997.8570","article-title":"Changes in the Dengue Virus Major Envelope Protein on Passaging and Their Localization on the Three-Dimensional Structure of the Protein","volume":"232","author":"Lee","year":"1997","journal-title":"Virology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.virol.2009.09.001","article-title":"Structure of yellow fever virus envelope protein domain III","volume":"394","author":"Volk","year":"2009","journal-title":"Virology"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1006\/viro.1998.9057","article-title":"Mutation in a 17D-204 Vaccine Substrain-Specific Envelope Protein Epitope Alters the Pathogenesis of Yellow Fever Virus in Mice","volume":"244","author":"Ryman","year":"1998","journal-title":"Virology"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/564\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,23]],"date-time":"2026-05-23T04:31:20Z","timestamp":1779510680000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/564"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,15]]},"references-count":31,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["v18050564"],"URL":"https:\/\/doi.org\/10.3390\/v18050564","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,15]]}}}