1
|
Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND. A new lineage nomenclature to aid genomic surveillance of dengue virus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.16.24307504. [PMID: 38798319 PMCID: PMC11118645 DOI: 10.1101/2024.05.16.24307504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org .
Collapse
|
2
|
Carrasco-Hernández R, Valenzuela-Ponce H, Soto-Nava M, García-Morales C, Matías-Florentino M, Wertheim JO, Smith DM, Reyes-Terán G, Ávila-Ríos S. Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical predictors. Epidemics 2024; 47:100770. [PMID: 38761432 DOI: 10.1016/j.epidem.2024.100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/07/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
In the context of infectious diseases, the dynamic interplay between ever-changing host populations and viral biology demands a more flexible modeling approach than common fixed correlations. Embracing random-effects regression models allows for a nuanced understanding of the intricate ecological and evolutionary dynamics underlying complex phenomena, offering valuable insights into disease progression and transmission patterns. In this article, we employed a random-effects regression to model an observed decreasing median plasma viral load (pVL) among individuals with HIV in Mexico City during 2019-2021. We identified how these functional slope changes (i.e. random slopes by year) improved predictions of the observed pVL median changes between 2019 and 2021, leading us to hypothesize underlying ecological and evolutionary factors. Our analysis involved a dataset of pVL values from 7325 ART-naïve individuals living with HIV, accompanied by their associated clinical and viral molecular predictors. A conventional fixed-effects linear model revealed significant correlations between pVL and predictors that evolved over time. However, this fixed-effects model could not fully explain the reduction in median pVL; thus, prompting us to adopt random-effects models. After applying a random effects regression model-with random slopes and intercepts by year-, we observed potential "functional changes" within the local HIV viral population, highlighting the importance of ecological and evolutionary considerations in HIV dynamics: A notably stronger negative correlation emerged between HIV pVL and the CpG content in the pol gene, suggesting a changing immune landscape influenced by CpG-induced innate immune responses that could impact viral load dynamics. Our study underscores the significance of random effects models in capturing dynamic correlations and the crucial role of molecular characteristics like CpG content. By enriching our understanding of changing host-virus interactions and HIV progression, our findings contribute to the broader relevance of such models in infectious disease research. They shed light on the changing interplay between host and pathogen, driving us closer to more effective strategies for managing infectious diseases. SIGNIFICANCE OF THE STUDY: This study highlights a decreasing trend in median plasma viral loads among ART-naïve individuals living with HIV in Mexico City between 2019 and 2021. It uncovers various predictors significantly correlated with pVL, shedding light on the complex interplay between host-virus interactions and disease progression. By employing a random-slopes model, the researchers move beyond traditional fixed-effects models to better capture dynamic correlations and evolutionary changes in HIV dynamics. The discovery of a stronger negative correlation between pVL and CpG content in HIV-pol sequences suggests potential changes in the immune landscape and innate immune responses, opening avenues for further research into adaptive changes and responses to environmental shifts in the context of HIV infection. The study's emphasis on molecular characteristics as predictors of pVL adds valuable insights to epidemiological and evolutionary studies of viruses, providing new avenues for understanding and managing HIV infection at the population level.
Collapse
Affiliation(s)
- Rocío Carrasco-Hernández
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico.
| | - Humberto Valenzuela-Ponce
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Maribel Soto-Nava
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Claudia García-Morales
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gustavo Reyes-Terán
- Coordinación de Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Secretaría de Salud, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico; Centro de Investigación en Enfermedades Infecciosas (CIENI), Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Tlalpan, Ciudad de México 14080, Mexico
| |
Collapse
|
3
|
Pimentel V, Pingarilho M, Sebastião CS, Miranda M, Gonçalves F, Cabanas J, Costa I, Diogo I, Fernandes S, Costa O, Corte-Real R, Martins MRO, Seabra SG, Abecasis AB, Gomes P. Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal. Viruses 2024; 16:622. [PMID: 38675962 PMCID: PMC11054263 DOI: 10.3390/v16040622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The global scale-up of antiretroviral treatment (ART) offers significant health benefits by suppressing HIV-1 replication and increasing CD4 cell counts. However, incomplete viral suppression poses a potential threat for the emergence of drug resistance mutations (DRMs), limiting ART options, and increasing HIV transmission. OBJECTIVE We investigated the patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) among HIV-1 patients in Portugal. METHODS Data were obtained from 1050 HIV-1 patient samples submitted for HIV drug resistance (HIVDR) testing from January 2022 to June 2023. Evaluation of DRM affecting viral susceptibility to nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs) was performed using an NGS technology, the Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay. RESULTS About 71% of patients were ART naïve and 29% were experienced. Overall, 20% presented with any DRM. The prevalence of TDR and ADR was 12.6% and 41.1%, respectively. M184V, T215S, and M41L mutations for NRTI, K103N for NNRTI, and M46I/L for PIs were frequent in naïve and treated patients. E138K and R263K mutations against INSTIs were more frequent in naïve than treated patients. TDR and ADR to INSTIs were 0.3% and 7%, respectively. Patients aged 50 or over (OR: 1.81, p = 0.015), originating from Portuguese-speaking African countries (PALOPs) (OR: 1.55, p = 0.050), HIV-1 subtype G (OR: 1.78, p = 0.010), and with CD4 < 200 cells/mm3 (OR: 1.70, p = 0.043) were more likely to present with DRMs, while the males (OR: 0.63, p = 0.003) with a viral load between 4.1 to 5.0 Log10 (OR: 0.55, p = 0.003) or greater than 5.0 Log10 (OR: 0.52, p < 0.001), had lower chances of presenting with DRMs. CONCLUSIONS We present the first evidence on TDR and ADR to INSTI regimens in followed up patients presenting for healthcare in Portugal. We observed low levels of TDR to INSTIs among ART-naïve and moderate levels in ART-exposed patients. Regimens containing PIs could be an alternative second line in patients with intermediate or high-level drug resistance, especially against second-generation INSTIs (dolutegravir, bictegravir, and cabotegravir).
Collapse
Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Cruz S. Sebastião
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Fátima Gonçalves
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Joaquim Cabanas
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Inês Costa
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
| | - Olga Costa
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - Rita Corte-Real
- Biologia Molecular, Serviço de Patologia Clínica, Centro Hospitalar de Lisboa Central, 1150-199 Lisbon, Portugal; (O.C.); (R.C.-R.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Sofia G. Seabra
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Ana B. Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (M.P.); (C.S.S.); (M.M.); (M.R.O.M.); (S.G.S.); (A.B.A.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade Local de Saúde Lisboa Ocidental, Hospital Egas Moniz, 1349-019 Lisbon, Portugal; (F.G.); (J.C.); (I.C.); (I.D.); (S.F.); (P.G.)
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, 2829-511 Almada, Portugal
| |
Collapse
|
4
|
Zacharopoulou P, Lee M, Oliveira T, Thornhill J, Robinson N, Brown H, Kinloch S, Goulder P, Fox J, Fidler S, Ansari MA, Frater J. Prevalence of resistance-associated viral variants to the HIV-specific broadly neutralising antibody 10-1074 in a UK bNAb-naïve population. Front Immunol 2024; 15:1352123. [PMID: 38562938 PMCID: PMC10982389 DOI: 10.3389/fimmu.2024.1352123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Broadly neutralising antibodies (bNAbs) targeting HIV show promise for both prevention of infection and treatment. Among these, 10-1074 has shown potential in neutralising a wide range of HIV strains. However, resistant viruses may limit the clinical efficacy of 10-1074. The prevalence of both de novo and emergent 10-1074 resistance will determine its use at a population level both to protect against HIV transmission and as an option for treatment. To help understand this further, we report the prevalence of pre-existing mutations associated with 10-1074 resistance in a bNAb-naive population of 157 individuals presenting to UK HIV centres with primary HIV infection, predominantly B clade, receiving antiretroviral treatment. Single genome analysis of HIV proviral envelope sequences showed that 29% of participants' viruses tested had at least one sequence with 10-1074 resistance-associated mutations. Mutations interfering with the glycan binding site at HIV Env position 332 accounted for 95% of all observed mutations. Subsequent analysis of a larger historic dataset of 2425 B-clade envelope sequences sampled from 1983 to 2019 revealed an increase of these mutations within the population over time. Clinical studies have shown that the presence of pre-existing bNAb mutations may predict diminished therapeutic effectiveness of 10-1074. Therefore, we emphasise the importance of screening for these mutations before initiating 10-1074 therapy, and to consider the implications of pre-existing resistance when designing prevention strategies.
Collapse
Affiliation(s)
| | - Ming Lee
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, United States
| | - John Thornhill
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Nicola Robinson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Helen Brown
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sabine Kinloch
- Institute of Immunity and Transplantation, Royal Free Hospital, London, United Kingdom
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Julie Fox
- Department of Infection, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Sarah Fidler
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford National Institute of Health Biomedical Research Centre, Oxford, United Kingdom
| |
Collapse
|
5
|
Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303990. [PMID: 38558994 PMCID: PMC10980117 DOI: 10.1101/2024.03.14.24303990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was estimated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Evolutionary dynamics were assessed among demographic and behavioral sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by more than four-fold. Inter-subtype HIV diversity has generally increased. While p24 intra-subtype genetic diversity and divergence leveled off after 2014, diversity and divergence of gp41 increased through 2017. Inter- and intra-subtype viral diversity increased across all population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics in declining African HIV epidemics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.
Collapse
Affiliation(s)
- Seungwon Kim
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Michael A. Martin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Redd
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Joshua T. Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven J. Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, England, United Kingdom
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Kalisizo, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - M. Kate Grabowski
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| |
Collapse
|
6
|
Hanke K, Rykalina V, Koppe U, Gunsenheimer-Bartmeyer B, Heuer D, Meixenberger K. Developing a next level integrated genomic surveillance: Advances in the molecular epidemiology of HIV in Germany. Int J Med Microbiol 2024; 314:151606. [PMID: 38278002 DOI: 10.1016/j.ijmm.2024.151606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Advances in the molecular epidemiological studies of the Human Immunodeficiency Virus (HIV) at the Robert Koch Institute (RKI) by laboratory and bioinformatic automation should allow the processing of larger numbers of samples and more comprehensive and faster data analysis in order to provide a higher resolution of the current HIV infection situation in near real-time and a better understanding of the dynamic of the German HIV epidemic. The early detection of the emergence and transmission of new HIV variants is important for the adaption of diagnostics and treatment guidelines. Likewise, the molecular epidemiological detection and characterization of spatially limited HIV outbreaks or rapidly growing sub-epidemics is of great importance in order to interrupt the transmission pathways by regionally adapting prevention strategies. These aims are becoming even more important in the context of the SARS-CoV2 pandemic and the Ukrainian refugee movement, which both have effects on the German HIV epidemic that should be monitored to identify starting points for targeted public health measures in a timely manner. To this end, a next level integrated genomic surveillance of HIV is to be established.
Collapse
Affiliation(s)
- Kirsten Hanke
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
| | - Vera Rykalina
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Uwe Koppe
- Unit 34: HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | | | - Dagmar Heuer
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Karolin Meixenberger
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| |
Collapse
|
7
|
Abrantes R, Pimentel V, Miranda MNS, Silva AR, Diniz A, Ascenção B, Piñeiro C, Koch C, Rodrigues C, Caldas C, Morais C, Faria D, Gomes da Silva E, Teófilo E, Monteiro F, Roxo F, Maltez F, Rodrigues F, Gaião G, Ramos H, Costa I, Germano I, Simões J, Oliveira J, Ferreira J, Poças J, Saraiva da Cunha J, Soares J, Fernandes S, Mansinho K, Pedro L, Aleixo MJ, Gonçalves MJ, Manata MJ, Mouro M, Serrado M, Caixeiro M, Marques N, Costa O, Pacheco P, Proença P, Rodrigues P, Pinho R, Tavares R, Correia de Abreu R, Côrte-Real R, Serrão R, Sarmento e Castro R, Nunes S, Faria T, Baptista T, Simões D, Mendão L, Martins MRO, Gomes P, Pingarilho M, Abecasis AB. Determinants of HIV late presentation among men who have sex with men in Portugal (2014-2019): who's being left behind? Front Public Health 2024; 12:1336845. [PMID: 38500732 PMCID: PMC10947991 DOI: 10.3389/fpubh.2024.1336845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/26/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction HIV late presentation (LP) remains excessive in Europe. We aimed to analyze the factors associated with late presentation in the MSM population newly diagnosed with HIV in Portugal between 2014 and 2019. Methods We included 391 newly HIV-1 diagnosed Men who have Sex with Men (MSM), from the BESTHOPE project, in 17 countrywide Portuguese hospitals. The data included clinical and socio-behavioral questionnaires and the viral genomic sequence obtained in the drug resistance test before starting antiretrovirals (ARVs). HIV-1 subtypes and epidemiological surveillance mutations were determined using different bioinformatics tools. Logistic regression was used to estimate the association between predictor variables and late presentation (LP). Results The median age was 31 years, 51% had a current income between 501-1,000 euros, 28% were migrants. 21% had never been tested for HIV before diagnosis, with 42.3% of MSM presenting LP. 60% were infected with subtype B strains. In the multivariate regression, increased age at diagnosis, higher income, lower frequency of screening, STI ever diagnosed and higher viral load were associated with LP. Conclusion Our study suggests that specific subgroups of the MSM population, such older MSM, with higher income and lower HIV testing frequency, are not being targeted by community and clinical screening services. Overall, targeted public health measures should be strengthened toward these subgroups, through strengthened primary care testing, expanded access to PrEP, information and promotion of HIV self-testing and more inclusive and accessible health services.
Collapse
Affiliation(s)
- Ricardo Abrantes
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Mafalda N. S. Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Ana Rita Silva
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - António Diniz
- U. Imunodeficiência, Hospital Pulido Valente, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - Bianca Ascenção
- Serviço de Infeciologia, Centro Hospitalar de Setúbal, Setúbal, Portugal
| | - Carmela Piñeiro
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Carmo Koch
- Centro de Biologia Molecular, Serviço de Imunohemoterapia do Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Catarina Rodrigues
- Serviço de Medicina 1.4, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Cátia Caldas
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Célia Morais
- Serviço de Patologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Domitília Faria
- Serviço de Medicina 3, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | | | - Eugénio Teófilo
- Serviço de Medicina 2.3, Hospital de Santo António dos Capuchos, Centro Hospitalar de Lisboa Central, Lisbon, Portugal
| | - Fátima Monteiro
- Centro de Biologia Molecular, Serviço de Imunohemoterapia do Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Fausto Roxo
- Hospital de Dia de Doenças Infeciosas, Hospital Distrital de Santarém, Santarém, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infeciosas, Hospital Curry Cabral, Centro Hospitalar de Lisboa, Lisbon, Portugal
| | - Fernando Rodrigues
- Serviço de Patologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Guilhermina Gaião
- Serviço de Patologia Clínica, Hospital de Sta Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - Helena Ramos
- Serviço de Patologia Clínica, Centro Hospitalar do Porto, Porto, Portugal
| | - Inês Costa
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
| | - Isabel Germano
- Serviço de Medicina 1.4, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Joana Simões
- Serviço de Medicina 1.4, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Joaquim Oliveira
- Serviço de Infeciologia, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - José Ferreira
- Serviço de Medicina 2, Hospital de Faro, Centro Hospitalar Universitário do Algarve, Faro, Portugal
| | - José Poças
- Serviço de Infeciologia, Centro Hospitalar de Setúbal, Setúbal, Portugal
| | - José Saraiva da Cunha
- Serviço de Infeciologia, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Jorge Soares
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Liliana Pedro
- Serviço de Medicina 3, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | | | | | - Maria José Manata
- Serviço de Doenças Infeciosas, Hospital Curry Cabral, Centro Hospitalar de Lisboa, Lisbon, Portugal
| | - Margarida Mouro
- Serviço de Infeciologia, Hospital de Aveiro, Centro Hospitalar Baixo Vouga, Aveiro, Portugal
| | - Margarida Serrado
- U. Imunodeficiência, Hospital Pulido Valente, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - Micaela Caixeiro
- Serviço de Infeciologia, Hospital Dr. Fernando da Fonseca, Amadora, Portugal
| | - Nuno Marques
- Serviço de Infeciologia, Hospital Garcia da Orta, Almada, Portugal
| | - Olga Costa
- Serviço de Patologia Clínica, Biologia Molecular, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Patrícia Pacheco
- Serviço de Infeciologia, Hospital Dr. Fernando da Fonseca, Amadora, Portugal
| | - Paula Proença
- Serviço de Infeciologia, Hospital de Faro, Centro Hospitalar Universitário do Algarve, Faro, Portugal
| | - Paulo Rodrigues
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - Raquel Pinho
- Serviço de Medicina 3, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | - Raquel Tavares
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - Ricardo Correia de Abreu
- Serviço de Infeciologia, Unidade de Local de Saúde de Matosinhos, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Rita Côrte-Real
- Serviço de Patologia Clínica, Biologia Molecular, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Rosário Serrão
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | | | - Sofia Nunes
- Serviço de Infeciologia, Hospital de Aveiro, Centro Hospitalar Baixo Vouga, Aveiro, Portugal
| | - Telo Faria
- Unidade Local de Saúde do Baixo Alentejo, Hospital José Joaquim Fernandes, Beja, Portugal
| | - Teresa Baptista
- Serviço de Doenças Infeciosas, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Daniel Simões
- Grupo de Ativistas em Tratamentos (GAT), Lisbon, Portugal
| | - Luis Mendão
- Grupo de Ativistas em Tratamentos (GAT), Lisbon, Portugal
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Almada, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Ana B. Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | | |
Collapse
|
8
|
Nduva GM, Otieno F, Kimani J, Sein Y, Arimide DA, Mckinnon LR, Cholette F, Lawrence MK, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Medstrand P, Sanders EJ, Esbjörnsson J, Hassan AS. Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020. J Antimicrob Chemother 2024; 79:287-296. [PMID: 38091580 PMCID: PMC10832587 DOI: 10.1093/jac/dkad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.
Collapse
Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Yiakon Sein
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | - Dawit A Arimide
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Lyle R Mckinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Morris K Lawrence
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Gaudensia Mutua
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Susan M Graham
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Department of Medicine, Global Health and Epidemiology, University of Washington, Seattle, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Matt A Price
- IAVI, NewYork, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Eduard J Sanders
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| |
Collapse
|
9
|
Topcu C, Georgiou V, Rodosthenous JH, Siakallis G, Gavala EK, Dimitriou CR, Zeniou E, Foley BT, Kostrikis LG. Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus. Viruses 2023; 16:19. [PMID: 38275954 PMCID: PMC10819958 DOI: 10.3390/v16010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Molecular investigations of the HIV-1 pol region (2253-5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790-8795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.
Collapse
Affiliation(s)
- Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Johana Hezka Rodosthenous
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | | | - Elena Katerina Gavala
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Christiana Reveka Dimitriou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Evgenia Zeniou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Brian Thomas Foley
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60–68 Phaneromenis Street, 1011 Nicosia, Cyprus
| |
Collapse
|
10
|
Valenzuela-Ponce H, Carbajal C, Soto-Nava M, Tapia-Trejo D, García-Morales C, Murillo W, Lorenzana I, Reyes-Terán G, Ávila-Ríos S. Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome. Microbiol Spectr 2023; 11:e0161323. [PMID: 37962394 PMCID: PMC10714756 DOI: 10.1128/spectrum.01613-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE We identify both canonical and novel human leukocyte antigen (HLA)-HIV associations, providing a first step toward improved understanding of HIV immune control among the understudied Honduras Mestizo population. Our results are relevant to understanding the protective or detrimental effects of HLA subtypes in Latin America because their unique HLA diversity poses challenges for designing vaccines against HIV and interpreting results from such vaccine trials. Likewise, the description of the HLA profile in an understudied population that shows a unique HLA immunogenetic background is not only relevant for HIV immunology but also relevant in population genetics, molecular anthropology, susceptibility to other infections, autoimmune diseases, and allograft transplantation.
Collapse
Affiliation(s)
- Humberto Valenzuela-Ponce
- CIENI Centro de Investigación en Enfermedades Respiratorias, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Candy Carbajal
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Maribel Soto-Nava
- CIENI Centro de Investigación en Enfermedades Respiratorias, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- CIENI Centro de Investigación en Enfermedades Respiratorias, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Claudia García-Morales
- CIENI Centro de Investigación en Enfermedades Respiratorias, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Wendy Murillo
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Gustavo Reyes-Terán
- Comisión Coordinadora de Institutos Nacional de Salud y Hospitales de Alta Especialidad, Secretar ´ıa de Salud, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- CIENI Centro de Investigación en Enfermedades Respiratorias, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| |
Collapse
|
11
|
Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
Collapse
Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| |
Collapse
|
12
|
Polotan FGM, Salazar CRP, Morito HLE, Abulencia MFB, Pantoni RAR, Mercado ES, Hué S, Ditangco RA. Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018. Virus Evol 2023; 9:vead073. [PMID: 38131006 PMCID: PMC10735293 DOI: 10.1093/ve/vead073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n = 1144) collected between 2008 and 2018 from three island groups were collated from the Research Institute for Tropical Medicine drug resistance genotyping database. Estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates, and geographic spread of CRF01_AE was performed with BEAST. Re and Ne were compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of June 1996 [95 per cent highest posterior density (HPD): December 1991, October 1999]. An increasing CRF01_AE Ne was observed from the tMRCA to 2013. The CRF01_AE Re reached peaks of 2.46 [95 per cent HPD: 1.76, 3.27] in 2007 and 2.52 [95 per cent HPD: 1.83, 3.34] in 2015. A decrease of CRF01_AE Re occurred in the intervening years of 2007 to 2011, reaching as low as 1.43 [95 per cent HPD: 1.06, 1.90] in 2011, followed by a rebound. The CRF01_AE epidemic most likely started in Luzon and then spread to the other island groups of the country. Both CRF01_AE and Subtype B exhibited similar patterns of Re fluctuation over time. These results characterize the subtype-specific phylodynamic history of the largest CRF01_AE cluster in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.
Collapse
Affiliation(s)
- Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Carl Raymund P Salazar
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6700 EH, The Netherlands
| | - Hannah Leah E Morito
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Miguel Francisco B Abulencia
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Roslind Anne R Pantoni
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Edelwisa S Mercado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
| | - Rossana A Ditangco
- AIDS Research Group, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| |
Collapse
|
13
|
Antonova A, Kazennova E, Lebedev A, Ozhmegova E, Kuznetsova A, Tumanov A, Bobkova M. Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses 2023; 15:2312. [PMID: 38140553 PMCID: PMC10748268 DOI: 10.3390/v15122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.
Collapse
Affiliation(s)
- Anastasiia Antonova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Elena Kazennova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksey Lebedev
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Ekaterina Ozhmegova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Anna Kuznetsova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksandr Tumanov
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia;
| |
Collapse
|
14
|
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d'Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos RD. HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. Lancet HIV 2023; 10:e733-e741. [PMID: 37832567 PMCID: PMC10913014 DOI: 10.1016/s2352-3018(23)00228-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir in first-line and second-line antiretroviral therapy (ART) might facilitate emerging resistance. The DTG RESIST study combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for dolutegravir resistance. METHODS We included cohorts with INSTI resistance data from two collaborations (ART Cohort Collaboration, International epidemiology Databases to Evaluate AIDS in Southern Africa), and the UK Collaborative HIV Cohort. Eight cohorts from Canada, France, Germany, Italy, the Netherlands, Switzerland, South Africa, and the UK contributed data on individuals who were viraemic on dolutegravir-based ART and underwent genotypic resistance testing. Individuals with unknown dolutegravir initiation date were excluded. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. FINDINGS We included 599 people with genotypic resistance testing on dolutegravir-based ART between May 22, 2013, and Dec 20, 2021. Most had HIV-1 subtype B (n=351, 59%), a third had been exposed to first-generation INSTIs (n=193, 32%), 70 (12%) were on dolutegravir dual therapy, and 18 (3%) were on dolutegravir monotherapy. INSTI DRMs were detected in 86 (14%) individuals; 20 (3%) had more than one mutation. Most (n=563, 94%) were susceptible to dolutegravir, seven (1%) had potential low, six (1%) low, 17 (3%) intermediate, and six (1%) high-level dolutegravir resistance. The risk of dolutegravir resistance was higher on dolutegravir monotherapy (adjusted odds ratio [aOR] 34·1, 95% CI 9·93-117) and dolutegravir plus lamivudine dual therapy (aOR 9·21, 2·20-38·6) compared with combination ART, and in the presence of potential low or low (aOR 5·23, 1·32-20·7) or intermediate or high-level (aOR 13·4, 4·55-39·7) nucleoside reverse transcriptase inhibitor (NRTI) resistance. INTERPRETATION Among people with viraemia on dolutegravir-based ART, INSTI DRMs and dolutegravir resistance were rare. NRTI resistance substantially increased the risk of dolutegravir resistance, which is of concern, notably in resource-limited settings. Monitoring is important to prevent resistance at the individual and population level and ensure the long-term sustainability of ART. FUNDING US National Institutes of Health, Swiss National Science Foundation.
Collapse
Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Suzanne M Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany; Department I of Internal Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - M John Gill
- Southern Alberta Clinic, Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jonathan A C Sterne
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
15
|
Moraka NO, Choga WT, Pema MN, Chawawa MK, Gobe I, Mokomane M, Bareng OT, Bhebhe L, Kelentse N, Mulenga G, Pretorius Holme M, Mohammed T, Koofhethile CK, Makhema JM, Shapiro R, Lockman S, Moyo S, Gaseitsiwe S. Predicted resistance to broadly neutralizing antibodies (bnAbs) and associated HIV-1 envelope characteristics among seroconverting adults in Botswana. Sci Rep 2023; 13:18134. [PMID: 37875518 PMCID: PMC10598268 DOI: 10.1038/s41598-023-44722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
We used HIV-1C sequences to predict (in silico) resistance to 33 known broadly neutralizing antibodies (bnAbs) and evaluate the different HIV-1 Env characteristics that may affect virus neutralization. We analyzed proviral sequences from adults with documented HIV-1 seroconversion (N = 140) in Botswana (2013-2018). HIV-1 env sequences were used to predict bnAb resistance using bNAb-ReP, to determine the number of potential N-linked glycosylation sites (PNGS) and evaluate Env variable region characteristics (VC). We also assessed the presence of signature mutations that may affect bnAb sensitivity in vitro. We observe varied results for predicted bnAb resistance among our cohort. 3BNC117 showed high predicted resistance (72%) compared to intermediate levels of resistance to VRC01 (57%). We predict low resistance to PGDM100 and 10-1074 and no resistance to 4E10. No difference was observed in the frequency of PNGS by bNAb susceptibility patterns except for higher number of PNGs in V3 bnAb resistant strains. Associations of VC were observed for V1, V4 and V5 loop length and net charge. We also observed few mutations that have been reported to confer bnAb resistance in vitro. Our results support use of sequence data and machine learning tools to predict the best bnAbs to use within populations.
Collapse
Affiliation(s)
- Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Marea N Pema
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Moses Kudzai Chawawa
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Margaret Mokomane
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Lynette Bhebhe
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Graceful Mulenga
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | | | - Terence Mohammed
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Catherine K Koofhethile
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Roger Shapiro
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Shahin Lockman
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Bontleng, Private Bag BO320, Gaborone, Botswana.
| |
Collapse
|
16
|
Fiebig U, Altmann B, Hauser A, Koppe U, Hanke K, Gunsenheimer-Bartmeyer B, Bremer V, Baumgarten A, Bannert N. Transmitted drug resistance and subtype patterns of viruses from reported new HIV diagnoses in Germany, 2017-2020. BMC Infect Dis 2023; 23:673. [PMID: 37817087 PMCID: PMC10563336 DOI: 10.1186/s12879-023-08649-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The transmission of resistant HIV variants jeopardizes the effective use of antiretrovirals for therapy and prophylaxis. Molecular surveillance of new HIV diagnoses with a focus on prevalence and type of resistance associated mutations and the subtype of circulating viruses is mandatory. METHOD From 2017 to 2020, 11,527 new HIV diagnoses were reported in Germany to the Robert Koch Institute (RKI). Protease (PR) and reverse-transcriptase (RT) sequences were obtained from 4559 (39.6%) cases, and PR, RT and integrase (IN) sequences were obtained from 3097 (26.9%) cases. The sequences were analyzed with data from the national HIV reports. RESULTS Among all cases in the analysis, the proportion of primary resistance was 4.3% for nucleoside reverse-transcriptase inhibitors (NRTIs), 9.2% for non-NRTI (NNRTIs), 3.3% for protease inhibitors (PIs) and 1.4% for integrase inhibitors (INIs). Dual-class resistance was highest for NRTIs/NNRTIs with 1.2%. There was no trend in the proportion of viruses resistant to drug classes. Most individual key mutations associated with relevant resistance had a prevalence below 1% including K65R (0.1%) and M184V (0.6%). A notable exception was K103NS, with a prevalence of 2.9% and a significant increase (pTrend=0.024) during 2017-2020. In this period, diagnoses of infections with HIV-1 subtype B were the most common at 58.7%, but its prevalence was declining (pTrend=0.049) while the frequency of minority subtypes (each < 1%) increased (pTrend=0.007). Subtype B was highest (75.6%) in men who have sex with men (MSM) and lowest in reported heterosexual transmissions (HETs, 22.6%). CONCLUSION The percentage of primary resistance was high but at a stable level. A genotypic determination of resistance is therefore still required before the start of therapy. The subtype diversity of circulating HIV-1 is increasing.
Collapse
Affiliation(s)
- Uwe Fiebig
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Britta Altmann
- Unit 18 "HIV and other Retroviruses", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Andrea Hauser
- Unit 18 "HIV and other Retroviruses", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Uwe Koppe
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Kirsten Hanke
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Barbara Gunsenheimer-Bartmeyer
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Viviane Bremer
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Axel Baumgarten
- Center for Infectiology Berlin-Prenzlauer Berg, Nordufer 20, 13353, Berlin, Germany
| | - Norbert Bannert
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.
| |
Collapse
|
17
|
Maruapula D, Moraka NO, Bareng OT, Mokgethi PT, Choga WT, Seatla KK, Kelentse N, Koofhethille CK, Zuze BJL, Gaolathe T, Pretorius-Holme M, Makhema J, Novitsky V, Shapiro R, Moyo S, Lockman S, Gaseitsiwe S. Archived rilpivirine-associated resistance mutations among ART-naive and virologically suppressed people living with HIV-1 subtype C in Botswana: implications for cabotegravir/rilpivirine use. J Antimicrob Chemother 2023; 78:2489-2495. [PMID: 37585352 PMCID: PMC10545497 DOI: 10.1093/jac/dkad258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023] Open
Abstract
OBJECTIVES Pre-existing rilpivirine resistance-associated mutations (RVP-RAMs) have been found to predict HIV-1 virological failure in those switching to long-acting injectable cabotegravir/rilpivirine. We here evaluated the prevalence of archived RPV-RAMs in a cohort of people living with HIV (PWH). METHODS We analysed near full-length HIV-1 pol sequences from proviral DNA for the presence of RPV-RAMs, which were defined according to the 2022 IAS-USA drug resistance mutation list and Stanford HIV drug resistance database. RESULTS RPV-RAMs were identified in 757/5805 sequences, giving a prevalence of 13.0% (95% CI 12%-13.9%). Amongst the ART-naive group, 137/1281 (10.7%, 95% CI 9.1%-12.5%) had at least one RPV-RAM. Of the 4524 PWH with viral suppression on ART (VL <400 copies/mL), 620 (13.7%, 95% CI 12.7%-14.7%) had at least one RPV-RAM. E138A was the most prevalent RPV-RAM in the ART-naive group (7.9%) and the ART-suppressed group (9.3%). The rest of the mutations observed (L100I, K101E, E138G, E138K, E138Q, Y181C, H221Y, M230L, A98G, V179D, G190A, G190E and M230I) were below a prevalence of 1%. CONCLUSIONS RPV-RAMs were present in 10.7% of ART-naive and 13.7% of ART-suppressed PWH in Botswana. The most common RPV-RAM in both groups was E138A. Since individuals with the E138A mutation may be more likely to fail cabotegravir/rilpivirine, monitoring RPV-RAMs will be crucial for effective cabotegravir/rilpivirine implementation in this setting.
Collapse
Affiliation(s)
| | - Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Faculty of Health Sciences, Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Faculty of Health Sciences, Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Faculty of Science, Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Faculty of Health Sciences, Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Catherine K Koofhethille
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Molly Pretorius-Holme
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
18
|
Faraci G, Park SY, Love TMT, Dubé MP, Lee HY. Precision detection of recent HIV infections using high-throughput genomic incidence assay. Microbiol Spectr 2023; 11:e0228523. [PMID: 37712639 PMCID: PMC10580985 DOI: 10.1128/spectrum.02285-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 09/16/2023] Open
Abstract
HIV incidence is a key measure for tracking disease spread and identifying populations and geographic regions where new infections are most concentrated. The HIV sequence population provides a robust signal for the stage of infection. Large-scale and high-precision HIV sequencing is crucial for effective genomic incidence surveillance. We produced 1,034 full-length envelope gene sequences from a seroconversion cohort by conducting HIV microdrop sequencing and measuring the genomic incidence assay's genome similarity index (GSI) dynamics. The measured dynamics of 9 of 12 individuals aligned with the GSI distribution estimated independently using 417 publicly available incident samples. We enhanced the capacity to identify individuals with recent infections, achieving predicted detection accuracies of 92% (89%-94%) for cases within 6 months and 81% (74%-87%) for cases within 9 months. These accuracy levels agreed with the observed detection accuracy intervals of an independent validation data set. Additionally, we produced 131 full-length envelope gene sequences from eight individuals with chronic HIV infection. This analysis confirmed a false recency rate (FRR) of 0%, which was consistent with 162 publicly available chronic samples. The mean duration of recent infection (MDRI) was 238 (209-267) days, indicating an 83% improvement in performance compared to current recent infection testing algorithms. The shifted Poisson mixture model was then used to estimate the time since infection, and the model estimates showed an 88% consistency with the days post infection derived from HIV RNA test dates and/or seroconversion dates. HIV microdrop sequencing provides unique prospects for large-scale incidence surveillance using high-throughput sequencing. IMPORTANCE Accurate identification of recently infected individuals is vital for prioritizing specific populations for interventions, reducing onward transmission risks, and optimizing public health services. However, current HIV-specific antibody-based methods have not been satisfactory in accurately identifying incident cases, hindering the use of HIV recency testing for prevention efforts and partner protection. Genomic incidence assays offer a promising alternative for identifying recent infections. In our study, we used microdroplet technologies to produce a large number of complete HIV envelope gene sequences, enabling the accurate detection of early infection signs. We assessed the dynamics of the incidence assay's metrics and compared them with statistical models. Our approach demonstrated high accuracy in identifying individuals with recent infections, achieving predicted detection rates exceeding 90% within 6 months and over 80% within 9 months of infection. This high-resolution method holds significant potential for enhancing the effectiveness of HIV incidence screening for case-based surveillance in public health initiatives.
Collapse
Affiliation(s)
- Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tanzy M. T. Love
- Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Michael P. Dubé
- Division of Infectious Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
19
|
Moraka NO, Choga WT, Pema MN, Chawawa MK, Gobe I, Mokomane M, Bareng OT, Bhebhe L, Kelentse N, Mulenga G, Pretorius-Holme M, Mohammed T, Koofhethile CK, Makhema JM, Shapiro R, Lockman S, Moyo S, Gaseitsiwe S. Predicted broadly neutralizing antibody (bnAb) resistance and associated envelope characteristics of adults with HIV-1 seroconversion in Botswana. RESEARCH SQUARE 2023:rs.3.rs-3194948. [PMID: 37693564 PMCID: PMC10491331 DOI: 10.21203/rs.3.rs-3194948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
We used HIV-1C sequences to predict (in silico) resistance to 33 known broadly neutralizing antibodies (bNAbs) and evaluate the different HIV-1 env characteristics that may affect virus neutralization. We analyzed proviral sequences from adults with documented HIV-1 seroconversion (N=140) in Botswana (2013-2018). HIV-1 env sequences were used to predict bnAb resistance using bNAb-ReP, to determine the number of potential N-linked glycosylation sites (PNGS) and evaluate env variable region characteristics (VC). We also assessed the presence of signature mutations that may affect bnAb sensitivity in vitro. We observe varied results for predicted bnAb resistance among our cohort. 3BNC117 showed high predicted resistance (72%) compared to intermediate levels of resistance to VRC01 (57%). We predict low resistance to PGDM100 and 10-1074 and no resistance to 4E10. No difference was observed in the frequency of PNGS by bNAb susceptibility patterns except for higher number of PNGs in V3 bnAb resistant strains. Associations of VC were observed for V1, V4 and V5 loop length and net charge. We also observed few mutations that have been reported to confer bnAb resistance in vitro. Our results support use of sequence data and machine learning tools to predict the best bnAbs to use within populations.
Collapse
|
20
|
Lan Y, Ling X, Deng X, Lin Y, Li J, Li L, He R, Cai W, Li F, Li L, Hu F. Drug Resistance Profile Among HIV-1 Infections Experiencing ART with Low-Level Viral Load in Guangdong China During 2011-2022: A Retrospective Study. Infect Drug Resist 2023; 16:4953-4964. [PMID: 37546367 PMCID: PMC10402888 DOI: 10.2147/idr.s419610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023] Open
Abstract
Background Antiretroviral therapy (ART) efficiently reduces the morbidities and mortalities caused by HIV-1 infection and prevents the HIV epidemic. However, virologic failure (VF) occurs in some patients receiving ART experience, especially increases in those patients with intermittent or persistent low-level viremia (LLV). The presence of drug resistance mutations (DRMs) in LLV was a strong predictor of subsequent VF. The data on drug resistance (DR) or DRMs for HIV-1 infections at low-level viral load (LLVL) are limited in China. Objective To monitor the prevalence of HIV-1 drug resistance and to evaluate the risk factors associated with drug resistance in LLVL HIV-1 infections during ART in Guangdong, China. Methods Plasma samples with LLVL during ART in Guangdong Province between Jan 2011 and Dec 2022 were subjected to a modified reverse-transcription PCR with a pre-step of virus concentration by ultracentrifugation before extraction and the Sanger sequencing. Then, the genotypic resistance test was performed and DR was analyzed by the Stanford HIVDB program. Finally, DR-associated factors were identified by logistic regression analysis. Results We found that CRF01_AE (53.57%) and CRF07_BC (25.07%) were the dominant HIV-1 genotypes in LLVL in Guangdong between 2011 and 2022 but that the percentage of CRF01_AE showed a trend of decrease over time. M46 (1.49%), M184 (30.91%), and K103 (21.46%) were the dominant PI-, NRTI-, and NNRTI-associated mutations, respectively. The total DR rate was 47.06%. Specifically, PI (3.71%) showed a significantly lower DR rate than NNRTI (40.74%) and NRTI (34.14%). Duration of ART, initial ART regimen, ethnicity, and WHO clinical stages were associated with DR. Conclusion The drug resistance rate among the LLVL during ART in Guangdong, China is high. The risk factors associated with HIV drug resistance should be seriously considered for better control.
Collapse
Affiliation(s)
- Yun Lan
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Xuemei Ling
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
- Guangdong Center for Diagnosis and Treatment of AIDS, Guangzhou, 510060, People’s Republic of China
| | - Xizi Deng
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Yaqing Lin
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Junbin Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
- Guangdong Center for Diagnosis and Treatment of AIDS, Guangzhou, 510060, People’s Republic of China
| | - Liya Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Ruiying He
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Linghua Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| |
Collapse
|
21
|
Novitsky V, Nyandiko W, Vreeman R, DeLong AK, Howison M, Manne A, Aluoch J, Chory A, Sang F, Ashimosi C, Jepkemboi E, Orido M, Hogan JW, Kantor R. Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth. Viruses 2023; 15:1416. [PMID: 37515104 PMCID: PMC10383797 DOI: 10.3390/v15071416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Drug resistance remains a global challenge in children and adolescents living with HIV (CALWH). Characterizing resistance evolution, specifically using next generation sequencing (NGS) can potentially inform care, but remains understudied, particularly in antiretroviral therapy (ART)-experienced CALWH in resource-limited settings. We conducted reverse-transcriptase NGS and investigated short-and long-term resistance evolution and its predicted impact in a well-characterized cohort of Kenyan CALWH failing 1st-line ART and followed for up to ~8 years. Drug resistance mutation (DRM) evolution types were determined by NGS frequency changes over time, defined as evolving (up-trending and crossing the 20% NGS threshold), reverting (down-trending and crossing the 20% threshold) or other. Exploratory analyses assessed potential impacts of minority resistance variants on evolution. Evolution was detected in 93% of 42 participants, including 91% of 22 with short-term follow-up, 100% of 7 with long-term follow-up without regimen change, and 95% of 19 with long-term follow-up with regimen change. Evolving DRMs were identified in 60% and minority resistance variants evolved in 17%, with exploratory analysis suggesting greater rate of evolution of minority resistance variants under drug selection pressure and higher predicted drug resistance scores in the presence of minority DRMs. Despite high-level pre-existing resistance, NGS-based longitudinal follow-up of this small but unique cohort of Kenyan CALWH demonstrated continued DRM evolution, at times including low-level DRMs detected only by NGS, with predicted impact on care. NGS can inform better understanding of DRM evolution and dynamics and possibly improve care. The clinical significance of these findings should be further evaluated.
Collapse
Affiliation(s)
- Vlad Novitsky
- Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Winstone Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
- College of Health Sciences, Moi University, Eldoret 30100, Kenya
| | - Rachel Vreeman
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
- Department of Global Health and Health System Design, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Arnhold Institute for Global Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allison K DeLong
- School of Public Health, Brown University, Providence, RI 02912, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, RI 02903, USA
| | - Akarsh Manne
- Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Josephine Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
| | - Ashley Chory
- Department of Global Health and Health System Design, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Festus Sang
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
| | - Celestine Ashimosi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
| | - Eslyne Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
| | - Millicent Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
| | - Joseph W Hogan
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret 30100, Kenya
- School of Public Health, Brown University, Providence, RI 02912, USA
| | - Rami Kantor
- Alpert Medical School, Brown University, Providence, RI 02912, USA
| |
Collapse
|
22
|
Sanaubarova A, Pujol-Hodge E, Dzissyuk N, Lemey P, Vermund SH, Leigh Brown AJ, Ali S. High-Level Drug-Resistant Mutations among HIV-1 Subtype A6 and CRF02_AG in Kazakhstan. Viruses 2023; 15:1407. [PMID: 37515095 PMCID: PMC10384832 DOI: 10.3390/v15071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/30/2023] Open
Abstract
HIV incidence in Kazakhstan increased by 73% between 2010 and 2020, with an estimated 35,000 people living with HIV (PLHIV) in 2020. The development of antiretroviral drug resistance is a major threat to effective antiretroviral therapy (ART), yet studies on the prevalence of drug resistance in Kazakhstan are sparse. In this study on the molecular epidemiology of HIV in Kazakhstan, we analyzed 968 partial HIV-1 pol sequences that were collected between 2017 and 2020 from PLHIV across all regions of Kazakhstan, covering almost 3% of PLHIV in 2020. Sequences predominantly represented subtypes A6 (57%) and CRF02_AG (41%), with 32% of sequences exhibiting high-level drug resistance. We further identified distinct drug-resistant mutations (DRMs) in the two subtypes: subtype A6 showed a propensity for DRMs A62V, G190S, K101E, and D67N, while CRF02_AG showed a propensity for K103N and V179E. Codon usage analysis revealed that different mutational pathways for the two subtypes may explain the difference in G190S and V179E frequencies. Phylogenetic analysis highlighted differences in the timing and geographic spread of both subtypes within the country, with A62V-harboring subtype A6 sequences clustering on the phylogeny, indicative of sustained transmission of the mutation. Our findings suggest an HIV epidemic characterized by high levels of drug resistance and differential DRM frequencies between subtypes. This emphasizes the importance of drug resistance monitoring within Kazakhstan, together with DRM and subtype screening at diagnosis, to tailor drug regimens and provide effective, virally suppressive ART.
Collapse
Affiliation(s)
- Ainur Sanaubarova
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan;
| | - Emma Pujol-Hodge
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK; (E.P.-H.); (A.J.L.B.)
| | - Natalya Dzissyuk
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty 010000, Kazakhstan;
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;
| | - Sten H. Vermund
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA;
| | - Andrew J. Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK; (E.P.-H.); (A.J.L.B.)
| | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan;
| |
Collapse
|
23
|
Alexiev I, Shankar A, Pan Y, Grigorova L, Partsuneva A, Dimitrova R, Gancheva A, Kostadinova A, Elenkov I, Yancheva N, Grozdeva R, Strashimirov D, Stoycheva M, Baltadzhiev I, Doichinova T, Pekova L, Kosmidis M, Emilova R, Nikolova M, Switzer WM. Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012-2020). Viruses 2023; 15:v15040941. [PMID: 37112921 PMCID: PMC10146724 DOI: 10.3390/v15040941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988-2011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012-2020 using polymerase sequences from 1053 of 2010 (52.4%) antiretroviral therapy (ART)-naive individuals. Sequences were analyzed for DRM using the WHO HIV SDRM list implemented in the calculated population resistance tool at Stanford University. Genetic diversity was inferred using automated subtyping tools and phylogenetics. Cluster detection and characterization was performed using MicrobeTrace. The overall rate of SDRMs was 5.7% (60/1053), with 2.2% having resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 1.8% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 2.1% to protease inhibitors (PIs), and 0.4% with dual-class SDRMs. We found high HIV-1 diversity, with the majority being subtype B (60.4%), followed by F1 (6.9%), CRF02_AG (5.2%), A1 (3.7%), CRF12_BF (0.8%), and other subtypes and recombinant forms (23%). Most (34/60, 56.7%) of the SDRMs were present in transmission clusters of different subtypes composed mostly of male-to-male sexual contact (MMSC), including a 14-member cluster of subtype B sequences from 12 MMSC and two males reporting heterosexual contact; 13 had the L90M PI mutation and one had the T215S NRTI SDRM. We found a low SDRM prevalence amid high HIV-1 diversity among ART-naive patients in Bulgaria during 2012-2020. The majority of SDRMs were found in transmission clusters containing MMSC, indicative of onward spread of SDRM in drug-naive individuals. Our study provides valuable information on the transmission dynamics of HIV drug resistance in the context of high genetic diversity in Bulgaria, for the development of enhanced prevention strategies to end the epidemic.
Collapse
Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anupama Shankar
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Alexandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Rusina Grozdeva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Mariana Stoycheva
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Ivan Baltadzhiev
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Tsetsa Doichinova
- Department of Infectious Diseases, Medical University, 5800 Pleven, Bulgaria
| | - Lilia Pekova
- Clinic of Infectious Diseases, Medical University, 6000 Stara Zagora, Bulgaria
| | - Minas Kosmidis
- Clinic of Infectious Diseases, Medical University, 9002 Varna, Bulgaria
| | - Radoslava Emilova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Maria Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - William M Switzer
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| |
Collapse
|
24
|
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, d’Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R. sHIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.05.23288183. [PMID: 37066200 PMCID: PMC10104228 DOI: 10.1101/2023.04.05.23288183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Background The widespread use of the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG) in first- and second-line antiretroviral therapy (ART) may facilitate emerging resistance. We combined data from HIV cohorts to examine patterns of drug resistance mutations (DRMs) and identify risk factors for DTG resistance. Methods Eight cohorts from Canada, Europe, and South Africa contributed data on individuals with genotypic resistance testing on DTG-based ART. Resistance levels were categorised using the Stanford algorithm. We identified risk factors for resistance using mixed-effects ordinal logistic regression models. Results We included 750 people with genotypic resistance testing on DTG-based ART between 2013 and 2022. Most had HIV subtype B (N=444, 59·2%) and were treatment-experienced; 134 (17.9%) were on DTG dual and 19 (2.5%) on DTG monotherapy. INSTI DRMs were detected in 100 (13·3%) individuals; 21 (2·8%) had more than one mutation. Most (N=713, 95·1%) were susceptible to DTG, 8 (1·1%) had potential-low, 5 (0·7%) low, 18 (2·4%) intermediate and 6 (0·8%) high-level DTG resistance. The risk of DTG resistance was higher on DTG monotherapy (adjusted odds ratio (aOR) 37·25, 95% CI 11·17 to 124·2) and DTG lamivudine dual therapy (aOR 6·59, 95% CI 1·70 to 25·55) compared to combination ART, and higher in the presence of potential-low/low (aOR 4.62, 95% CI 1.24 to 17.2) or intermediate/high-level (aOR 7·01, 95% CI 2·52 to 19·48) nucleoside reverse transcriptase inhibitors (NRTI) resistance. Viral load on DTG showed a trend towards increased DTG resistance (aOR 1·42, 95% CI 0·92 to 2·19 per standard deviation of log10 area under the viral load curve). Interpretation Among people experiencing virological failure on DTG-based ART, INSTI DRMs were uncommon, and DTG resistance was rare. DTG monotherapy and NRTI resistance substantially increased the risk for DTG resistance, which is of concern, notably in resource-limited settings.
Collapse
Affiliation(s)
- Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
| | - Suzanne M. Ingle
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Hajra Okhai
- Institute for Global Health, University College London, UK
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Johannes Mouton
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Melanie Stecher
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf
| | - Antonella d’Arminio Monforte
- Italian Cohort Naive Antiretrovirals, (ICONA) L’Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Milano, Italy
| | - M. John Gill
- Southern Alberta Clinic, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Gary Maartens
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Richard Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Switzerland
- Population Health Sciences, Bristol Medical School, University of Bristol, UK
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roger Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
25
|
Shchemelev AN, Ostankova YV, Valutite DE, Serikova EN, Zueva EB, Semenov AV, Totolian AA. RISK ASSESSMENT OF FIRST-LINE TREATMENT FAILURE IN UNTREATED HIV PATIENTS IN NORTHWESTERN FEDERAL DISTRICT OF THE RUSSIAN FEDERATION. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2023. [DOI: 10.15789/2220-7619-rao-2122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The HIV infection epidemic in Russia continues to evolve, and HIV infection cases have been registered in all territorial entities of the Russian Federation. 2021 Treatment coverage was 82.2% and 56.4% individuals under dispensary observation and living with diagnosed HIV infection. 79.9% receiving ART subjects were shown to achieve undetectable viral load.
Highly active antiretroviral therapy (HAART) currently represents a combination of three (less frequently four) antiretroviral drugs targeting pathways involved in various stages of HIV replication in vivo. Treatment failure is a problem facing doctors and patients using HAART. The most common cause of therapeutic failure is the development of HIV drug resistance. The emergence of resistance is associated with processes involving mutation occurring in the viral genome influenced by evolutionary factors.
Therefore, it is important clinically and programmatically to learn more about the rate of first-line treatment failure, the rate of switching to a second-line ART regimen, and to identify patients at risk to develop strategies for preventing development of further failure cases.
The study was aimed at analyzing ineffectiveness of first-line ART therapy in patients in Northwestern Federal District of the Russian Federation.
Materials and methods
Sequencing reactions were performed using the AmpliSens HIV Resist-Seq. Assembly of consensus sequences from fragments obtained during sequencing was carried out using Unipro UGENE software. Isolate genotyping was performed using the MEGA-X software with the Neighbor-joining algorithm.
Results
The HIV pol genes in 239 patients with first-line ART failure and 100 nave patients were sequenced; all sequences genotyped as HIV-1 sub-subtype A6. According to analysis, 82% of patients had at least one significant mutation associated with drug resistance for the corresponding viral subtype. In total, we encountered 87 different drug resistance mutations.
Conclusion
We have shown increased proportion of patients with first-line ART failure among all patients with treatment failure. The main cause for such changes is probably related to the prevalence of primary drug resistance, estimated here at 8%. Specific differences were found between drug resistance mutation profiles in patients without suppressed viral load and patients with virological breakthrough. The overall results of the study indicate a need to diagnose and characterize HIV drug resistance prior to initiation of therapy in order to avoid ineffective first-line antiretroviral treatment.
Collapse
|
26
|
Mustafa A, Akbay B, Davlidova S, Abidi SH, Ali S. Origin and evolution of subtype B variants in the former Soviet Union countries. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105402. [PMID: 36623715 DOI: 10.1016/j.meegid.2022.105402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023]
Abstract
Contrary to the global trend, between 2010 and 2020, an increase of 43% new HIV infections was recorded in Eastern Europe and Central Asia. Analyses of phylogenetic relationship, and routes and modes of transmission of the HIV-1 subtype B across the former Soviet Union (FSU) region are currently lacking. The objective of this analysis was to investigate the origin and transmission routes of HIV subtype B in FSU countries. We performed phylogenetic and phylodynamic analyses using 21,007 publicly available subtype B sequences from Europe and Asia, including thirteen FSU countries. Our study suggests that BFSU strain evolved more recently in FSU countries (Russia, Kyrgyzstan, Uzbekistan, Tajikistan, Belarus, Ukraine, Lithuania, Latvia, Georgia, Armenia, Azerbaijan) compared to the Western B variant in Western Europe (Austria, Belgium, Germany, Luxembourg, Netherlands, Switzerland). The primary high-risk group responsible for the transmission of subtype B was found to be MSM/homosexual. Intermixing of phylogenetic clusters among high-risk groups and bridging with the general population indicated that the HIV epidemic is no longer confined to distinct key populations - emphasizing an urgent need to improve the HIV harm-reduction efforts among high risk as well as general populations.
Collapse
Affiliation(s)
- Aidana Mustafa
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Burkitkan Akbay
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Salima Davlidova
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Syed Hani Abidi
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan.
| |
Collapse
|
27
|
Abadi SAR, Mohammadi A, Koohi S. An automated ultra-fast, memory-efficient, and accurate method for viral genome classification. J Biomed Inform 2023; 139:104316. [PMID: 36781036 DOI: 10.1016/j.jbi.2023.104316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/30/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
The classification of different organisms into subtypes is one of the most important tools of organism studies, and among them, the classification of viruses itself has been the focus of many studies due to their use in virology and epidemiology. Many methods have been proposed to classify viruses, some of which are designed for a specific family of organisms and some of which are more general. But still, especially for certain categories such as Influenza and HIV, classification is facing performance challenges as well as processing and memory bottlenecks. In this way, we designed an automated classifier, called PC-mer, that is based on k-mer and physicochemical characteristics of nucleotides, which reduces the number of features about 2 k times compared to the alternative methods based on k-mer, and compared to integer and one-hot encoding methods, it is possible to keep the number of features constant despite the growth of the sequence length. In this way, it also increases the training speed by an average of 17.93 times. This improvement in processing complexity is provided while PC-mer can also improve the classifying performance for a variety of virus families.
Collapse
Affiliation(s)
| | - Amirhossein Mohammadi
- No 717, Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Somayyeh Koohi
- No 717, Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
| |
Collapse
|
28
|
HIV Drug Resistance in Adults Initiating or Reinitiating Antiretroviral Therapy in Uruguay-Results of a Nationally Representative Survey, 2018-2019. Viruses 2023; 15:v15020490. [PMID: 36851704 PMCID: PMC9961578 DOI: 10.3390/v15020490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
The first nationally representative cross-sectional HIV drug resistance (HIVDR) survey was conducted in Uruguay in 2018-2019 among adults diagnosed with HIV and initiating or reinitiating antiretroviral therapy (ART). Protease, reverse transcriptase, and integrase genes of HIV-1 were sequenced. A total of 206 participants were enrolled in the survey; 63.2% were men, 85.7% were >25 years of age, and 35.6% reported previous exposure to antiretroviral (ARV) drugs. The prevalence of HIVDR to efavirenz or nevirapine was significantly higher (OR: 1.82, p < 0.001) in adults with previous ARV drug exposure (20.3%, 95% CI: 18.7-22.0%) compared to adults without previous ARV drug exposure (12.3%, 11.0-13.8%). HIVDR to any nucleoside reverse transcriptase inhibitors was 10.3% (9.4-11.2%). HIVDR to ritonavir-boosted protease inhibitors was 1.5% (1.1-2.1%); resistance to ritonavir-boosted darunavir was 0.9% (0.4-2.1%) among adults without previous ARV drug exposure and it was not observed among adults with previous ARV drug exposure. Resistance to integrase inhibitors was 12.7% (11.7-13.8%), yet HIVDR to dolutegravir, bictegravir, and cabotegravir was not observed. The high level (>10%) of HIVDR to efavirenz highlights the need to accelerate the transition to the WHO-recommended dolutegravir-based ART. Access to dolutegravir-based ART should be prioritised for people reporting previous ARV drug exposure.
Collapse
|
29
|
Manyana S, Pillay M, Gounder L, Khan A, Moodley P, Naidoo K, Chimukangara B. Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings. AIDS Res Ther 2023; 20:9. [PMID: 36759801 PMCID: PMC9912687 DOI: 10.1186/s12981-023-00505-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND As use of dolutegravir (DTG) becomes more common in resource limited settings (RLS), the demand for integrase resistance testing is increasing. Affordable methods for genotyping all relevant HIV-1 pol genes (i.e., protease (PR), reverse transcriptase (RT) and integrase (IN)) are required to guide choice of future antiretroviral therapy (ART). We designed an in-house HIV-1 drug resistance (HIVDR) genotyping method that is affordable and suitable for use in RLS. METHODS We obtained remnant plasma samples from CAPRISA 103 study and amplified HIV-1 PR, RT and IN genes, using an innovative PCR assay. We validated the assay using remnant plasma samples from an external quality assessment (EQA) programme. We genotyped samples by Sanger sequencing and assessed HIVDR mutations using the Stanford HIV drug resistance database. We compared drug resistance mutations with previous genotypes and calculated method cost-estimates. RESULTS From 96 samples processed, we obtained sequence data for 78 (81%), of which 75 (96%) had a least one HIVDR mutation, with no major-IN mutations observed. Only one sample had an E157Q INSTI-accessory mutation. When compared to previous genotypes, 18/78 (23%) had at least one discordant mutation, but only 2/78 (3%) resulted in different phenotypic predictions that could affect choice of subsequent regimen. All CAPRISA 103 study sequences were HIV-1C as confirmed by phylogenetic analysis. Of the 7 EQA samples, 4 were HIV-1C, 2 were HIV-1D, and 1 was HIV-1A. Genotypic resistance data generated using the IDR method were 100% concordant with EQA panel results. Overall genotyping cost per sample was estimated at ~ US$43-$US49, with a processing time of ~ 2 working days. CONCLUSIONS We successfully designed an in-house HIVDR method that is suitable for genotyping HIV-1 PR, RT and IN genes, at an affordable cost and shorter turnaround time. This HIVDR genotyping method accommodates changes in ART regimens and will help to guide HIV-1 treatment decisions in RLS.
Collapse
Affiliation(s)
- Sontaga Manyana
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Melendhran Pillay
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Lilishia Gounder
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Aabida Khan
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Pravi Moodley
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Benjamin Chimukangara
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
| |
Collapse
|
30
|
Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K. Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry? JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
31
|
Kotokwe K, Moyo S, Zahralban-Steele M, Holme MP, Melamu P, Koofhethile CK, Choga WT, Mohammed T, Nkhisang T, Mokaleng B, Maruapula D, Ditlhako T, Bareng O, Mokgethi P, Boleo C, Makhema J, Lockman S, Essex M, Ragonnet-Cronin M, Novitsky V, Gaseitsiwe S. Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana. Viruses 2023; 15:403. [PMID: 36851617 PMCID: PMC9963705 DOI: 10.3390/v15020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
It remains unknown whether the C-C motif chemokine receptor type 5 (CCR5) coreceptor is still the predominant coreceptor used by Human Immunodeficiency Virus-1 (HIV-1) in Botswana, where the HIV-1 subtype C predominates. We sought to determine HIV-1C tropism in Botswana using genotypic tools, taking into account the effect of antiretroviral treatment (ART) and virologic suppression. HIV-1 gp120 V3 loop sequences from 5602 participants were analyzed for viral tropism using three coreceptor use predicting algorithms/tools: Geno2pheno, HIV-1C Web Position-Specific Score Matrices (WebPSSM) and the 11/25 charge rule. We then compared the demographic and clinical characteristics of people living with HIV (PLWH) harboring R5- versus X4-tropic viruses using χ2 and Wilcoxon rank sum tests for categorical and continuous data analysis, respectively. The three tools congruently predicted 64% of viruses as either R5-tropic or X4-tropic. Geno2pheno and the 11/25 charge rule had the highest concordance at 89%. We observed a significant difference in ART status between participants harboring X4- versus R5-tropic viruses. X4-tropic viruses were more frequent among PLWH receiving ART (χ2 test, p = 0.03). CCR5 is the predominant coreceptor used by HIV-1C strains circulating in Botswana, underlining the strong potential for CCR5 inhibitor use, even in PLWH with drug resistance. We suggest that the tools for coreceptor prediction should be used in combination.
Collapse
Affiliation(s)
- Kenanao Kotokwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Melissa Zahralban-Steele
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Pinkie Melamu
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | | | - Terence Mohammed
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tapiwa Nkhisang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tsotlhe Ditlhako
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Ontlametse Bareng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Corretah Boleo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Manon Ragonnet-Cronin
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | | |
Collapse
|
32
|
Gabrielaite M, Bennedbæk M, Rasmussen MS, Kan V, Furrer H, Flisiak R, Losso M, Lundgren JD, Marvig RL. Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load. PLoS Comput Biol 2023; 19:e1010756. [PMID: 36595537 PMCID: PMC9838853 DOI: 10.1371/journal.pcbi.1010756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2023] [Accepted: 11/23/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, the association between intrahost diversity and disease progression markers has not been investigated in large and diverse cohorts for which the majority of the genome has been deep-sequenced. Viral load (VL) is a key progression marker and understanding of its relationship to viral intrahost genetic diversity could help design future strategies for HIV monitoring and treatment. METHODS We analysed deep-sequenced viral genomes from 2,650 treatment-naive HIV-infected persons to measure the intrahost genetic diversity of 2,447 genomic codon positions as calculated by Shannon entropy. We tested for associations between VL and amino acid (AA) entropy accounting for sex, age, race, duration of infection, and HIV population structure. RESULTS We confirmed that the intrahost genetic diversity is highest in the env gene. Furthermore, we showed that mean Shannon entropy is significantly associated with VL, especially in infections of >24 months duration. We identified 16 significant associations between VL (p-value<2.0x10-5) and Shannon entropy at AA positions which in our association analysis explained 13% of the variance in VL. Finally, equivalent analysis based on variation in HIV consensus sequences explained only 2% of VL variance. CONCLUSIONS Our results elucidate that viral intrahost genetic diversity is associated with VL and could be used as a better disease progression marker than HIV consensus sequence variants, especially in infections of longer duration. We emphasize that viral intrahost diversity should be considered when studying viral genomes and infection outcomes. TRIAL REGISTRATION Samples included in this study were derived from participants who consented in the clinical trial, START (NCT00867048) (23), run by the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT). All the participant sites are listed here: http://www.insight-trials.org/start/my_phpscript/participating.php?by=site.
Collapse
Affiliation(s)
- Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- * E-mail: (MG); (MB)
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MG); (MB)
| | - Malthe Sebro Rasmussen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Section of Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Virginia Kan
- Veterans Affairs Medical Center and The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, United States of America
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland
| | - Marcelo Losso
- Hospital General De Agudos J M Ramos Mejía, Buenos Aires, Argentina
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
33
|
Shchemelev AN, Boumbaly S, Ostankova YV, Zueva EB, Semenov AV, Totolian AA. Prevalence of drug resistant HIV-1 forms in patients without any history of antiretroviral therapy in the Republic of Guinea. J Med Virol 2023; 95:e28184. [PMID: 36175006 DOI: 10.1002/jmv.28184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
To study the structure of human immunodeficiency virus (HIV)-1 drug resistance (DR) in patients with newly diagnosed infection. Residents of the Republic of Guinea (N = 2168) were tested for HIV using enzyme-linked immunosorbent assay (ELISA). Individuals with a positive result were further examined for the presence of viral load in blood plasma. HIV was analyzed using Sanger sequencing. The obtained sequences were genotyped using REGA (version 3.0) and analyzed in MEGA 7. Analysis for the presence of DR mutations was performed using the Stanford University HIV DR Database. Serological markers of HIV were detected in 239 people, which represents 11.02% of the entire sample. HIV RNA was detected in 58 people. The following subtypes were seen: HIV CRF02_AG (41.9%); A1 (29.1%); A3 (12.9%); URF A1_G (12.9%); and G (3.2%). In 25% of patients, at least one significant mutation was encountered leading directly to HIV DR. The mutations encountered cause resistance to NRTI and NNRTI; one case of multiple resistance was identified. Major resistance to protease inhibitor was not seen. The detection of HIV-1 mutations associated with DR, in individuals who have never received antiretroviral therapy, is a cause for concern. It suggests that: new infections are occurring with strains that already have resistance; and the expansion of resistance is not always directly associated with selective drug pressure. Among the likely reasons for the high prevalence of primary HIV DR in the Republic of Guinea, drug availability is probably the key. The consequence of this is the lack of adherence of patients to treatment, the formation and transmission of resistant variants of the virus in the population. These findings suggest the need to test patients for resistant virus variants before initiating treatment.
Collapse
Affiliation(s)
| | - Sanaba Boumbaly
- Institute Research Biology Appliquee De Guinee, Kindia, Republic of Guinea
| | | | - Elena B Zueva
- Saint Petersburg Pasteur Institute, St. Petersburg, Russia
| | | | | |
Collapse
|
34
|
HIV-1 subtype B spread through cross-border clusters in the Balkans: a molecular analysis in view of incidence trends. AIDS 2023; 37:125-135. [PMID: 36129113 DOI: 10.1097/qad.0000000000003394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To analyze phylogenetic relations and assess the role of cross-border clusters in the spread of HIV-1 subtype B across the Balkans, given the general trends of new HIV diagnoses in seven Balkan countries. DESIGN Retrospective phylogenetic and trend analysis. METHODS In-depth phylogenetic, phylodynamic and phylogeographic analysis performed on 2415 HIV-1 subtype B sequences from 1999 to 2019 using maximal likelihood and Bayesian methods. The joinpoint regression analysis of new HIV diagnoses by country and modes of transmission using 2004-2019 ECDC data. RESULTS Ninety-three HIV-1 Subtype B transmission clusters (68% of studied sequences) were detected of which four cross-border clusters (11% of studied sequences). Phylodynamic analysis showed activity of cross-border clusters up until the mid-2000s, with a subsequent stationary growth phase. Phylogeography analyses revealed reciprocal spread patterns between Serbia, Slovenia and Montenegro and several introductions to Romania from these countries and Croatia. The joinpoint analysis revealed a reduction in new HIV diagnoses in Romania, Greece and Slovenia, whereas an increase in Serbia, Bulgaria, Croatia and Montenegro, predominantly among MSM. CONCLUSION Differing trends of new HIV diagnoses in the Balkans mirror differences in preventive policies implemented in participating countries. Regional spread of HIV within the countries of former Yugoslavia has continued to play an important role even after country break-up, whereas the spread of subtype B through multiple introductions to Romania suggested the changing pattern of travel and migration linked to European integration of Balkan countries in the early 2000s.
Collapse
|
35
|
Springfield O, Brouwer KC, Avila-Rios S, Morales-Miranda S, Mehta SR. Molecular epidemiology of HIV-1 among adult female sex workers at the Guatemala-Mexico border. Glob Public Health 2023; 18:2278873. [PMID: 37944916 PMCID: PMC10808948 DOI: 10.1080/17441692.2023.2278873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
ABSTRACTSex workers have been demonstrated to have increased vulnerabilities to HIV and a high population prevalence of the disease. Despite their increased risk, sex workers have been underrepresented in molecular epidemiology studies assessing HIV in Mesoamerica. This study aims to describe the sociodemographic characteristics and phylogenetic profile of HIV-1 within a cohort of HIV-positive female sex workers (FSW) situated at the Guatemala-Mexico border. HIV viral sequences were collected from a cohort of FSW ≥18 years of age from San Marcos, Guatemala (n = 6) and compared to viral sequences collected as part of the Mesoamerican Drug Resistance Monitoring Programme to assess HIV viral diversity in Mexico and Guatemala (n = 3956). All of the FSW sampled were determined to have genetically unrelated HIV infections, suggesting multiple introductions of the virus and/or the potential existence of populations not captured by current surveillance efforts. Many reported numerous vulnerabilities that may have heightened their risk of acquiring and transmitting HIV through sex work activities. Our phylogenetic analysis indicated that national surveillance programmes may not fully capture the viral diversity among FSW and their clients within this region. Additional research is needed to fully capture HIV diversity and transmission in Mesoamerica, especially in the Guatemala-Mexico border region.
Collapse
Affiliation(s)
- Olivia Springfield
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - Kimberly C. Brouwer
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Sonia Morales-Miranda
- Consorcio de Investigación sobre VIH SIDA TB Consorcio de Investigación en Salud, Cuernavaca, Morelos, México
| | - Sanjay R. Mehta
- University of California San Diego School of Medicine, La Jolla, California, USA
- San Diego Veterans Affairs Medical Center, San Diego, California, USA
| |
Collapse
|
36
|
Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
Collapse
Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
| |
Collapse
|
37
|
Novitsky V, Nyandiko W, Vreeman R, DeLong AK, Manne A, Scanlon M, Ngeresa A, Aluoch J, Sang F, Ashimosi C, Jepkemboi E, Orido M, Hogan JW, Kantor R. Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance. Microbiol Spectr 2022; 10:e0345422. [PMID: 36445146 PMCID: PMC9769539 DOI: 10.1128/spectrum.03454-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 drug resistance testing in children and adolescents in low-resource settings is both important and challenging. New (more sensitive) drug resistance testing technologies may improve clinical care, but evaluation of their added value is limited. We assessed the potential added value of using next-generation sequencing (NGS) over Sanger sequencing for detecting nucleoside reverse transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations (DRMs). Participants included 132 treatment-experienced Kenyan children and adolescents with diverse HIV-1 subtypes and with already high levels of drug resistance detected by Sanger sequencing. We examined overall and DRM-specific resistance and its predicted impact on antiretroviral therapy and evaluated the discrepancy between Sanger sequencing and six NGS thresholds (1%, 2%, 5%, 10%, 15%, and 20%). Depending on the NGS threshold, agreement between the two technologies was 62% to 88% for any DRM, 83% to 92% for NRTI DRMs, and 73% to 94% for NNRTI DRMs, with more DRMs detected at low NGS thresholds. NGS identified 96% to 100% of DRMs detected by Sanger sequencing, while Sanger identified 83% to 99% of DRMs detected by NGS. Higher discrepancy between technologies was associated with higher DRM prevalence. Even in this resistance-saturated cohort, 12% of participants had higher, potentially clinically relevant predicted resistance detected only by NGS. These findings, in a young, vulnerable Kenyan population with diverse HIV-1 subtypes and already high resistance levels, suggest potential benefits of more sensitive NGS over existing technology. Good agreement between technologies at high NGS thresholds supports their interchangeable use; however, the significance of DRMs identified at lower thresholds to patient care should be explored further. IMPORTANCE HIV-1 drug resistance in children and adolescents remains a significant problem in countries facing the highest burden of the HIV epidemic. Surveillance of HIV-1 drug resistance in children and adolescents is an important public health strategy, particularly in resource-limited settings, and yet, it is limited due mostly to cost and infrastructure constraints. Whether newer and more sensitive next-generation sequencing (NGS) adds substantial value beyond traditional Sanger sequencing in detecting HIV-1 drug resistance in real life settings remains an open and debatable question. In this paper, we attempt to address this issue by performing a comprehensive comparison of drug resistance identified by Sanger sequencing and six NGS thresholds. We conducted this study in a well-characterized, vulnerable cohort of children and adolescents living with diverse HIV-1 subtypes in Kenya and, importantly, failing antiretroviral therapy (ART) with already extensive drug resistance. Our findings suggest a potential added value of NGS over Sanger even in this unique cohort.
Collapse
Affiliation(s)
- V. Novitsky
- Brown University, Providence, Rhode Island, USA
| | - W. Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
| | - R. Vreeman
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | | | - A. Manne
- Brown University, Providence, Rhode Island, USA
| | - M. Scanlon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | - A. Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - F. Sang
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - C. Ashimosi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - E. Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - M. Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. W. Hogan
- Brown University, Providence, Rhode Island, USA
| | - R. Kantor
- Brown University, Providence, Rhode Island, USA
| | - for the RESistance in a PEdiatric CohorT (RESPECT) Study
- Brown University, Providence, Rhode Island, USA
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| |
Collapse
|
38
|
Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database. Viruses 2022; 14:v14122768. [PMID: 36560771 PMCID: PMC9783618 DOI: 10.3390/v14122768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008-2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15-24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil.
Collapse
|
39
|
Bailón L, Llano A, Cedeño S, Escribà T, Rosás-Umbert M, Parera M, Casadellà M, Lopez M, Pérez F, Oriol-Tordera B, Ruiz-Riol M, Coll J, Perez F, Rivero À, Leselbaum AR, McGowan I, Sengupta D, Wee EG, Hanke T, Paredes R, Alarcón-Soto Y, Clotet B, Noguera-Julian M, Brander C, Molto J, Mothe B, Benet S, Cobarsi P, Geleziunas R, Leselbaum AR, Loste C, Meulbroek M, Miranda C, Muñoz J, Naval J, Nieto A, Pujol F, Puig J. Safety, immunogenicity and effect on viral rebound of HTI vaccines in early treated HIV-1 infection: a randomized, placebo-controlled phase 1 trial. Nat Med 2022; 28:2611-2621. [PMID: 36302893 DOI: 10.1038/s41591-022-02060-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 09/28/2022] [Indexed: 01/15/2023]
Abstract
HIVACAT T-cell immunogen (HTI) is a novel human immunodeficiency virus (HIV) vaccine immunogen designed to elicit cellular immune responses to HIV targets associated with viral control in humans. The AELIX-002 trial was a randomized, placebo-controlled trial to evaluate as a primary objective the safety of a combination of DNA.HTI (D), MVA.HTI (M) and ChAdOx1.HTI (C) vaccines in 45 early-antiretroviral (ART)-treated individuals (44 men, 1 woman; NCT03204617). Secondary objectives included T-cell immunogenicity, the effect on viral rebound and the safety of an antiretroviral treatment interruption (ATI). Adverse events were mostly mild and transient. No related serious adverse events were observed. We show here that HTI vaccines were able to induce strong, polyfunctional and broad CD4 and CD8 T-cell responses. All participants experienced detectable viral rebound during ATI, and resumed ART when plasma HIV-1 viral load reached either >100,000 copies ml-1, >10,000 copies ml-1 for eight consecutive weeks, or after 24 weeks of ATI. In post-hoc analyses, HTI vaccines were associated with a prolonged time off ART in vaccinees without beneficial HLA (human leukocyte antigen) class I alleles. Plasma viral load at the end of ATI and time off ART positively correlated with vaccine-induced HTI-specific T-cell responses at ART cessation. Despite limited efficacy of the vaccines in preventing viral rebound, their ability to elicit robust T-cell responses towards HTI may be beneficial in combination cure strategies, which are currently being tested in clinical trials.
Collapse
Affiliation(s)
- Lucia Bailón
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,Department of Medicine, Autonomous University of Barcelona, Catalonia, Spain
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Samandhy Cedeño
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Tuixent Escribà
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Miriam Rosás-Umbert
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Miriam Lopez
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Francisco Pérez
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain
| | - Josep Coll
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,Projecte Dels Noms-Hispanosida, Bcn Checkpoint, Barcelona, Spain
| | - Felix Perez
- Projecte Dels Noms-Hispanosida, Bcn Checkpoint, Barcelona, Spain
| | - Àngel Rivero
- Projecte Dels Noms-Hispanosida, Bcn Checkpoint, Barcelona, Spain
| | - Anne R Leselbaum
- Projecte Dels Noms-Hispanosida, Bcn Checkpoint, Barcelona, Spain
| | - Ian McGowan
- AELIX Therapeutics S.L, Barcelona, Spain.,University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Edmund G Wee
- The Jenner Institute, The Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tomáš Hanke
- The Jenner Institute, The Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic - Central University of Catalonia (UVic - UCC), Vic, Barcelona, Spain.,Germans Trias I Pujol Research Institte, Badalona, Spain
| | - Yovaninna Alarcón-Soto
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,Departament d'Estadística I Investigació Operativa, Universitat Politècnica de Catalunya/BARCELONATECH, Barcelona, Spain
| | - Bonaventura Clotet
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic - Central University of Catalonia (UVic - UCC), Vic, Barcelona, Spain
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic - Central University of Catalonia (UVic - UCC), Vic, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,AELIX Therapeutics S.L, Barcelona, Spain.,Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic - Central University of Catalonia (UVic - UCC), Vic, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Jose Molto
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain. .,CIBERINFEC, ISCIII, Madrid, Spain. .,Germans Trias I Pujol Research Institte, Badalona, Spain.
| | - Beatriz Mothe
- Fundació Lluita Contra les Infeccions, Infectious Diseases Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain.,CIBERINFEC, ISCIII, Madrid, Spain.,Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic - Central University of Catalonia (UVic - UCC), Vic, Barcelona, Spain.,Germans Trias I Pujol Research Institte, Badalona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Bareng OT, Seselamarumo S, Seatla KK, Choga WT, Bakae B, Maruapula D, Kelentse N, Moraka NO, Mokaleng B, Mokgethi PT, Ditlhako TR, Pretorius-Holme M, Mbulawa MB, Lebelonyane R, Bile EC, Gaolathe T, Shapiro R, Makhema JM, Lockman S, Essex M, Novitsky V, Mpoloka SW, Moyo S, Gaseitsiwe S. Doravirine-associated resistance mutations in antiretroviral therapy naïve and experienced adults with HIV-1 subtype C infection in Botswana. J Glob Antimicrob Resist 2022; 31:128-134. [PMID: 35973671 PMCID: PMC9750894 DOI: 10.1016/j.jgar.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES There are limited data on the prevalence of doravirine (DOR)-associated drug resistance mutations in people with HIV (PWH) in Botswana. This cross-sectional, retrospective study aimed to explore the prevalence of DOR-associated resistance mutations among ART-naïve and -experienced PWH in Botswana enrolled in the population-based Botswana Combination Prevention Project (BCPP). METHODS A total of 6078 HIV-1C pol sequences were analysed for DOR-associated resistance mutations using the Stanford HIV drug resistance database, and their levels were predicted according to the Stanford DRM penalty scores and resistance interpretation. Virologic failure was defined as HIV-1 RNA load (VL) >400 copies/mL. RESULTS Among 6078 PWH, 5999 (99%) had known ART status, and 4529/5999 (79%) were on ART at time of sampling. The suppression rate among ART-experienced was 4517/4729 (96%). The overall prevalence of any DOR-associated resistance mutations was 181/1473 (12.3% [95% confidence interval {CI}: 10.7-14.1]); by ART status: 42/212 (19.8% [95% CI: 14.7-25.4]) among ART-failing individuals (VL ≥400 copies/mL) and 139/1261 (11.0% [95% CI: 9.3-12.9]) among ART-naïve individuals (P < 0.01). Intermediate DOR-associated resistance mutations were observed in 106/1261 (7.8% [95% CI: 6.9-10.1]) in ART-naïve individuals and 29/212 (13.7% [95% CI: 9.4-8.5]) among ART-experienced participants (P < 0.01). High-level DOR-associated resistance mutations were observed in 33/1261 (2.6% [95% CI: 1.8-3.7]) among ART-naïve and 13/212 (6.1% [95% CI: 3.6-10.8]) among ART-failing PWH (P < 0.01). PWH failing ART with at least one EFV/NVP-associated resistance mutation had high prevalence 13/67 (19.4%) of high-level DOR-associated resistance mutations. CONCLUSION DOR-associated mutations were rare (11.0%) among ART-naive PWH but present in 62.7% of Botswana individuals who failed NNRTI-based ART with at least one EFV/NVP-associated resistance mutation. Testing for HIV drug resistance should underpin the use of DOR in PWH who have taken first-generation NNRTIs.
Collapse
Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Sekgabo Seselamarumo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Blessing Bakae
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Molly Pretorius-Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Ebi Celestin Bile
- FHI 360, Department of Clinical Sciences, Durham, North Carolina, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
| |
Collapse
|
41
|
Topcu C, Georgiou V, Rodosthenous JH, Demetriades I, Foley BT, G Kostrikis L. Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men. Virulence 2022; 13:1331-1348. [PMID: 35979885 PMCID: PMC9397478 DOI: 10.1080/21505594.2022.2106021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Prospective molecular studies of HIV-1 pol region (2253-5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017-2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790-8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.
Collapse
Affiliation(s)
- Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | - Johana Hezka Rodosthenous
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | | | - Brian Thomas Foley
- Los Alamos National Laboratory, T-6 Theoretical Biology and Biophysics, Los Alamos, NM, USA
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus.,Cyprus Academy of Sciences, Letters, and Arts, Nicosia, Cyprus
| |
Collapse
|
42
|
Mukhatayeva A, Mustafa A, Dzissyuk N, Issanov A, Mukhatayev Z, Bayserkin B, Vermund SH, Ali S. Antiretroviral therapy resistance mutations among HIV infected people in Kazakhstan. Sci Rep 2022; 12:17195. [PMID: 36229577 PMCID: PMC9562405 DOI: 10.1038/s41598-022-22163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/10/2022] [Indexed: 01/05/2023] Open
Abstract
In Kazakhstan, the number of people living with HIV (PLHIV) has increased steadily by 39% since 2010. Development of antiretroviral therapy (ART) resistance mutations (ARTRM) is a major hurdle in achieving effective treatment and prevention against HIV. Using HIV pol sequences from 602 PLHIV from Kazakhstan, we analyzed ARTRMs for their association with factors that may promote development of ARTRMs. 56% PLHIV were infected with HIV subtype A6 and 42% with CRF02_AG. The ARTRM Q174K was associated with increased viral load and decreased CD4+ cell count, while infection with CRF02_AG was associated with a lower likelihood of Q174K. Interestingly, CRF02_AG was positively associated with the ARTRM L10V that, in turn, was observed frequently with darunavir administration. Infection with CRF02_AG was positively associated with the ARTRM S162A that, in turn, was frequently observed with the administration of nevirapine, also associated with lower CD4 counts. Zidovudine or Nevirapine receipt was associated with the development of the ARTRM E138A, that, in turn, was associated with lower CD4 counts. Determination of a patient's HIV variant can help guide ART choice in Kazakhstan. For example, PLHIV infected with CRF02_AG will benefit less from darunavir and nevirapine, and emtricitabine should replace zidovudine.
Collapse
Affiliation(s)
- Ainur Mukhatayeva
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Aidana Mustafa
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Natalya Dzissyuk
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | - Alpamys Issanov
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Zhussipbek Mukhatayev
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Bauyrzhan Bayserkin
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | | | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan.
| |
Collapse
|
43
|
Clipman SJ, Solomon SS, Srikrishnan AK, McFall AM, Gomathi S, Saravanan S, Anand S, Vasudevan CK, Kumar MS, Celentano DD, Mehta SH, Lucas GM. Antiretroviral Drug Resistance in HIV Sequences From People Who Inject Drugs and Men Who Have Sex With Men Across 21 Cities in India. Open Forum Infect Dis 2022; 9:ofac481. [PMID: 36225747 PMCID: PMC9547506 DOI: 10.1093/ofid/ofac481] [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: 06/20/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background Drug resistance testing is limited in public-sector human immunodeficiency virus (HIV) care in India, and there are few systematic samplings for prevalent drug resistance mutations (DRMs), particularly among men who have sex with men (MSM) and people who inject drugs (PWID). Methods We conducted genotypic resistance testing on 915 HIV sequences sampled from viremic self-reported antiretroviral therapy (ART) experienced and naive PWID and MSM recruited from 21 cities across India in 2016-2017. We analyzed factors associated with resistance using logistic regression and evaluated evidence for transmitted resistance using phylogenetic analyses. Results Of the 915 participants sequenced, median age was 31, 436 were MSM, and 191 were ART experienced. Overall, 62.8% of ART-experienced participants and 14.4% of ART-naive participants were found to have low-level resistance or higher to 1 or more classes of drugs. Prevalence of tenofovir disoproxil fumarate resistance was 25.7% in ART-experienced participants and 1.11% in ART-naive participants. The highest proportion of drug resistance was seen across nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, and resistance was significantly more common among MSM participants than PWID. Phylogenetic analyses revealed that 54.6% of ART-naive participants with resistance who clustered had shared DRMs, suggesting transmitted resistance may have occurred. Conclusions Patients experiencing virologic failure on first-line therapy switched blindly to tenofovir/lamivudine/dolutegravir may effectively be receiving dolutegravir monotherapy due to resistance to tenofovir and lamivudine. While dolutegravir is expected to have full activity in the majority of patients in India, follow-up is needed to understand how resistance may affect long-term outcomes.
Collapse
Affiliation(s)
- Steven J Clipman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sunil S Solomon
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Allison M McFall
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Santhanam Anand
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
| | | | | | - David D Celentano
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Shruti H Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gregory M Lucas
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
44
|
Beesham I, Parikh UM, Mellors JW, Joseph Davey DL, Heffron R, Palanee-Phillips T, Bosman SL, Beksinska M, Smit J, Ahmed K, Makkan H, Selepe P, Louw C, Kotze P, Hofmeyr GJ, Singata‐Madliki M, Rees H, Baeten JM, Wallis C. High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study. J Acquir Immune Defic Syndr 2022; 91:130-137. [PMID: 36094478 PMCID: PMC9651927 DOI: 10.1097/qai.0000000000003027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pretreatment HIV drug resistance (PDR) undermines individual treatment success and threatens the achievement of UNAIDS 95-95-95 targets. In many African countries, limited data are available on PDR as detection of recent HIV infection is uncommon and access to resistance testing is limited. We describe the prevalence of PDR among South African women with recent HIV infection from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial. METHODS HIV-uninfected, sexually active women, aged 18-35 years, and seeking contraception were enrolled in the ECHO Trial at sites in South Africa, from 2015 to 2018. HIV testing was done at trial entry and repeated quarterly. We tested stored plasma samples collected at HIV diagnosis from women who seroconverted during follow-up and had a viral load >1000 copies/mL for antiretroviral resistant mutations using a validated laboratory-developed population genotyping assay, which sequences the full protease and reverse transcriptase regions. Mutation profiles were determined using the Stanford Drug Resistance Database. RESULTS We sequenced 275 samples. The median age was 23 years, and majority (98.9%, n = 272) were infected with HIV-1 subtype C. The prevalence of surveillance drug resistance mutations (SDRMs) was 13.5% (n = 37). Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations were found in 12.4% of women (n = 34). Few women had NRTI (1.8%, n = 5) and protease inhibitor (1.1%, n = 3) mutations. Five women had multiple NRTI and NNRTI SDRMs. CONCLUSIONS The high levels of PDR, particularly to NNRTIs, strongly support the recent change to the South African national HIV treatment guidelines to transition to a first-line drug regimen that excludes NNRTIs.
Collapse
Affiliation(s)
- Ivana Beesham
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Urvi M. Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dvora L. Joseph Davey
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Renee Heffron
- Department of Global Health and Department of Epidemiology, University of Washington, Seattle, WA
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shannon L. Bosman
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Mags Beksinska
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Jennifer Smit
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Khatija Ahmed
- Setshaba Research Centre, Soshanguve, South Africa
- Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Heeran Makkan
- The Aurum Institute, Klerksdorp, South Africa
- Department of Interdisciplinary Social Science, Public Health, Utrecht University, Utrecht, The Netherlands
| | | | - Cheryl Louw
- Madibeng Centre for Research, Brits, South Africa
- Department of Family Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Philip Kotze
- Qhakaza Mbokodo Research Clinic, Ladysmith, South Africa
| | - G. Justus Hofmeyr
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana
| | - Mandisa Singata‐Madliki
- Effective Care Research Unit, Universities of the Witwatersrand, Walter Sisulu and Fort Hare and Eastern Cape Department of Health, East London, South Africa
- Effective Care Research Unit, Universities of the Witwatersrand and Fort Hare and Eastern Cape Department of Health, East London, South Africa
| | - Helen Rees
- Wits Reproductive Health and HIV Institute (Wits RHI), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jared M. Baeten
- Department of Global Health, Department of Epidemiology, Department of Medicine, University of Washington, Seattle, WA
- Currently, Gilead Sciences, Foster City, CA; and
| | - Carole Wallis
- BARC-SA and Lancet Laboratories, Johannesburg, South Africa
| |
Collapse
|
45
|
Autopsy Study Defines Composition and Dynamics of the HIV-1 Reservoir after Allogeneic Hematopoietic Stem Cell Transplantation with CCR5Δ32/Δ32 Donor Cells. Viruses 2022; 14:v14092069. [PMID: 36146874 PMCID: PMC9503691 DOI: 10.3390/v14092069] [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: 08/30/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Allo-HSCT with CCR5Δ32/Δ32 donor cells is the only curative HIV-1 intervention. We investigated the impact of allo-HSCT on the viral reservoir in PBMCs and post-mortem tissue in two patients. IciS-05 and IciS-11 both received a CCR5Δ32/Δ32 allo-HSCT. Before allo-HSCT, ultrasensitive HIV-1 RNA quantification; HIV-1-DNA quantification; co-receptor tropism analysis; deep-sequencing and viral characterization in PBMCs and bone marrow; and post-allo-HSCT, ultrasensitive RNA and HIV-1-DNA quantification were performed. Proviral quantification, deep sequencing, and viral characterization were done in post-mortem tissue samples. Both patients harbored subtype B CCR5-tropic HIV-1 as determined genotypically and functionally by virus culture. Pre-allo-HSCT, HIV-1-DNA could be detected in both patients in bone marrow, PBMCs, and T-cell subsets. Chimerism correlated with detectable HIV-1-DNA LTR copies in cells and tissues. Post-mortem analysis of IciS-05 revealed proviral DNA in all tissue biopsies, but not in PBMCs. In patient IciS-11, who was transplanted twice, no HIV-1-DNA could be detected in PBMCs at the time of death, whereas HIV-1-DNA was detectable in the lymph node. In conclusion, shortly after CCR5Δ32/Δ32, allo-HSCT HIV-1-DNA became undetectable in PBMCs. However, HIV-1-DNA variants identical to those present before transplantation persisted in post-mortem-obtained tissues, indicating that these tissues play an important role as viral reservoirs.
Collapse
|
46
|
Henerico S, Lyimo E, Makubi AN, Magesa D, Desderius B, Mueller A, Changalucha J, Kalluvya SE, Van Zyl G, Preiser W, Mshana SE, Kasang C. Primary resistance against integrase strand transfer inhibitors in integrase strand transfer inhibitor-naive patients failing first- and second-line ART in Tanzania. J Antimicrob Chemother 2022; 77:3138-3143. [PMID: 36101479 DOI: 10.1093/jac/dkac295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Sub-Saharan African countries are introducing integrase strand transfer inhibitors (INSTIs) in their ART programmes as the preferred first-line regimen, and dolutegravir is the INSTI of choice due to its potency, tolerability and high genetic barrier to resistance. Dolutegravir was introduced into the first-line ART regimen in Tanzania in 2019. However, there is a paucity of data on the occurrence of mutations in HIV lineages circulating in Tanzania. This study aimed to determine the prevalence of INSTI primary resistance mutations in Tanzanian patients exposed to ART but not INSTIs. METHODS Plasma samples from 50 INSTI-naive patients failing first- or second-line ART [median (IQR) age: 40 (21.93-46.41) years; 68% women] were subjected to Sanger sequencing of the HIV integrase gene. Participants had been on ART for a median (IQR) duration of 7.32 (4.73-9.29) years, with 80% and 20% failing first- and second-line ART, respectively. RESULTS No major INSTI mutations were found, but 2 (4%) participants had the accessory mutation T97A. Using the REGA HIV-1 subtyping tool, HIV subtype A1 (53.1%) was found to be dominant, followed by subtypes C (30.6%) and D (16.3%). CONCLUSIONS This study found no current evidence for transmitted resistance against INSTIs among unexposed patients failing ART and supports the scale-up of INSTI-based regimens. However, the presence of accessory mutations calls for the surveillance of INSTI resistance mutations to ensure that the anticipated long-term desired outcomes are achieved.
Collapse
Affiliation(s)
| | - Eric Lyimo
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | - Abel N Makubi
- The Ministry of Health, Dodoma, United Republic of Tanzania
| | - Daniel Magesa
- Centers for Disease Control and Prevention, United Republic of Tanzania branch, Dar es Salaam, United Republic of Tanzania
| | - Bernard Desderius
- Bugando Medical Centre, Mwanza, United Republic of Tanzania.,Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Andreas Mueller
- Klinikum Wuerzburg Mitte gGmbH, Missioklinik, Department of Tropical Medicine, Würzburg, Germany
| | - John Changalucha
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | | | - Gert Van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Stephen E Mshana
- Catholic University of Health and Allied Sciences-Bugando, Mwanza, United Republic of Tanzania
| | - Christa Kasang
- German Leprosy and Tuberculosis Relief Association (DAHW), Würzburg, Germany.,Medmissio, Würzburg, Germany
| |
Collapse
|
47
|
Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T. Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018. Viruses 2022; 14:v14091992. [PMID: 36146798 PMCID: PMC9505726 DOI: 10.3390/v14091992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain effective, levels of transmitted drug resistance (TDR) need to be monitored over time. To determine the temporal trends of TDR in Mozambique, a search for studies in PubMed and sequences in GenBank was performed. Only studies covering the pol region that described HIVDR and genetic diversity from treatment naïve patients were included. A dataset from seven published studies and one novel unpublished study conducted between 1999 and 2018 were included. The Calibrated Population Resistance tool (CPR) and REGA HIV-1 Subtyping Tool version 3 for sequences pooled by sampling year were used to determine resistance mutations and subtypes, respectively. The prevalence of HIVDR amongst treatment-naïve individuals increased over time, reaching 14.4% in 2018. The increase was most prominent for non-nucleoside reverse transcriptase inhibitors (NNRTIs), reaching 12.7% in 2018. Subtype C was predominant in all regions, but a higher genetic variability (19% non-subtype C) was observed in the north region of Mozambique. These findings confirm a higher diversity of HIV in the north of the country and an increased prevalence of NNRTI resistance among treatment naïve individuals over time.
Collapse
Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- Correspondence: (N.I.); (T.d.O.)
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Isabel Mahumane
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Hernane Gemusse
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Adilson Bauhofer
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Adolfo Vubil
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Pirolita Mambo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Dulce Bila
- Elizabeth Glaser Pediatric AIDS Foundation in Mozambique, Avenida Agostinho Neto, Maputo 620, Mozambique
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
- Correspondence: (N.I.); (T.d.O.)
| |
Collapse
|
48
|
Parbie PK, Abana CZY, Kushitor D, Asigbee TW, Ntim NAA, Addo-Tetebo G, Ansong MRD, Ofori SB, Mizutani T, Runtuwene LR, Nishizawa M, Ishikawa K, Kiyono H, Ampofo WK, Matano T, Bonney EY, Kikuchi T. High-level resistance to non-nucleos(t)ide reverse transcriptase inhibitor based first-line antiretroviral therapy in Ghana; A 2017 study. Front Microbiol 2022; 13:973771. [PMID: 36090108 PMCID: PMC9459847 DOI: 10.3389/fmicb.2022.973771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
Expanding access to effective antiretroviral therapy (ART) is a major tool for management of Human Immunodeficiency Virus (HIV) infection. However, rising levels of HIV drug-resistance have significantly hampered the anticipated success of ART in persons living with HIV (PLWH), particularly those from Africa. Though great strides have been made in Ghana toward achieving the UNAIDS “95-95-95” target, a substantial number of PLWH receiving ART have not attained viral suppression. This study investigated patterns of drug resistance mutations in ART naïve as well as ART-experienced PLWH receiving first-line regimen drugs from Ghana. In a cross-sectional study, blood samples were collected from HIV-1 infected adults (≥18 years) attending HIV/AIDS clinic at the Eastern Regional Hospital, Koforidua, Ghana from September to October 2017. Viral RNA isolated from plasma were subjected to genotypic drug resistance testing for Protease Inhibitors (PI), Reverse Transcriptase Inhibitors (RTI), and Integrase Strand Transfer Inhibitors (INSTI). A total of 95 (84 ART experienced, 11 ART naïve) HIV-1 infected participants were sampled in this study. Sixty percent (50/84) of the ART-experienced participants were controlling viremia (viral load < 1,000 copies/ml). Of the 95 patient samples, 32, 34, and 33 were successfully sequenced for protease, reverse-transcriptase, and integrase regions, respectively. The dominant HIV-1 subtypes detected were CRF02_AG (70%), and A3 (10%). Major drug resistance associated mutations were only detected for reverse transcriptase inhibitors. The predominant drug resistance mutations were against nucleos(t)ide reverse transcriptase inhibitors (NRTI)—M184V/I and non-nucleos(t)ide reverse transcriptase inhibitors (NNRTI)—K103N. In the ART-experienced group, M184V/I and K103N were detected in 54% (15/28) and 46% (13/28) of individuals, respectively. Both mutations were each detected in 33% (2/6) of ART naïve individuals. Multiclass resistance to NRTI and NNRTI was detected in 57% of ART-experienced individuals and two ART naïve individuals. This study reports high-level resistance to NNRTI-based antiretroviral therapy in PLWH in Ghana. However, the absence of major PI and INSTI associated-mutations is a good signal that the current WHO recommendation of Dolutegravir in combination with an NRTI backbone will yield maximum benefits as first-line regimen for PLWH in Ghana.
Collapse
Affiliation(s)
- Prince Kofi Parbie
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Zaab-Yen Abana
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Center for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dennis Kushitor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Theodore Worlanyo Asigbee
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Nana Afia Asante Ntim
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Gifty Addo-Tetebo
- Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | | | - Sampson Badu Ofori
- Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | | | | | - Masako Nishizawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Kiyono
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Future Medicine Education and Research Organization, Institute for Global Prominent Research, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Medicine, Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV) University of California San Diego, San Diego, CA, United States
| | | | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Evelyn Yayra Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- *Correspondence: Evelyn Yayra Bonney,
| | - Tadashi Kikuchi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Tadashi Kikuchi,
| |
Collapse
|
49
|
de Azevedo SSD, Delatorre E, Gaido CM, Silva-de-Jesus C, Guimarães ML, Couto-Fernandez JC, Morgado MG. HIV-1 Diversity and Drug Resistance in Treatment-Naïve Children and Adolescents from Rio de Janeiro, Brazil. Viruses 2022; 14:v14081761. [PMID: 36016383 PMCID: PMC9413768 DOI: 10.3390/v14081761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/02/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) can be transmitted via parenteral, sexual, or vertical exposure routes. The number of HIV-1 cases detected yearly in children and adolescents in Brazil did not decrease over the last decade, representing ~5% of total cases described in the country. In recent years, the HIV-1 diversity and the prevalence of transmitted drug resistance mutations (TDRM) are moving toward a marked increase. In this study, we retrospectively evaluated the diversity of HIV-1 subtypes and the TDRM prevalence in 135 treatment-naïve HIV-1 vertically infected children and adolescents born in between 1993 and 2012. These children were assessed in either 2001–2007 or 2008–2012 when they were 0 to 17 years old. The individuals assessed in 2001–2007 (n = 38) had median CD4+ T cell counts of 1218 cells/mm3 (IQR: 738–2.084) and median HIV-1 plasma viral load of 4.18 log10 copies/mL (IQR: 3.88–4.08). The individuals (n = 97) evaluated in 2008–2012 showed median CD4+ T cell counts of 898.5 cells/mm3 (IQR: 591.3–1.821) and median HIV-1 plasma viral load of 4.69 log10 copies/mL (IQR: 4.26–5.33). A steady decrease in the median CD4 T+ cell counts was observed with age progression, as expected. The majority HIV-1 pol sequences (87%) were classified as pure HIV-1 subtypes (77% subtype B, 9% subtype F1 and 1.5% subtype C), while 13% of sequences were classified as recombinants (CRF45_cpx, n = 4; CRF28/29_BF1, n = 2; CRF02_AG, n = 1; CRF40_BF1, n = 1, CRF99_BF1, n = 1, URF_BF1, n = 8). The overall prevalence of TDRM was 14% (19/135), conferring resistance to the nucleoside reverse transcriptase inhibitors (NRTI, 13/135–9.6%), non-nucleoside reverse transcriptase inhibitors (NNRTI, 8/135–5.9%), and protease inhibitors (PI, 2/135–1.5%). The main TDRM observed for NNRTI was the K103N (n = 8), while the mutations T215I/Y/D/E (n = 7) and M184V (n = 4) were the main TDRM for NRTI. Only two TDRM were observed for PI in one individual each (M46I and V82A). Most TDRM were found in the HIV-1 subtype B (84%) sequences. This study reveals an HIV-1 epidemic with high diversity and moderate prevalence of TDRM in the pediatric population of Rio de Janeiro, indicating the existence of possible problems in the clinical management of prophylactic therapy to prevent mother-to-child transmission and future treatment options for the affected children.
Collapse
Affiliation(s)
- Suwellen Sardinha Dias de Azevedo
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
- Correspondence: or ; Tel.: +55-21-3865-8147; Fax: +55-21-3865-8173
| | - Edson Delatorre
- Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia—Universidade Federal do Espírito Santo—UFES, Espírito Santo 29500-000, Brazil
| | - Cibele Marina Gaido
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Carlos Silva-de-Jesus
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | | | - José Carlos Couto-Fernandez
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| |
Collapse
|
50
|
Blenkinsop A, Monod M, Sighem AV, Pantazis N, Bezemer D, Op de Coul E, van de Laar T, Fraser C, Prins M, Reiss P, de Bree GJ, Ratmann O. Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam. eLife 2022; 11:76487. [PMID: 35920649 PMCID: PMC9545569 DOI: 10.7554/elife.76487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, we aimed to estimate the number and proportion of Amsterdam HIV infections that originated within the city, from Amsterdam residents. We also aimed to estimate the proportion of recent HIV infections during the 5-year period 2014–2018 in Amsterdam that remained undiagnosed. Methods: We located diagnosed HIV infections in Amsterdam using postcode data (PC4) at time of registration in the ATHENA observational HIV cohort, and used HIV sequence data to reconstruct phylogeographically distinct, partially observed Amsterdam transmission chains. Individual-level infection times were estimated from biomarker data, and used to date the phylogenetically observed transmission chains as well as to estimate undiagnosed proportions among recent infections. A Bayesian Negative Binomial branching process model was used to estimate the number, size, and growth of the unobserved Amsterdam transmission chains from the partially observed phylogenetic data. Results: Between 1 January 2014 and 1 May 2019, there were 846 HIV diagnoses in Amsterdam residents, of whom 516 (61%) were estimated to have been infected in 2014–2018. The rate of new Amsterdam diagnoses since 2014 (104 per 100,000) remained higher than the national rates excluding Amsterdam (24 per 100,000), and in this sense Amsterdam remained a HIV hotspot in the Netherlands. An estimated 14% [12–16%] of infections in Amsterdan MSM in 2014–2018 remained undiagnosed by 1 May 2019, and 41% [35–48%] in Amsterdam heterosexuals, with variation by region of birth. An estimated 67% [60–74%] of Amsterdam MSM infections in 2014–2018 had an Amsterdam resident as source, and 56% [41–70%] in Amsterdam heterosexuals, with heterogeneity by region of birth. Of the locally acquired infections, an estimated 43% [37–49%] were in foreign-born MSM, 41% [35–47%] in Dutch-born MSM, 10% [6–18%] in foreign-born heterosexuals, and 5% [2–9%] in Dutch-born heterosexuals. We estimate the majority of Amsterdam MSM infections in 2014–2018 originated in transmission chains that pre-existed by 2014. Conclusions: This combined phylogenetic, epidemiologic, and modelling analysis in the UNAIDS Fast-Track City Amsterdam indicates that there remains considerable potential to prevent HIV infections among Amsterdam residents through city-level interventions. The burden of locally acquired infection remains concentrated in MSM, and both Dutch-born and foreign-born MSM would likely benefit most from intensified city-level interventions. Funding: This study received funding as part of the H-TEAM initiative from Aidsfonds (project number P29701). The H-TEAM initiative is being supported by Aidsfonds (grant number: 2013169, P29701, P60803), Stichting Amsterdam Dinner Foundation, Bristol-Myers Squibb International Corp. (study number: AI424-541), Gilead Sciences Europe Ltd (grant number: PA-HIV-PREP-16-0024), Gilead Sciences (protocol numbers: CO-NL-276-4222, CO-US-276-1712, CO-NL-985-6195), and M.A.C AIDS Fund.
Collapse
Affiliation(s)
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, United Kingdom
| | | | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, University of Athens, Athens, Greece
| | | | - Eline Op de Coul
- Center for Infectious Diseases Prevention and Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Thijs van de Laar
- Department of Donor Medicine Research, Sanquin, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maria Prins
- Academic Medical Center, Amsterdam, Netherlands
| | - Peter Reiss
- Department of Global Health, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Godelieve J de Bree
- Department of Global Health, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, United Kingdom
| |
Collapse
|