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Zhukova A, Voznica J, Dávila Felipe M, To TH, Pérez L, Martínez Y, Pintos Y, Méndez M, Gascuel O, Kouri V. Cuban history of CRF19 recombinant subtype of HIV-1. PLoS Pathog 2021; 17:e1009786. [PMID: 34370795 PMCID: PMC8376097 DOI: 10.1371/journal.ppat.1009786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/19/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022] Open
Abstract
CRF19 is a recombinant form of HIV-1 subtypes D, A1 and G, which was first sampled in Cuba in 1999, but was already present there in 1980s. CRF19 was reported almost uniquely in Cuba, where it accounts for ∼25% of new HIV-positive patients and causes rapid progression to AIDS (∼3 years). We analyzed a large data set comprising ∼350 pol and env sequences sampled in Cuba over the last 15 years and ∼350 from Los Alamos database. This data set contained both CRF19 (∼315), and A1, D and G sequences. We performed and combined analyses for the three A1, G and D regions, using fast maximum likelihood approaches, including: (1) phylogeny reconstruction, (2) spatio-temporal analysis of the virus spread, and ancestral character reconstruction for (3) transmission mode and (4) drug resistance mutations (DRMs). We verified these results with a Bayesian approach. This allowed us to acquire new insights on the CRF19 origin and transmission patterns. We showed that CRF19 recombined between 1966 and 1977, most likely in Cuban community stationed in Congo region. We further investigated CRF19 spread on the Cuban province level, and discovered that the epidemic started in 1970s, most probably in Villa Clara, that it was at first carried by heterosexual transmissions, and then quickly spread in the 1980s within the "men having sex with men" (MSM) community, with multiple transmissions back to heterosexuals. The analysis of the transmission patterns of common DRMs found very few resistance transmission clusters. Our results show a very early introduction of CRF19 in Cuba, which could explain its local epidemiological success. Ignited by a major founder event, the epidemic then followed a similar pattern as other subtypes and CRFs in Cuba. The reason for the short time to AIDS remains to be understood and requires specific surveillance, in Cuba and elsewhere.
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Affiliation(s)
- Anna Zhukova
- Unité Bioinformatique Evolutive, Département de Biologie Computationelle, Institut Pasteur, Paris, France
- Hub Bioinformatique et Biostatistique, Département de Biologie Computationelle, Institut Pasteur, Paris, France
- * E-mail: (AZ); (OG); (VK)
| | - Jakub Voznica
- Unité Bioinformatique Evolutive, Département de Biologie Computationelle, Institut Pasteur, Paris, France
- Université de Paris, Paris, France
| | - Miraine Dávila Felipe
- Unité Bioinformatique Evolutive, Département de Biologie Computationelle, Institut Pasteur, Paris, France
| | - Thu-Hien To
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lissette Pérez
- Institute of Tropical Medicine Pedro Kourí, Virology Department, Havana City, Cuba
| | - Yenisleidys Martínez
- Institute of Tropical Medicine Pedro Kourí, Virology Department, Havana City, Cuba
| | - Yanet Pintos
- Institute of Tropical Medicine Pedro Kourí, Virology Department, Havana City, Cuba
| | - Melissa Méndez
- Institute of Tropical Medicine Pedro Kourí, Virology Department, Havana City, Cuba
| | - Olivier Gascuel
- Unité Bioinformatique Evolutive, Département de Biologie Computationelle, Institut Pasteur, Paris, France
- * E-mail: (AZ); (OG); (VK)
| | - Vivian Kouri
- Institute of Tropical Medicine Pedro Kourí, Virology Department, Havana City, Cuba
- * E-mail: (AZ); (OG); (VK)
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Sam M, Masaba JPM, Alio D, Byakika-Tusiime J. Treatment Failure and Associated Factors among Individuals on Second Line Antiretroviral Therapy in Eastern Uganda: A Retrospective Cohort Study. Infect Dis (Lond) 2021; 14:11786337211014518. [PMID: 34121842 PMCID: PMC8175835 DOI: 10.1177/11786337211014518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/05/2021] [Indexed: 11/15/2022] Open
Abstract
Background: ART failure is a growing public health problem and a major threat to the progress of HIV/AIDS control. In Uganda however, little is documented on treatment outcomes and their associated factors among individuals on second line ART regimen. The rapid scale-up of ART over the past has resulted in substantial reductions in morbidity and mortality. However, as millions of people must be maintained on ART for life, individuals with ART treatment failure are increasingly encountered and the numbers are expected to rise. This could be attributed to factors such as sub-standard regimens, limited access to routine viral load monitoring, treatment interruptions, suboptimal adherence, among others. The purpose of this study was to estimate 5-year cumulative treatment failure and the associated factors among individuals on second line ART regimen Eastern Uganda. Materials and methods: A retrospective analysis of 541 records of HIV positive individuals, switched to second line ART regimen from January 2012 to December 2017. Inferential statistics including the Chi square test and multivariable logistic regression analysis was applied to determine associations of treatment failure against of the selected demographic, laboratory and clinical factors was performed. Associations between treatment failure and the predictors was based on a P-value of less than 5% and confidence intervals level of 95%. Results: We reviewed 541 records of individuals on second line ART regimen, of which 350 (64.7%) were female, 226 (41.8%) were married, and 197 (36.4%) were older than 35 years. The mean age at ART initiation was 30 years (SD = 14.8), while the mean weight at ART initiation was 47 kg (SD = 18.6), (range 4-97 kg). The overall proportion of treatment failure was 23%. The cumulative mortality risk for 5 years was 12.4% and the mortality rate was 2.5 deaths per 100 individuals per year. The odds of developing treatment failure among individuals switched to ATV/r-based regimen were 44% lower as compared to individuals who were switched to LPV/r (ORadj0.56, 95% CI 0.35-0.90, P = .016). while the odds of experiencing treatment failure among individuals that used AZT at ART initiation were 43% lower as compared to individuals that used a TDF based regimen at ART initiation (ORadj0.57, 95% CI 0.33-0.98, P = .041). Conclusion: The 5 year cumulative incidence of treatment failure in a cohort of 541 individuals was 23%. The type of protease inhibitor (PI) used in second line regimen and use of AZT at ART initiation were significantly associated with treatment failure. Our study also shows that the cumulative mortality risk while on second line ART regimen was 12.4% while the mortality rate was 2.5 deaths per 100 individuals per year. Given the high level of treatment failure among individuals on second line ART regimen, yet the current ART protocols limits the use of third line ART regimens to only regional referral hospitals, the Ministry of Health should strengthen the surveillance systems for identifying individuals failing on second line ART regimen even at district hospitals and lower health facilities to facilitate timely switch to optimal regimen. The Ministry of health through the Quality Improvement Division should conduct routine onsite support supervision to sites offering ART to ensure that treatment guides and other standard of care like timely switch to appropriate regimens among others are being adhered to. Knowledge gaps identified can also be addressed through onsite Continuous Medical Educations.
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Affiliation(s)
| | | | - Deborah Alio
- Department of Natural Resources, Faculty of Health Sciences, Busitema University, Mbale, Uganda
| | - Jayne Byakika-Tusiime
- Department of Public Health, School of Health Sciences, Soroti University, Soroti, Uganda
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Vannappagari V, Ragone L, Henegar C, van Wyk J, Brown D, Demarest J, Quercia R, St Clair M, Underwood M, Gatell JM, de Ruiter A, Aboud M. Prevalence of pretreatment and acquired HIV-1 mutations associated with resistance to lamivudine or rilpivirine: a systematic review. Antivir Ther 2020; 24:393-404. [PMID: 31503008 DOI: 10.3851/imp3331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Pretreatment and acquired drug resistance mutations (DRMs) can limit antiretroviral therapy effectiveness. METHODS We review prevalence of DRMs with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs), focusing on lamivudine and rilpivirine, from 127 articles with >100,000 individuals with HIV-1 infection. RESULTS Estimated global prevalence of pretreatment resistance to any NRTI was 4% and to any NNRTI was 6%. Most prevalent DRMs resistant to lamivudine or rilpivirine were at positions E138 (4%), V179 (1%) and M184 (1%). Estimated acquired DRM prevalence was 58% for any NRTIs and 67% for any NNRTIs, most frequently at positions M184 (58%) and Y181 (21%). CONCLUSIONS This review suggests low risk of lamivudine- or rilpivirine-resistant mutations in treatment-naive, HIV-1-infected individuals.
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Affiliation(s)
| | - Leigh Ragone
- ViiV Healthcare, Research Triangle Park, NC, USA
| | | | | | | | | | | | | | | | - Jose M Gatell
- Hospital Clinic/IDIBAPS, University of Barcelona, Barcelona, Spain.,ViiV Healthcare, Barcelona, Spain
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Machado LY, Blanco M, López LS, Díaz HM, Dubed M, Valdés N, Noa E, Martínez L, Pérez MT, Romay DM, Rivero CB, Joanes J, Cancio I, Lantero MI, Rodríguez M. National survey of pre-treatment HIV drug resistance in Cuban patients. PLoS One 2019; 14:e0221879. [PMID: 31479466 PMCID: PMC6719847 DOI: 10.1371/journal.pone.0221879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/17/2019] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) recommends a method to estimate nationally representative pretreatment HIV drug resistance (PDR) in order to evaluate the effectiveness of first -line treatments. The objective of the present study was to determine the prevalence of PDR in Cuban adults infected with HIV-1. Materials and methods A cross-sectional study in Cuban adults infected with HIV-1 over 18 years was conducted. The probability proportional to size method for the selection of municipalities and patients without a prior history of antiretroviral treatment during the period from January 2017 to June 2017 was used. The plasma from 141 patients from 15 municipalities for the determination of viral subtype and HIV drug resistance was collected. Some clinical and epidemiological variables were evaluated. Results 80. 9% of the patients corresponded to the male sex and 76.3% were men who have sex with other men (MSM). The median CD4 count was 371 cells / mm3 and the median viral load was 68000 copies / mL. The predominant genetic variants were subtype B (26.9%), CRF19_cpx (24.1%), CRF 20, 23, 24_BG (23.4%) and CRF18_cpx (12%). Overall, the prevalence of PDR was 29.8% (95%, CI 22.3–38.1). The prevalence was 12.8% (95%, CI 6.07–16.9) for any nucleoside reverse transcriptase inhibitor (NRTI), 23.4% (95%, CI 16.7–31.3) for any non-reverse transcriptase inhibitor (NNRTI) and 1.4% (95%, CI 0.17–5.03) for any protease inhibitor (PI). The most frequent mutations detected were K103N (12.9%), G190A (6.4%) and Y181C (4.8%). Conclusions The NNRTI prevalence above 10% in our study indicates that the first-line antiretroviral therapy in Cuba may be less effective and supports the need to look for new treatment options that contribute to therapeutic success and help the country achieve the global goals 90-90-90 set forth by UNAIDS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - José Joanes
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - Isis Cancio
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
| | - María I. Lantero
- Department of STI/HIV/AIDS, Ministry of Public Health, Havana, Cuba
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Ndashimye E, Arts EJ. The urgent need for more potent antiretroviral therapy in low-income countries to achieve UNAIDS 90-90-90 and complete eradication of AIDS by 2030. Infect Dis Poverty 2019; 8:63. [PMID: 31370888 PMCID: PMC6676518 DOI: 10.1186/s40249-019-0573-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background Over 90% of Human Immunodeficiency Virus (HIV) infected individuals will be on treatment by 2020 under UNAIDS 90–90-90 global targets. Under World Health Organisation (WHO) “Treat All” approach, this number will be approximately 36.4 million people with over 98% in low-income countries (LICs). Main body Pretreatment drug resistance (PDR) largely driven by frequently use of non-nucleoside reverse transcriptase inhibitors (NNRTIs), efavirenz and nevirapine, has been increasing with roll-out of combined antiretroviral therapy (cART) with 29% annual increase in some LICs countries. PDR has exceeded 10% in most LICs which warrants change of first line regimen to more robust classes under WHO recommendations. If no change in regimens is enforced in LICs, it’s estimated that over 16% of total deaths, 9% of new infections, and 8% of total cART costs will be contributed by HIV drug resistance by 2030. Less than optimal adherence, and adverse side effects associated with currently available drug regimens, all pose a great threat to achievement of 90% viral suppression and elimination of AIDS as a public health threat by 2030. This calls for urgent introduction of policies that advocate for voluntary and compulsory drug licensing of new more potent drugs which should also emphasize universal access of these drugs to all individuals worldwide. Conclusions The achievement of United Nations Programme on HIV and AIDS 2020 and 2030 targets in LICs depends on access to active cART with higher genetic barrier to drug resistance, better safety, and tolerability profiles. It’s also imperative to strengthen quality service delivery in terms of retention of patients to treatment, support for adherence to cART, patient follow up and adequate drug stocks to help achieve a free AIDS generation. Electronic supplementary material The online version of this article (10.1186/s40249-019-0573-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada. .,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, 1151 Richmond St., DSB Rm.3007, London, ON, N6A5C1, Canada
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Indriati DW, Kotaki T, Khairunisa SQ, Witaningrum AM, Matondang MQY, Ueda S, Nasronudin, Purnama A, Kurniawan D, Kameoka M. Appearance of Drug Resistance Mutations Among the Dominant HIV-1 Subtype, CRF01_AE in Maumere, Indonesia. Curr HIV Res 2019; 16:158-166. [PMID: 29732988 DOI: 10.2174/1570162x16666180502114344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVES Human Immunodeficiency Virus (HIV) is still a major health issue in Indonesia. In recent years, the appearance of drug resistance-associated mutations has reduced the effectiveness of Antiretroviral Therapy (ART). We conducted genotypic studies, including the detection of drug resistance-associated mutations (from first-line regimen drugs), on HIV-1 genes derived from infected individuals in Maumere, West Nusa Tenggara. Maumere, a transit city in West Nusa Tenggara, which has a high HIV-1 transmission rate. METHOD We collected 60 peripheral blood samples from 53 ART-experienced and 7 ART-naive individuals at TC Hillers Hospital, Maumere between 2014 and 2015. The amplification and a sequencing analysis of pol genes encoding protease (the PR gene) and reverse transcriptase (the RT gene) as well as the viral env and gag genes were performed. HIV-1 subtyping and the detection of drug resistance-associated mutations were then conducted. RESULTS Among 60 samples, 46 PR, 31 RT, 30 env, and 20 gag genes were successfully sequenced. The dominant HIV-1 subtype circulating in Maumere was CRF01_AE. Subtype B and recombinant viruses containing gene fragments of CRF01_AE, subtypes A, B, C, and/or G were also identified as minor populations. The major drug resistance-associated mutations, M184V, K103N, Y188L, and M230I, were found in the RT genes. However, no major drug resistance-associated mutations were detected in the PR genes. CONCLUSION CRF01_AE was the major HIV-1 subtype prevalent in Maumere. The appearance of drug resistance-associated mutations found in the present study supports the necessity of monitoring the effectiveness of ART in Maumere.
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Affiliation(s)
- Dwi Wahyu Indriati
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Health, Faculty of Vocational Studies, Universitas Airlangga, Surabaya, Indonesia
| | - Tomohiro Kotaki
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Siti Qamariyah Khairunisa
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Adiana Mutamsari Witaningrum
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Muhammad Qushai Yunifiar Matondang
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Nasronudin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | | | - Masanori Kameoka
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan.,Center for Infectious Diseases, Kobe University, Graduate School of Medicine, Hyogo, Japan
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Hamers RL, Rinke de Wit TF, Holmes CB. HIV drug resistance in low-income and middle-income countries. Lancet HIV 2018; 5:e588-e596. [PMID: 30193863 DOI: 10.1016/s2352-3018(18)30173-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/02/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
Abstract
After 15 years of global scale-up of antiretroviral therapy (ART), rising prevalence of HIV drug resistance in many low-income and middle-income countries (LMICs) poses a growing threat to the HIV response, with the potential to drive an increase in mortality, HIV incidence, and costs. To achieve UNAIDS global targets, enhanced strategies are needed to improve quality of ART services and durability of available ART regimens, and to curb resistance. These strategies include roll out of drugs with greater efficacy and higher genetic barriers to resistance than those that are currently widely used, universal access to and improved effectiveness of viral load monitoring, patient-centred care delivery models, and reliable drug supply chains, in conjunction with frameworks for resistance monitoring and prevention. In this Review, we assess contemporary data on HIV drug resistance in LMICs and their implications for the HIV response, highlighting the potential impact and resistance risks of novel ART strategies and knowledge gaps.
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Affiliation(s)
- Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
| | - Tobias F Rinke de Wit
- Department of Global Health, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands; Joep Lange Institute, Amsterdam, Netherlands
| | - Charles B Holmes
- Centre for Infectious Diseases Research Zambia, Lusaka, Zambia; Center for Global Health and Quality, Georgetown University Medical Center, Washington, DC, USA; Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Baltimore, MD, USA
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Emergence as an outbreak of the HIV-1 CRF19_cpx variant in treatment-naïve patients in southern Spain. PLoS One 2018; 13:e0190544. [PMID: 29309418 PMCID: PMC5757947 DOI: 10.1371/journal.pone.0190544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background CRF19_cpx is a complex circulating recombination form (CRF) of HIV-1. We describe the characteristics of an outbreak of the CRF19_cpx variant among treatment-naïve patients in southern Spain. Methods The study was undertaken at the Virgen de la Victoria Hospital, a reference centre for the analysis of HIV-1 genotype in Malaga (Spain). Subtyping was performed through REGA v3.0 and the relationship of our CRF19_cpx sequences, among themselves and regarding other reference sequences from the same variant, was defined by phylogenetic analysis. We used PhyML program to perform a reconstruction of the phylogeny by Maximum Likelihood method as well as further confirmation of the transmission clusters by Bayesian inference. Additionally, we collected demographic, clinical and immunovirological data. Results Between 2011 and 2016, we detected 57 treatment-naïve patients with the CRF19_cpx variant. Of these, 55 conformed a very well-defined transmission cluster, phylogenetically close to CRF19_cpx sequences from the United Kingdom. The origin of this subtype in Malaga was dated between 2007 and 2010. Over 50% of the patients presented the non-nucleoside reverse transcriptase inhibitor G190A resistance mutation. This variant was mostly represented by young adult Spanish men who had sex with men. Almost half of them were recent seroconverters, though a similar percentage was diagnosed at a late state of HIV infection. Five cases of AIDS and one non-AIDS defined death occurred during follow-up. The majority of patients treated with first-line combination antiretroviral therapy (ART) responded. Conclusions We report the largest HIV-1 CRF19_cpx cohort of treatment-naïve patients outside Cuba, almost all emerging as an outbreak in the South of Spain. Half the cases had the G190A resistance mutation. Unlike previous studies, the variant from Malaga seems less pathogenic, with few AIDS events and an excellent response to ART.
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Hofstra LM, Sánchez Rivas E, Nijhuis M, Bank LEA, Wilkinson E, Kelly K, Mudrikova T, Schuurman R, de Oliveira T, de Kort J, Wensing AMJ. High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients. Clin Infect Dis 2017; 64:1092-1097. [PMID: 28329390 PMCID: PMC5848377 DOI: 10.1093/cid/cix056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/24/2017] [Indexed: 11/22/2022] Open
Abstract
Background. In Western countries emergence of human immunodeficiency virus (HIV) drug resistance has tremendously decreased, and transmission of drug resistance has merely stabilized in recent years. However, in many endemic settings with limited resources rates of emerging and transmitted drug resistance are not regularly assessed. Methods. We performed a survey including all HIV-infected individuals who received resistance testing in 2010–2015 in Aruba, a highly endemic HIV area in the Caribbean. Transmitted HIV drug resistance was determined using World Health Organization (WHO) criteria. Transmission dynamics were investigated using phylogenetic analyses. In a subset, baseline samples were re-analyzed using next generation sequencing (NGS). Results. Baseline resistance testing was performed in 104 newly diagnosed untreated individuals (54% of all newly diagnosed individuals in 2010–2015): 86% were men, 39% were foreign-born, and 22% had AIDS at diagnosis. And 33% (95% CI: 24–42%) was infected with a drug-resistant HIV variant. The prevalence of resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) reached 45% (95% CI: 27–64%) in 2015, all based on the prevalence of mutation K103N. NGS did not demonstrate additional minority K103N-variants compared to routine resistance testing. K103N-harboring strains were introduced into the therapy-unexposed population via at least 6 independent transmissions epidemiologically linked to the surrounding countries. Virological failure of the WHO-recommended first-line NNRTI-based regimen was higher in the presence of K103N. Conclusions. The prevalence of resistant HIV in Aruba has increased to alarming levels, compromising the WHO-recommended first-line regimen. As adequate surveillance as advocated by the WHO is limited, the Caribbean region could face an unidentified rise of NNRTI-resistant HIV.
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Affiliation(s)
- L Marije Hofstra
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.,Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Elena Sánchez Rivas
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Leonie E A Bank
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.,Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, The Netherlands
| | - Eduan Wilkinson
- Africa Centre for Population Health, Myeki, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Karina Kelly
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, The Netherlands
| | - Rob Schuurman
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Tulio de Oliveira
- Africa Centre for Population Health, Myeki, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Jaclyn de Kort
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
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Lavu E, Kave E, Mosoro E, Markby J, Aleksic E, Gare J, Elsum IA, Nano G, Kaima P, Dala N, Gurung A, Bertagnolio S, Crowe SM, Myatt M, Hearps AC, Jordan MR. High Levels of Transmitted HIV Drug Resistance in a Study in Papua New Guinea. PLoS One 2017; 12:e0170265. [PMID: 28146591 PMCID: PMC5287486 DOI: 10.1371/journal.pone.0170265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/30/2016] [Indexed: 11/26/2022] Open
Abstract
Introduction Papua New Guinea is a Pacific Island nation of 7.3 million people with an estimated HIV prevalence of 0.8%. ART initiation and monitoring are guided by clinical staging and CD4 cell counts, when available. Little is known about levels of transmitted HIV drug resistance in recently infected individuals in Papua New Guinea. Methods Surveillance of transmitted HIV drug resistance in a total of 123 individuals recently infected with HIV and aged less than 30 years was implemented in Port Moresby (n = 62) and Mount Hagen (n = 61) during the period May 2013-April 2014. HIV drug resistance testing was performed using dried blood spots. Transmitted HIV drug resistance was defined by the presence of one or more drug resistance mutations as defined by the World Health Organization surveillance drug resistance mutations list. Results The prevalence of non-nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 16.1% (95% CI 8.8%-27.4%) and 8.2% (95% CI 3.2%-18.2%) in Port Moresby and Mount Hagen, respectively. The prevalence of nucleoside reverse transcriptase inhibitor transmitted HIV drug resistance was 3.2% (95% CI 0.2%-11.7%) and 3.3% (95% CI 0.2%-11.8%) in Port Moresby and Mount Hagen, respectively. No protease inhibitor transmitted HIV drug resistance was observed. Conclusions The level of non-nucleoside reverse transcriptase inhibitor drug resistance in antiretroviral drug naïve individuals recently infected with HIV in Port Moresby is amongst the highest reported globally. This alarming level of transmitted HIV drug resistance in a young sexually active population threatens to limit the on-going effective use of NNRTIs as a component of first-line ART in Papua New Guinea. To support the choice of nationally recommended first-line antiretroviral therapy, representative surveillance of HIV drug resistance among antiretroviral therapy initiators in Papua New Guinea should be urgently implemented.
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Affiliation(s)
- Evelyn Lavu
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Ellan Kave
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Euodia Mosoro
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Jessica Markby
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Eman Aleksic
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Janet Gare
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
- Institute for Medical Research, Goroka, Papua New Guinea
| | - Imogen A. Elsum
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Gideon Nano
- National Department of Health, Port Moresby, Papua New Guinea
| | | | - Nick Dala
- National Department of Health, Port Moresby, Papua New Guinea
| | - Anup Gurung
- World Health Organization, Port Moresby, Papua New Guinea
| | | | - Suzanne M. Crowe
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Mark Myatt
- Brixton Health, Llawryglyn, Powys, Wales, United Kingdom
| | - Anna C. Hearps
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | - Michael R. Jordan
- Division of Geographic Medicine and Infection Disease, Tufts Medical Center, Boston, Massachusetts, United States of America
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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11
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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Avila-Rios S, Sued O, Rhee SY, Shafer RW, Reyes-Teran G, Ravasi G. Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. PLoS One 2016; 11:e0158560. [PMID: 27355626 PMCID: PMC4927069 DOI: 10.1371/journal.pone.0158560] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/19/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND HIV transmitted drug resistance (TDR) remains at moderate level in Latin America and the Caribbean (LAC). However, different epidemiologic scenarios could influence national and sub-regional TDR levels and trends. METHODS AND FINDINGS We performed a systematic review of currently available publications on TDR in antiretroviral treatment-naïve adults in LAC. Ninety-eight studies published between January 2000 and June 2015 were included according to critical appraisal criteria and classified by sub-region: Brazil (50), Mesoamerica (17), Southern Cone (16), Andean (8) and Caribbean (7). From these, 81 studies encompassing 11,441 individuals with data on DR mutation frequency were included in a meta-analysis. Overall TDR prevalence in LAC was 7.7% (95% CI: 7.2%-8.2%). An increasing trend was observed for overall TDR when comparing 2000-2005 (6.0%) and 2006-2015 (8.2%) (p<0.0001), which was associated with significant NNRTI TDR increase (p<0.0001). NRTI TDR decreased (4.5% vs. 2.3%, p<0.0001). NNRTI TDR increase was associated mainly with K101E, K103N and G190A. NRTI TDR decrease was associated mainly with M184V, K70R and T215Y. All sub-regions reached moderate overall TDR levels. The rapid increase in TDR to all antiretroviral classes in the Caribbean is notable, as well as the significant increase in NNRTI TDR reaching moderate levels in the Southern Cone. NRTI TDR was dominant in 2000-2005, mainly in the Caribbean, Mesoamerica and Brazil. This dominance was lost in 2006-2015 in all sub-regions, with the Southern Cone and the Caribbean switching to NNRTI dominance. PI TDR remained mostly constant with a significant increase only observed in the Caribbean. CONCLUSIONS Given the high conceptual and methodological heterogeneity of HIV TDR studies, implementation of surveys with standardized methodology and national representativeness is warranted to generate reliable to inform public health policies. The observed increasing trend in NNRTI TDR supports the need to strengthen TDR surveillance and programme monitoring and evaluation in LAC.
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Affiliation(s)
- Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Omar Sued
- Clinical Research Section, Huésped Foundation, Buenos Aires, Argentina
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Gustavo Reyes-Teran
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Giovanni Ravasi
- Pan American Health Organization (PAHO), Washington DC, United States of America
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13
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Phylogeny and drug resistance of HIV PR gene among HIV patients receiving RT inhibitors in Iran. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2015.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Collins-Fairclough AM, Dennis AM, Nelson JA, Weir SS, Figueroa JP. HIV Drug Resistance Surveillance Among Jamaican Men Who Have Sex with Men Should Be Prioritized for Reducing HIV Transmission. AIDS Res Hum Retroviruses 2015; 31:841-4. [PMID: 26133540 DOI: 10.1089/aid.2015.0040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of human immunodeficiency virus type 1 (HIV-1) is highest among men who have sex with men (MSM) in Jamaica but no genotypic data are available on the virus strains that are responsible for the epidemic among this key population. HIV-1 polymerase (pol) genes from 65 MSM were sequenced and used to predict drug resistance mutations. An HIV drug resistance prevalence of 28% (minimum 13%) was observed among this cohort, with the most frequent mutations conferring resistance to efavirenz, nevirapine, and lamivudine. Phylogenetic analysis of the sequences revealed 10 times the number of linked HIV infections among this cohort than respondent reporting. HIV treatment and prevention efforts in Jamaica could benefit significantly from Pol genotyping of the HIV strains infecting socially vulnerable MSM prior to initiating antiretroviral therapy (ART), as this would guide suppressive ART and unearth HIV transmission clusters to enable more effective delivery of treatment and prevention programs.
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Affiliation(s)
- Aneisha M. Collins-Fairclough
- Biology Division, School of Natural and Applied Sciences, Faculty of Science and Sport, University of Technology, Kingston, Jamaica
| | - Ann M. Dennis
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julie A.E. Nelson
- University of North Carolina Center for AIDS Research and Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sharon S. Weir
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - J. Peter Figueroa
- Department of Community Health and Psychiatry, University of the West Indies, Mona, Kingston, Jamaica
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Abstract
BACKGROUND HIV-1 CRF19_cpx, is a recombinant variant found almost exclusively in Cuba and recently associated to a faster AIDS onset. Infection with this variant leads to higher viral loads and levels of RANTES and CXCR4 co-receptor use. OBJECTIVES The goal of this study was to assess the presence of CRF19_cpx in the Spanish province of Valencia, given its high pathogenicity. STUDY DESIGN 1294 HIV-1 protease-reverse transcriptase (PR/RT) sequences were obtained in Valencia (Spain), between 2005 and 2014. After subtyping, the detected CRF19_cpx sequences were aligned with 201 CRF19_cpx and 66 subtype D sequences retrieved from LANL, and subjected to maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. The presence of resistance mutations in the PR/RT region of these sequences was also analyzed. RESULTS Among the 9 CRF19_cpx sequences from different patients found (prevalence <0.1%), 7 grouped in two well-supported clades (groups A, n=4, and B, n=3), suggesting the existence of at least two independent introductions which subsequently started to expand in the studied Spanish region. Unprotected sex between men was the only known transmission route. Coalescent analyses suggested that the introductions in Valencia occurred between 2008 and 2010. Resistance mutations in the RT region were found in all sequences from group A (V139D) and in two sequences from group B (E138A). CONCLUSIONS This study reports for the first time the recent expansion of CRF19_cpx outside Cuba. Our results suggest that CRF19_cpx might become an emerging HIV variant in Spain, affecting Spanish native MSM and not only Cuban migrants.
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Kouri V, Khouri R, Alemán Y, Abrahantes Y, Vercauteren J, Pineda-Peña AC, Theys K, Megens S, Moutschen M, Pfeifer N, Van Weyenbergh J, Pérez AB, Pérez J, Pérez L, Van Laethem K, Vandamme AM. CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba. EBioMedicine 2015; 2:244-54. [PMID: 26137563 PMCID: PMC4484819 DOI: 10.1016/j.ebiom.2015.01.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
Background Clinicians reported an increasing trend of rapid progression (RP) (AIDS within 3 years of infection) in Cuba. Methods Recently infected patients were prospectively sampled, 52 RP at AIDS diagnosis (AIDS-RP) and 21 without AIDS in the same time frame (non-AIDS). 22 patients were sampled at AIDS diagnosis (chronic-AIDS) retrospectively assessed as > 3 years infected. Clinical, demographic, virological, epidemiological and immunological data were collected. Pol and env sequences were used for subtyping, transmission cluster analysis, and prediction of resistance, co-receptor use and evolutionary fitness. Host, immunological and viral predictors of RP were explored through data mining. Findings Subtyping revealed 26 subtype B strains, 6 C, 6 CRF18_cpx, 9 CRF19_cpx, 29 BG-recombinants and other subtypes/URFs. All patients infected with CRF19 belonged to the AIDS-RP group. Data mining identified CRF19, oral candidiasis and RANTES levels as the strongest predictors of AIDS-RP. CRF19 was more frequently predicted to use the CXCR4 co-receptor, had higher fitness scores in the protease region, and patients had higher viral load at diagnosis. Interpretation CRF19 is a recombinant of subtype D (C-part of Gag, PR, RT and nef), subtype A (N-part of Gag, Integrase, Env) and subtype G (Vif, Vpr, Vpu and C-part of Env). Since subtypes D and A have been associated with respectively faster and slower disease progression, our findings might indicate a fit PR driving high viral load, which in combination with co-infections may boost RANTES levels and thus CXCR4 use, potentially explaining the fast progression. We propose that CRF19 is evolutionary very fit and causing rapid progression to AIDS in many newly infected patients in Cuba. We propose that CRF19 is evolutionary very fit, causing rapid progression to AIDS in many newly infected patients in Cuba. CRF19 is a recombinant of subtype D, subtype A and subtype G, with a subtype D protease estimated to be particularly fit. A fit protease with high viral load and co-infections, may boost RANTES levels and thus CXCR4 use, hence fast progression.
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Affiliation(s)
- Vivian Kouri
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Ricardo Khouri
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; LIMI-LIP, Centro de Pesquisa Gonçalo Moniz, FIOCRUZ, Salvador-Bahia, Brazil
| | - Yoan Alemán
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Yeissel Abrahantes
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Jurgen Vercauteren
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Andrea-Clemencia Pineda-Peña
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
| | - Kristof Theys
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Sarah Megens
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Michel Moutschen
- AIDS Reference Center, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Johan Van Weyenbergh
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Ana B Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Jorge Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Lissette Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Kristel Van Laethem
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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17
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Sagna T, Bisseye C, Compaore TR, Kagone TS, Djigma FW, Ouermi D, Pirkle CM, Zeba MTA, Bazie VJT, Douamba Z, Moret R, Pietra V, Koama A, Gnoula C, Sia JD, Nikiema JB, Simpore J. Prevention of mother-to-child HIV-1 transmission in Burkina Faso: evaluation of vertical transmission by PCR, molecular characterization of subtypes and determination of antiretroviral drugs resistance. Glob Health Action 2015; 8:26065. [PMID: 25630709 PMCID: PMC4309832 DOI: 10.3402/gha.v8.26065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/20/2014] [Accepted: 12/21/2014] [Indexed: 11/27/2022] Open
Abstract
Background Vertical human immunodeficiency virus (HIV) transmission is a public health problem in Burkina Faso. The main objective of this study on the prevention of mother-to-child HIV-1 transmission was to determine the residual risk of HIV transmission in infants born to mothers receiving highly active antiretroviral therapy (HAART). Moreover, we detect HIV antiretroviral (ARV) drug resistance among mother–infant pairs and identify subtypes and circulating recombinant forms (CRF) in Burkina Faso. Design In this study, 3,215 samples of pregnant women were analyzed for HIV using rapid tests. Vertical transmission was estimated by polymerase chain reaction in 6-month-old infants born to women who tested HIV positive. HIV-1 resistance to ARV, subtypes, and CRFs was determined through ViroSeq kit using the ABI PRISM 3,130 sequencer. Results In this study, 12.26% (394/3,215) of the pregnant women were diagnosed HIV positive. There was 0.52% (2/388) overall vertical transmission of HIV, with rates of 1.75% (2/114) among mothers under prophylaxis and 0.00% (0/274) for those under HAART. Genetic mutations were also isolated that induce resistance to ARV such as M184V, Y115F, K103N, Y181C, V179E, and G190A. There were subtypes and CRF of HIV-1 present, the most common being: CRF06_CPX (58.8%), CRF02_AG (35.3%), and subtype G (5.9%). Conclusions ARV drugs reduce the residual rate of HIV vertical transmission. However, the virus has developed resistance to ARV, which could limit future therapeutic options when treatment is needed. Resistance to ARV therefore requires a permanent interaction between researchers, physicians, and pharmacists, to strengthen the network of monitoring and surveillance of drug resistance in Burkina Faso.
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Affiliation(s)
- Tani Sagna
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa; Institute of Research in Health Sciences, IRSS, Bobo-Dioulasso, Burkina Faso;
| | - Cyrille Bisseye
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa; Laboratory of Molecular and Cellular Biology, University of Sciences and Techniques of Masuku (USTM), Franceville, Gabon
| | - Tegewende R Compaore
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa; Saint Camille Medical Centre, Ouagadougou, Burkina Faso
| | - Therese S Kagone
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Florencia W Djigma
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Djeneba Ouermi
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa; Saint Camille Medical Centre, Ouagadougou, Burkina Faso
| | - Catherine M Pirkle
- Population Health and Optimal Health Practices Research Unit, CHU de Québec Research Centre, Quebec, Canada
| | - Moctar T A Zeba
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Valerie J T Bazie
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Zoenabo Douamba
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Remy Moret
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | | | - Adjirita Koama
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Charlemagne Gnoula
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Joseph D Sia
- Saint Camille Medical Centre, Ouagadougou, Burkina Faso
| | - Jean-Baptiste Nikiema
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa
| | - Jacques Simpore
- Biomolecular Research Centre Pietro Annigoni (CERBA/LABIOGENE), University of Ouagadougou, Burkina Faso, West Africa; Saint Camille Medical Centre, Ouagadougou, Burkina Faso
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Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS One 2014; 9:e106045. [PMID: 25148215 PMCID: PMC4141835 DOI: 10.1371/journal.pone.0106045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/29/2014] [Indexed: 11/18/2022] Open
Abstract
The Human immunodeficiency virus type-1 (HIV-1) epidemic in the Caribbean region is mostly driven by subtype B; but information about the pattern of viral spread in this geographic region is scarce and different studies point to quite divergent models of viral dissemination. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in the Caribbean. A total of 1,806 HIV-1 subtype B pol sequences collected from 17 different Caribbean islands between 1996 and 2011 were analyzed together with sequences from the United States (n = 525) and France (n = 340) included as control. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in the Caribbean are driven by dissemination of the pandemic clade (BPANDEMIC) responsible for most subtype B infections across the world, and older non-pandemic lineages (BCAR) characteristics of the Caribbean region. The non-pandemic BCAR strains account for >40% of HIV-1 infections in most Caribbean islands; with exception of Cuba and Puerto Rico. Bayesian phylogeographic analyses indicate that BCAR strains probably arose in the island of Hispaniola (Haiti/Dominican Republic) around the middle 1960s and were later disseminated to Trinidad and Tobago and to Jamaica between the late 1960s and the early 1970s. In the following years, the BCAR strains were also disseminated from Hispaniola and Trinidad and Tobago to other Lesser Antilles islands at multiple times. The BCAR clades circulating in Hispaniola, Jamaica and Trinidad and Tobago appear to have experienced an initial phase of exponential growth, with mean estimated growth rates of 0.35-0.45 year(-1), followed by a more recent stabilization since the middle 1990s. These results demonstrate that non-pandemic subtype B lineages have been widely disseminated through the Caribbean since the late 1960s and account for an important fraction of current HIV-1 infections in the region.
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Affiliation(s)
- Marina Cabello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
- INDICASAT-AIP, City of Knowledge, Clayton, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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Mendoza Y, Bello G, Castillo Mewa J, Martínez AA, González C, García-Morales C, Avila-Ríos S, Reyes-Terán G, Pascale JM. Molecular epidemiology of HIV-1 in Panama: origin of non-B subtypes in samples collected from 2007 to 2013. PLoS One 2014; 9:e85153. [PMID: 24454808 PMCID: PMC3890310 DOI: 10.1371/journal.pone.0085153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 11/23/2013] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic studies have suggested that the HIV-1 epidemic in the Americas is mainly dominated by HIV subtype B. However, countries of South America and the Caribbean have recently reported changes in their circulating HIV-1 genetic profiles. The aim of this study was to characterize the molecular profile of the HIV-1 epidemic in Panama by the analysis of 655 polymerase gene (pol) sequences that were obtained from HIV-infected Panamanians diagnosed between 1987 and 2013. Blood samples were collected from recently infected, antiretroviral drug-naïve and treatment-experienced subjects since mid-2007 to 2013. Viral RNA from plasma was extracted and sequences of HIV protease and reverse transcriptase genes were obtained. Bootscanning and phylogenetic methods were used for HIV subtyping and to trace the putative origin of non-B subtype strains. Our results showed that HIV-1 infections in Panama are dominated by subtype B (98.9%). The remaining 1.1% is represented by a diverse collection of recombinant variants including: three URFs_BC, one CRF20_BG, and one CRF28/29_BF, in addition to one subtype F1 and one subtype C, none of which were previously reported in Panama. The non-B subtype variants detected in Panama were probably introduced from Brazil (subtype F1 and CRF28/29_BF), Cuba (CRF20_BG), Dominican Republic (URFs_BC) and India (subtype C). Panama is the geographical vertex that connects the North with South America and the Caribbean through trade and cultural relations, which may explain the observed introductions of non-B subtype HIV-1 variants from both the Caribbean and South America into this Central American country.
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Affiliation(s)
- Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
- INDICASAT-AIP, 219, City of Knowledge, Clayton, Panama City, Panama
- * E-mail:
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Juan Castillo Mewa
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Alexander A. Martínez
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- INDICASAT-AIP, 219, City of Knowledge, Clayton, Panama City, Panama
| | - Claudia González
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Claudia García-Morales
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Juan M. Pascale
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
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20
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Abstract
Previous studies have shown that the HIV-1 epidemic in Cuba displayed a complex molecular epidemiologic profile with circulation of several subtypes and circulating recombinant forms (CRF); but the evolutionary and population history of those viral variants remains unknown. HIV-1 pol sequences of the most prevalent Cuban lineages (subtypes B, C and G, CRF18_cpx, CRF19_cpx, and CRFs20/23/24_BG) isolated between 1999 and 2011 were analyzed. Maximum-likelihood analyses revealed multiple introductions of subtype B (n≥66), subtype C (n≥10), subtype G (n≥8) and CRF18_cpx (n≥2) viruses in Cuba. The bulk of HIV-1 infections in this country, however, was caused by dissemination of a few founder strains probably introduced from North America/Europe (clades BCU-I and BCU-II), east Africa (clade CCU-I) and central Africa (clades GCU, CRF18CU and CRF19CU), or locally generated (clades CRFs20/23/24_BG). Bayesian-coalescent analyses show that the major HIV-1 founder strains were introduced into Cuba during 1985–1995; whereas the CRFs_BG strains emerged in the second half of the 1990s. Most HIV-1 Cuban clades appear to have experienced an initial period of fast exponential spread during the 1990s and early 2000s, followed by a more recent decline in growth rate. The median initial growth rate of HIV-1 Cuban clades ranged from 0.4 year−1 to 1.6 year−1. Thus, the HIV-1 epidemic in Cuba has been a result of the successful introduction of a few viral strains that began to circulate at a rather late time of the AIDS pandemic, but then were rapidly disseminated through local transmission networks.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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