{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T11:38:05Z","timestamp":1768217885010,"version":"3.49.0"},"reference-count":65,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PICIII16\/00033"],"award-info":[{"award-number":["PICIII16\/00033"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI19CIII\/00042"],"award-info":[{"award-number":["PI19CIII\/00042"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI22CIII\/00065"],"award-info":[{"award-number":["PI22CIII\/00065"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Osakidetza-Servicio Vasco de Salud, Government of Basque Country","award":["MVI 1001\/16"],"award-info":[{"award-number":["MVI 1001\/16"]}]},{"name":"Conseller\u00eda de Sanidade, Government of Galicia","award":["MVI 281\/22"],"award-info":[{"award-number":["MVI 281\/22"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Previous studies have reported the propagation of diverse HIV-1 CRFs of South American origin in Europe. Here, through protease-reverse transcriptase (Pr-RT) and integrase sequence analyses, we identify a Spanish cluster (BC3) branching with a Brazilian virus (10BR_RJ009) previously classified as CRF146_BC. In Pr-RT, BC3 comprised 14 viruses and was nested within a larger cluster, comprising 22 Brazilian viruses and 1 Spanish virus branching outside of BC3. Near full-length genome analyses of five BC3 viruses revealed mosaic structures identical to 10BR_RJ009, with two breakpoints delimiting a ~0.3 kb subtype B fragment within an otherwise subtype C genome. Two other Brazilian viruses previously classified as CRF146_BC (10BR_RJ039 and 01_BR_RGS69) had one and two additional short subtype B fragments, respectively, and failed to group with the 10BR_RJ009\/BC3 cluster in subtype C fragments. Based on these results, we contend that 10BR_RJ009 and BC3 viruses, but not 10BR_RJ039 and 01_BR_RGS69, should be classified as CRF146_BC. Bayesian analyses estimated the CRF146_BC emergence in Brazil to be around 1999 and its introduction in Europe around 2011. CRF146_BC is the 10th CRF of South American origin reported to circulate in Europe, reflecting the relationship between South American and European HIV-1 epidemics.<\/jats:p>","DOI":"10.3390\/v18010101","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T08:20:37Z","timestamp":1768206037000},"page":"101","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Viruses Previously Classified as CRF146_BC, a Circulating Recombinant Form of HIV-1 Recently Reported in Brazil, Represent Different Recombinant Forms, One of Which Is Circulating in Spain"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3989-7399","authenticated-orcid":false,"given":"Ana","family":"Donoso","sequence":"first","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6958-4951","authenticated-orcid":false,"given":"Mar\u00eda","family":"Moreno-Lorenzo","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0754-8533","authenticated-orcid":false,"given":"Elena","family":"Delgado","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8964-0551","authenticated-orcid":false,"given":"Javier E.","family":"Ca\u00f1ada-Garc\u00eda","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4013-8509","authenticated-orcid":false,"given":"Jos\u00e9 Antonio","family":"Iribarren","sequence":"additional","affiliation":[{"name":"Hospital Universitario Donostia, 20014 San Sebasti\u00e1n, Gipuzkoa, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yolanda","family":"Salicio","sequence":"additional","affiliation":[{"name":"Hospital Universitario Donostia, 20014 San Sebasti\u00e1n, Gipuzkoa, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6908-4757","authenticated-orcid":false,"given":"Sonia","family":"Benito","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0404-9453","authenticated-orcid":false,"given":"Clara","family":"Lorente-Sorolla","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8922-5182","authenticated-orcid":false,"given":"Jorge","family":"Del Romero-Guerrero","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"},{"name":"Fundaci\u00f3n de Investigaci\u00f3n Biom\u00e9dica, Centro Sanitario Sandoval, Hospital Cl\u00ednico San Carlos, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda Bego\u00f1a","family":"Baza-Caraciolo","sequence":"additional","affiliation":[{"name":"Centro Sanitario Sandoval, Instituto de Medicina de Laboratorio (IML), Hospital Cl\u00ednico San Carlos, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2413-9229","authenticated-orcid":false,"given":"Francisco","family":"D\u00edez-Fuertes","sequence":"additional","affiliation":[{"name":"AIDS Immunopathogenesis Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pilar","family":"Zamarr\u00f3n","sequence":"additional","affiliation":[{"name":"Hospital Universitario Puerta de Hierro, 28222 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raquel","family":"T\u00e9llez","sequence":"additional","affiliation":[{"name":"Hospital Universitario Fundaci\u00f3n Jim\u00e9nez D\u00edaz, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Miqueleiz","sequence":"additional","affiliation":[{"name":"Hospital Universitario de Navarra, 31008 Pamplona, Navarra, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmen","family":"G\u00f3mez-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Hospital Universitario Araba, 01009 Vitoria, \u00c1lava, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8222-6729","authenticated-orcid":false,"given":"Sandra","family":"Cortizo","sequence":"additional","affiliation":[{"name":"Complejo Hospitalario Universitario de Vigo, 36208 Vigo, Pontevedra, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0560-3260","authenticated-orcid":false,"given":"Luis","family":"Morano","sequence":"additional","affiliation":[{"name":"Hospital Universitario \u00c1lvaro Cunqueiro, 36312 Vigo, Pontevedra, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0622-7527","authenticated-orcid":false,"given":"Michael M.","family":"Thomson","sequence":"additional","affiliation":[{"name":"HIV Biology and Variability Unit, Centro Nacional de Microbiolog\u00eda, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.1128\/JVI.80.5.2472-2482.2006","article-title":"Extensive recombination among human immunodeficiency virus type 1 quasispecies makes an important contribution to viral diversity in individual patients","volume":"80","author":"Charpentier","year":"2006","journal-title":"J. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Moradigaravand, D., Kouyos, R., Hinkley, T., Haddad, M., Petropoulos, C.J., Engelst\u00e4dter, J., and Bonhoeffer, S. (2014). Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004439"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ympev.2015.09.001","article-title":"Influence of mutation and recombination on HIV-1 in vitro fitness","volume":"94","author":"Arenas","year":"2016","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1084\/jem.20080281","article-title":"Immune-driven recombination and loss of control after HIV superinfection","volume":"205","author":"Streeck","year":"2008","journal-title":"J. Exp. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1038\/s41467-018-04217-5","article-title":"Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection","volume":"9","author":"Song","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"7620","DOI":"10.1128\/JVI.00083-07","article-title":"Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment","volume":"81","author":"Nora","year":"2007","journal-title":"J. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.meegid.2007.02.001","article-title":"Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy","volume":"7","author":"Crandall","year":"2007","journal-title":"Infect. Genet. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1097\/00002030-200216004-00002","article-title":"Genetic recombination and its role in the development of the HIV-1 pandemic","volume":"16","author":"Delgado","year":"2002","journal-title":"AIDS"},{"key":"ref_9","unstructured":"(2025, November 15). HIV Sequence Database, Available online: https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1093\/jac\/dkt305","article-title":"Predominance of CXCR4 tropism in HIV-1 CRF14_BG strains from newly diagnosed infections","volume":"69","author":"Delgado","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.ebiom.2015.01.015","article-title":"CRF19_cpx is an evolutionary fit HIV-1 variant strongly associated with rapid progression to AIDS in Cuba","volume":"2","author":"Kouri","year":"2015","journal-title":"EBioMedicine"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1073\/pnas.1814714116","article-title":"Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade","volume":"116","author":"Song","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Bacqu\u00e9, J., Delgado, E., Gil, H., Ibarra, S., Benito, S., Garc\u00eda-Arata, I., Moreno-Lorenzo, M., S\u00e1ez de Adana, E.S., G\u00f3mez-Gonz\u00e1lez, C., and S\u00e1nchez, M. (2023). Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1301374"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1093\/infdis\/169.1.48","article-title":"Two antigenically distinct subtypes of human immunodeficiency virus type 1: Viral genotype predicts neutralization serotype","volume":"169","author":"Mascola","year":"1994","journal-title":"J. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"12623","DOI":"10.1128\/JVI.01705-14","article-title":"Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies","volume":"88","author":"Hraber","year":"2014","journal-title":"J. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Pessoa, R., Loureiro, P., Esther Lopes, M., Carneiro-Proietti, A.B., Sabino, E.C., Busch, M.P., and Sanabani, S.S. (2016). Ultra-Deep sequencing of HIV-1 near full-length and partial proviral genomes reveals high genetic diversity among Brazilian blood donors. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0152499"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1089\/aid.2009.0167","article-title":"Near full-length genome characterization of HIV type 1 unique BC recombinant forms from Southern Brazil","volume":"25","author":"Passaes","year":"2009","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e230214","DOI":"10.1590\/0074-02760230214","article-title":"Description of the new HIV-1 intersubtype B\/C circulating recombinant form (CRF146_BC) detected in Brazil","volume":"119","author":"Oliveira","year":"2024","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Delgado, E., Cuevas, M.T., Dom\u00ednguez, F., Vega, Y., Cabello, M., Fern\u00e1ndez-Garc\u00eda, A., P\u00e9rez-Losada, M., Castro, M.\u00c1., Montero, V., and S\u00e1nchez, M. (2015). Phylogeny and phylogeography of a recent HIV-1 subtype F outbreak among men who have sex with men in Spain deriving from a cluster with a wide geographic circulation in Western Europe. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0143325"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Gil, H., Delgado, E., Benito, S., Moreno-Lorenzo, M., and Thomson, M.M. (2022). Spanish Group for the Study of Antiretroviral Drug Resistance. Factors associated with HIV-1 resistance to integrase strand transfer inhibitors in Spain: Implications for dolutegravir-containing regimens. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1051096"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1097\/00126334-200204150-00016","article-title":"Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure","volume":"29","author":"Delgado","year":"2002","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.meegid.2004.07.010","article-title":"The analysis of near full-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile, Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF","volume":"5","author":"Sierra","year":"2005","journal-title":"Infect. Genet. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Ca\u00f1ada, J.E., Delgado, E., Gil, H., S\u00e1nchez, M., Benito, S., Garc\u00eda-Bodas, E., G\u00f3mez-Gonz\u00e1lez, C., Canut-Blasco, A., Portu-Zapirain, J., and S\u00e1ez de Adana, E. (2021). Identification of a new HIV-1 BC intersubtype circulating recombinant form (CRF108_BC) in Spain. Viruses, 13.","DOI":"10.3390\/v13010093"},{"key":"ref_24","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":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_26","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":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_28","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":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1089\/aid.1995.11.1423","article-title":"Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning","volume":"11","author":"Salminen","year":"1995","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.1093\/molbev\/msx149","article-title":"SMS: Smart Model Selection in PhyML","volume":"34","author":"Lefort","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/s41586-018-0043-0","article-title":"Renewing Felsenstein\u2019s phylogenetic bootstrap in the era of big data","volume":"556","author":"Lemoine","year":"2018","journal-title":"Nature"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.virol.2011.03.021","article-title":"Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning","volume":"415","author":"Thomson","year":"2011","journal-title":"Virology"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"10501","DOI":"10.1128\/JVI.78.19.10501-10506.2004","article-title":"Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1","volume":"78","author":"Travers","year":"2004","journal-title":"J. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1089\/aid.2013.0240","article-title":"Coreceptor usage, diversity, and divergence in drug-naive and drug-exposed individuals from Malawi, infected with HIV-1 subtype C for more than 20 years","volume":"30","author":"Seager","year":"2014","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Hill, G., P\u00e9rez-Losada, M., Delgado, E., Benito, S., Montero, V., Gil, H., S\u00e1nchez, M., Ca\u00f1ada-Garc\u00eda, J.E., Garc\u00eda-Bodas, E., and Crandall, K.A. (2022). The origin, epidemiology, and phylodynamics of human immunodeficiency virus type 1 CRF47_BF. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.863123"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Mauer, K.M., Schmidt, H., Dittrich, M., Fr\u00f6bius, A.C., Hellmann, S.L., Zischler, H., Hankeln, T., and Herlyn, H. (2021). Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07857-y"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1016\/S0959-437X(98)80028-2","article-title":"How good are deep phylogenetic trees?","volume":"8","author":"Philippe","year":"1998","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1096-0031.2005.00059.x","article-title":"A review of long-branch attraction","volume":"21","author":"Bergsten","year":"2005","journal-title":"Cladistics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1016\/j.ympev.2009.08.012","article-title":"Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations","volume":"54","author":"Binley","year":"2010","journal-title":"Mol. Phylogenet Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1080\/10635150290069913","article-title":"An approximately unbiased test of phylogenetic tree selection","volume":"51","author":"Shimodaira","year":"2002","journal-title":"Syst. Biol."},{"key":"ref_46","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":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/molbev\/msj021","article-title":"Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences","volume":"23","author":"Shapiro","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: A coalescent-based model for multiple loci","volume":"30","author":"Gill","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1089\/aid.2014.0075","article-title":"Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia","volume":"30","author":"Shcherbakova","year":"2014","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1097\/QAI.0b013e318046ea47","article-title":"Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba","volume":"45","author":"Sierra","year":"2007","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Fern\u00e1ndez-Garc\u00eda, A., Delgado, E., Cuevas, M.T., Vega, Y., Montero, V., S\u00e1nchez, M., Carrera, C., L\u00f3pez-\u00c1lvarez, M.J., Miralles, C., and P\u00e9rez-Castro, S. (2016). Identification of an HIV-1 BG intersubtype recombinant form (CRF73_BG), partially related to CRF14_BG, which is circulating in Portugal and Spain. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0148549"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Ca\u00f1ada-Garc\u00eda, J.E., Delgado, E., Gil, H., Benito, S., S\u00e1nchez, M., Ocampo, A., Cabrera, J.J., Miralles, C., Garc\u00eda-Bodas, E., and Mari\u00f1o, A. (2022). Viruses previously identified in Brazil as belonging to HIV-1 CRF72_BF1 represent two closely related circulating recombinant forms, one of which, designated CRF122_BF1, is also circulating in Spain. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.863084"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1089\/aid.2014.0364","article-title":"Near full-length characterization and population dynamics of the human immunodeficiency virus type I circulating recombinant form 42 (CRF42_BF) in Luxembourg","volume":"31","author":"Struck","year":"2015","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1089\/aid.2009.0311","article-title":"Identification of a new HIV type 1 circulating BF intersubtype recombinant form (CRF47_BF) in Spain","volume":"26","author":"Cuevas","year":"2010","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.meegid.2014.02.007","article-title":"Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men","volume":"23","author":"Simonetti","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Bacqu\u00e9, J., Delgado, E., Benito, S., Moreno-Lorenzo, M., Montero, V., Gil, H., S\u00e1nchez, M., Nieto-Toboso, M.C., Mu\u00f1oz, J., and Zubero-Sulibarria, M.Z. (2021). Identification of CRF66_BF, a new HIV-1 circulating recombinant form of South American origin. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.774386"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"11442","DOI":"10.1038\/s41598-021-90023-x","article-title":"Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America","volume":"11","author":"Delgado","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.meegid.2016.02.028","article-title":"Transmission dynamics of HIV-1 subtype B in the Basque Country, Spain","volume":"40","author":"Thomson","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Gil, H., Delgado, E., Benito, S., Georgalis, L., Montero, V., S\u00e1nchez, M., Ca\u00f1ada-Garc\u00eda, J.E., Garc\u00eda-Bodas, E., D\u00edaz, A., and Thomson, M.M. (2022). Transmission clusters, predominantly associated with men who have sex with men, play a main role in the propagation of HIV-1 in Northern Spain (2013-2018). Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.782609"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.1097\/QAD.0000000000000383","article-title":"Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions","volume":"28","author":"Brown","year":"2014","journal-title":"AIDS"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e309","DOI":"10.1016\/S2352-3018(18)30062-6","article-title":"Non-disclosed men who have sex with men in UK HIV transmission networks: Phylogenetic analysis of surveillance data","volume":"5","author":"Hodcroft","year":"2018","journal-title":"Lancet HIV"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e772","DOI":"10.1016\/S2352-3018(20)30252-6","article-title":"Global and regional epidemiology of HIV-1 recombinants in 1990\u20132015: A systematic review and global survey","volume":"7","author":"Hemelaar","year":"2020","journal-title":"Lancet HIV"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/1\/101\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T08:24:37Z","timestamp":1768206277000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/1\/101"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,12]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["v18010101"],"URL":"https:\/\/doi.org\/10.3390\/v18010101","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,12]]}}}