The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF

CRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerab...

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Main Authors: Gracelyn Hill, Marcos Pérez-Losada, Elena Delgado, Sonia Benito, Vanessa Montero, Horacio Gil, Mónica Sánchez, Javier E. Cañada-García, Elena García-Bodas, Keith A. Crandall, Michael M. Thomson, the Spanish Group for the Study of New HIV Diagnoses, José Luis Díaz de Tuesta del Arco, Silvia Hernáez, Sofía Ibarra-Ugarte, Josefa Muñoz, María Carmen Nieto-Toboso, Miren Zuriñe Zubero-Sulibarria, Elena Bereciartua-Bastarrica, Luis Elorduy, Goikoetxea-Agirre Ane Josune, Leyre López-Soria, María José López de Goikoetxea, Maitane Aranzamendi, Gustavo Cilla, José Antonio Iribarren, Yolanda Salicio, Carmen Gómez, José Joaquín Portu, Aitziber Aguinaga, Carmen Ezpeleta, Carmen Martín-Salas, María Gracia Ruiz-Alda, José Javier García-Irure, Fernando Buñuel, Francisco Jover-Díaz, Jorge Julio Cabrera, Antonio Ocampo, Celia Miralles, Julio Diz-Aren, Matilde Trigo, María José Gude, Ramón Rabuñal, Eva María Romay, Ricardo Fernández-Rodríguez, Juan García-Costa, Ana María Martínez-Sapiña, Jorge del Romero, Belén Lorenzo-Vidal, César Gómez
Format: Article
Language:English
Published: Frontiers Media S.A. 2022-05-01
Series:Frontiers in Microbiology
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fmicb.2022.863123/full
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author Gracelyn Hill
Marcos Pérez-Losada
Marcos Pérez-Losada
Marcos Pérez-Losada
Elena Delgado
Sonia Benito
Vanessa Montero
Horacio Gil
Mónica Sánchez
Javier E. Cañada-García
Elena García-Bodas
Keith A. Crandall
Keith A. Crandall
Michael M. Thomson
the Spanish Group for the Study of New HIV Diagnoses
José Luis Díaz de Tuesta del Arco
Silvia Hernáez
Sofía Ibarra-Ugarte
Josefa Muñoz
María Carmen Nieto-Toboso
Miren Zuriñe Zubero-Sulibarria
Elena Bereciartua-Bastarrica
Luis Elorduy
Goikoetxea-Agirre Ane Josune
Leyre López-Soria
María José López de Goikoetxea
Maitane Aranzamendi
Gustavo Cilla
José Antonio Iribarren
Yolanda Salicio
Carmen Gómez
José Joaquín Portu
Aitziber Aguinaga
Carmen Ezpeleta
Carmen Martín-Salas
María Gracia Ruiz-Alda
José Javier García-Irure
Fernando Buñuel
Francisco Jover-Díaz
Jorge Julio Cabrera
Antonio Ocampo
Celia Miralles
Julio Diz-Aren
Matilde Trigo
María José Gude
Ramón Rabuñal
Eva María Romay
Ricardo Fernández-Rodríguez
Juan García-Costa
Ana María Martínez-Sapiña
Jorge del Romero
Belén Lorenzo-Vidal
César Gómez
author_facet Gracelyn Hill
Marcos Pérez-Losada
Marcos Pérez-Losada
Marcos Pérez-Losada
Elena Delgado
Sonia Benito
Vanessa Montero
Horacio Gil
Mónica Sánchez
Javier E. Cañada-García
Elena García-Bodas
Keith A. Crandall
Keith A. Crandall
Michael M. Thomson
the Spanish Group for the Study of New HIV Diagnoses
José Luis Díaz de Tuesta del Arco
Silvia Hernáez
Sofía Ibarra-Ugarte
Josefa Muñoz
María Carmen Nieto-Toboso
Miren Zuriñe Zubero-Sulibarria
Elena Bereciartua-Bastarrica
Luis Elorduy
Goikoetxea-Agirre Ane Josune
Leyre López-Soria
María José López de Goikoetxea
Maitane Aranzamendi
Gustavo Cilla
José Antonio Iribarren
Yolanda Salicio
Carmen Gómez
José Joaquín Portu
Aitziber Aguinaga
Carmen Ezpeleta
Carmen Martín-Salas
María Gracia Ruiz-Alda
José Javier García-Irure
Fernando Buñuel
Francisco Jover-Díaz
Jorge Julio Cabrera
Antonio Ocampo
Celia Miralles
Julio Diz-Aren
Matilde Trigo
María José Gude
Ramón Rabuñal
Eva María Romay
Ricardo Fernández-Rodríguez
Juan García-Costa
Ana María Martínez-Sapiña
Jorge del Romero
Belén Lorenzo-Vidal
César Gómez
author_sort Gracelyn Hill
collection DOAJ
description CRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual contact (∼56% of the infections). Little is known, however, about the origin and diversity of this CRF or its epidemiological correlates, as very few samples have been available so far. This study conducts a phylogenetic analysis with representatives of all CRFx_BF sequence types along with HIV-1 M Group subtypes to validate that the CRF47_BF sequences share a unique evolutionary history. The CRFx_BF sequences cluster into a single, not well supported, clade that includes their dominant parent subtypes (B and F). This clade also includes subtype D and excludes sub-subtype F2. However, the CRF47_BF sequences all share a most recent common ancestor. Further analysis of this clade couples CRF47_BF protease-reverse transcriptase sequences and epidemiological data from an additional 87 samples collected throughout Spain, as well as additional CRF47_BF database sequences from Brazil and Spain to investigate the origin and phylodynamics of CRF47_BF. The Spanish region with the highest proportion of CRF47_BF samples in the data set was the Basque Country (43.7%) with Navarre next highest at 19.5%. We include in our analysis epidemiological data on host sex, mode of transmission, time of collection, and geographic region. The phylodynamic analysis indicates that CRF47_BF originated in Brazil around 1999–2000 and spread to Spain from Brazil in 2002–2003. The virus spread rapidly throughout Spain with an increase in population size from 2011 to 2015 and leveling off more recently. Three strongly supported clusters associated with Spanish regions (Basque Country, Navarre, and Aragon), together comprising 60.8% of the Spanish samples, were identified, one of which was also associated with transmission among men who have sex with men. The expansion in Spain of CRF47_BF, together with that of other CRFs and subtype variants of South American origin, previously reported, reflects the increasing relationship between the South American and European HIV-1 epidemics.
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spelling doaj.art-e5985d8df59241f385ffe846371564e12022-12-22T00:26:53ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-05-011310.3389/fmicb.2022.863123863123The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BFGracelyn Hill0Marcos Pérez-Losada1Marcos Pérez-Losada2Marcos Pérez-Losada3Elena Delgado4Sonia Benito5Vanessa Montero6Horacio Gil7Mónica Sánchez8Javier E. Cañada-García9Elena García-Bodas10Keith A. Crandall11Keith A. Crandall12Michael M. Thomson13the Spanish Group for the Study of New HIV DiagnosesJosé Luis Díaz de Tuesta del ArcoSilvia HernáezSofía Ibarra-UgarteJosefa MuñozMaría Carmen Nieto-TobosoMiren Zuriñe Zubero-SulibarriaElena Bereciartua-BastarricaLuis ElorduyGoikoetxea-Agirre Ane JosuneLeyre López-SoriaMaría José López de GoikoetxeaMaitane AranzamendiGustavo CillaJosé Antonio IribarrenYolanda SalicioCarmen GómezJosé Joaquín PortuAitziber AguinagaCarmen EzpeletaCarmen Martín-SalasMaría Gracia Ruiz-AldaJosé Javier García-IrureFernando BuñuelFrancisco Jover-DíazJorge Julio CabreraAntonio OcampoCelia MirallesJulio Diz-ArenMatilde TrigoMaría José GudeRamón RabuñalEva María RomayRicardo Fernández-RodríguezJuan García-CostaAna María Martínez-SapiñaJorge del RomeroBelén Lorenzo-VidalCésar GómezComputational Biology Institute, George Washington University, Washington, DC, United StatesComputational Biology Institute, George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United StatesCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, PortugalHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainComputational Biology Institute, George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United StatesHIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, SpainCRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual contact (∼56% of the infections). Little is known, however, about the origin and diversity of this CRF or its epidemiological correlates, as very few samples have been available so far. This study conducts a phylogenetic analysis with representatives of all CRFx_BF sequence types along with HIV-1 M Group subtypes to validate that the CRF47_BF sequences share a unique evolutionary history. The CRFx_BF sequences cluster into a single, not well supported, clade that includes their dominant parent subtypes (B and F). This clade also includes subtype D and excludes sub-subtype F2. However, the CRF47_BF sequences all share a most recent common ancestor. Further analysis of this clade couples CRF47_BF protease-reverse transcriptase sequences and epidemiological data from an additional 87 samples collected throughout Spain, as well as additional CRF47_BF database sequences from Brazil and Spain to investigate the origin and phylodynamics of CRF47_BF. The Spanish region with the highest proportion of CRF47_BF samples in the data set was the Basque Country (43.7%) with Navarre next highest at 19.5%. We include in our analysis epidemiological data on host sex, mode of transmission, time of collection, and geographic region. The phylodynamic analysis indicates that CRF47_BF originated in Brazil around 1999–2000 and spread to Spain from Brazil in 2002–2003. The virus spread rapidly throughout Spain with an increase in population size from 2011 to 2015 and leveling off more recently. Three strongly supported clusters associated with Spanish regions (Basque Country, Navarre, and Aragon), together comprising 60.8% of the Spanish samples, were identified, one of which was also associated with transmission among men who have sex with men. The expansion in Spain of CRF47_BF, together with that of other CRFs and subtype variants of South American origin, previously reported, reflects the increasing relationship between the South American and European HIV-1 epidemics.https://www.frontiersin.org/articles/10.3389/fmicb.2022.863123/fullHIVphylodynamicscirculating recombinant form (CRF)SpainepidemiologyCRF47_BF
spellingShingle Gracelyn Hill
Marcos Pérez-Losada
Marcos Pérez-Losada
Marcos Pérez-Losada
Elena Delgado
Sonia Benito
Vanessa Montero
Horacio Gil
Mónica Sánchez
Javier E. Cañada-García
Elena García-Bodas
Keith A. Crandall
Keith A. Crandall
Michael M. Thomson
the Spanish Group for the Study of New HIV Diagnoses
José Luis Díaz de Tuesta del Arco
Silvia Hernáez
Sofía Ibarra-Ugarte
Josefa Muñoz
María Carmen Nieto-Toboso
Miren Zuriñe Zubero-Sulibarria
Elena Bereciartua-Bastarrica
Luis Elorduy
Goikoetxea-Agirre Ane Josune
Leyre López-Soria
María José López de Goikoetxea
Maitane Aranzamendi
Gustavo Cilla
José Antonio Iribarren
Yolanda Salicio
Carmen Gómez
José Joaquín Portu
Aitziber Aguinaga
Carmen Ezpeleta
Carmen Martín-Salas
María Gracia Ruiz-Alda
José Javier García-Irure
Fernando Buñuel
Francisco Jover-Díaz
Jorge Julio Cabrera
Antonio Ocampo
Celia Miralles
Julio Diz-Aren
Matilde Trigo
María José Gude
Ramón Rabuñal
Eva María Romay
Ricardo Fernández-Rodríguez
Juan García-Costa
Ana María Martínez-Sapiña
Jorge del Romero
Belén Lorenzo-Vidal
César Gómez
The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
Frontiers in Microbiology
HIV
phylodynamics
circulating recombinant form (CRF)
Spain
epidemiology
CRF47_BF
title The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
title_full The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
title_fullStr The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
title_full_unstemmed The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
title_short The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF
title_sort origin epidemiology and phylodynamics of human immunodeficiency virus type 1 crf47 bf
topic HIV
phylodynamics
circulating recombinant form (CRF)
Spain
epidemiology
CRF47_BF
url https://www.frontiersin.org/articles/10.3389/fmicb.2022.863123/full
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