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Gil H, Delgado E, Benito S, Georgalis L, Montero V, Sánchez M, Cañada-García JE, García-Bodas E, Díaz A, Thomson MM. 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 2022; 13:782609. [PMID: 35432279 PMCID: PMC9009226 DOI: 10.3389/fmicb.2022.782609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses of HIV-1-infected individuals whose transmission is related group phylogenetically in transmission clusters (TCs). The study of the phylogenetic relations of these viruses and the factors associated with these individuals is essential to analyze the HIV-1 epidemic. In this study, we examine the role of TCs in the epidemiology of HIV-1 infection in Galicia and the Basque County, two regions of northern Spain. A total of 1,158 HIV-1-infected patients from both regions with new diagnoses (NDs) in 2013–2018 were included in the study. Partial HIV-1 pol sequences were analyzed phylogenetically by approximately maximum-likelihood with FastTree 2. In this analysis, 10,687 additional sequences from samples from HIV-1-infected individuals collected in Spain in 1999–2019 were also included to assign TC membership and to determine TCs’ sizes. TCs were defined as those which included viruses from ≥4 individuals, at least 50% of them Spaniards, and with ≥0.95 Shimodaira-Hasegawa-like node support in the phylogenetic tree. Factors associated to TCs were evaluated using odds ratios (OR) and their 95% CI. Fifty-one percent of NDs grouped in 162 TCs. Male patients (OR: 2.6; 95% CI: 1.5–4.7) and men having sex with men (MSM; OR: 2.1; 95% CI: 1.4–3.2) had higher odds of belonging to a TC compared to female and heterosexual patients, respectively. Individuals from Latin America (OR: 0.3; 95% CI: 0.2–0.4), North Africa (OR: 0.4; 95% CI: 0.2–1.0), and especially Sub-Saharan Africa (OR: 0.02; 95% CI: 0.003–0.2) were inversely associated to belonging to TCs compared to native Spaniards. Our results show that TCs are important components of the HIV-1 epidemics in the two Spanish regions studied, where transmission between MSM is predominant. The majority of migrants were infected with viruses not belonging to TCs that expand in Spain. Molecular epidemiology is essential to identify local peculiarities of HIV-1 propagation. The early detection of TCs and prevention of their expansion, implementing effective control measures, could reduce HIV-1 infections.
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Affiliation(s)
- Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Michael M. Thomson, ; Horacio Gil,
| | - 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
| | - Leonidas Georgalis
- 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
| | - 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
| | - Asunción Díaz
- HIV Surveillance and Behavioral Monitoring Unit, Centro Nacional de Epidemiología, 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
- *Correspondence: Michael M. Thomson, ; Horacio Gil,
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González-Domenech CM, Sena-Corrales G, Viciana-Ramos I, Palacios-Muñoz R, Mora-Navas L, Clavijo-Frutos E, Santos-González J. High Prevalence of Sequences Included in Transmission Clusters Within Newly Diagnosed HIV-1 Patients in Southern Spain (2004-2015). Microb Drug Resist 2020; 26:1090-1097. [PMID: 32240038 DOI: 10.1089/mdr.2019.0344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The presence of transmission clusters (TCs) and their epidemiological characteristics in a treatment-naive cohort of HIV-1 patients in southern Spain over a decade (2004-2015) were evaluated. Protease and reverse transcriptase sequences provided by each genotype test were used in the phylogenetic study, performed first by the neighbor-joining method and then confirmed by Bayesian analysis. We collected clinical, immunovirological, and demographic data for all patients included. Our cohort comprised 757 patients, 428 (56.5%) belonging to a TC. Overall, we found 123 TCs, 21 of them comprising five or more individuals and three with ≥10 sequences. Forty-three TCs (35.0%) remained active. The clustered patients were mainly men (92.8%) who had sex with men (MSM) (81.5%), Spanish (80.6%), and young adults (median age at diagnosis of 32.6 years). They had lower percentages of late diagnosis and AIDS cases (42.1% and 13.6%, respectively), whereas the presence of recent seroconverters (31.1%), HIV-1 B subtypes (79.4%), and transmission drug resistance (20.3%) increased within TCs, with regard to not-clustered individuals. Among the TCs of non-B variants, circulating recombinant forms (CRF) were predominant (87.5%), with the highest frequencies for CRF19_cpx (17.0% of non-B subtype sequences in TCs); CRF02_AG (15.9%); and CRF01_AE (9.1%). In conclusion, over half of our cohort was included within a TC. More than a third of TCs found could be considered active transmission events. Belonging to a TC was related to MSM, Spanish origin, recent seroconversion, high prevalence of resistance mutations, and B HIV subtype. Among the non-B genetic forms in TCs, we found a high prevalence of CRF19_cpx, CRF02_AG, and CRF01_AE variants.
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Affiliation(s)
- Carmen M González-Domenech
- Clinical Research Group in HIV Infection, Endovascular Infection and Bacteremia, Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain
| | - Gabriel Sena-Corrales
- Clinical Research Group in HIV Infection, Endovascular Infection and Bacteremia, Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain
| | - Isabel Viciana-Ramos
- Clinical Research Group in HIV Infection, Endovascular Infection and Bacteremia, Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain.,Infectious Diseases and Clinical Microbiology Unit, Virgen de la Victoria Hospital, Malaga, Spain
| | - Rosario Palacios-Muñoz
- Clinical Research Group in HIV Infection, Endovascular Infection and Bacteremia, Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain.,Infectious Diseases and Clinical Microbiology Unit, Virgen de la Victoria Hospital, Malaga, Spain
| | - Laura Mora-Navas
- Infectious Diseases and Clinical Microbiology Unit, Virgen de la Victoria Hospital, Malaga, Spain
| | | | - Jesús Santos-González
- Clinical Research Group in HIV Infection, Endovascular Infection and Bacteremia, Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain.,Infectious Diseases and Clinical Microbiology Unit, Virgen de la Victoria Hospital, Malaga, Spain
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Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach. PLoS One 2017; 12:e0186928. [PMID: 29084239 PMCID: PMC5662216 DOI: 10.1371/journal.pone.0186928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/10/2017] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic studies are a valuable tool to understand viral transmission patterns and the role of immigration in HIV-1 spread. We analyzed the spatio-temporal relationship of different HIV-1 non-B subtype variants over time using phylogenetic analysis techniques. We collected 693 pol (PR+RT) sequences that were sampled from 2005 to 2012 from naïve patients in different hospitals in southern Spain. We used REGA v3.0 to classify them into subtypes and recombinant forms, which were confirmed by phylogenetic analysis through maximum likelihood (ML) using RAxML. For the main HIV-1 non-B variants, publicly available, genetically similar sequences were sought using HIV-BLAST. The presence of HIV-1 lineages circulating in our study population was established using ML and Bayesian inference (BEAST v1.7.5) and transmission networks were identified. We detected 165 (23.4%) patients infected with HIV-1 non-B variants: 104 (63%) with recombinant viruses in pol: CRF02_AG (71, 43%), CRF14_BG (8, 4.8%), CRF06_cpx (5, 3%) and nine other recombinant forms (11, 6.7%) and unique recombinants (9, 5.5%). The rest (61, 37%) were infected with non-recombinant subtypes: A1 (30, 18.2%), C (7, [4.2%]), D (3, [1.8%]), F1 (9, 5.5%) and G (12, 7.3%). Most patients infected with HIV-1 non-B variants were men (63%, p < 0.001) aged over 35 (73.5%, p < 0.001), heterosexuals (92.2%, p < 0.001), from Africa (59.5%, p < 0.001) and living in the El Ejido area (62.4%, p<0.001). We found lineages of epidemiological relevance (mainly within Subtype A1), imported primarily through female sex workers from East Europe. We detected 11 transmission clusters of HIV-1 non-B Subtypes, which included patients born in Spain in half of them. We present the phylogenetic profiles of the HIV-1 non-B variants detected in southern Spain, and explore their putative geographical origins. Our data reveals a high HIV-1 genetic diversity likely due to the import of viral lineages that circulate in other countries. The highly immigrated El Ejido area acts as a gateway through which different subtypes are introduced into other regions, hence the importance of setting up epidemiological control measures to prevent future outbreaks.
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Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, the United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
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Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain. PLoS One 2016; 11:e0168099. [PMID: 28002469 PMCID: PMC5176287 DOI: 10.1371/journal.pone.0168099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/23/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain. PATIENTS & METHODS We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6. RESULTS Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations. CONCLUSIONS We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.
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Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | - Ana B. Lozano
- Servicio de Infecciosas, Hospital de Poniente, Almería, Spain
| | - Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
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Viciana I, González-Domenech CM, Palacios R, Delgado M, Del Arco A, Tellez F, Jarilla F, Fernández S, Clavijo E, Santos J. Clinical, virological and phylogenetic characterization of a multiresistant HIV-1 strain outbreak in naive patients in southern Spain. J Antimicrob Chemother 2015; 71:357-61. [PMID: 26483513 DOI: 10.1093/jac/dkv332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/15/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We describe the characteristics of an HIV-1 strain with six viral reverse transcriptase mutations (D67N, T69N/D, V118I, V179D, T215S and K219Q), which we have called the Malaga strain. This strain was detected in treatment-naive patients from southern Spain. METHODS The study was undertaken at the Virgen de la Victoria Hospital, Malaga, a reference centre for the study of HIV-1 genotype resistance in Andalusia (the 'Costa del Sol'), Spain. Genotypic resistance testing was done in an automated sequencer. Phylogenetic analysis was performed using a 630 bp region of the reverse transcriptase with the mutations mentioned. RESULTS Between 2007 and 2014, we detected the Malaga strain in 30 treatment-naive patients. All were MSM, seen at five hospitals on the Costa del Sol. In all cases, the HIV-1 was subtype B with viral tropism R5. Phylogenetic analysis based on the reverse transcriptase sequence showed consistent grouping (with a bootstrap value of the common node of 100%) of the isolates that shared the mutation pattern mentioned. This strain has not been detected elsewhere or in previously treated patients. All of the patients treated with first-line combination ART responded. CONCLUSIONS We report a cluster of an HIV-1 strain with multiple resistance mutations that was transmitted over a period of >8 years, affecting 30 naive patients from the same geographical area. The strain was susceptible to first-line combination ART.
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Affiliation(s)
- I Viciana
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | | | - R Palacios
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | - M Delgado
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Regional Carlos Haya, Málaga, Spain
| | - A Del Arco
- UGC de Enfermedades Infecciosas, Hospital Costa del Sol, Marbella, Spain
| | - F Tellez
- UGC de Enfermedades Infecciosas y Microbiología Clínica, Hospital La Línea, AGS Campo de Gibraltar, Cádiz, Spain
| | - F Jarilla
- Servicio de Medicina Interna, Hospital Comarcal de Antequera, Malaga, Spain
| | - S Fernández
- Servicio de Medicina Interna, Hospital Comarcal de la Axarquía, Vélez-Málaga, Spain
| | - E Clavijo
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain
| | - J Santos
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
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