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Nalwanga D, Musiime V. Children living with HIV: a narrative review of recent advances in pediatric HIV research and their implications for clinical practice. Ther Adv Infect Dis 2022; 9:20499361221077544. [PMID: 35186289 PMCID: PMC8855388 DOI: 10.1177/20499361221077544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the great strides that have been made in prevention of mother to child
transmission (PMTCT), children continue to acquire HIV. The reduction in
transmission is variable, for example in Africa, great gains have been made in
Eastern and Southern Africa, but critical gaps remain in West and Central
Africa. These gaps are also observed in the treatment of children living with
HIV. Although there is increased access to lifesaving antiretroviral therapy
(ART), management of pediatric HIV infection continues to be a challenge to
clinicians in low-income countries where the disease burden is
disproportionately high. On the contrary, recent advances in ART drug types and
formulations provide great hope. In this narrative review, we present key
updates in HIV care and promising ART research among children and adolescents
living with HIV. We particularly highlight the dolutegravir (DTG) research which
informed the change of the World Health Organization (WHO) ART guidelines in
this age group. Significant gaps remain around management of children presenting
with advanced disease to minimize mortality and in the long-term care and
treatment of adolescents living with HIV. Research to address these sensitive
areas is crucial for the realization of global, regional, and national pediatric
HIV targets.
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Affiliation(s)
- Damalie Nalwanga
- Department of Pediatrics and Child Health, Makerere University Lung Institute, P. O. Box 7072 Kampala, 256 Uganda
| | - Victor Musiime
- Department of Pediatrics and Child Health, Makerere University, Kampala, Uganda; Joint Clinical Research Centre, Kampala, Uganda
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2
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Brenner BG, Ibanescu RI, Osman N, Cuadra-Foy E, Oliveira M, Chaillon A, Stephens D, Hardy I, Routy JP, Thomas R, Baril JG, Leblanc R, Tremblay C, Roger M. The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020). Viruses 2021; 13:1643. [PMID: 34452506 PMCID: PMC8402830 DOI: 10.3390/v13081643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/23/2023] Open
Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
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Affiliation(s)
- Bluma G. Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine (Surgery, Infectious Disease), McGill University, Montréal, QC H3A 2M7, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Nathan Osman
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ernesto Cuadra-Foy
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Maureen Oliveira
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 93903, USA;
| | - David Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, Canada;
| | - Isabelle Hardy
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, Canada;
| | - Réjean Thomas
- Clinique Médicale l’Actuel, Montréal, QC H2L 4P9, Canada;
| | - Jean-Guy Baril
- Clinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, Canada;
| | - Roger Leblanc
- Clinique Médicale OPUS, Montréal, QC H3A 1T1, Canada;
| | - Cecile Tremblay
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Michel Roger
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
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3
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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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Younger J, Raboud J, Szadkowski L, Harrigan R, Walmsley S, Bayoumi AM, Klein MB, Cooper C, Burchell AN, Loutfy M, Hull M, Wong A, Thomas R, Hogg R, Montaner J, Tsoukas C, Antoniou T. Tenofovir and emtricitabine resistance among antiretroviral-naive patients in the Canadian Observational Cohort Collaboration: implications for PrEP. Antivir Ther 2020; 24:211-220. [PMID: 30873953 DOI: 10.3851/imp3302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND The real-world effectiveness of pre-exposure prophylaxis (PrEP) may be influenced by circulating HIV strains resistant to either tenofovir or emtricitabine. Yet, few studies have examined rates of resistance to these drugs in clinical settings. METHODS We conducted a retrospective cohort study of antiretroviral-naive participants in the Canadian Observational Cohort collaboration who initiated antiretroviral therapy between 2006 and 2014. In separate analyses, we determined the prevalence of pretherapy resistance and cumulative incidence of follow-up resistance to tenofovir and emtricitabine. We used multivariable proportional hazards models to examine associations between baseline variables and the development of resistance. RESULTS We studied 6,622 antiretroviral-naive participants initiating therapy, of whom 5,428 (82.0%) had a baseline resistance test. Baseline resistance to tenofovir and emtricitabine was observed in 83 (1.5%) and 21 (0.4%) patients, respectively. Among patients without baseline resistance, the cumulative incidence of resistance to tenofovir and emtricitabine 5 years following treatment initiation was 0.0070 (95% CI 0.0046, 0.0095) and 0.033 (95% CI 0.028, 0.038), respectively. Following multivariable analysis, a baseline viral load ≥100,000 copies/ml was associated with emergence of tenofovir (hazard ratio [HR] 2.88; 95% CI 1.35, 6.15) and emtricitabine (HR 2.27; 95% CI 1.64, 3.15) resistance. Initiating an integrase inhibitor-based regimen and CD4+ T-cell count below 200 cells/mm3 were also associated with resistance to each drug. CONCLUSIONS We observed a low prevalence of baseline resistance and a low incidence of emergence of resistance to tenofovir and emtricitabine among antiretroviral-naive patients in routine clinical care.
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Affiliation(s)
- Jaime Younger
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Janet Raboud
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Leah Szadkowski
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sharon Walmsley
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada
| | - Ahmed M Bayoumi
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Marina B Klein
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Department of Medicine, McGill University Health Centre Research Institute, Montréal, QC, Canada
| | - Curtis Cooper
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Ann N Burchell
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada.,Department of Family and Community Medicine, St Michael's Hospital and University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Mona Loutfy
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada.,Maple Leaf Medical Clinic, Toronto, ON, Canada
| | - Mark Hull
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Alex Wong
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,Division of Infectious Diseases, Department of Medicine, University of Saskatchewan, Regina, SK, Canada
| | | | - Robert Hogg
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Vancouver, BC, Canada
| | - Julio Montaner
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Chris Tsoukas
- Faculty of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Tony Antoniou
- Department of Family and Community Medicine, St Michael's Hospital and University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
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Kronfli N, Linthwaite B, Sheehan N, Cox J, Hardy I, Lebouché B, de Pokomandy A, Frenette C, Roger M, Klein MB. Delayed linkage to HIV care among asylum seekers in Quebec, Canada. BMC Public Health 2019; 19:1683. [PMID: 31842822 PMCID: PMC6916083 DOI: 10.1186/s12889-019-8052-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023] Open
Abstract
Background Migrants represent an increasing proportion of people living with HIV in many developed countries. We aimed to describe the HIV care cascade and baseline genotypic resistance for newly diagnosed asylum seekers referred to the McGill University Health Centre (MUHC) in Montreal, Quebec, Canada. Methods We conducted a retrospective cohort study of patients linked to the MUHC from June 1, 2017 to October 31, 2018. We calculated the median time (days; interquartile range (IQR)) from: 1) entry into Canada to immigration medical examination (IME) (i.e. HIV screening); 2) IME to patient notification of diagnosis; 3) notification to linkage to HIV care (defined as a CD4 or viral load (VL) measure); 4) linkage to HIV care to combination antiretroviral therapy (cART) prescription; and 5) cART prescription to viral suppression (defined as a VL < 20 copies/mL). We reviewed baseline genotypes and interpreted mutations using the Stanford University HIV Drug Resistance Database. We calculated the proportion with full resistance to > 1 antiretroviral. Results Overall, 43% (60/139) of asylum seekers were newly diagnosed in Canada. Among these, 62% were late presenters (CD4 < 350 cells/μl), 22% presented with advanced HIV (CD4 < 200 cells/μl), and 25% with high-level viremia (VL > 100,000 copies/ml). Median time from entry to IME: 27 days [IQR:13;55]; IME to notification: 28 days [IQR:21;49]; notification to linkage: 6 days [IQR:2;19]; linkage to cART prescription: 11 days [IQR:6;17]; and cART to viral suppression: 42 days [IQR:31;88]; 45% were linked to HIV care within 30 days. One-fifth (21%) had baseline resistance to at least one antiretroviral agent; the K103 N/S mutation was the most common mutation. Conclusions While the majority of newly diagnosed asylum seekers were late presenters, only 45% were linked to care within 30 days. Once linked, care and viral suppression were rapid. Delays in screening and linkage to care present increased risk for onward transmission, and in the context of 21% baseline resistance, consideration of point-of-care testing and immediate referral at IME screening should be made.
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Affiliation(s)
- Nadine Kronfli
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada. .,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
| | - Blake Linthwaite
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Nancy Sheehan
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada.,Faculté de Pharmacie, Université de Montréal, Montreal, Quebec, Canada
| | - Joseph Cox
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Isabelle Hardy
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Bertrand Lebouché
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Family Medicine, McGill University, Montreal, QC, Canada
| | - Alexandra de Pokomandy
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Family Medicine, McGill University, Montreal, QC, Canada
| | - Charles Frenette
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada
| | - Michel Roger
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada.,Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Marina B Klein
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, Glen site, McGill University Health Centre, 1001 Decarie Boulevard D02.4110, Montreal, Quebec, H4A 3J1, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,CIHR Canadian HIV Trials Network, Vancouver, British Columbia, Canada
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6
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Villandré L, Labbe A, Brenner B, Ibanescu RI, Roger M, Stephens DA. Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada. PLoS One 2019; 14:e0213366. [PMID: 30840706 PMCID: PMC6402664 DOI: 10.1371/journal.pone.0213366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/19/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Phylogenetics has been used to investigate HIV transmission among men who have sex with men. This study compares several methodologies to elucidate the role of transmission chains in the dynamics of HIV spread in Quebec, Canada. METHODS The Quebec Human Immunodeficiency Virus (HIV) genotyping program database now includes viral sequences from close to 4,000 HIV-positive individuals classified as Men who have Sex with Men (MSMs), collected between 1996 and early 2016. Assessment of chain expansion may depend on the partitioning scheme used, and so, we produce estimates from several methods: the conventional Bayesian and maximum likelihood-bootstrap methods, in combination with a variety of schemes for applying a maximum distance criterion, and two other algorithms, DM-PhyClus, a Bayesian algorithm that produces a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast non-phylogenetic approach. Sequences obtained from individuals in the Primary HIV Infection (PHI) stage serve to identify incident cases. We focus on the period ranging from January 1st 2012 to February 1st 2016. RESULTS AND CONCLUSION The analyses reveal considerable overlap between chain estimates obtained from conventional methods, thus leading to similar estimates of recent temporal expansion. The Gap Procedure and DM-PhyClus suggest however moderately different chains. Nevertheless, all estimates stress that longer older chains are responsible for a sizeable proportion of the sampled incident cases among MSMs. Curbing the HIV epidemic will require strategies aimed specifically at preventing such growth.
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Affiliation(s)
- Luc Villandré
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Decision Sciences, HEC Montréal, Montreal, Québec, Canada
| | - Aurélie Labbe
- Department of Decision Sciences, HEC Montréal, Montreal, Québec, Canada
| | - Bluma Brenner
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Québec, Canada
| | | | - Michel Roger
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, Québec, Canada
| | - David A. Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, Québec, Canada
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Brenner BG, Ibanescu RI, Oliveira M, Roger M, Hardy I, Routy JP, Kyeyune F, Quiñones-Mateu ME, Wainberg MA. HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters. J Antimicrob Chemother 2018; 72:2171-2183. [PMID: 28472323 PMCID: PMC7263826 DOI: 10.1093/jac/dkx118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among
MSM in Quebec. While most HIV-1 strains (n = 2011) were
associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed
large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and
2015. Herein, tissue culture selections ascertained if large cluster lineages possessed
higher replicative fitness than singleton/small cluster isolates, allowing for viral
escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster
(n = 11) or singleton/small cluster
(n = 6) networks were passagedin
vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine
for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective
drug pressure. Results: Large cluster HIV-1 isolates selected for resistance to
dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small
clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K
(n = 7), S153Y
(n = 1) or H51Y
(n = 1) mutations as the dominant quasi-species within
8–12 weeks as compared with small cluster lineages where R263K
(n = 1/6), S153Y (1/6) or WT species (4/6) were
observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised
viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With
elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G,
N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations
leading to viral escape (>10 μM) by week 24. Conclusions: Further studies are needed to understand virological features of
large cluster viruses that may favour their transmissibility, replicative competence and
potential to escape selective antiretroviral drug pressure.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | | | - Fred Kyeyune
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Brenner BG, Ibanescu RI, Hardy I, Roger M. Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in "Real-World" Settings. Viruses 2017; 10:v10010010. [PMID: 29283390 PMCID: PMC5795423 DOI: 10.3390/v10010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/15/2022] Open
Abstract
HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
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Sepúlveda-Torres LDC, Rishishwar L, Rogers ML, Ríos-Olivares E, Boukli N, Jordan IK, Cubano LA. A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002-2011. PLoS One 2017; 12:e0177452. [PMID: 28493944 PMCID: PMC5426751 DOI: 10.1371/journal.pone.0177452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Puerto Rico has one of the highest rates of HIV/AIDS seen for any US state or territory, and antiretroviral therapy has been a mainstay of efforts to mitigate the HIV/AIDS public health burden on the island. We studied the evolutionary dynamics of HIV-1 mutation and antiretroviral drug resistance in Puerto Rico by monitoring the population frequency of resistance-associated mutations from 2002 to 2011. Whole blood samples from 4,475 patients were analyzed using the TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System in the Immunoretrovirus Research Laboratory at Universidad Central del Caribe. Results show that 64.0% of female and 62.9% of male patients had HIV-1 mutations that confer resistance to at least one antiretroviral medication. L63P and M184V were the dominant mutations observed for the protease (PRO) and reverse transcriptase (RT) encoding genes, respectively. Specific resistance mutations, along with their associated drug resistance profiles, can be seen to form temporal clusters that reveal a steadily changing landscape of resistance trends over time. Both women and men showed resistance mutations for an average of 4.8 drugs over the 10-year period, further underscoring the strong selective pressure exerted by antiretrovirals along with the rapid adaptive response of HIV. Nevertheless, both female and male patients showed a precipitous decrease for overall drug resistance, and for PRO mutations in particular, over the entire course of the study, with the most rapid decrease in frequency seen after 2006. The reduced HIV-1 mutation and drug resistance trends that we observed are consistent with previous reports from multi-year studies conducted around the world. Reduced resistance can be attributed to the use of more efficacious antiretroviral drug therapy, including the introduction of multi-drug combination therapies, which limited the ability of the virus to mount rapid adaptive responses to antiretroviral selection pressure.
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Affiliation(s)
- Lycely del C. Sepúlveda-Torres
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Maria Luisa Rogers
- Natural Sciences Department, Sacred Heart University, San Juan, Puerto Rico, United States of America
| | - Eddy Ríos-Olivares
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Nawal Boukli
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Luis A. Cubano
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
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Abstract
OBJECTIVE HIV-1 epidemics among MSM remain unchecked despite advances in treatment and prevention paradigms. This study combined viral phylogenetic and behavioural risk data to better understand underlying factors governing the temporal growth of the HIV epidemic among MSM in Quebec (2002-2015). METHODS Phylogenetic analysis of pol sequences was used to deduce HIV-1 transmission dynamics (cluster size, size distribution and growth rate) in first genotypes of treatment-naïve MSM (2002-2015, n = 3901). Low sequence diversity of first genotypes (0-0.44% mixed base calls) was used as an indication of early-stage infection. Behavioural risk data were obtained from the Montreal rapid testing site and primary HIV-1-infection cohorts. RESULTS Phylogenetic analyses uncovered high proportion of clustering of new MSM infections. Overall, 27, 45, 48, 53 and 57% of first genotypes within one (singleton, n = 1359), 2-4 (n = 692), 5-9 (n = 367), 10-19 (n = 405) and 20+ (n = 1277) cluster size groups were early infections (<0.44% diversity). Thirty viruses within large 20+ clusters disproportionately fuelled the epidemic, representing 13, 25 and 42% of infections, first genotyped in 2004-2007 (n = 1314), 2008-2011 (n = 1356) and 2012-2015 (n = 1033), respectively. Of note, 35, 21 and 14% of MSM belonging to 20+, 2-19 and one (singleton) cluster groups were under 30 years of age, respectively. Half of persons seen at the rapid testing site (2009-2011, n = 1781) were untested in the prior year. Poor testing propensity was associated with fewer reported partnerships. CONCLUSION Addressing the heterogeneity in transmission dynamics among HIV-1-infected MSM populations may help guide testing, treatment and prevention strategies.
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Duani H, Aleixo AW, Tupinambás U. Trends and predictors of HIV-1 acquired drug resistance in Minas Gerais, Brazil: 2002-2012. Braz J Infect Dis 2016; 21:148-154. [PMID: 28017554 PMCID: PMC9427561 DOI: 10.1016/j.bjid.2016.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/01/2016] [Accepted: 11/30/2016] [Indexed: 10/26/2022] Open
Abstract
Several studies show that the prevalence of multidrug-resistant HIV-1 virus is declining over time. A retrospective cohort study was carried out to evaluate the trends of drug resistance in antiretroviral treatment-exposed individuals in a state of a middle-income country, Minas Gerais, southeast region of Brazil. We analyzed 2115 HIV-1 sequences from 2002 up to 2012, from 52 cities of Minas Gerais. The groups were analyzed according to the definitions: "IAS - 3 class mutations", if ≥1 drug resistance mutation from IAS 2015 list (DRM) was present in each class; "No fully susceptible drugs" as the absence of any fully susceptible drug in Stanford algorithm; and "GSS≥2″, when a maximum calculated GSS (genotypic susceptibility score) was ≥2 or ≥3, counting only drugs available in Brazil and USA at given calendar years. Time trends of resistance were analyzed by Cochran-Armitage test. We observed a decrease in the rate resistance mutations for PI, NRTI, "IAS - 3 class mutations", and "No fully susceptible drugs" over these 11 years, from 69.2% to 20.7%, 92.3% to 90.2%, 46.2% to 22.5%, and 12.8% to 5.7%, respectively (p<0.05). Resistance to NNRTI increased from 74.4% to 81.6%, mainly because of K103N mutation. The GSS score ≥2 increased during the years from 35.9% to 87.3% (p<0.001). We demonstrate that resistance to PI and to the three main classes simultaneously are declining, although the number of patients on of antiretroviral therapy has doubled in the last ten years in Brazil (125,000 in 2002 to 400,000 in 2014). Broader resistance testing and the availability of more therapeutic options might have influenced this decline. The increase in NNRTI resistance can limit this class as first line treatment in Brazil in the future.
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Affiliation(s)
- Helena Duani
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Pós-Graduação em Ciências da Saúde, Infectologia e Medicina Tropical, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Laboratório de Imunologia e Biologia Molecular (DIP-UFMG), Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Hospital das Clínicas, Belo Horizonte, MG, Brazil.
| | - Agdemir Waleria Aleixo
- Universidade Federal de Minas Gerais (UFMG), Laboratório de Imunologia e Biologia Molecular (DIP-UFMG), Belo Horizonte, MG, Brazil
| | - Unaí Tupinambás
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Pós-Graduação em Ciências da Saúde, Infectologia e Medicina Tropical, Belo Horizonte, MG, Brazil
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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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Brenner BG, Wainberg MA. Clinical benefit of dolutegravir in HIV-1 management related to the high genetic barrier to drug resistance. Virus Res 2016; 239:1-9. [PMID: 27422477 DOI: 10.1016/j.virusres.2016.07.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
Abstract
This manuscript reviews the reasons why Integrase inhibitors should now routinely constitute a part of first line antiretroviral therapy for the treatment of HIV disease. The use of these drugs that are generally well tolerated has resulted in far less drug resistance than was the case with most other categories of antiviral compounds. In addition, the integrase inhibitor family of drugs has been less prone to the problem of transmitted drug resistance which is due to a wide variety of substitutions in the HIV genome that can be sexually transmitted from one person to another. However, the use of integrase inhibitors in first line therapy may unfortunately not soon happen in developing country settings where non-nucleoside reverse transcriptase inhibitors continue to be a mainstay of initial therapy, primarily for reasons of cost. As long as this situation continues, problems of drug resistance and transmitted drug resistance will be common in such settings. Current evidence also suggests that the use of dolutegravir as a first line integrase inhibitor may limit development of drug resistance to an extent that exceeds the use of other members of this family of drugs. This may be due to particular patterns of resistance involving dolutegravir, whereby the mutations that are associated with resistance against this compound may actually diminish both HIV replication capacity as well as integrase enzymatic activity in a far-reaching and unique manner. This gives potential hope that the use of dolutegravir in first line therapy could actually form part of the long-sought goal of attainment of a functional cure for HIV disease.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
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A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS 2015; 29:1917-25. [PMID: 26355570 DOI: 10.1097/qad.0000000000000768] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Antiretroviral-naive HIV-positive individuals contribute to the transmission of drug-resistant viruses, compromising first-line therapy. Using phylogenetic inference, we quantified the proportion of transmitted drug-resistance originating from a treatment-naive source. METHODS Using a novel phylotype-based approach, 24 550 HIV-1 subtype B partial pol gene sequences from the UK HIV Drug Resistance database were analysed. Ongoing transmission of drug resistance amongst HIV-positive individuals was identified as phylotypes of at least three sequences with at least one shared drug resistance mutation, a maximum intra-clade genetic distance of 4.0% and a basal branch support at least 90%. The time of persistence of the transmission chains was estimated using a fast least-squares molecular clock inference approach. RESULTS Around 70% of transmitted drug-resistance had a treatment-naive source. The most commonly transmitted mutations were L90M in the protease gene and K103N, T215D and T215S in reverse transcriptase. Reversion to wild type occurred at a low frequency and drug-independent reservoirs of resistance have persisted for up to 13 years. CONCLUSION These results illustrate the impact of viral fitness on the establishment of resistance reservoirs and support the notion that earlier diagnoses and treatment of HIV infections are warranted for counteracting the spread of antiretroviral resistance. Phylotype-based phylogenetic inference is an attractive approach for the routine surveillance of transmitted drug resistance in HIV as well as in other pathogens for which genotypic resistance data are available.
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