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Silhol R, Maheu-Giroux M, Soni N, Simo Fotso A, Rouveau N, Vautier A, Doumenc-Aïdara C, Geoffroy O, N'Guessan KN, Sidibé Y, Kabemba OK, Gueye PA, Ndeye PD, Mukandavire C, Vickerman P, Keita A, Ndour CT, Larmarange J, Boily MC. Potential population-level effects of HIV self-test distribution among key populations in Côte d'Ivoire, Mali, and Senegal: a mathematical modelling analysis. Lancet HIV 2024; 11:e531-e541. [PMID: 38991596 DOI: 10.1016/s2352-3018(24)00126-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND During 2019-21, the AutoTest VIH, Libre d'accéder à la connaissance de son Statut (ATLAS) programme distributed around 380 000 HIV self-testing kits to key populations, including female sex workers, men who have sex with men, and their partners, in Côte d'Ivoire, Mali, and Senegal. We aimed to estimate the effects of the ATLAS programme and national scale-up of HIV self-test distribution on HIV diagnosis, HIV treatment coverage, HIV incidence, and HIV-related mortality. METHODS We adapted a deterministic compartmental model of HIV transmission in Côte d'Ivoire, parameterised and fitted to country-specific demographic, behavioural, HIV epidemiological, and intervention data in Côte d'Ivoire, Mali, and Senegal separately during 1980-2020. We simulated dynamics of new HIV infections, HIV diagnoses, and HIV-related deaths within scenarios with and without HIV self-test distribution among key populations. Models were separately parameterised and fitted to country-specific sets of epidemiological and intervention outcomes (stratified by sex, risk, age group, and HIV status, if available) over time within a Bayesian framework. We estimated the effects on the absolute increase in the proportion of people with HIV diagnosed at the end of 2021 for the ATLAS-only scenario and at the end of 2028 and 2038 for the HIV self-testing scale-up scenario. We estimated cumulative numbers of additional HIV diagnoses and initiations of antiretroviral therapy and the proportion and absolute numbers of new HIV infections and HIV-related deaths averted during 2019-21 and 2019-28 for the ATLAS-only scenario and during 2019-28 and 2019-38 for the HIV self-testing scale-up scenario. FINDINGS Our model estimated that ATLAS could have led to 700 (90% uncertainty interval [UI] 500-900) additional HIV diagnoses in Côte d'Ivoire, 500 (300-900) in Mali, and 300 (50-700) in Senegal during 2019-21, a 0·4 percentage point (90% UI 0·3-0·5) increase overall by the end of 2021. During 2019-28, ATLAS was estimated to avert 1900 (90% UI 1300-2700) new HIV infections and 600 (400-800) HIV-related deaths across the three countries, of which 38·6% (90% UI 31·8-48·3) of new infections and 70·1% (60·4-77·3) of HIV-related deaths would be among key populations. ATLAS would avert 1·5% (0·8-3·1) of all HIV-related deaths across the three countries during this period. Scaling up HIV self-testing would avert 16·2% (90% UI 10·0-23·1) of all new HIV infections during 2019-28 in Senegal, 5·3% (3·0-8·9) in Mali, and 1·6% (1·0-2·4) in Côte d'Ivoire. HIV self-testing scale-up among key populations was estimated to increase HIV diagnosis by the end of 2028 to 1·3 percentage points (90% UI 0·8-1·9) in Côte d'Ivoire, 10·6 percentage points (5·3-16·8) in Senegal, and 3·6 percentage points (2·0-6·4) in Mali. INTERPRETATION Scaling up HIV self-test distribution among key populations in western Africa could attenuate disparities in access to HIV testing and reduce infections and deaths among key populations and their partners. FUNDING Unitaid, Solthis, the UK Medical Research Council Centre for Global Infectious Disease Analysis, the EU European & Developing Countries Clinical Trials Partnership programme, and the Wellcome Trust. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Romain Silhol
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Mathieu Maheu-Giroux
- Department of Epidemiology and Biostatistics, School of Population and Global Health, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Nirali Soni
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Arlette Simo Fotso
- Centre Population et Développement, Université Paris Cité, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Paris, France; French Institute for Demographic Studies, Institut National d'Études Démographiques, Paris, France
| | - Nicolas Rouveau
- Centre Population et Développement, Université Paris Cité, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Anthony Vautier
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Dakar, Senegal
| | | | - Olivier Geoffroy
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Abidjan, Côte d'Ivoire
| | | | - Younoussa Sidibé
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Bamako, Mali
| | - Odé Kanku Kabemba
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Bamako, Mali
| | - Papa Alioune Gueye
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Dakar, Senegal
| | - Pauline Dama Ndeye
- Solidarité Thérapeutique et Initiatives pour la Santé, Solthis, Dakar, Senegal
| | - Christinah Mukandavire
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Peter Vickerman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Cheikh Tidiane Ndour
- Division de Lutte contre le Sida et les Infections Sexuellement Transmissibles, Ministère de la Santé et de l'Action Sociale Institut d'Hygiène Sociale, Dakar, Senegal
| | - Joseph Larmarange
- Centre Population et Développement, Université Paris Cité, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Paris, France; French Institute for Demographic Studies, Institut National d'Études Démographiques, Paris, France
| | - Marie-Claude Boily
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
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Fabeni L, Armenia D, Abbate I, Gagliardini R, Mazzotta V, Bertoli A, Gennari W, Forbici F, Berno G, Piermatteo L, Borghi V, Pinnetti C, Vergori A, Mondi A, Parruti G, Di Sora F, Iannetta M, Lichtner M, Latini A, Mussini C, Sarmati L, Perno CF, Girardi E, Antinori A, Ceccherini-Silberstein F, Maggi F, Santoro MM. HIV-1 transmitted drug resistance in newly diagnosed individuals in Italy over the period 2015-21. J Antimicrob Chemother 2024:dkae189. [PMID: 39028674 DOI: 10.1093/jac/dkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/22/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Transmitted drug resistance (TDR) is still a critical aspect for the management of individuals living with HIV-1. Thus, its evaluation is crucial to optimize HIV care. METHODS Overall, 2386 HIV-1 protease/reverse transcriptase and 1831 integrase sequences from drug-naïve individuals diagnosed in north and central Italy between 2015 and 2021 were analysed. TDR was evaluated over time. Phylogeny was generated by maximum likelihood. Factors associated with TDR were evaluated by logistic regression. RESULTS Individuals were mainly male (79.1%) and Italian (56.2%), with a median (IQR) age of 38 (30-48). Non-B infected individuals accounted for 44.6% (N = 1065) of the overall population and increased over time (2015-2021, from 42.1% to 51.0%, P = 0.002). TDR prevalence to any class was 8.0% (B subtype 9.5% versus non-B subtypes 6.1%, P = 0.002) and remained almost constant over time. Overall, 300 transmission clusters (TCs) involving 1155 (48.4%) individuals were identified, with a similar proportion in B and non-infected individuals (49.7% versus 46.8%, P = 0.148). A similar prevalence of TDR among individuals in TCs and those out of TCs was found (8.2% versus 7.8%, P = 0.707).By multivariable analysis, subtypes A, F, and CFR02_AG were negatively associated with TDR. No other factors, including being part of TCs, were significantly associated with TDR. CONCLUSIONS Between 2015 and 2021, TDR prevalence in Italy was 8% and remained almost stable over time. Resistant strains were found circulating regardless of being in TCs, but less likely in non-B subtypes. These results highlight the importance of a continuous surveillance of newly diagnosed individuals for evidence of TDR to inform clinical practice.
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Affiliation(s)
- Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Armenia
- Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Roberta Gagliardini
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ada Bertoli
- Laboratory of Virology, Department of Laboratory Medicine, University Hospital Tor Vergata, Rome, Italy
| | - William Gennari
- Molecular Microbiology and Virology Unit, Department of Laboratory Medicine and Pathological Anatomy, Policlinic of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Vanni Borghi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Carmela Pinnetti
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Annalisa Mondi
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giustino Parruti
- Infectious Diseases Unit, Pescara General Hospital, Pescara, Italy
| | - Fiorella Di Sora
- Unit of Clinical Immunology, San Giovanni Addolorata Hospital, Rome, Italy
| | - Marco Iannetta
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Miriam Lichtner
- Infectious Diseases Unit, Santa Maria Goretti Hospital, Sapienza University of Rome, Polo Pontino, Latina, Italy
- Sant'Andrea Hospital, Clinical Infectious Diseases, Rome, Italy
| | - Alessandra Latini
- Sexually Transmitted Infection/Human Immunodeficiency Virus Unit, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Loredana Sarmati
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesú Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
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Lemée V, Gréaume S, Gautier J, Dzamitika SA, Coignard C, Jortani SA, Grillet B, Badawi M, Plantier JC. Performance evaluation of the new Access HIV Ag/Ab combo assay on the DxI 9000 Access Immunoassay Analyzer. J Clin Virol 2024; 174:105712. [PMID: 39047323 DOI: 10.1016/j.jcv.2024.105712] [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: 04/12/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Fourth-generation HIV immunoassays have been developed to reduce the window period of detection during seroconversion period, allowing for the detection of early and established infections. The aim of this work was to evaluate a newly developed assay, Access HIV Ag/Ab combo on the novel high throughput DxI 9000 Access Immunoassay Analyzer (Beckman Coulter, Inc.). The assay allows for simultaneous qualitative detection and differentiation of HIV-1 p24 antigen and HIV-1/2 antibodies. Assay performance was compared to two gold standard assays, the Abbott Architect HIV Ag/Ab Combo and Roche Elecsys HIV Duo, and assessed in a multicenter study, using a wide panel of samples (n > 9000, clinical samples and viral lysates) representative of genetic diversity for both antibodies and antigens, early phases of infection, negative, and cross-reacting samples. The clinical sensitivity was 100 % for clinical samples as well as for viral lysates. Data on viral lysates and early detection on seroconversion panels showed a better result with the Access assay. Analytical sensitivity showed a limit of p24 detection determined around 0.2 IU/mL. The overall specificity was 99.91 %, and no interference was found using the potentially cross-reactive samples. In conclusion, the Access HIV Ag/Ab combo assay demonstrated its ability for accurate diagnosis of chronic as well as primary HIV infections on the DxI 9000 Analyzer, despite the high level of genetic diversity of these viruses.
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Affiliation(s)
- V Lemée
- CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France; Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - S Gréaume
- Etablissement Français du Sang (EFS) Hauts-de-France - Normandie (HFNO), Bois Guillaume, France
| | | | | | - C Coignard
- Eurofins Biomnis, Ivry-sur-Seine, France
| | - S A Jortani
- Kentucky Clinical Trials Laboratory (KCTL), Louisville, KY, USA; University of Louisville School of Medicine, Louisville, KY, USA
| | - B Grillet
- Beckman Coulter Immunotech, Marseille, France
| | - M Badawi
- Beckman Coulter Immunotech, Marseille, France
| | - J-C Plantier
- CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France; Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France.
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4
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Mahomed S. Broadly neutralizing antibodies for HIV prevention: a comprehensive review and future perspectives. Clin Microbiol Rev 2024; 37:e0015222. [PMID: 38687039 DOI: 10.1128/cmr.00152-22] [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] [Indexed: 05/02/2024] Open
Abstract
SUMMARYThe human immunodeficiency virus (HIV) epidemic remains a formidable global health concern, with 39 million people living with the virus and 1.3 million new infections reported in 2022. Despite anti-retroviral therapy's effectiveness in pre-exposure prophylaxis, its global adoption is limited. Broadly neutralizing antibodies (bNAbs) offer an alternative strategy for HIV prevention through passive immunization. Historically, passive immunization has been efficacious in the treatment of various diseases ranging from oncology to infectious diseases. Early clinical trials suggest bNAbs are safe, tolerable, and capable of reducing HIV RNA levels. Although challenges such as bNAb resistance have been noted in phase I trials, ongoing research aims to assess the additive or synergistic benefits of combining multiple bNAbs. Researchers are exploring bispecific and trispecific antibodies, and fragment crystallizable region modifications to augment antibody efficacy and half-life. Moreover, the potential of other antibody isotypes like IgG3 and IgA is under investigation. While promising, the application of bNAbs faces economic and logistical barriers. High manufacturing costs, particularly in resource-limited settings, and logistical challenges like cold-chain requirements pose obstacles. Preliminary studies suggest cost-effectiveness, although this is contingent on various factors like efficacy and distribution. Technological advancements and strategic partnerships may mitigate some challenges, but issues like molecular aggregation remain. The World Health Organization has provided preferred product characteristics for bNAbs, focusing on optimizing their efficacy, safety, and accessibility. The integration of bNAbs in HIV prophylaxis necessitates a multi-faceted approach, considering economic, logistical, and scientific variables. This review comprehensively covers the historical context, current advancements, and future avenues of bNAbs in HIV prevention.
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Affiliation(s)
- Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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5
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Ode H, Matsuda M, Shigemi U, Mori M, Yamamura Y, Nakata Y, Okazaki R, Kubota M, Setoyama Y, Imahashi M, Yokomaku Y, Iwatani Y. Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations. Sci Rep 2024; 14:12099. [PMID: 38802662 PMCID: PMC11130118 DOI: 10.1038/s41598-024-63054-3] [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: 04/12/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024] Open
Abstract
HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different drug target proteins. Since the number of targets has increased with the addition of a new class of antiretroviral drugs, a simple high-throughput system for assessing nucleotide sequences throughout the HIV-1 genome is required. Here, we developed a new solution using nanopore sequencing of viral pangenomes amplified by PCR. Benchmark tests using HIV-1 molecular clones demonstrated an accuracy of up to 99.9%. In addition, validation tests of our protocol in 106 clinical samples demonstrated high concordance of drug resistance and tropism genotypes (92.5% and 98.1%, respectively) between the nanopore sequencing-based results and archived clinical determinations made based on Sanger sequencing data. These results suggest that our new approach will be a powerful solution for the comprehensive survey of HIV-1 drug resistance mutations in clinical settings.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Mikiko Mori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yoshimi Yamamura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Reiko Okazaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yuka Setoyama
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan.
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
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Koornneef A, Vanshylla K, Hardenberg G, Rutten L, Strokappe NM, Tolboom J, Vreugdenhil J, Boer KFD, Perkasa A, Blokland S, Burger JA, Huang WC, Lovell JF, van Manen D, Sanders RW, Zahn RC, Schuitemaker H, Langedijk JPM, Wegmann F. CoPoP liposomes displaying stabilized clade C HIV-1 Env elicit tier 2 multiclade neutralization in rabbits. Nat Commun 2024; 15:3128. [PMID: 38605096 PMCID: PMC11009251 DOI: 10.1038/s41467-024-47492-1] [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: 09/21/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
One of the strategies towards an effective HIV-1 vaccine is to elicit broadly neutralizing antibody responses that target the high HIV-1 Env diversity. Here, we present an HIV-1 vaccine candidate that consists of cobalt porphyrin-phospholipid (CoPoP) liposomes decorated with repaired and stabilized clade C HIV-1 Env trimers in a prefusion conformation. These particles exhibit high HIV-1 Env trimer decoration, serum stability and bind broadly neutralizing antibodies. Three sequential immunizations of female rabbits with CoPoP liposomes displaying a different clade C HIV-1 gp140 trimer at each dosing generate high HIV-1 Env-specific antibody responses. Additionally, serum neutralization is detectable against 18 of 20 multiclade tier 2 HIV-1 strains. Furthermore, the peak antibody titers induced by CoPoP liposomes can be recalled by subsequent heterologous immunization with Ad26-encoded membrane-bound stabilized Env antigens. Hence, a CoPoP liposome-based HIV-1 vaccine that can generate cross-clade neutralizing antibody immunity could potentially be a component of an efficacious HIV-1 vaccine.
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Affiliation(s)
| | | | | | - Lucy Rutten
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | | | | | | | | | - Sven Blokland
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Wei-Chiao Huang
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Jonathan F Lovell
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | | | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Roland C Zahn
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | - Johannes P M Langedijk
- Janssen Vaccines & Prevention, Leiden, The Netherlands.
- ForgeBio, Amsterdam, The Netherlands.
| | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands.
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Marichannegowda M, Heredia A, Wang Y, Song H. Genetic signatures in the highly virulent subtype B HIV-1 conferring immune escape to V1/V2 and V3 broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584899. [PMID: 38559199 PMCID: PMC10980024 DOI: 10.1101/2024.03.13.584899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV-1 is considered to become less susceptible to existing neutralizing antibodies over time. Our study on the virulent B (VB) HIV-1 identified genetic signatures responsible for immune escape from broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 glycan epitopes. We found that the absence of N295 and N332 glycans in the high mannose patch, which are crucial for neutralization by V3 glycan bNAbs and are typically conserved in subtype B HIV-1, is a notable feature in more than half of the VB variants. Neutralization assays confirmed that the loss of these two glycans in VB HIV-1 leads to escape from V3 glycan bNAbs. Additionally, all VB variants we investigated have an insertion in V2, contributing to immune escape from V1/V2 bNAbs PG9 and PG16. These findings suggest potential co-evolution of HIV-1 virulence and antigenicity, underscoring the need to monitor both the pathogenicity and neutralization susceptibility of newly emerged HIV-1 strains.
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Arman MS, Hasan MZ. A computational exploration of global and temporal dynamics of selection pressure on HIV-1 Vif polymorphism. Virus Res 2024; 341:199323. [PMID: 38237808 PMCID: PMC10831783 DOI: 10.1016/j.virusres.2024.199323] [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: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Virion infectivity factor (Vif), an accessory protein of HIV-1 (human immunodeficiency virus type 1), antagonizes host APOBEC3 protein (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3) or A3 via proteasomal degradation, facilitating viral replication. HLA (Human leukocyte antigens) alleles, host restriction factors, and error-prone reverse transcription contribute to the global polymorphic dynamics of HIV, impacting effective vaccine design. Our computational analysis of over 50,000 HIV-1 M vif sequences from the Los Alamos National Laboratory (LANL) database (1998-2021) revealed positive selection pressure on the vif gene (nonsynonymous to synonymous ratio, dn/ds=1.58) and an average entropy score of 0.372 in protein level. Interestingly, over the years (1998-2021), a decreasing trend of dn/ds (1.68 to 1.47) and an increasing trend of entropy (0.309 to 0.399) was observed. The predicted mutational frequency against Vif consensus sequence decreased over time (slope = -0.00024, p < 0.0001). Sequence conservation was observed in Vif functional motifs F1, F2, F3, G, BC box, and CBF β binding region, while variability was observed mainly in N- and C- terminal and Zinc finger region, which were dominantly under immune pressure by host HLA-I-restricted CD8+ T cell. Computational analysis of ∆∆Gstability through protein stability prediction tools suggested that missense mutation may affect Vif stability, especially in the Vif-A3 binding interface. Notably, mutations R17K and Y44F in F1 and G box were predicted to destabilize the Vif-A3 binding interface by altering bond formations with adjacent amino acids. Therefore, our analysis demonstrates Vif adaptation with host physiology by maintaining sequence conservation, especially in A3 interacting functional motifs, highlighting important therapeutic candidate regions of Vif against HIV-1 infections.
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Affiliation(s)
- Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Zafrul Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
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Azzman N, Gill MSA, Hassan SS, Christ F, Debyser Z, Mohamed WAS, Ahemad N. Pharmacological advances in anti-retroviral therapy for human immunodeficiency virus-1 infection: A comprehensive review. Rev Med Virol 2024; 34:e2529. [PMID: 38520650 DOI: 10.1002/rmv.2529] [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: 11/13/2023] [Revised: 01/23/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
The discovery of anti-retroviral (ARV) drugs over the past 36 years has introduced various classes, including nucleoside/nucleotide reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitor, fusion, and integrase strand transfer inhibitors inhibitors. The introduction of combined highly active anti-retroviral therapies in 1996 was later proven to combat further ARV drug resistance along with enhancing human immunodeficiency virus (HIV) suppression. As though the development of ARV therapies was continuously expanding, the variation of action caused by ARV drugs, along with its current updates, was not comprehensively discussed, particularly for HIV-1 infection. Thus, a range of HIV-1 ARV medications is covered in this review, including new developments in ARV therapy based on the drug's mechanism of action, the challenges related to HIV-1, and the need for combination therapy. Optimistically, this article will consolidate the overall updates of HIV-1 ARV treatments and conclude the significance of HIV-1-related pharmacotherapy research to combat the global threat of HIV infection.
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Affiliation(s)
- Nursyuhada Azzman
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA, Cawangan Pulau Pinang Kampus Bertam, Permatang Pauh, Pulau Pinang, Malaysia
| | - Muhammad Shoaib Ali Gill
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Wan Ahmad Syazani Mohamed
- Nutrition Unit, Nutrition, Metabolism and Cardiovascular Research Centre (NMCRC), Level 3, Block C, Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia (MOH), Shah Alam, Selangor, Malaysia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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Bacqué J, Delgado E, Gil H, Ibarra S, Benito S, García-Arata I, Moreno-Lorenzo M, de Adana ES, Gómez-González C, Sánchez M, Montero V, Thomson MM. Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe. Front Microbiol 2023; 14:1301374. [PMID: 38125564 PMCID: PMC10731470 DOI: 10.3389/fmicb.2023.1301374] [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: 09/24/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The high recombinogenic potential of HIV-1 has resulted in the generation of countless unique recombinant forms (URFs) and around 120 reported circulating recombinant forms (CRFs). Here we identify through analyses of near full-length genomes (NFLG) a new HIV-1 CRF derived from subtypes B and F1. Methods HIV-1 protease-reverse transcriptase (Pr-RT) sequences were obtained by RT-PCR amplification from plasma RNA. Near full-length genome sequences were obtained after amplification by RT-PCR in 5 overlapping fragments. Phylogenetic sequence analyses were performed via maximum likelihood. Mosaic structures were analyzed by bootscanning and phylogenetic analyses of genome segments. Temporal and geographical estimations of clade emergence were performed with a Bayesian coalescent method. Results Through phylogenetic analyses of HIV-1 Pr-RT sequences obtained by us from samples collected in Spain and downloaded from databases, we identified a BF1 recombinant cluster segregating from previously reported CRFs comprising 52 viruses, most from Brazil (n = 26), Spain (n = 11), and Italy (n = 9). The analyses of NFLG genomes of 4 viruses of the cluster, 2 from Spain and 2 from Italy, allowed to identify a new CRF, designated CRF75_BF1, which exhibits a complex mosaic structure with 20 breakpoints. All 4 patients harboring CRF75_BF1 viruses studied by us had CD4+ T-cell lymphocyte counts below 220/mm3 less than one year after diagnosis, a proportion significantly higher (p = 0.0074) than the 29% found in other patients studied in Spain by us during the same period. The origin of the clade comprising CRF75_BF1 and related viruses was estimated around 1984 in Brazil, with subsequent introduction of CRF75_BF1 in Italy around 1992, and migration from Italy to Spain around 1999. Conclusion A new HIV-1 CRF, designated CRF75_BF1, has been identified. CRF75_BF1 is the 6th CRF of South American origin initially identified in Western Europe, reflecting the increasing relationship of South American and European HIV-1 epidemics. The finding of low CD4+ T-cell lymphocyte counts early after diagnosis in patients harboring CRF75_BF1 viruses warrants further investigation on the virulence of this variant.
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Affiliation(s)
- Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Ibarra
- Department of Infectious Diseases, Hospital Universitario Basurto, Bilbao, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel García-Arata
- Department of Microbiology, Hospital Universitario de Fuenlabrada, Madrid, Spain
| | - María Moreno-Lorenzo
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Sáez de Adana
- Bioaraba, Microbiology, Infectious Diseases, Antimicrobials and Gene Therapy Research Group, Vitoria-Gasteiz, Spain
- Osakidetza-Basque Health Service, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Carmen Gómez-González
- Bioaraba, Microbiology, Infectious Diseases, Antimicrobials and Gene Therapy Research Group, Vitoria-Gasteiz, Spain
- Osakidetza-Basque Health Service, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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