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Guo X, Yu D, Liu M, Li H, Chen M, Wang X, Zhai X, Zhang B, Wang Y, Yang C, Wang C, Liu Y, Han J, Wang X, Li J, Jia L, Li L. A unified classification system for HIV-1 5' long terminal repeats. PLoS One 2024; 19:e0301809. [PMID: 38696412 PMCID: PMC11065288 DOI: 10.1371/journal.pone.0301809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024] Open
Abstract
The HIV-1 provirus mainly consists of internal coding region flanked by 1 long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic and phylogenetic classifications for HIV-1 5' LTRs, which hinders our elaboration on 5' LTR and a better understanding of the viral origin, spread and therapy. Here, by analyzing all available resources of 5' LTR sequences in public databases following 4 recognized principles for the reference classification, 83 representatives and 14 consensus sequences were identified as representatives of 2 groups, 6 subtypes, 6 sub-subtypes, and 9 CRFs. To test the reliability of the supplemented classification system, the constructed references were applied to identify the 5' LTR assignment of the 22 clinical isolates in China. The results revealed that 16 out of 22 tested strains showed a consistent subtype classification with the previous LTR-independent classification system. However, 6 strains, for which recombination events within 5' LTR were demonstrated, unexpectedly showed a different subtype classification, leading a significant change of binding sites for important transcription factors including SP1, p53, and NF-κB. The binding change of these transcriptional factors would probably affect the transcriptional activity of 5' LTR. This study supplemented a unified classification system for HIV-1 5' LTRs, which will facilitate HIV-1 characterization and be helpful for both basic and clinical research fields.
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Affiliation(s)
- Xing Guo
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Dan Yu
- Laboratory of Dermatology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Mengying Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Xinyu Wang
- Laboratory of Dermatology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xiuli Zhai
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Caiqing Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Bacqué J, Delgado E, Gil H, Ibarra S, Benito S, García-Arata I, Moreno-Lorenzo M, de Adana ES, Gómez-González C, Sánchez M, Montero V, Thomson MM. Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe. Front Microbiol 2023; 14:1301374. [PMID: 38125564 PMCID: PMC10731470 DOI: 10.3389/fmicb.2023.1301374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The high recombinogenic potential of HIV-1 has resulted in the generation of countless unique recombinant forms (URFs) and around 120 reported circulating recombinant forms (CRFs). Here we identify through analyses of near full-length genomes (NFLG) a new HIV-1 CRF derived from subtypes B and F1. Methods HIV-1 protease-reverse transcriptase (Pr-RT) sequences were obtained by RT-PCR amplification from plasma RNA. Near full-length genome sequences were obtained after amplification by RT-PCR in 5 overlapping fragments. Phylogenetic sequence analyses were performed via maximum likelihood. Mosaic structures were analyzed by bootscanning and phylogenetic analyses of genome segments. Temporal and geographical estimations of clade emergence were performed with a Bayesian coalescent method. Results Through phylogenetic analyses of HIV-1 Pr-RT sequences obtained by us from samples collected in Spain and downloaded from databases, we identified a BF1 recombinant cluster segregating from previously reported CRFs comprising 52 viruses, most from Brazil (n = 26), Spain (n = 11), and Italy (n = 9). The analyses of NFLG genomes of 4 viruses of the cluster, 2 from Spain and 2 from Italy, allowed to identify a new CRF, designated CRF75_BF1, which exhibits a complex mosaic structure with 20 breakpoints. All 4 patients harboring CRF75_BF1 viruses studied by us had CD4+ T-cell lymphocyte counts below 220/mm3 less than one year after diagnosis, a proportion significantly higher (p = 0.0074) than the 29% found in other patients studied in Spain by us during the same period. The origin of the clade comprising CRF75_BF1 and related viruses was estimated around 1984 in Brazil, with subsequent introduction of CRF75_BF1 in Italy around 1992, and migration from Italy to Spain around 1999. Conclusion A new HIV-1 CRF, designated CRF75_BF1, has been identified. CRF75_BF1 is the 6th CRF of South American origin initially identified in Western Europe, reflecting the increasing relationship of South American and European HIV-1 epidemics. The finding of low CD4+ T-cell lymphocyte counts early after diagnosis in patients harboring CRF75_BF1 viruses warrants further investigation on the virulence of this variant.
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Affiliation(s)
- Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Ibarra
- Department of Infectious Diseases, Hospital Universitario Basurto, Bilbao, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel García-Arata
- Department of Microbiology, Hospital Universitario de Fuenlabrada, Madrid, Spain
| | - María Moreno-Lorenzo
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Sáez de Adana
- Bioaraba, Microbiology, Infectious Diseases, Antimicrobials and Gene Therapy Research Group, Vitoria-Gasteiz, Spain
- Osakidetza-Basque Health Service, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Carmen Gómez-González
- Bioaraba, Microbiology, Infectious Diseases, Antimicrobials and Gene Therapy Research Group, Vitoria-Gasteiz, Spain
- Osakidetza-Basque Health Service, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Hill G, Pérez-Losada M, Delgado E, Benito S, Montero V, Gil H, Sánchez M, Cañada-García JE, García-Bodas E, Crandall KA, Thomson MM. The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF. Front Microbiol 2022; 13:863123. [PMID: 35685934 PMCID: PMC9172993 DOI: 10.3389/fmicb.2022.863123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
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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Affiliation(s)
- Gracelyn Hill
- Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E Cañada-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Cañada-García JE, Delgado E, Gil H, Benito S, Sánchez M, Ocampo A, Cabrera JJ, Miralles C, García-Bodas E, Mariño A, Ordóñez P, Gude MJ, Ezpeleta C, Thomson MM. 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 2022; 13:863084. [PMID: 35694315 PMCID: PMC9185580 DOI: 10.3389/fmicb.2022.863084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Those derived from recombination between subtype B and subsubtype F1, with 18 reported, most of them of South American origin, are among the most diverse. In this study, we identified a HIV-1 BF1 recombinant cluster that is expanding in Spain, transmitted mainly via heterosexual contact, which, analyzed in near full-length genomes in four viruses, exhibited a coincident BF1 mosaic structure, with 12 breakpoints, that fully coincided with that of two viruses (10BR_MG003 and 10BR_MG005) from Brazil, previously classified as CRF72_BF1. The three remaining Brazilian viruses (10BR_MG002, 10BR_MG004, and 10BR_MG008) previously identified as CRF72_BF1 exhibited mosaic structures highly similar, but not identical, to that of the Spanish viruses and to 10BR_MG003 and 10BR_MG005, with discrepant subtypes in two short genome segments, located in pol and gp120env. Based on these results, we propose that the five viruses from Brazil previously identified as CRF72_BF1 actually belong to two closely related CRFs, one comprising 10BR_MG002, 10BR_MG004, and 10BR_MG008, which keep their CRF72_BF1 designation, and the other, designated CRF122_BF1, comprising 10BR_MG003, 10BR_MG005, and the viruses of the identified Spanish cluster. Three other BF1 recombinant genomes, two from Brazil and one from Italy, previously identified as unique recombinant forms, were classified as CRF72_BF1. CRF122_BF1, but not CRF72_BF1, was associated with protease L89M substitution, which was reported to contribute to antiretroviral drug resistance. Phylodynamic analyses estimate the emergence of CRF122_BF1 in Brazil around 1987. Given their close phylogenetic relationship and similar structures, the grouping of CRF72_BF1 and CRF122_BF1 in a CRF family is proposed.
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Affiliation(s)
- Javier E. Cañada-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Antonio Ocampo
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Jorge Julio Cabrera
- Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Celia Miralles
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Ana Mariño
- Infectious Diseases Unit, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Patricia Ordóñez
- Department of Microbiology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - María José Gude
- Department of Microbiology, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Carmen Ezpeleta
- Department of Clinical Microbiology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- *Correspondence: Michael M. Thomson,
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Bacqué J, Delgado E, Benito S, Moreno-Lorenzo M, Montero V, Gil H, Sánchez M, Nieto-Toboso MC, Muñoz J, Zubero-Sulibarria MZ, Ugalde E, García-Bodas E, Cañada JE, Del Romero J, Rodríguez C, Rodríguez-Avial I, Elorduy-Otazua L, Portu JJ, García-Costa J, Ocampo A, Cabrera JJ, Thomson MM. Identification of CRF66_BF, a New HIV-1 Circulating Recombinant Form of South American Origin. Front Microbiol 2021; 12:774386. [PMID: 34867914 PMCID: PMC8634668 DOI: 10.3389/fmicb.2021.774386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/25/2021] [Indexed: 12/03/2022] Open
Abstract
Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Among 110 reported in the literature, 17 are BF1 intersubtype recombinant, most of which are of South American origin. Among these, all 5 identified in the Southern Cone and neighboring countries, except Brazil, derive from a common recombinant ancestor related to CRF12_BF, which circulates widely in Argentina, as deduced from coincident breakpoints and clustering in phylogenetic trees. In a HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 20 samples from 3 separate regions which were of F1 subsubtype, related to the Brazilian strain, in protease-reverse transcriptase (Pr-RT) and of subtype B in integrase. Remarkably, 14 individuals from this cluster (designated BF9) were Paraguayans and only 4 were native Spaniards. HIV-1 transmission was predominantly heterosexual, except for a subcluster of 6 individuals, 5 of which were men who have sex with men. Ten additional database sequences, from Argentina (n = 4), Spain (n = 3), Paraguay (n = 1), Brazil (n = 1), and Italy (n = 1), branched within the BF9 cluster. To determine whether it represents a new CRF, near full-length genome (NFLG) sequences were obtained for 6 viruses from 3 Spanish regions. Bootscan analyses showed a coincident BF1 recombinant structure, with 5 breakpoints, located in p17gag, integrase, gp120, gp41-rev overlap, and nef, which was identical to that of two BF1 recombinant viruses from Paraguay previously sequenced in NFLGs. Interestingly, none of the breakpoints coincided with those of CRF12_BF. In a maximum likelihood phylogenetic tree, all 8 NFLG sequences grouped in a strongly supported clade segregating from previously identified CRFs and from the CRF12_BF “family” clade. These results allow us to identify a new HIV-1 CRF, designated CRF66_BF. Through a Bayesian coalescent analysis, the most recent common ancestor of CRF66_BF was estimated around 1984 in South America, either in Paraguay or Argentina. Among Pr-RT sequences obtained by us from HIV-1-infected Paraguayans living in Spain, 14 (20.9%) of 67 were of CRF66_BF, suggesting that CRF66_BF may be one of the major HIV-1 genetic forms circulating in Paraguay. CRF66_BF is the first reported non-Brazilian South American HIV-1 CRF_BF unrelated to CRF12_BF.
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Affiliation(s)
- Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Moreno-Lorenzo
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Josefa Muñoz
- Hospital Universitario de Basurto, Bilbao, Spain
| | | | | | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | | | | | - Antonio Ocampo
- Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | | | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America. Sci Rep 2021; 11:11442. [PMID: 34075073 PMCID: PMC8169922 DOI: 10.1038/s41598-021-90023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/28/2021] [Indexed: 01/10/2023] Open
Abstract
Circulating recombinant forms (CRFs) contribute substantially to the HIV-1 pandemic. Among 105 CRFs described in the literature, 16 are BF intersubtype recombinants, most of South American origin, of which CRF12_BF is the most widely spread. A BF recombinant cluster identified in Bolivia was suggested to represent a new CRF_BF. Here we find that it belongs to a larger cluster incorporating 39 viruses collected in 7 countries from 3 continents, 22 of them in Spain, most from Bolivian or Peruvian individuals, and 12 in South America (Bolivia, Argentina, and Peru). This BF cluster comprises three major subclusters, two associated with Bolivian and one with Peruvian individuals. Near full-length genome sequence analyses of nine viruses, collected in Spain, Bolivia, and Peru, revealed coincident BF mosaic structures, with 13 breakpoints, 6 and 7 of which coincided with CRF12_BF and CRF17_BF, respectively. In a phylogenetic tree, they grouped in a clade closely related to these CRFs, and more distantly to CRF38_BF and CRF44_BF, all circulating in South America. These results allowed to identify a new HIV-1 CRF, designated CRF89_BF. Through phylodynamic analyses, CRF89_BF emergence was estimated in Bolivia around 1986. CRF89_BF is the fifth CRF member of the HIV-1 recombinant family related to CRF12_BF.
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Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain. Viruses 2021; 13:v13010093. [PMID: 33445523 PMCID: PMC7826730 DOI: 10.3390/v13010093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.
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Li J, Gao Q, Zhang M, Liu J, Jia Y, Feng Y, Xia X, Dong X. A newly emerging HIV-1 circulating recombinant form (CRF110_BC) comprising subtype B and C among intravenous drug users in Yunnan, China. J Infect 2020; 82:e8-e10. [PMID: 33352212 DOI: 10.1016/j.jinf.2020.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Jianjian Li
- Clinical Laboratory, Yunnan Provincial Infectious Diseases Hospital, 28 km away from Shi'an highway, Yunnan, Kunming, China
| | - Qinghua Gao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Mi Zhang
- Clinical Laboratory, Yunnan Provincial Infectious Diseases Hospital, 28 km away from Shi'an highway, Yunnan, Kunming, China
| | - Jiafa Liu
- Clinical Laboratory, Yunnan Provincial Infectious Diseases Hospital, 28 km away from Shi'an highway, Yunnan, Kunming, China
| | - Yuanyuan Jia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
| | - Xingqi Dong
- Clinical Laboratory, Yunnan Provincial Infectious Diseases Hospital, 28 km away from Shi'an highway, Yunnan, Kunming, China.
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9
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Bagaglio S, Uberti-Foppa C, Sagnelli C, Lai A, Hasson H, Salpietro S, Messina E, Morsica G, Zaffina C, Sica A, Lazzarin A, Angeletti S, Sagnelli E, Foley B, Ciccozzi M. HIV-1 recombinant forms in immigrants regularly residing in Milan, northern Italy. Infection 2020; 48:553-558. [PMID: 32430647 DOI: 10.1007/s15010-020-01434-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
To assess the HIV -1subtypes distribution in HIV-1 positive migrants living in Milan we studied 77 HIV-1 patients followed at the San Raffaele Hospital of Milan. Twenty subjects were born in Europe, 43 in the Americas, 10 in Africa and 4 in Asia. Unsafe heterosexual activity prevailed in migrants born in Africa and male homosexuality in those born in European, American and Asian countries (p = 0.05). The phylogeny showed that 38/77 (49.3%) subjects carried HIV-B subtype while the remaining strains were classified as not pure HIV-1 B subtypes 13/77 (16.9%) or recombinant forms 26/77 (33.8%). Female gender more frequently showed HIV-1 non-B strains and rarely HIV-1 B subtypes (12/39, 30.8% vs. 3/38, 7.9%, p = 0.02). Transmitted drug resistance was identified in 10/77 (13%) patients predominately with B subtype. Our data underscore a large heterogeneity in HIV-1 subtypes and a large proportion of recombinant forms.
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Affiliation(s)
- Sabrina Bagaglio
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Caterina Uberti-Foppa
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Caterina Sagnelli
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Hamid Hasson
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Salpietro
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Emanuela Messina
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Morsica
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Zaffina
- Medical Statistics and Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Antonello Sica
- Department of Precision Medicine, Campania University Luigi Vanvitelli, Naples, Italy
| | - Adriano Lazzarin
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Angeletti
- Laboratory Clinical Science, Campus Bio-Medico University, Rome, Italy
| | - Evangelista Sagnelli
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy.
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Massimo Ciccozzi
- Laboratory Clinical Science, Campus Bio-Medico University, Rome, Italy
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10
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Lepore L, Fabrizio C, Bavaro DF, Milano E, Volpe A, Lagioia A, Angarano G, Saracino A, Monno L. Gp120 substitutions at positions associated with resistance to fostemsavir in treatment-naive HIV-1-positive individuals. J Antimicrob Chemother 2020; 75:1580-1587. [DOI: 10.1093/jac/dkaa034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
Fostemsavir, a novel attachment inhibitor targeting the HIV-1 gp120, has demonstrated wide in vitro activity. However, the high rate of HIV gp120 substitutions could jeopardize its efficacy. We investigated envelope (env) substitutions at positions associated with resistance to fostemsavir in patients with a new HIV-1 diagnosis according to HIV subtype and tropism.
Methods
Gp120 sequences from 409 subjects were retrospectively analysed and the presence of the L116P, A204D, S375H/M/T, M426L, M434I and M475I mutations was evaluated. Other amino acid changes at the same positions were also recorded. The variability at each amino acid position was evaluated using Shannon entropy.
Results
The frequency of mutations was: S375T (13.2%); M426L (6.8%); M434I (2.9%); M475I (2.7%); S375H (1.0%)/M (0.8%) and L116P (0.31%). Statistically significant differences were found at positions 375 (R5/non-R5 strains and B/non-B subtypes) and 426 (B/non-B subtypes); post hoc analysis revealed that significance for position 375 was steered by S375T while for position 426 significance was governed by unusual substitutions, in particular M426R (B/non-B, P < 0.00001). The variability of env constant domains appeared to be more relevant in the non-B virus population.
Conclusions
In conclusion, gp120 substitutions were detected in different subtypes and in both R5 and non-R5 variants. Despite the great variability of gp120, the frequency of mutations was low overall and the predominant substitution was S375T, the role of which in reducing fostemsavir efficacy is less substantial.
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Affiliation(s)
- Luciana Lepore
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Claudia Fabrizio
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Malattie Infettive e Tropicali, Ospedale Oncologico San Giuseppe Moscati, Taranto, Italy
| | - Davide Fiore Bavaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Eugenio Milano
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Anna Volpe
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonella Lagioia
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Gioacchino Angarano
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
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11
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Fabeni L, Alteri C, Berno G, Scutari R, Orchi N, De Carli G, Bertoli A, Carioti L, Gori C, Forbici F, Salpini R, Vergori A, Gagliardini R, Cicalini S, Mondi A, Pinnetti C, Mazzuti L, Turriziani O, Colafigli M, Borghi V, Montella F, Pennica A, Lichtner M, Girardi E, Andreoni M, Mussini C, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Characterisation of HIV-1 molecular transmission clusters among newly diagnosed individuals infected with non-B subtypes in Italy. Sex Transm Infect 2019; 95:619-625. [PMID: 31076456 DOI: 10.1136/sextrans-2019-054017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE We evaluated the characteristics of HIV-1 molecular transmission clusters (MTCs) in 1890 newly diagnosed individuals infected with non-B subtypes between 2005 and 2017 in Italy. METHODS Phylogenetic analyses were performed on pol sequences to characterise subtypes/circulating recombinant forms and identify MTCs. MTCs were divided into small (SMTCs, 2-3 sequences), medium (MMTCs, 4-9 sequences) and large (LMTCs, ≥10 sequences). Factors associated with MTCs were evaluated using logistic regression analysis. RESULTS 145 MTCs were identified and involved 666 individuals (35.2%); 319 of them (16.9%) were included in 13 LMTCs, 111 (5.9%) in 20 MMTCs and 236 (12.5%) in 112 SMTCs. Compared with individuals out of MTCs, individuals involved in MTCs were prevalently Italian (72.7% vs 30.9%, p<0.001), male (82.9% vs 62.3%, p<0.001) and men who have sex with men (MSM) (43.5% vs 14.5%, p<0.001). Individuals in MTCs were also younger (median (IQR) years: 41 (35-49) vs 43 (36-51), p<0.001) and had higher CD4 cell count in comparison with individuals out of MTCs (median (IQR): 109/L: 0.4 (0.265-0.587) vs 0.246 (0.082-0.417), p<0.001). The viral load remained stable between the two groups (median (IQR) log10 copies/mL: 4.8 (4.2-5.5) vs 5.0 (4.3-5.5), p=0.87). Logistic regression confirmed that certain factors such as being MSM, of Italian origin, younger age and higher CD4 cell count were significantly associated with MTCs. CONCLUSIONS Our findings show that HIV-1 newly diagnosed individuals infected with non-B subtypes are involved in several MTCs in Italy. These MTCs include mainly Italians and MSM and highlight the complex phenomenon characterising the HIV-1 spread. This is important especially in view of monitoring the HIV epidemic and guiding the public health response.
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Affiliation(s)
- Lavinia Fabeni
- Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Claudia Alteri
- Oncology and Oncohematology, University of Milan, Milan, Italy
| | - Giulia Berno
- Laboratory of Virology, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Rossana Scutari
- Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Nicoletta Orchi
- AIDS Reference Center, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | | | - Ada Bertoli
- Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Luca Carioti
- Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Caterina Gori
- Laboratory of Virology, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Federica Forbici
- Laboratory of Virology, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Romina Salpini
- Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | | | - Annalisa Mondi
- Clinical Department, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Carmela Pinnetti
- Clinical Department, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Laura Mazzuti
- Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | | | - Vanni Borghi
- Infectious Diseases, University Hospital of Modena, Modena, Italy
| | | | | | - Miriam Lichtner
- Infectious Diseases Unit, "Sapienza" University, Polo Pontino, Latina, Italy
| | - Enrico Girardi
- Clinical Epidemiology, INMI "Lazzaro Spallanzani" IRCCS, Rome, Lazio, Italy
| | - Massimo Andreoni
- Infectious Diseases, University Hospital "Tor Vergata", Rome, Italy
| | - Cristina Mussini
- Infectious Diseases, University Hospital of Modena, Modena, Italy
| | - Andrea Antinori
- Clinical Department, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | | | - Carlo Federico Perno
- Oncology and Oncohematology, University of Milan, Milan, Italy.,Laboratory of Virology, INMI "Lazzaro Spallanzani"-IRCCS, Rome, Italy
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12
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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13
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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14
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Reis MNG, Guimarães ML, Bello G, Stefani MMA. Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms. Front Microbiol 2019; 10:97. [PMID: 30804902 PMCID: PMC6378278 DOI: 10.3389/fmicb.2019.00097] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/16/2019] [Indexed: 01/22/2023] Open
Abstract
Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous pol region studies (2003–2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in pol were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B (n = 629), 6.4% subtype C (n = 53), 4.2% subtype F1 (n = 35), 13.4% intersubtype recombinants: 10.5% BF1 (n = 87), 2.3% BC (n = 19), 0.4% F1CB (n = 3), and 0.2% CF1 (n = 2). Two full and one partial BF1C genomes allowed the characterization of the CRF81_cpx that has 9 breakpoints dividing the genome into 10 subregions. Basic Local Alignment Search Tool searches (Los Alamos HIV Sequence Database) identified six other sequences with the same recombination profile in pol, five from Brazil, and one from Italy. The estimated median TMRCA of CRF81_cpx was 1999 (1992–2003). CRF60_BC-like sequences, originally described in Italy, were also found. Two full and one near full-length BF1 genomes led to the characterization of the new CRF99_BF1 that has six recombination breakpoints dividing the genome into seven subregions. Two new URFs BF1, with six recombination breakpoints and seven subregions were also characterized. The description of the first Brazilian BF1C CRF81_cpx and of the new CRF99_BF1 corroborate the important role of CRFs in the HIV/AIDS epidemic throughout Brazil. Our data also highlight the value of HIV-1 full-genome sequence studies in order to fully reveal the complexity of the epidemic in a huge country as Brazil.
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Affiliation(s)
- Mônica N G Reis
- Laboratório de Imunologia da Aids e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Monick L Guimarães
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mariane M A Stefani
- Laboratório de Imunologia da Aids e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
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15
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Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
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Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
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16
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Lunar MM, Židovec Lepej S, Tomažič J, Vovko TD, Pečavar B, Turel G, Maver M, Poljak M. HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011-2016 update. PLoS One 2018; 13:e0196670. [PMID: 29698470 PMCID: PMC5919638 DOI: 10.1371/journal.pone.0196670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/17/2018] [Indexed: 01/30/2023] Open
Abstract
HIV-positive individuals that have a detected transmitted drug resistance (TDR) at baseline have a higher risk of virological failure with antiretroviral therapy (ART). This study offers an update on the prevalence of TDR in Slovenia, looks for onward transmission of TDR, and reassesses the need for baseline drug resistance testing. Blinded questionnaires and partial pol sequences were obtained from 54.5% (168/308) of all of the patients diagnosed with HIV-1 from 2011 to 2016. Subtype B was detected in 82.7% (139/168) of patients, followed by subtype A (8.3%), subtype C (2.4%), and CRF01_AE (1.8%). Surveillance drug resistance mutations (SDRMs) were found in four individuals (2.4%), all of them men who have sex with men (MSM) and infected with subtype B. K103N was detected in two patients and T68D and T215D in one person each, corresponding to a prevalence of 0%, 1.2%, and 1.2% of TDR to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs), and non-NRTIs (NNRTIs), respectively. The impact of mutations on drug susceptibility was found to be most pronounced for NNRTIs. No forward spread of TDR within the country was observed; however, phylogenetic analysis revealed several new introductions of HIV into Slovenia in recent years, possibly due to increased risky behavior by MSM. This was indirectly confirmed by a substantial increase in syphilis cases and HIV-1 non-B subtypes during the study period. A drug-resistant HIV variant with good transmission fitness is thus more likely to be imported into Slovenia in the near future, and so TDR should be closely monitored.
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Affiliation(s)
- Maja M. Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Janez Tomažič
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Tomaž D. Vovko
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Blaž Pečavar
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Gabriele Turel
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Manja Maver
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Trends in Drug Resistance Prevalence, HIV-1 Variants and Clinical Status in HIV-1-infected Pediatric Population in Madrid: 1993 to 2015 Analysis. Pediatr Infect Dis J 2018; 37:e48-e57. [PMID: 28991889 DOI: 10.1097/inf.0000000000001760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The expanded use of long-term antiretroviral treatments in infected children may exacerbate the problem of drug resistance mutations selection, which can compromise treatment efficiency. OBJECTIVE We describe the temporal trends of HIV drug resistance mutations and the HIV-1 variants during 23 years (1993 to March 2016) in the Madrid cohort of HIV-infected children and adolescents. METHODS We selected patients with at least one available HIV-1 pol sequence/genotypic resistance profile, establishing different groups according to the sampling year of first resistance data. We determined the prevalence of transmitted drug resistance mutations or acquired drug resistance mutations (DRM), the drug susceptibility among resistant viruses and HIV-1 variants characterized by phylogeny across time. RESULTS A total of 245 pediatric patients were selected, being mainly female, Spanish native, perinatally infected and carrying HIV-1 subtype B. At first sampling, most pediatric patients were on antiretroviral therapy and heavily pretreated. During 1993 to 2016, transmitted drug resistance mutations was found in 13 (26%) of 50 naive children [non-nucleoside reverse transcriptase inhibitors (NNRTI), 14.6%; nucleoside reverse transcriptase inhibitors (NRTI), 10.4%; protease inhibitors, 8.7%]. DRM appeared in 139 (73.2%) of 190 pretreated patients (NRTI, 64.5%; NNRTI, 36%; protease inhibitors, 35.1%). DRM to NNRTI was higher in last 5 years. Non-B variants infected 14.5% of children and adolescents of the Madrid Cohort, being mainly intersubtype recombinants (76.5%), including complex unique recombinant strains. They caused 3.4% infections before 2000, rising to 85.7% during 2011 to 2016. CONCLUSIONS Periodic surveillance resistance and molecular epidemiology studies in long-term pretreated HIV-infected pediatric populations are required to optimize treatment regimens. Results will permit a better understanding of long-time dynamics of viral resistance and HIV-1 variants in Spain.
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Yebra G, Frampton D, Gallo Cassarino T, Raffle J, Hubb J, Ferns RB, Waters L, Tong CYW, Kozlakidis Z, Hayward A, Kellam P, Pillay D, Clark D, Nastouli E, Leigh Brown AJ. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS One 2018; 13:e0192081. [PMID: 29389981 PMCID: PMC5794160 DOI: 10.1371/journal.pone.0192081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND & METHODS The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. RESULTS The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. CONCLUSIONS The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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Affiliation(s)
- Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Frampton
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | | | - Jade Raffle
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
| | - Jonathan Hubb
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
| | - R. Bridget Ferns
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- NIHR UCLH/UCL Biomedical Research Centre, London, United Kingdom
| | - Laura Waters
- Department of HIV Medicine, Mortimer Market Centre, Central & North West London NHS Trust, London, United Kingdom
| | - C. Y. William Tong
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Queen Mary University, London, United Kingdom
| | - Zisis Kozlakidis
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- UCL Institute of Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Andrew Hayward
- UCL Institute of Epidemiology and Health Care, London, United Kingdom
| | - Paul Kellam
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Deenan Pillay
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | - Duncan Clark
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- School of Life Sciences, University of Glasgow. Glasgow, United Kingdom
| | - Eleni Nastouli
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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Beloukas A, Psarris A, Giannelou P, Kostaki E, Hatzakis A, Paraskevis D. Molecular epidemiology of HIV-1 infection in Europe: An overview. INFECTION GENETICS AND EVOLUTION 2016; 46:180-189. [PMID: 27321440 DOI: 10.1016/j.meegid.2016.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.
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Affiliation(s)
- Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alexandros Psarris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polina Giannelou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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