1
|
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.
Collapse
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
| |
Collapse
|
2
|
Di Giambenedetto S, Zazzi M, Corsi P, Gonnelli A, Di Pietro M, Giacometti A, Almi P, Trezzi M, Boeri E, Gianotti N, Menzo S, Gobbo RD, Francisci D, Nerli A, Galli L, Luca AD. Evolution and predictors of HIV type-1 drug resistance in patients failing combination antiretroviral therapy in Italy. Antivir Ther 2009. [DOI: 10.1177/135965350901400308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background This study aimed to examine the evolution of genotypic drug resistance prevalence in treatment-failing patients in the multicentre, Italian, Antiretroviral Resistance Cohort Analysis (ARCA). Methods Patients with a drug resistance genotype test performed between 1999 and 2006 at failure of a combination antiretroviral therapy and with complete treatment history were selected. The prevalence of resistance was measured overall, per calendar year, per drug class and per treatment line at failure. Results The overall resistance prevalence was 81%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs) declined after 2002 (68% in 2006; χ2 for trend P=0.004); resistance to non-NRTIs (NNRTIs) stabilized after 2004; and resistance to protease inhibitors (PIs) declined after 2001 (43% in 2006; P=0.004). In first-line failures, NRTI resistance decreased after 2002 ( P=0.006), NNRTI resistance decreased after 2003 ( P=0.001) and PI resistance decreased after 2001 ( P<0.001). Independent predictors of resistance to any class were HIV type-1 transmission by heterosexual contacts as compared with injecting drug use, a higher number of experienced regimens, prior history of suboptimal therapy, higher viral load and CD4+ T-cell counts, more recent calendar year and viral subtype B carriage, whereas the use of PI-based versus NNRTI-based regimens at failure was associated with a reduced risk of resistance. There was an increase of type-1 thymidine analogue and of protease mutations L33F, I47A/V, I50V and I54L/M, whereas L90M decreased over calendar years. Conclusions During more recent years, emerging drug resistance has decreased, particularly in first-line failures. The prevalence continues to be high in multiregimen-failing patients.
Collapse
Affiliation(s)
| | - Maurizio Zazzi
- Department of Molecular Biology, University of Siena, Siena, Italy
| | - Paola Corsi
- Division of Infectious Diseases, Careggi University Hospital, Firenze, Italy
| | - Angela Gonnelli
- Unit of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Massimo Di Pietro
- Division of Infectious Diseases, SM Annunziata Hospital, Firenze, Italy
| | - Andrea Giacometti
- Institute of Clinical Infectious Diseases, University Hospital of Ancona, Ancona, Italy
| | - Paolo Almi
- Unit of Infectious Diseases, Hospital of Massa, Massa, Italy
| | - Michele Trezzi
- Unit of Infectious Diseases, Hospital of Grosseto, Grosseto, Italy
| | - Enzo Boeri
- Infectious Diseases Clinic, San Raffaele Hospital, Milan, Italy
| | - Nicola Gianotti
- Infectious Diseases Clinic, San Raffaele Hospital, Milan, Italy
| | - Stefano Menzo
- Institute of Microbiology, University of Ancona, Ancona, Italy
| | - Romana Del Gobbo
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| | - Daniela Francisci
- Unit of Infectious Diseases, Perugia University Hospital, Perugia, Italy
| | | | - Luisa Galli
- Unit of Infectious Diseases, Meyer Hospital, Firenze, Italy
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| |
Collapse
|
3
|
Audelin AM, Lohse N, Obel N, Gerstoft J, Jørgensen LB. The incidence rate of HIV type-1 drug resistance in patients on antiretroviral therapy: a nationwide population-based Danish cohort study 1999–2005. Antivir Ther 2009; 14:995-1000. [DOI: 10.3851/imp1412] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
4
|
Lohse N, Jørgensen LB, Kronborg G, Møller A, Kvinesdal B, Sørensen HT, Obel N, Gerstoft J, Gerstat J, Obel N, Kronborg G, Pedersen C, Larsen CS, Pedersen G, Laursen AL, Kvinesdal B, Møller A. Genotypic Drug Resistance and Long-Term Mortality in Patients with Triple-Class Antiretroviral Drug Failure. Antivir Ther 2007. [DOI: 10.1177/135965350701200606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objective To examine the prevalence of drug-resistance-associated mutations in HIV patients with triple-drug class virological failure (TCF) and their association with long-term mortality. Design Population-based study from the Danish HIV Cohort Study (DHCS). Methods We included all patients in the DHCS who experienced TCF between January 1995 and November 2004, and we performed genotypic resistance tests for International AIDS Society (IAS)-USA primary mutations on virus from plasma samples taken around the date of TCF. We computed time to all-cause death from date of TCF. The relative risk of death according to the number of mutations and individual mutations was estimated by Cox regression analysis and adjusted for potential confounders. Results Resistance tests were done for 133 of the 179 patients who experienced TCF. The median number of resistance mutations was eight (interquartile range 2–10), and 81 (61%) patients had mutations conferring resistance towards all three major drug classes. In a regression model adjusted for CD4+ T-cell count, HIV RNA, year of TCF, age, gender and previous inferior antiretroviral therapy, harbouring ≥9 versus ≤8 mutations was associated with increased mortality (mortality rate ratio [MRR] 2.3 [95% confidence interval (CI) 1.1–4.8]), as were the individual mutations T215Y (MRR 3.4 [95% CI 1.6–7.0]), G190A/S (MRR 3.2 [95% CI 1.6–6.6]) and V82F/A/T/S (MRR 2.5 [95% CI 1.2–5.3]). Conclusions In HIV patients with TCF, the total number of genotypic resistance mutations and specific single mutations predicted mortality.
Collapse
Affiliation(s)
- Nicolai Lohse
- Department of Clinical Epidemiology, Århus University Hospital, Århus, Denmark
- The Danish HIV Cohort Study, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Gitte Kronborg
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Axel Møller
- Department of Infectious Diseases, Kolding Hospital, Kolding, Denmark
| | - Birgit Kvinesdal
- Department of Infectious Diseases, Helsingør Hospital, Helsingør, Denmark
| | - Henrik T Sørensen
- Department of Clinical Epidemiology, Århus University Hospital, Århus, Denmark
- School of Public Health, Boston University, Boston, MA, USA
| | - Niels Obel
- The Danish HIV Cohort Study, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | - Jan Gerstoft
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J Gerstat
- Departments of Infectious Diseases at Copenhagen University Hospitals, Rigshospitalet
| | - N Obel
- Departments of Infectious Diseases at Copenhagen University Hospitals, Rigshospitalet
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Giambenedetto SD, Bracciale L, Colatigli M, Pannetti C, Bacarelli A, Prosperi M, Fadda G, Cauda R, De Luca A. Declining Prevalence of HIV-1 Drug Resistance in Treatment-Failing Patients: A Clinical Cohort Study. Antivir Ther 2007. [DOI: 10.1177/135965350701200516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objectives A major barrier to successful viral suppression in HIV type 1 (HIV-1)-infected individuals is the emergence of virus resistant to antiretroviral drugs. We explored the evolution of genotypic drug resistance prevalence in treatment-failing patients from 1999 to 2005 in a clinical cohort. Patients and Methods Prevalence of major International AIDS Society-USA HIV-1 drug resistance mutations was measured over calendar years in a population with treatment failure and undergoing resistance testing. Predictors of the presence of resistance mutations were analysed by logistic regression. Results Significant reductions of the prevalence of resistance to all three drug classes examined were observed. This was accompanied by a reduction in the proportion of treatment-failing patients. Independent predictors of drug resistance were the earlier calendar year, prior use of suboptimal nucleoside analogue therapy, male sex and higher CD4 levels at testing. Conclusions In a single clinical cohort, we observed a decrease in the prevalence of resistance to all three examined antiretroviral drug classes over time. If this finding is confirmed in multicentre cohorts it may translate into reduced transmission of drug-resistant virus from treated patients.
Collapse
Affiliation(s)
| | - Laura Bracciale
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| | - Manuela Colatigli
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| | | | | | - Mattia Prosperi
- Department of Computer Science and Automation, University of Roma Tre, Rome, Italy
| | - Giovanni Fadda
- Institute of Microbiology, Catholic University, Rome, Italy
| | - Roberto Cauda
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| |
Collapse
|