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Saha T, Lyons N, Yue Yung DB, Quiñones-Mateu ME, Pletzer D, Das SC. Repurposing ebselen as an inhalable dry powder to treat respiratory tract infections. Eur J Pharm Biopharm 2024; 195:114170. [PMID: 38128743 DOI: 10.1016/j.ejpb.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
Respiratory tract infections (RTIs) are one of the leading causes of death globally, lately exacerbated by the increasing prevalence of antimicrobial resistance. While antimicrobial resistance could be overcome by developing new antimicrobial agents, the use of a safe repurposed agent having potent antimicrobial activity against various RTIs can be an efficient and cost-effective alternative to overcome the long and complex process of developing and testing new drugs. Ebselen, a synthetic organoselenium drug originally developed to treat noise-inducing hearing problems, has shown promising antimicrobial activity in vitro against several respiratory pathogens including viruses (e.g., SARS-CoV-2, influenza A virus) and bacteria (e.g., Mycobacterium tuberculosis, Streptococcus pneumoniae, and Staphylococcus aureus). Inhaled drug delivery is considered a promising approach for treating RTIs, as it can ensure effective drug concentrations at a lower dose, thereby minimizing the side effects that are often encountered by using oral or injectable drugs. In this study, we developed inhalable ebselen dry powder formulations using a spray-drying technique. The amino acids leucine, methionine, and tryptophan were incorporated with ebselen to enhance the yield and aerosolization of the dry powders. The amino acid-containing ebselen dry powders showed a better yield (37-56.4 %) than the amino acid-free formulation (30.9 %). All dry powders were crystalline in nature. The mass median aerodynamic diameter (MMAD) was less than 5 µm for amino acids containing dry powders (3-4 µm) and slightly higher (5.4 µm) for amino acid free dry powder indicating their suitability for inhalation. The aerosol performance was higher when amino acids were used, and the leucine-containing ebselen dry powder showed the highest emitted dose (84 %) and fine particle fraction (68 %). All amino acid formulations had similar cytotoxicity as raw ebselen, tested in respiratory cell line (A549 cells), with half-maximal inhibitory concentrations (IC50) between 100 and 250 μg/mL. Raw ebselen and amino acid-containing dry powders showed similar potent antibacterial activity against the Gram-positive bacteria S. aureus and S. pneumoniae with minimum inhibitory concentrations of 0.31 μg/mL and 0.16 μg/mL, respectively. On the other hand, raw ebselen and the formulations showed limited antimicrobial activity against the Gram-negative pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae. In summary, in this study we were able to develop amino-acid-containing inhalable dry powders of ebselen that could be used against different respiratory pathogens, especially Gram-positive bacteria, which could ensure more drug deposition in the respiratory tract, including the lungs. DPIs are generally used to treat lung (lower respiratory tract) diseases. However, DPIs can also be used to treat both upper and lower RTIs. The deposition of the dry powder in the respiratory tract is dependent on its physicochemical properties and this properties can be modulated to target the intended site of infection (upper and/or lower respiratory tract). Further studies will allow the development of similar formulations of individual and/or combination of antimicrobials that could be used to inhibit a number of respiratory pathogens.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Nikita Lyons
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Deborah Bow Yue Yung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniel Pletzer
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Shyamal C Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
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2
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Basak I, Harfoot R, Palmer JE, Kumar A, Quiñones-Mateu ME, Schweitzer L, Hughes SM. Neuroproteomic Analysis after SARS-CoV-2 Infection Reveals Overrepresented Neurodegeneration Pathways and Disrupted Metabolic Pathways. Biomolecules 2023; 13:1597. [PMID: 38002279 PMCID: PMC10669333 DOI: 10.3390/biom13111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Besides respiratory illness, SARS-CoV-2, the causative agent of COVID-19, leads to neurological symptoms. The molecular mechanisms leading to neuropathology after SARS-CoV-2 infection are sparsely explored. SARS-CoV-2 enters human cells via different receptors, including ACE-2, TMPRSS2, and TMEM106B. In this study, we used a human-induced pluripotent stem cell-derived neuronal model, which expresses ACE-2, TMPRSS2, TMEM106B, and other possible SARS-CoV-2 receptors, to evaluate its susceptibility to SARS-CoV-2 infection. The neurons were exposed to SARS-CoV-2, followed by RT-qPCR, immunocytochemistry, and proteomic analyses of the infected neurons. Our findings showed that SARS-CoV-2 infects neurons at a lower rate than other human cells; however, the virus could not replicate or produce infectious virions in this neuronal model. Despite the aborted SARS-CoV-2 replication, the infected neuronal nuclei showed irregular morphology compared to other human cells. Since cytokine storm is a significant effect of SARS-CoV-2 infection in COVID-19 patients, in addition to the direct neuronal infection, the neurons were treated with pre-conditioned media from SARS-CoV-2-infected lung cells, and the neuroproteomic changes were investigated. The limited SARS-CoV-2 infection in the neurons and the neurons treated with the pre-conditioned media showed changes in the neuroproteomic profile, particularly affecting mitochondrial proteins and apoptotic and metabolic pathways, which may lead to the development of neurological complications. The findings from our study uncover a possible mechanism behind SARS-CoV-2-mediated neuropathology that might contribute to the lingering effects of the virus on the human brain.
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Affiliation(s)
- Indranil Basak
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand (M.E.Q.-M.)
| | - Jennifer E. Palmer
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, University of Otago, Dunedin 9016, New Zealand
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand (M.E.Q.-M.)
| | - Lucia Schweitzer
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie M. Hughes
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
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3
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Saha T, Sinha S, Harfoot R, Quiñones-Mateu ME, Das SC. Inhalable dry powder containing remdesivir and disulfiram: Preparation and in vitro characterization. Int J Pharm 2023; 645:123411. [PMID: 37703955 DOI: 10.1016/j.ijpharm.2023.123411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The respiratory tract, as the first and most afflicted target of many viruses such as SARS-CoV-2, seems to be the logical choice for delivering antiviral agents against this and other respiratory viruses. A combination of remdesivir and disulfiram, targeting two different steps in the viral replication cycle, has showed synergistic activity against SARS-CoV-2 in-vitro. In this study, we have developed an inhalable dry powder containing a combination of remdesivir and disulfiram utilizing the spray-drying technique, with the final goal of delivering this drug combination to the respiratory tract. The prepared dry powders were spherical, and crystalline. The particle size was between 1 and 5 μm indicating their suitability for inhalation. The spray-dried combinational dry powder containing remdesivir and disulfiram (RDSD) showed a higher emitted dose (ED) of >88% than single dry powder of remdesivir (RSD) (∼72%) and disulfiram (DSD) (∼84%), with a fine particle fraction (FPF) of ∼55%. Addition of L-leucine to RDSD showed >60% FPF with a similar ED. The in vitro aerosolization was not significantly affected after the stability study conducted at different humidity conditions. Interestingly, the single (RSD and DSD) and combined (RDSD) spray-dried powders showed limited cellular toxicity (CC50 values from 39.4 to >100 µM), while maintaining their anti-SARS-CoV-2 in vitro (EC50 values from 4.43 to 6.63 µM). In a summary, a combinational dry powder formulation containing remdesivir and disulfiram suitable for inhalation was developed by spray-drying technique which showed high cell viability in the respiratory cell line (Calu-3 cells) retaining their anti-SARS-CoV-2 property. In the future, in vivo studies will test the ability of these formulations to inhibit SARS-CoV-2 which is essential for clinical translation.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Shyamal C Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
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4
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Saha T, Sinha S, Harfoot R, Quiñones-Mateu ME, Das SC. Spray-Dried Inhalable Microparticles Combining Remdesivir and Ebselen against SARS-CoV-2 Infection. Pharmaceutics 2023; 15:2229. [PMID: 37765198 PMCID: PMC10535576 DOI: 10.3390/pharmaceutics15092229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
There is a continuous effort to develop efficient treatments for coronavirus disease 2019 (COVID-19) and other viral respiratory diseases. Among the different strategies, inhaled treatment is considered one of the most logical and efficient approaches to treating COVID-19, as the causative "SARS-CoV-2 virus RNA" predominantly infects the respiratory tract. COVID-19 treatments initially relied on repurposed drugs, with a few additional strategies developed during the last two years, and all of them are based on monotherapy. However, drug combinations have been found to be more effective than monotherapy in other viral diseases such as HIV, influenza, and hepatitis C virus. In the case of SARS-CoV-2 infection, in vitro studies have shown synergistic antiviral activity combining remdesivir with ebselen, an organoselenium compound. Therefore, these drug combinations could ensure better therapeutic outcomes than the individual agents. In this study, we developed a dry powder formulation containing remdesivir and ebselen using a spray-drying technique and used L-leucine as an aerosolization enhancer. The prepared dry powders were spherical and crystalline, with a mean particle size between 1 and 3 µm, indicating their suitability for inhalation. The emitted dose (ED) and fine particle fraction (FPF) of remdesivir- and ebselen-containing dry powders were ~80% and ~57% when prepared without L-leucine. The ED as well as the FPF significantly increased with values of >86% and >67%, respectively, when L-leucine was incorporated. More importantly, the single and combinational dry powder of remdesivir and ebselen showed minimal cytotoxicity (CC50 > 100 μM) in Calu-3 cells, retaining their anti-SARS-CoV-2 properties (EC50 2.77 to 18.64 μM). In summary, we developed an inhalable dry powder combination of remdesivir and ebselen using a spray-drying technique. The spray-dried inhalable microparticles retained their limited cytotoxicity and specific antiviral properties. Future in vivo studies are needed to verify the potential use of these remdesivir/ebselen combinational spray-dried inhalable microparticles to block the SARS-CoV-2 replication in the respiratory tract.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand;
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Shyamal C. Das
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand;
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5
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Crump JA, Vakaoti P, Moore-Jones M, Tan L, Ergler CR, Fenton E, Anderson EMR, Bremer PJ, Sharples KJ, Walls T, Quiñones-Mateu ME, Kolandai K, Hadingham J, Hill PC, Knowles S. Health nationalism in Aotearoa New Zealand during COVID-19: problems for global health equity. Nat Med 2023; 29:1887-1889. [PMID: 37464060 DOI: 10.1038/s41591-023-02436-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- John A Crump
- Centre for International Health, Division of Health Sciences, University of Otago, Dunedin, New Zealand.
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand.
| | - Patrick Vakaoti
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Te Tumu - School of Māori, Pacific, and Indigenous Studies, Division of Humanities, University of Otago, Dunedin, New Zealand
| | - Michael Moore-Jones
- English Literature Programme, School of English, Film, Theatre, Media and Communication, and Art History, Victoria University of Wellington, Wellington, New Zealand
| | - Lena Tan
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Politics Programme, Division of Humanities, University of Otago, Dunedin, New Zealand
| | - Christina R Ergler
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- School of Geography, Division of Humanities, University of Otago, Dunedin, New Zealand
| | - Elizabeth Fenton
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Bioethics Centre, Dunedin School of Medicine, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Emma M R Anderson
- Bioethics Centre, Dunedin School of Medicine, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Philip J Bremer
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Department of Food Science, Division of Sciences, University of Otago, Dunedin, New Zealand
| | - Katrina J Sharples
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Department of Mathematics and Statistics, Division of Sciences, University of Otago, Dunedin, New Zealand
| | - Tony Walls
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Department of Paediatrics, Division of Health Sciences, University of Otago, Christchurch, New Zealand
| | - Miguel E Quiñones-Mateu
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Komathi Kolandai
- COMPASS Research Centre and Public Policy Institute, Faculty of Arts, University of Auckland, Auckland, New Zealand
| | - Jacqui Hadingham
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
| | - Philip C Hill
- Centre for International Health, Division of Health Sciences, University of Otago, Dunedin, New Zealand
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
| | - Stephen Knowles
- Otago Global Health Institute, University of Otago, Dunedin, New Zealand
- Department of Economics, Otago Business School, Division of Commerce, University of Otago, Dunedin, New Zealand
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6
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Slama L, Hardy WD, Quiñones-Mateu ME, Kuritzkes DR. Alternative options for treatment-experienced people with HIV. AIDS 2023; 37:1165-1166. [PMID: 37139652 DOI: 10.1097/qad.0000000000003550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Laurence Slama
- Department of Infectious Diseases, Hôtel-Dieu Hospital, Assistance Publique-Hôpitaux de Paris
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, INRAE, Center for Research in Epidemiology and Statistics (CRESS), Paris, France
| | - W David Hardy
- Division of Infectious Diseases, Los Angeles County-University of Southern California Medical Center and Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology & Laboratory Medicine, Schulich Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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7
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Waqqar S, Lee K, Lawley B, Bilton T, Quiñones-Mateu ME, Bostina M, Burga LN. Directed Evolution of Seneca Valley Virus in Tumorsphere and Monolayer Cell Cultures of a Small-Cell Lung Cancer Model. Cancers (Basel) 2023; 15:cancers15092541. [PMID: 37174006 PMCID: PMC10177334 DOI: 10.3390/cancers15092541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
The Seneca Valley virus (SVV) is an oncolytic virus from the picornavirus family, characterized by a 7.3-kilobase RNA genome encoding for all the structural and functional viral proteins. Directed evolution by serial passaging has been employed for oncolytic virus adaptation to increase the killing efficacy towards certain types of tumors. We propagated the SVV in a small-cell lung cancer model under two culture conditions: conventional cell monolayer and tumorspheres, with the latter resembling more closely the cellular structure of the tumor of origin. We observed an increase of the virus-killing efficacy after ten passages in the tumorspheres. Deep sequencing analyses showed genomic changes in two SVV populations comprising 150 single nucleotides variants and 72 amino acid substitutions. Major differences observed in the tumorsphere-passaged virus population, compared to the cell monolayer, were identified in the conserved structural protein VP2 and in the highly variable P2 region, suggesting that the increase in the ability of the SVV to kill cells over time in the tumorspheres is acquired by capsid conservation and positively selecting mutations to counter the host innate immune responses.
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Affiliation(s)
- Shakeel Waqqar
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Kai Lee
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Timothy Bilton
- Invermay Agricultural Centre, AgResearch, Mosgiel 9092, New Zealand
| | | | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
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8
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Pankhurst TE, Buick KH, Lange JL, Marshall AJ, Button KR, Palmer OR, Farrand KJ, Montgomerie I, Bird TW, Mason NC, Kuang J, Compton BJ, Comoletti D, Salio M, Cerundolo V, Quiñones-Mateu ME, Painter GF, Hermans IF, Connor LM. MAIT cells activate dendritic cells to promote T FH cell differentiation and induce humoral immunity. Cell Rep 2023; 42:112310. [PMID: 36989114 PMCID: PMC10045373 DOI: 10.1016/j.celrep.2023.112310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Protective immune responses against respiratory pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus, are initiated by the mucosal immune system. However, most licensed vaccines are administered parenterally and are largely ineffective at inducing mucosal immunity. The development of safe and effective mucosal vaccines has been hampered by the lack of a suitable mucosal adjuvant. In this study we explore a class of adjuvant that harnesses mucosal-associated invariant T (MAIT) cells. We show evidence that intranasal immunization of MAIT cell agonists co-administered with protein, including the spike receptor binding domain from SARS-CoV-2 virus and hemagglutinin from influenza virus, induce protective humoral immunity and immunoglobulin A production. MAIT cell adjuvant activity is mediated by CD40L-dependent activation of dendritic cells and subsequent priming of T follicular helper cells. In summary, we show that MAIT cells are promising vaccine targets that can be utilized as cellular adjuvants in mucosal vaccines.
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Affiliation(s)
- Theresa E Pankhurst
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kaitlin H Buick
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Joshua L Lange
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Andrew J Marshall
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Kaileen R Button
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Olga R Palmer
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kathryn J Farrand
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Isabelle Montgomerie
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Thomas W Bird
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Ngarangi C Mason
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Joanna Kuang
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Benjamin J Compton
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Mariolina Salio
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Gavin F Painter
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Lisa M Connor
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand.
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9
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Montgomerie I, Bird TW, Palmer OR, Mason NC, Pankhurst TE, Lawley B, Hernández LC, Harfoot R, Authier-Hall A, Anderson DE, Hilligan KL, Buick KH, Mbenza NM, Mittelstädt G, Maxwell S, Sinha S, Kuang J, Subbarao K, Parker EJ, Sher A, Hermans IF, Ussher JE, Quiñones-Mateu ME, Comoletti D, Connor LM. Incorporation of SARS-CoV-2 spike NTD to RBD protein vaccine improves immunity against viral variants. iScience 2023; 26:106256. [PMID: 36845030 PMCID: PMC9940465 DOI: 10.1016/j.isci.2023.106256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Emerging SARS-CoV-2 variants pose a threat to human health worldwide. SARS-CoV-2 receptor binding domain (RBD)-based vaccines are suitable candidates for booster vaccines, eliciting a focused antibody response enriched for virus neutralizing activity. Although RBD proteins are manufactured easily, and have excellent stability and safety properties, they are poorly immunogenic compared to the full-length spike protein. We have overcome this limitation by engineering a subunit vaccine composed of an RBD tandem dimer fused to the N-terminal domain (NTD) of the spike protein. We found that inclusion of the NTD (1) improved the magnitude and breadth of the T cell and anti-RBD response, and (2) enhanced T follicular helper cell and memory B cell generation, antibody potency, and cross-reactive neutralization activity against multiple SARS-CoV-2 variants, including B.1.1.529 (Omicron BA.1). In summary, our uniquely engineered RBD-NTD-subunit protein vaccine provides a promising booster vaccination strategy capable of protecting against known SARS-CoV-2 variants of concern.
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Affiliation(s)
- Isabelle Montgomerie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Thomas W Bird
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Olga R Palmer
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | | | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Leonor C Hernández
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Danielle E Anderson
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerry L Hilligan
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Laboratory of Parasitic Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin H Buick
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Naasson M Mbenza
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Samara Maxwell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Joanna Kuang
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Emily J Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Alan Sher
- Laboratory of Parasitic Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand
| | - Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Lisa M Connor
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
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10
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Zaccarelli M, Musiime V, Quiñones-Mateu ME. Monitoring antiretroviral therapy in low and middle-income countries: current status and future considerations. AIDS 2022; 36:2071-2073. [PMID: 36305186 DOI: 10.1097/qad.0000000000003381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Mauro Zaccarelli
- HIV/Infectious Diseases Unit, "Villa Maraini" Foundation, Rome/Infectious Diseases Unit, "San Camillo de Lellis" Hospital, Rieti, Italy
| | - Victor Musiime
- Department of Paediatrics and Child Health, School of Medicine, College of Health Sciences, Makerere University/Research Department, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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11
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Saha T, Quiñones-Mateu ME, Das SC. Inhaled therapy for COVID-19: Considerations of drugs, formulations and devices. Int J Pharm 2022; 624:122042. [PMID: 35868481 PMCID: PMC9296254 DOI: 10.1016/j.ijpharm.2022.122042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/04/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for the COVID-19 pandemic, has outspread at full tilt across the world. Although several effective vaccines continue to be deployed, reliable antiviral treatments have yet to be developed against this disease. Currently, available therapeutics for COVID-19 include repurposed, and a few novel drugs. Many drugs have been promising in preclinical studies, but a majority of these drugs have shown little or no efficacy in clinical studies. One of the major reasons is the insufficient drug concentration in the lung, the primary target site of infection for SARS-CoV-2, from the administration of drugs through oral or intravenous routes. Higher effective doses administered through these routes could also lead to adverse side effects. For this reason, inhaled treatments are being tested as an efficient approach for COVID-19, allowing lower doses of drugs ensuring higher concentrations of the drug(s) in the lung. The inhaled treatment combining two or more antiviral drugs will increase potency and reduce the possibility of selecting for SARS-CoV-2 variants with reduced drug susceptibility. Finally, the appropriate drug combination needs to be delivered using a suitable system. Here, we review the current treatment for COVID-19 and their limitations, discussing the advantages of mono and combinational inhaled therapy with a brief outline of the recently reformulated anti-SARS-CoV-2 agents as inhaled formulations. The selection of appropriate delivery devices for inhalation and associated key considerations including the formulation challenges are also discussed.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand
| | - Shyamal C Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
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12
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Stanton JAL, O'Brien R, Hall RJ, Chernyavtseva A, Ha HJ, Jelley L, Mace PD, Klenov A, Treece JM, Fraser JD, Clow F, Clarke L, Su Y, Kurup HM, Filichev VV, Rolleston W, Law L, Rendle PM, Harris LD, Wood JM, Scully TW, Ussher JE, Grant J, Hore TA, Moser TV, Harfoot R, Lawley B, Quiñones-Mateu ME, Collins P, Blaikie R. Uncoupling Molecular Testing for SARS-CoV-2 From International Supply Chains. Front Public Health 2022; 9:808751. [PMID: 35141190 PMCID: PMC8818800 DOI: 10.3389/fpubh.2021.808751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022] Open
Abstract
The rapid global rise of COVID-19 from late 2019 caught major manufacturers of RT-qPCR reagents by surprise and threw into sharp focus the heavy reliance of molecular diagnostic providers on a handful of reagent suppliers. In addition, lockdown and transport bans, necessarily imposed to contain disease spread, put pressure on global supply lines with freight volumes severely restricted. These issues were acutely felt in New Zealand, an island nation located at the end of most supply lines. This led New Zealand scientists to pose the hypothetical question: in a doomsday scenario where access to COVID-19 RT-qPCR reagents became unavailable, would New Zealand possess the expertise and infrastructure to make its own reagents onshore? In this work we describe a review of New Zealand's COVID-19 test requirements, bring together local experts and resources to make all reagents for the RT-qPCR process, and create a COVID-19 diagnostic assay referred to as HomeBrew (HB) RT-qPCR from onshore synthesized components. This one-step RT-qPCR assay was evaluated using clinical samples and shown to be comparable to a commercial COVID-19 assay. Through this work we show New Zealand has both the expertise and, with sufficient lead time and forward planning, infrastructure capacity to meet reagent supply challenges if they were ever to emerge.
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Affiliation(s)
- Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- *Correspondence: Jo-Ann L. Stanton
| | - Rory O'Brien
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- MicroGEM NZ Ltd., Dunedin, New Zealand
| | - Richard J. Hall
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Anastasia Chernyavtseva
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Hye Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Lauren Jelley
- Clinical Virology, Institute of Environmental Science and Research Limited (ESR), Upper Hutt, New Zealand
| | - Peter D. Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alexander Klenov
- Hudak Lab, Department of Biology, York University, Toronto, ON, Canada
| | - Jackson M. Treece
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - John D. Fraser
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Fiona Clow
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Lewis Clarke
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Yongdong Su
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | | | | | - Lee Law
- South Pacific Sera, Timaru, New Zealand
| | - Phillip M. Rendle
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Lawrence D. Harris
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - James M. Wood
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Thomas W. Scully
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Molecular Pathology, Southern Community Laboratories, Dunedin, New Zealand
| | - Jenny Grant
- Molecular Pathology, Southern Community Laboratories, Dunedin, New Zealand
| | - Timothy A. Hore
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tim V. Moser
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Richard Blaikie
- Research and Enterprise, University of Otago, Dunedin, New Zealand
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13
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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14
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Harfoot R, Yung DBY, Anderson WA, Wild CEK, Coetzee N, Hernández LC, Lawley B, Pletzer D, Derraik JGB, Anderson YC, Quiñones-Mateu ME. Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators. Pathogens 2022; 11:83. [PMID: 35056031 PMCID: PMC8780977 DOI: 10.3390/pathogens11010083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
The arrival of SARS-CoV-2 to Aotearoa/New Zealand in February 2020 triggered a massive response at multiple levels. Procurement and sustainability of medical supplies to hospitals and clinics during the then upcoming COVID-19 pandemic was one of the top priorities. Continuing access to new personal protective equipment (PPE) was not guaranteed; thus, disinfecting and reusing PPE was considered as a potential alternative. Here, we describe part of a local program intended to test and implement a system to disinfect PPE for potential reuse in New Zealand. We used filtering facepiece respirator (FFR) coupons inoculated with SARS-CoV-2 or clinically relevant multidrug-resistant pathogens (Acinetobacter baumannii Ab5075, methicillin-resistant Staphylococcus aureus USA300 LAC and cystic-fibrosis isolate Pseudomonas aeruginosa LESB58), to evaluate the potential use of ultraviolet-C germicidal irradiation (UV-C) or dry heat treatment to disinfect PPE. An applied UV-C dose of 1000 mJ/cm2 was sufficient to completely inactivate high doses of SARS-CoV-2; however, irregularities in the FFR coupons hindered the efficacy of UV-C to fully inactivate the virus, even at higher UV-C doses (2000 mJ/cm2). Conversely, incubating contaminated FFR coupons at 65 °C for 30 min or 70 °C for 15 min, was sufficient to block SARS-CoV-2 replication, even in the presence of mucin or a soil load (mimicking salivary or respiratory secretions, respectively). Dry heat (90 min at 75 °C to 80 °C) effectively killed 106 planktonic bacteria; however, even extending the incubation time up to two hours at 80 °C did not completely kill bacteria when grown in colony biofilms. Importantly, we also showed that FFR material can harbor replication-competent SARS-CoV-2 for up to 35 days at room temperature in the presence of a soil load. We are currently using these findings to optimize and establish a robust process for decontaminating, reusing, and reducing wastage of PPE in New Zealand.
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Affiliation(s)
- Rhodri Harfoot
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
| | - Deborah B. Y. Yung
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
| | - William A. Anderson
- Department of Chemical Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Cervantée E. K. Wild
- Department of Paediatrics, Child and Youth Health, University of Auckland, Auckland 1010, New Zealand; (C.E.K.W.); (N.C.); (J.G.B.D.)
| | - Nicolene Coetzee
- Department of Paediatrics, Child and Youth Health, University of Auckland, Auckland 1010, New Zealand; (C.E.K.W.); (N.C.); (J.G.B.D.)
| | - Leonor C. Hernández
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
| | - Blair Lawley
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
| | - Daniel Pletzer
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
| | - José G. B. Derraik
- Department of Paediatrics, Child and Youth Health, University of Auckland, Auckland 1010, New Zealand; (C.E.K.W.); (N.C.); (J.G.B.D.)
| | - Yvonne C. Anderson
- Department of Paediatrics, Child and Youth Health, University of Auckland, Auckland 1010, New Zealand; (C.E.K.W.); (N.C.); (J.G.B.D.)
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (R.H.); (D.B.Y.Y.); (L.C.H.); (B.L.); (D.P.)
- Webster Centre for Infectious Diseases, University of Otago, Dunedin 9016, New Zealand
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15
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Cruz-Lebrón A, Johnson R, Mazahery C, Troyer Z, Joussef-Piña S, Quiñones-Mateu ME, Strauch CM, Hazen SL, Levine AD. Chronic opioid use modulates human enteric microbiota and intestinal barrier integrity. Gut Microbes 2021; 13:1946368. [PMID: 34313547 PMCID: PMC8317955 DOI: 10.1080/19490976.2021.1946368] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the past three decades the United States has experienced a devastating opioid epidemic. One of the many debilitating side effects of chronic opioid use is opioid-induced bowel dysfunction. We investigated the impact of methadone maintenance treatment (MMT) on the gut microbiome, the gut bacterial metabolite profile, and intestinal barrier integrity. An imbalance in key bacterial communities required for production of short-chain fatty acids (SCFAs), mucus degradation, and maintenance of barrier integrity was identified. Consistent with dysbiosis, levels of fecal SCFAs were reduced in MMT. We demonstrated that metabolites synthesized by Akkermansia muciniphila modulate intestinal barrier integrity in vitro by strengthening the pore pathway and regulating tight junction protein expression. This study provides essential information about the therapeutic potential of A. muciniphila and warrants development of new clinical strategies that aim to normalize the gut microbiome in individuals affected by chronic opioid use.
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Affiliation(s)
- Angélica Cruz-Lebrón
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Ramona Johnson
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Claire Mazahery
- Department of Pathology, Case Western Reserve University, Cleveland, USA
| | - Zach Troyer
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | | | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Christopher M Strauch
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland, USA
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland, USA
| | - Alan D. Levine
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA,Department of Pathology, Case Western Reserve University, Cleveland, USA,Departments of Pharmacology, Medicine, and Pediatrics, Case Western Reserve University, Cleveland, USA,CONTACT Alan D. Levine Case Western Reserve University School of Medicine (Wood W217C), 10900 Euclid Avenue, Cleveland, Ohio44106-4960
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16
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Ndashimye E, Li Y, Reyes PS, Avino M, Olabode AS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Barr SD, Arts EJ. High-level resistance to bictegravir and cabotegravir in subtype A- and D-infected HIV-1 patients failing raltegravir with multiple resistance mutations. J Antimicrob Chemother 2021; 76:2965-2974. [PMID: 34453542 DOI: 10.1093/jac/dkab276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/02/2021] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES The second-generation integrase strand transfer inhibitor (INSTI) bictegravir is becoming accessible in low- and middle-income countries (LMICs), and another INSTI, cabotegravir, has recently been approved as a long-acting injectable. Data on bictegravir and cabotegravir susceptibility in raltegravir-experienced HIV-1 subtype A- and D-infected patients carrying drug resistance mutations (DRMs) remain very scarce in LMICs. PATIENTS AND METHODS HIV-1 integrase (IN)-recombinant viruses from eight patients failing raltegravir-based third-line therapy in Uganda were genotypically and phenotypically tested for susceptibility to bictegravir and cabotegravir. Ability of these viruses to integrate into human genomes was assessed in MT-4 cells. RESULTS HIV-1 IN-recombinant viruses harbouring single primary mutations (N155H or Y143R/S) or in combination with secondary INSTI mutations (T97A, M50I, L74IM, E157Q, G163R or V151I) were susceptible to both bictegravir and cabotegravir. However, combinations of primary INSTI-resistance mutations such as E138A/G140A/G163R/Q148R or E138K/G140A/S147G/Q148K led to decreased susceptibility to both cabotegravir (fold change in EC50 values from 429 to 1000×) and bictegravir (60 to 100×), exhibiting a high degree of cross-resistance. However, these same IN-recombinant viruses showed impaired integration capacity (14% to 48%) relative to the WT HIV-1 NL4-3 strain in the absence of drug. CONCLUSIONS Though not currently widely accessible in most LMICs, bictegravir and cabotegravir offer a valid alternative to HIV-infected individuals harbouring subtype A and D HIV-1 variants with reduced susceptibility to first-generation INSTIs but previous exposure to raltegravir may reduce efficacy, more so with cabotegravir.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | | | - Fred Kyeyune
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Stephen D Barr
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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17
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Ndashimye E, Avino M, Olabode AS, Poon AFY, Gibson RM, Li Y, Meadows A, Tan C, Reyes PS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Arts EJ. Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. J Antimicrob Chemother 2021; 75:3525-3533. [PMID: 32853364 DOI: 10.1093/jac/dkaa355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/03/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Increasing first-line treatment failures in low- and middle-income countries (LMICs) have led to increased use of integrase strand transfer inhibitors (INSTIs) such as dolutegravir. However, HIV-1 susceptibility to INSTIs in LMICs, especially with previous raltegravir exposure, is poorly understood due to infrequent reporting of INSTI failures and testing for INSTI drug resistance mutations (DRMs). METHODS A total of 51 non-subtype B HIV-1 infected patients failing third-line (raltegravir-based) therapy in Uganda were initially selected for the study. DRMs were detected using Sanger and deep sequencing. HIV integrase genes of 13 patients were cloned and replication capacities (RCs) and phenotypic susceptibilities to dolutegravir, raltegravir and elvitegravir were determined with TZM-bl cells. Spearman's correlation coefficient was used to determine cross-resistance between INSTIs. RESULTS INSTI DRMs were detected in 47% of patients. HIV integrase-recombinant virus carrying one primary INSTI DRM (N155H or Y143R/S) was susceptible to dolutegravir but highly resistant to raltegravir and elvitegravir (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to raltegravir, elvitegravir and even dolutegravir. The former multi-DRM virus had WT RC whereas the latter had lower RCs than WT. CONCLUSIONS In HIV-1 subtype A- and D-infected patients failing raltegravir and harbouring INSTI DRMs, there is high-level resistance to elvitegravir and raltegravir. More routine monitoring of INSTI treatment may be advised in LMICs, considering that multiple INSTI DRMs may have accumulated during prolonged exposure to raltegravir during virological failure, leading to high-level INSTI resistance, including dolutegravir resistance.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Canada.,Department of Applied Mathematics, Western University, London, Canada
| | - Richard M Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Adam Meadows
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Christine Tan
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | | | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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18
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Ameratunga R, Woon ST, Steele R, Snell R, Medlicott N, Mears E, Leung E, Lehnert K, Jordan A, Das S, Abbott W, Longhurst H, Quiñones-Mateu ME. Perspective: the nose and the stomach play a critical role in the NZACE2-Pātari* (modified ACE2) drug treatment project of SARS-CoV-2 infection. Expert Rev Clin Immunol 2021; 17:553-560. [PMID: 33792473 PMCID: PMC8127172 DOI: 10.1080/1744666x.2021.1912596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: COVID-19 has caused calamitous health, economic and societal consequences globally. Currently, there is no effective treatment for the infection. Areas covered: We have recently described the NZACE2-Pātari project, which seeks to administer modified Angiotensin Converting Enzyme 2 (ACE2) molecules early in the infection to intercept and block SARS-CoV-2 binding to the pulmonary epithelium. Expert opinion: Since the nasopharyngeal mucosa is infected in the first asymptomatic phase of the infection, treatment of the nose is likely to be safe and potentially effective. The intercepted virus will be swallowed and destroyed in the stomach. There is however a limited window of opportunity to alter the trajectory of the infection in an individual patient, which requires access to rapid testing for SARS-CoV-2. The proposed strategy is analogous to passive immunization of viral infections such as measles and may be of particular benefit to immunodeficient and unvaccinated individuals.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical Immunology, Auckland Hospital, Auckland New Zealand.,Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand.,Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Russell Snell
- Centre for Brain Research, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand
| | | | - Emily Mears
- Centre for Brain Research, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- Centre for Brain Research, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand
| | - Anthony Jordan
- Department of Clinical Immunology, Auckland Hospital, Auckland New Zealand
| | - Shyamal Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - William Abbott
- Department of Surgery, Auckland Hospital, Auckland, New Zealand
| | - Hilary Longhurst
- Department of Clinical Immunology, Auckland Hospital, Auckland New Zealand
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19
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Datir R, Kemp S, El Bouzidi K, Mlchocova P, Goldstein R, Breuer J, Towers GJ, Jolly C, Quiñones-Mateu ME, Dakum PS, Ndembi N, Gupta RK. In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix. mBio 2020; 11:e02036-20. [PMID: 33144375 PMCID: PMC7642677 DOI: 10.1128/mbio.02036-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic changes in viruses from six Nigerian patients who failed PI-based regimens without known drug resistance-associated protease mutations in order to identify novel determinants of PI resistance. Target enrichment and next-generation sequencing (NGS) with the Illumina MiSeq system were followed by haplotype reconstruction. Full-length Gag-protease gene regions were amplified from baseline (pre-PI) and virologic failure (VF) samples, sequenced, and used to construct gag-pro-pseudotyped viruses. Phylogenetic analysis was performed using maximum-likelihood methods. Susceptibility to lopinavir (LPV) and darunavir (DRV) was measured using a single-cycle replication assay. Western blotting was used to analyze Gag cleavage. In one of six participants (subtype CRF02_AG), we found 4-fold-lower LPV susceptibility in viral clones during failure of second-line treatment. A combination of four mutations (S126del, H127del, T122A, and G123E) in the p17 matrix of baseline virus generated a similar 4-fold decrease in susceptibility to LPV but not darunavir. These four amino acid changes were also able to confer LPV resistance to a subtype B Gag-protease backbone. Western blotting demonstrated significant Gag cleavage differences between sensitive and resistant isolates in the presence of drug. Resistant viruses had around 2-fold-lower infectivity than sensitive clones in the absence of drug. NGS combined with haplotype reconstruction revealed that resistant, less fit clones emerged from a minority population at baseline and thereafter persisted alongside sensitive fitter viruses. We used a multipronged genotypic and phenotypic approach to document emergence and temporal dynamics of a novel protease inhibitor resistance signature in HIV-1 matrix, revealing the interplay between Gag-associated resistance and fitness.
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Affiliation(s)
| | - Steven Kemp
- University College London, London, United Kingdom
| | | | - Petra Mlchocova
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Judy Breuer
- University College London, London, United Kingdom
| | | | - Clare Jolly
- University College London, London, United Kingdom
| | | | - Patrick S Dakum
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nicaise Ndembi
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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20
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Ndembi N, Murtala-Ibrahim F, Tola M, Jumare J, Aliyu A, Alabi P, Mensah C, Abimiku A, Quiñones-Mateu ME, Crowell TA, Rhee SY, Shafer RW, Gupta R, Blattner W, Charurat ME, Dakum P. Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria. AIDS Res Ther 2020; 17:64. [PMID: 33143751 PMCID: PMC7640637 DOI: 10.1186/s12981-020-00317-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/10/2020] [Indexed: 01/09/2023] Open
Abstract
Background A substantial number of persons living with HIV (PLWH) in Nigeria do not experience durable viral suppression on first-line antiretroviral therapy (ART). Understanding risk factors for first-line treatment failure informs patient monitoring practices and distribution of limited resources for second-line regimens. We determined predictors of immunologic and virologic failures in a large ART delivery program in Abuja, Nigeria. Methods A retrospective cohort study was conducted at the University of Abuja Teaching Hospital, a tertiary health care facility, using data from February 2005 to December 2014 in Abuja, Nigeria. All PLWH aged ≥ 15 years who initiated ART with at least 6-month follow-up and one CD4 measurement were included. Immunologic failure was defined as a CD4 decrease to or below pre-ART level or persistent CD4 < 100 cells per mm3 after 6 months on ART. Virologic failure (VF) was defined as two consecutive HIV-1 RNA levels > 1000 copies/mL after at least 6 months of ART and enhanced adherence counselling. HIV drug resistance (Sanger sequences) was analyzed using the Stanford HIV database algorithm and scored for resistance to common nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Univariate and multivariate log binomial regression models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs). Results Of 12,452 patients followed, a total of 5928 initiated ART with at least 6 months of follow-up and one CD4 measurement. The entry point for 3924 (66.2%) was through the program’s own voluntary counseling and testing (VCT) center, while 1310 (22.1%) were referred from an outside clinic/program, 332 (5.6%) in-patients, and 373 (6.3%) through other entry points including prevention of mother to child transmission (PMTCT) and transferred from other programs. The mean CD4 at enrollment in care was 268 ± 23.7 cells per mm3, and the mean HIV-1 RNA was 3.3 ± 1.3.log10 copies/mL. A total of 3468 (80.5%) received nevirapine (NVP) and 2260 (19.5%) received efavirenz (EFV)—based regimens. A total of 2140 (36.1%) received tenofovir (TDF); 2662 (44.9%) zidovudine (AZT); and 1126 (19.0%) stavudine (d4T). Among those receiving TDF, 45.0% also received emtricitabine (FTC). In a multivariate model, immunologic failure was more common among PLWH with female gender as compared to male [RR (95% CI) 1.22 (1.07–1.40)] and less common among those who entered care at the program’s VCT center as compared to other entry points [0.79 (0.64–0.91)], WHO stage 3/4 as compared to 1/2 [0.19 (0.16–0.22)], or CD4 200 + cells per mm3 as compared to lower [0.19 (0.16–0.22)]. Virologic failure was more common among PLWH who entered care at the program’s VCT center as compared to other entry points [RR (95% CI) 1.45 (1.11–1.91) and those with CD4 < 200 cells per mm3 at entry into care as compared to higher [1.71 (1.36–2.16)]. Of 198 patient-derived samples sequenced during virologic failure, 42 (21%) were wild-type; 145 (73%) carried NNRTI drug resistance mutations; 151 (76.3%) M184I/V; 29 (14.6%) had ≥ 3 TAMs, and 37 (18.7%) had K65R, of whom all were on TDF-containing first-line regimens. Conclusions In this cohort of Nigerian PLWH followed for a period of 9 years, immunologic criteria poorly predicted virologic failure. Furthermore, a subset of samples showed that patients failing ART for extended periods of time had HIV-1 strains harboring drug resistance mutations.
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21
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Bonar MM, Tabler CO, Haqqani AA, Lapointe LE, Galiatsos JA, Joussef-Piña S, Quiñones-Mateu ME, Tilton JC. Nanoscale flow cytometry reveals interpatient variability in HIV protease activity that correlates with viral infectivity and identifies drug-resistant viruses. Sci Rep 2020; 10:18101. [PMID: 33093566 PMCID: PMC7583244 DOI: 10.1038/s41598-020-75118-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022] Open
Abstract
HIV encodes an aspartyl protease that is activated during, or shortly after, budding of viral particles from the surface of infected cells. Protease-mediated cleavage of viral polyproteins is essential to generating infectious viruses, a process known as ‘maturation’ that is the target of FDA-approved antiretroviral drugs. Most assays to monitor protease activity rely on bulk analysis of millions of viruses and obscure potential heterogeneity of protease activation within individual particles. In this study we used nanoscale flow cytometry in conjunction with an engineered FRET reporter called VIral ProteasE Reporter (VIPER) to investigate heterogeneity of protease activation in individual, patient-derived viruses. We demonstrate previously unappreciated interpatient variation in HIV protease processing efficiency that impacts viral infectivity. Additionally, monitoring of protease activity in individual virions distinguishes between drug sensitivity or resistance to protease inhibitors in patient-derived samples. These findings demonstrate the feasibility of monitoring enzymatic processes using nanoscale flow cytometry and highlight the potential of this technology for translational clinical discovery, not only for viruses but also other submicron particles including exosomes, microvesicles, and bacteria.
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Affiliation(s)
- Michał M Bonar
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Caroline O Tabler
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Aiman A Haqqani
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lauren E Lapointe
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jake A Galiatsos
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Samira Joussef-Piña
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - John C Tilton
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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22
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Cruz-Lebrón A, D’argenio Garcia L, Talla A, Joussef-Piña S, Quiñones-Mateu ME, Sékaly RP, de Carvalho KIL, Levine AD. Decreased Enteric Bacterial Composition and Diversity in South American Crohn's Disease Vary With the Choice of Treatment Strategy and Time Since Diagnosis. J Crohns Colitis 2020; 14:791-800. [PMID: 31758685 PMCID: PMC7346893 DOI: 10.1093/ecco-jcc/jjz189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The symptomology of Crohn's disease [CD], a chronic inflammatory disease of the digestive tract, correlates poorly with clinical, endoscopic or immunological assessments of disease severity. The prevalence of CD in South America is rising, reflecting changes in socio-economic stability. Many treatment options are available to CD patients, including biological agents and corticosteroids, each of which offers variable efficacy attributed to host genetics and environmental factors associated with alterations in the gut microbiota. METHODS Based on 16S rRNA gene sequencing and taxonomic differences, we compared the faecal microbial population of Brazilian patients with CD treated with corticosteroid or anti-tumour necrosis factor [anti-TNF] immunotherapy. Faecal calprotectin and plasma sCD14 levels were quantified as markers for local and systemic inflammation, respectively. RESULTS Anti-TNF treatment led to an increased relative abundance of Proteobacteria and a decreased level of Bacteroidetes. In contrast, corticoid treatment was associated with an increase in the relative abundance of Actinobacteria, which has been linked to inflammation in CD. Disruption of the faecal microbiota was related to decreased bacterial diversity and composition. Moreover, the choice of clinical regimen and time since diagnosis modulate the character of the resulting dysbiosis. CONCLUSIONS Enteric microbial populations in CD patients who have been treated are modulated by disease pathogenesis, local inflammatory microenvironment and treatment strategy. The dysbiosis that remains after anti-TNF treatment due to decreased bacterial diversity and composition abates restoration of the microbiota to a healthy state, suggesting that the identification and development of new clinical treatments for CD must include their capacity to normalize the gut microbiota.
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Affiliation(s)
- Angélica Cruz-Lebrón
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Aarthi Talla
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Samira Joussef-Piña
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | | | | | | | - Alan D Levine
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Departments of Pharmacology, Medicine, and Pediatrics, Case Western Reserve University, Cleveland, OH, USA
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23
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Ussher JE, Le Gros G, Quiñones-Mateu ME, Gulab SA, Yiannoutsos M. The case for New Zealand to have its own COVID-19 vaccine programme. N Z Med J 2020; 133:112-115. [PMID: 32325476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin
| | | | | | - Shivali A Gulab
- Ferrier Research Institute and Wellington UniVentures, Victoria University of Wellington, Wellington
| | - Melissa Yiannoutsos
- Ferrier Research Institute and Wellington UniVentures, Victoria University of Wellington, Wellington
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24
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Taiwo BO, Quiñones-Mateu ME, Smith K, Zheng L, Gulick R, Nyaku AN, Sax PE, Ha B, Kumwenda J, Olefsky M, Godfrey C, Wallis C. Prior Case of Resistance on Dolutegravir Plus Lamivudine Dual Therapy. AIDS Res Hum Retroviruses 2020; 36:254-255. [PMID: 31914799 DOI: 10.1089/aid.2019.0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Babafemi O. Taiwo
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | - Lu Zheng
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Roy Gulick
- Division of Infectious Diseases, Weill Cornell Medical College, New York, New York
| | - Amesika N. Nyaku
- Division of Infectious Diseases, Rutgers University, Newark, New Jersey
| | - Paul E. Sax
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Belinda Ha
- ViiV Healthcare, Research Triangle Park, North Carolina
| | | | - Maxine Olefsky
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Catherine Godfrey
- Division of AIDS, National Institutes of Allergy and Infectious Diseases, Bethesda, Maryland
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25
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Poon AFY, Ndashimye E, Avino M, Gibson R, Kityo C, Kyeyune F, Nankya I, Quiñones-Mateu ME, ARTS EJ. First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda. AIDS Res Ther 2019; 16:3. [PMID: 30670037 PMCID: PMC6343277 DOI: 10.1186/s12981-019-0218-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Background Our understanding of HIV-1 and antiretroviral treatment (ART) is strongly biased towards subtype B, the predominant subtype in North America and western Europe. Efforts to characterize the response to first-line treatments in other HIV-1 subtypes have been hindered by the availability of large study cohorts in resource-limited settings. To maximize our statistical power, we combined HIV-1 sequence and clinical data from every available study population associated with the Joint Clinical Research Centre (JCRC) in Uganda. These records were combined with contemporaneous ART-naive records from Uganda in the Stanford HIVdb database. Methods Treatment failures were defined by the presence of HIV genotype records with sample collection dates after the ART start dates in the JCRC database. Drug resistances were predicted by the Stanford HIVdb algorithm, and HIV subtype classification and recombination detection was performed with SCUEAL. We used Bayesian network analysis to evaluate associations between drug exposures and subtypes, and binomial regression for associations with recombination. Results This is the largest database of first-line treatment failures (\documentclass[12pt]{minimal}
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\begin{document}$$n=1724$$\end{document}n=1724) in Uganda to date, with a predicted statistical power of 80% to detect subtype associations at an odds ratio of \documentclass[12pt]{minimal}
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\begin{document}$$\ge 1.2$$\end{document}≥1.2. In the subset where drug regimen data were available, we observed that use of 3TC was associated with a higher rate of first line treatment failure, whereas regimens containing AZT and TDF were associated with reduced rates of failure. In the complete database, we found limited evidence of associations between HIV-1 subtypes and treatment failure, with the exception of a significantly lower frequency of failures among A/D recombinants that comprised about 7% of the population. First-line treatment failure was significantly associated with reduced numbers of recombination breakpoints across subtypes. Conclusions Expanding access to first-line ART should confer the anticipated public health benefits in Uganda, despite known differences in the pathogenesis of HIV-1 subtypes. Furthermore, the impact of ART may actually be enhanced by frequent inter-subtype recombination in this region. Electronic supplementary material The online version of this article (10.1186/s12981-019-0218-2) contains supplementary material, which is available to authorized users.
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26
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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27
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Orrú CD, Yuan J, Appleby BS, Li B, Li Y, Winner D, Wang Z, Zhan YA, Rodgers M, Rarick J, Wyza RE, Joshi T, Wang GX, Cohen ML, Zhang S, Groveman BR, Petersen RB, Ironside JW, Quiñones-Mateu ME, Safar JG, Kong Q, Caughey B, Zou WQ. Prion seeding activity and infectivity in skin samples from patients with sporadic Creutzfeldt-Jakob disease. Sci Transl Med 2018; 9:9/417/eaam7785. [PMID: 29167394 DOI: 10.1126/scitranslmed.aam7785] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/04/2017] [Accepted: 08/18/2017] [Indexed: 11/02/2022]
Abstract
Sporadic Creutzfeldt-Jakob disease (sCJD), the most common human prion disease, is transmissible through iatrogenic routes due to abundant infectious prions [misfolded forms of the prion protein (PrPSc)] in the central nervous system (CNS). Some epidemiological studies have associated sCJD risk with non-CNS surgeries. We explored the potential prion seeding activity and infectivity of skin from sCJD patients. Autopsy or biopsy skin samples from 38 patients [21 sCJD, 2 variant CJD (vCJD), and 15 non-CJD] were analyzed by Western blotting and real-time quaking-induced conversion (RT-QuIC) for PrPSc Skin samples from two patients were further examined for prion infectivity by bioassay using two lines of humanized transgenic mice. Western blotting revealed dermal PrPSc in one of five deceased sCJD patients and one of two vCJD patients. However, the more sensitive RT-QuIC assay detected prion seeding activity in skin from all 23 CJD decedents but not in skin from any non-CJD control individuals (with other neurological conditions or other diseases) during blinded testing. Although sCJD patient skin contained ~103- to 105-fold lower prion seeding activity than did sCJD patient brain tissue, all 12 mice from two transgenic mouse lines inoculated with sCJD skin homogenates from two sCJD patients succumbed to prion disease within 564 days after inoculation. Our study demonstrates that the skin of sCJD patients contains both prion seeding activity and infectivity, which raises concerns about the potential for iatrogenic sCJD transmission via skin.
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Affiliation(s)
- Christina D Orrú
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jue Yuan
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Brian S Appleby
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Neurology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Baiya Li
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Otolaryngology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi Province, People's Republic of China
| | - Yu Li
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Dane Winner
- University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Zerui Wang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Neurology, First Hospital of Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Yi-An Zhan
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Mark Rodgers
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jason Rarick
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Robert E Wyza
- Human Tissue Procurement Facility, Comprehensive Cancer Center Tissue Resources Core, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tripti Joshi
- Human Tissue Procurement Facility, Comprehensive Cancer Center Tissue Resources Core, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Gong-Xian Wang
- First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi Province, People's Republic of China
| | - Mark L Cohen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shulin Zhang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Bradley R Groveman
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Robert B Petersen
- Foundation Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI 48859, USA
| | - James W Ironside
- National CJD Research and Surveillance Unit, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Jiri G Safar
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Qingzhong Kong
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. .,Department of Neurology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Center for Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
| | - Wen-Quan Zou
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. .,Department of Neurology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi Province, People's Republic of China.,Department of Neurology, First Hospital of Jilin University, Changchun, Jilin Province, People's Republic of China.,National Center for Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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Ndashimye E, Avino M, Kyeyune F, Nankya I, Gibson RM, Nabulime E, Poon AF, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda. AIDS Res Hum Retroviruses 2018; 34:404-414. [PMID: 29353487 DOI: 10.1089/aid.2017.0205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To screen for drug resistance and possible treatment with Dolutegravir (DTG) in treatment-naive patients and those experiencing virologic failure during first-, second-, and third-line combined antiretroviral therapy (cART) in Uganda. Samples from 417 patients in Uganda were analyzed for predicted drug resistance upon failing a first- (N = 158), second- (N = 121), or third-line [all 51 involving Raltegravir (RAL)] treatment regimen. HIV-1 pol gene was amplified and sequenced from plasma samples. Drug susceptibility was interpreted using the Stanford HIV database algorithm and SCUEAL was used for HIV-1 subtyping. Frequency of resistance to nucleoside reverse transcriptase inhibitors (NRTIs) (95%) and non-NRTI (NNRTI, 96%) was high in first-line treatment failures. Despite lack of NNRTI-based treatment for years, NNRTI resistance remained stable in 55% of patients failing second-line or third-line treatment, and was also at 10% in treatment-naive Ugandans. DTG resistance (n = 366) was not observed in treatment-naive individuals or individuals failing first- and second-line cART, and only found in two patients failing third-line cART, while 47% of the latter had RAL- and Elvitegravir-resistant HIV-1. Secondary mutations associated with DTG resistance were found in 2%-10% of patients failing third-line cART. Of 14 drugs currently available for cART in Uganda, resistance was readily observed to all antiretroviral drugs (except for DTG) in Ugandan patients failing first-, second-, or even third-line treatment regimens. The high NNRTI resistance in first-line treatment in Uganda even among treatment-naive patients calls for the use of DTG to reach the UNAIDS 90:90:90 goals.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Richard M. Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F.Y. Poon
- Department of Microbiology and Immunology, Western University, London, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E. Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Eric J. Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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Abstract
Sierra Leone is a low-income West African country that has dealt with waves of economic, political, and public health challenges in its recent past, including a decade-long brutal civil war and the Ebola epidemic of 2014-2016. The HIV/AIDS epidemic, which has raged on in the country since 1987, has long been characterized as stable. The latest UNAIDS report estimates a countrywide HIV prevalence rate of 1.7% in 2016 among adults aged 15-49 years. However, there are indications that the epidemic may be in fact escalating and unless arrested urgently, has the potential to deteriorate into a major public health emergency. Although there are high levels of HIV awareness among adults (over 94%), uptake in voluntary HIV testing has remained low (<30%), and under one-third (29%) of the country's 60,000 people living with HIV/AIDS were on antiretroviral therapy in 2015. This review attempts to address the paucity of scientific information on the subject by presenting the historical and epidemiological background to the HIV/AIDS epidemic in Sierra Leone. Other aspects of the HIV/AIDS epidemic in Sierra Leone are examined, including routine HIV screening and diagnosis, linkage to and retention in HIV care, clinical characteristics and molecular epidemiology, treatment coverage, and prevention strategies. Finally, we identify four key areas of challenge that are hampering current efforts attempting to bring the epidemic under control, and perspective is offered on the way forward.
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Affiliation(s)
- George A Yendewa
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Eva Poveda
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur)-Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Spain
| | - Sahr A Yendewa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Foday Sahr
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- 34 Military Hospital, Republic of Sierra Leone Armed Forces, Freetown, Sierra Leone
| | - Miguel E Quiñones-Mateu
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathogenesis, Case Western Reserve University, Cleveland, Ohio, USA
- Center for AIDS Research at Case Western University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Robert A Salata
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
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Brenner BG, Ibanescu RI, Oliveira M, Roger M, Hardy I, Routy JP, Kyeyune F, Quiñones-Mateu ME, Wainberg MA. HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters. J Antimicrob Chemother 2018; 72:2171-2183. [PMID: 28472323 PMCID: PMC7263826 DOI: 10.1093/jac/dkx118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among
MSM in Quebec. While most HIV-1 strains (n = 2011) were
associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed
large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and
2015. Herein, tissue culture selections ascertained if large cluster lineages possessed
higher replicative fitness than singleton/small cluster isolates, allowing for viral
escape from integrase inhibitors. Methods: Primary HIV-1 isolates from large 20+ cluster
(n = 11) or singleton/small cluster
(n = 6) networks were passagedin
vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine
for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective
drug pressure. Results: Large cluster HIV-1 isolates selected for resistance to
dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small
clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K
(n = 7), S153Y
(n = 1) or H51Y
(n = 1) mutations as the dominant quasi-species within
8–12 weeks as compared with small cluster lineages where R263K
(n = 1/6), S153Y (1/6) or WT species (4/6) were
observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised
viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With
elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G,
N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations
leading to viral escape (>10 μM) by week 24. Conclusions: Further studies are needed to understand virological features of
large cluster viruses that may favour their transmissibility, replicative competence and
potential to escape selective antiretroviral drug pressure.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | | | - Fred Kyeyune
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Gibson RM, Nickel G, Crawford M, Kyeyune F, Venner C, Nankya I, Nabulime E, Ndashimye E, Poon AFY, Salata RA, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries. Infect Dis Poverty 2017; 6:163. [PMID: 29202874 PMCID: PMC5716384 DOI: 10.1186/s40249-017-0377-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
Background Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country. Methods We examined the drug resistance genotypes by Sanger sequencing of 262 HIV-infected patients failing a first line combined antiretroviral treatment containing either AZT or d4T, which represents approximately 5% of the patients at the Joint Clinical Research Center receiving a AZT or d4T containing treatment. Next generation sequencing (DEEPGEN™HIV) and multiplex oligonucleotide ligation assays (AfriPOLA) were then performed on a subset of patient samples to detect low frequency drug resistant mutations. CD4 cell counts, viral RNA loads, and treatment changes were analyzed in a cohort of treatment success and failures. Results Over 80% of patients failing first line AZT/d4T-containing cART had predicted drug resistance to 3TC (Lamivudine) and non-nucleoside RT inhibitors (NNRTIs) in the treatment regimen but only 45% had resistance AZT/d4T associated resistance mutations (TAMs). TAMs were however detected at low frequency within the patients HIV quasispecies (1–20%) in 21 of 34 individuals who were failing first-line AZT-containing cART and lacked TAMs by Sanger. Due to lack of TAMs by Sanger, AZT was typically maintained in second-line therapies and these patients had a low frequency of subsequent virologic success. Conclusions Our findings suggest that continued use of AZT and d4T in first-line treatment in low-to-middle income countries may lead to misdiagnosis of HIV-1 drug resistance and possibly enhance a succession of second- and third-line treatment failures. Electronic supplementary material The online version of this article (doi: 10.1186/s40249-017-0377-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard M Gibson
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Crawford
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Colin Venner
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Immaculate Nankya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.,Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Emmanuel Ndashimye
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Robert A Salata
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada. .,TREAT, Joint Clinical Research Centre, Kampala, Uganda.
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Weber J, Gibson RM, Sácká L, Strunin D, Hodek J, Weberová J, Pávová M, Alouani DJ, Asaad R, Rodriguez B, Lederman MM, Quiñones-Mateu ME. Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals. AIDS Res Ther 2017; 14:15. [PMID: 28331526 PMCID: PMC5359922 DOI: 10.1186/s12981-017-0144-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 01/15/2023] Open
Abstract
Background Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals—termed viremic non-progressors (VNP) or controllers—do not seem to progress to AIDS, maintaining high CD4+ T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers. Methods We analyzed HIV-1 isolates from three VNP individuals and compared the replicative fitness, near full-length HIV-1 genomes and intra-patient HIV-1 genetic diversity with viruses from three typical (TP) and one rapid (RP) progressor individuals. Results Viremic non-progressors and typical patients were infected for >10 years (range 10–17 years), with a mean CD4+ T-cell count of 472 cells/mm3 (442–529) and 400 cells/mm3 (126–789), respectively. VNP individuals had a less marked decline in CD4+ cells (mean −0.56, range −0.4 to −0.7 CD4+/month) than TP patients (mean −10.3, −8.2 to −13.1 CD4+/month). Interestingly, VNP individuals carried viruses with impaired replicative fitness, compared to HIV-1 isolates from the TP and RP patients (p < 0.05, 95% CI). Although analyses of the near full-length HIV-1 genomes showed no clear patterns of single-nucleotide polymorphisms (SNP) that could explain the decrease in replicative fitness, both the number of SNPs and HIV-1 population diversity correlated inversely with the replication capacity of the viruses (r = −0.956 and r = −0.878, p < 0.01, respectively). Conclusion It is likely that complex multifactorial parameters govern HIV-1 disease progression in each individual, starting with the infecting virus (phenotype, load, and quasispecies diversity) and the intrinsic ability of the host to respond to the infection. Here we analyzed a subset of viremic controller patients and demonstrated that similar to the phenomenon observed in patients with a discordant response to antiretroviral therapy (i.e., high CD4+ cell counts with detectable plasma HIV-1 RNA load), reduced viral replicative fitness seems to be linked to slow disease progression in these antiretroviral-naïve individuals. Electronic supplementary material The online version of this article (doi:10.1186/s12981-017-0144-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan Weber
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Richard M Gibson
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA
| | - Lenka Sácká
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Dmytro Strunin
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jan Hodek
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jitka Weberová
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Marcela Pávová
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - David J Alouani
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA
| | - Robert Asaad
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Benigno Rodriguez
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Michael M Lederman
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Miguel E Quiñones-Mateu
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA ; 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA ; 0000 0001 2164 3847grid.67105.35Department of Pathology, Case Western Reserve University, Cleveland, OH USA
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Aralaguppe SG, Winner D, Singh K, Sarafianos SG, Quiñones-Mateu ME, Sönnerborg A, Neogi U. Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa. J Med Virol 2016; 89:106-111. [PMID: 27328744 DOI: 10.1002/jmv.24610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND A lower virulence of HIV-1 subtype C (HIV-1C) is suggested to be related to the global dominance of HIV-1C. In this observational study, combining in vivo (clinical monitoring) and in vitro (genotypic, biochemical, and phenotypic assays), we explored whether HIV-1C from East Africa (HIV-1CEA ) is more pathogenic due to the evolution of a PYxE-insertion (CPYxEi ) in the gag-p6 that also could affect the therapy response. METHODS HIV-1B (n = 112) and HIV-1CEA (n = 128)-infected individuals residing in Sweden were analyzed with regard to Gag-p6 genotype and clinically monitored. Based on the Gag-p6 characteristics, three HIV-1CEA and one HIV-1 B patient-derived p2-INT-recombinant virus (gag-p2/NCp7/p1/p6/pol-PR/RT/IN) were constructed to analyze viral growth kinetics (VGKs) and drug sensitivity assays. Reverse transcriptase (RT) from the same samples was cloned into the heterodimer expression plasmid (pRT6H-PROT) to analyze catalytic efficiency of RT. RESULTS A higher viral failure rate and lower pre-therapy CD4+ T-cell counts were observed in HIV-1CEA -infected patients compared to HIV-1B-infected patients. In Gag-p6, PTAP-duplication was more common in HIV-1C. HIV-1CEA -infected patients with signature CPYxEi, evidenced very low pre-therapy CD4+ T-cell counts and suboptimal gain in CD4+ T-cells following therapy, as compared to the non-CPYxEi -strains indicating higher virulence. VGKs showed a statistically significant higher replication capacity (RC) for the CPYxEi viruses than the other two non-CPYxEi strains. No statistically significant difference was observed in the catalytic efficiency among HIV-1C RTs. CONCLUSIONS This is the first evidence of polymerase independent increased virulence and RC in HIV-1CEA following PYxE-insertion that is associated with suboptimal CD4+ T-cell gain following therapy initiation. J. Med. Virol. 89:106-111, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Dane Winner
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, Ohio
| | - Kamalendra Singh
- Department of Molecular Microbiology and Immunology, Christopher Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, Christopher Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | - Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.
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Rodríguez AK, Garzaro DJ, Loureiro CL, Gutiérrez CR, Ameli G, Jaspe RC, Porto L, Monsalve F, Pozada Á, Vázquez L, Quiñones-Mateu ME, Pujol FH, Rangel HR. HIV-1 and GBV-C co-infection in Venezuela. J Infect Dev Ctries 2014; 8:863-8. [PMID: 25022296 DOI: 10.3855/jidc.3830] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 10/25/2013] [Accepted: 11/22/2013] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Co-infection with GB virus C (GBV-C) in patients infected with human immunodeficiency virus 1 (HIV-1) has been associated with prolonged survival. The aim of this study was to evaluate the prevalence of GBV-C infection among HIV-1-infected patients in Venezuela, and to determine the effects of the co-infection on the levels of relevant cytokines. METHODOLOGY Plasma samples were collected from 270 HIV-1-seronegative and 255 HIV-1-seropositive individuals. GBV-C infection was determined by RT-PCR of the NS5 region and genotyped by sequence analysis of the 5´UTR region. HIV-1 strains were characterized by sequence analysis of pol, vif, env, and nef genes. Selected cytokines were evaluated by ELISA. RESULTS Ninety-seven of 525 (18.5%) plasma samples tested positive for GBV-C RNA. A significantly higher prevalence of GBV-C was found among HIV-1 patients compared to HIV-1-seronegative individuals (67/255, 26% versus 30/270, 11%; p < 0.001). Statistical difference was observed in the viral load between HIV-1+GBV-C+ and HIV-1+GBV-C- (p = 0.014), although no differences in CD4+ cell counts were found between both groups. TNFα concentration was higher in HIV-1+GBV-C- than in HIV-1+GBV-C+ patients (25.9 pg/mL versus 17.3 pg/mL; p = 0.02); RANTES expression levels were more variable in GBV-C co-infected patients and more frequently elevated in HIV-1 mono-infected patients compared to patients co-infected with GBV-C. CONCLUSIONS The previously observed beneficial effect of co-infection with HIV-1 and GBV-C on disease progression is complex and might be due in part to a change in the cytokine environment. More studies are required to understand the interaction between both viruses.
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Abstract
Researchers today have a many choices when deciding which sequencing technology to use for their clinical research. Sanger sequencing, long the "gold standard" in clinical research sequencing technology, has met significant competition with the advent of next generation sequencing (NGS). NGS technologies are now commonplace in clinical research laboratories where they have enabled rapid advances in the gathering and analysis of genetic information. However, with these advances have come additional challenges involving validation as these technologies become more widespread and move closer to future clinical application. In this webinar, our expert speakers will discuss the relative benefits of Sanger and NGS technologies and their application in different fields of clinical research.
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Quiñones-Mateu ME, Vanham G. HIV microbicides: where are we now? Curr HIV Res 2012; 10:1-2. [PMID: 22264039 DOI: 10.2174/157016212799304724] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/10/2011] [Accepted: 12/15/2011] [Indexed: 11/22/2022]
Abstract
Most human immunodeficiency virus (HIV) infections are acquired during sexual contact, across the genital or rectal mucosal epithelium. At present, HIV preventive strategies such as behavioral and structural interventions (e.g., counseling and condom use) or pre-exposure prophylaxis (e.g., topical microbicides or the oral administration of antiretroviral drugs) seem to be the only effective and most indicated methods against the establishment of systemic HIV infection. The recent success of the CAPRISA 004 phase II clinical trial, using a tenofovir-based gel, as well as the iPreX trial, using oral TRUVADA®, not only provided the proof-of-concept for reverse transcription inhibitor (RTI)-based vaginal microbicides but also demonstrated the real possibility of using topical or oral pre-exposure prophylaxis (PrEP) to prevent sexual HIV transmission. Unfortunately, more recent failures in the FEMPreP and VOICE trial, using similar regimes, suggest that there is still room for improvement. Therefore, ongoing and future studies will be key in the development of novel potent and safe strategies to block HIV transmission.
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Tebit DM, Ndembi N, Weinberg A, Quiñones-Mateu ME. Mucosal transmission of human immunodeficiency virus. Curr HIV Res 2012; 10:3-8. [PMID: 22264040 PMCID: PMC3744389 DOI: 10.2174/157016212799304689] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/01/2011] [Accepted: 11/11/2011] [Indexed: 02/07/2023]
Abstract
Since the beginning of the AIDS pandemic, and following the discovery of the human immunodeficiency virus (HIV) as the etiological agent of the disease, it was clear that the virus gains access to the human host predominantly through the mucosal tissue after sexual exposure. As a consequence, the female genital tract (vaginal and cervical), as well as the rectal, penile, and oral mucosae have been extensively studied over the last thirty years towards a better understanding of--and to develop strategies to prevent--sexual HIV transmission. This review seeks to describe the biology of the events leading to HIV infection through the human mucosa and introduce some of the approaches attempted to prevent the sexual transmission of HIV.
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Affiliation(s)
- Denis M. Tebit
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | | | - Aaron Weinberg
- School of Medicine, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio
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Jegede O, Khodyakova A, Chernov M, Weber J, Menéndez-Arias L, Gudkov A, Quiñones-Mateu ME. Identification of low-molecular weight inhibitors of HIV-1 reverse transcriptase using a cell-based high-throughput screening system. Antiviral Res 2011; 91:94-8. [PMID: 21600931 DOI: 10.1016/j.antiviral.2011.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 11/26/2022]
Abstract
A cell-based drug screening system that utilizes a green fluorescent protein (GFP)-tagged recombinant lentiviral vector has been used to screen a chemical library of 34,000 small molecules for antiretroviral compounds. Thirty-three initial hits were analyzed and four compounds were selected based on their anti-human immunodeficiency virus type 1 (HIV-1) activity (EC(50) values ranging from 0.17 to 1.9 μM) and low cellular toxicity (CC(50) values >50 μM). The four compounds blocked reverse transcription and were able to inhibit the replication of a panel of different HIV-1 strains, including non-B subtype and viruses resistant to different drug classes. Serial in vitro passages of HIV-1(B-HXB2) in the presence of increasing drug concentrations selected for viruses with reduced susceptibility. Mutations previously associated with resistance to non-nucleoside reverse transcriptase (RT) inhibitors (L100I and Y181C for CBL-17 and CBL-21, respectively) or linked to nucleoside analogue resistance (A62V for CBL-4.0 and CBL-4.1) were identified. Viruses with reduced susceptibility to CBL-17 and CBL-21 but not the ones resistant to CBL-4.0 or CBL-4.1 showed a decrease in replicative fitness. Interestingly, two of the small molecules (CBL-4.0 and CBL-4.1) are indolopyridinones that were previously described as nucleotide-competing RT inhibitors.
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Affiliation(s)
- Oyebisi Jegede
- Department of Molecular Genetics, Section of Virology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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Selhorst P, Vazquez AC, Terrazas-Aranda K, Michiels J, Vereecken K, Heyndrickx L, Weber J, Quiñones-Mateu ME, Ariën KK, Vanham G. Human immunodeficiency virus type 1 resistance or cross-resistance to nonnucleoside reverse transcriptase inhibitors currently under development as microbicides. Antimicrob Agents Chemother 2011; 55:1403-13. [PMID: 21282453 PMCID: PMC3067143 DOI: 10.1128/aac.01426-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 11/29/2010] [Accepted: 01/19/2011] [Indexed: 11/20/2022] Open
Abstract
Microbicides based on nonnucleoside reverse transcriptase inhibitors (NNRTIs) are currently being developed to protect women from HIV acquisition through sexual contact. However, the large-scale introduction of these products raises two major concerns. First, when these microbicides are used by undiagnosed HIV-positive women, they could potentially select for viral resistance, which may compromise subsequent therapeutic options. Second, NNRTI-based microbicides that are inactive against NNRTI-resistant strains might promote the selective transmission of these viruses. In order to address these concerns, drug resistance was selected in vitro by the serial passage of three viral isolates from subtypes B and C and CRF02_AG (a circulating recombinant form) in activated peripheral blood mononuclear cells (PBMCs) under conditions of increasing concentrations of three NNRTIs (i.e., TMC120, UC781, and MIV-160) that are currently being developed as candidate microbicides. TMC120 and MIV-160 displayed a high genetic barrier to resistance development, whereas resistance to UC781 emerged rapidly, similarly to efavirenz and nevirapine. Phenotypically, the selected viruses appeared to be highly cross-resistant to current first-line therapeutic NNRTIs (i.e., delavirdine, nevirapine, and efavirenz), although they retained some susceptibility to the more recently developed NNRTIs lersivirine and etravirine. The ability of UC781, TMC120, and MIV-160 to inhibit the in vitro-selected NNRTI-resistant viruses was also limited, although residual activity could be observed for the candidate microbicide NNRTI MIV-170. Interestingly, only four p2/p7/p1/p6/PR/RT/INT recombinant NNRTI-resistant viruses (i.e., TMC120-resistant VI829, EFV-resistant VI829, MIV-160-resistant VI829, and EFV-resistant MP568) showed impairments in replicative fitness. Overall, these in vitro analyses demonstrate that due to potential cross-resistance, the large-scale introduction of single-NNRTI-based microbicides should be considered with caution.
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Affiliation(s)
- Philippe Selhorst
- Department of Microbiology, Virology Unit, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium.
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Zapata W, Rodriguez B, Weber J, Estrada H, Quiñones-Mateu ME, Zimermman PA, Lederman MM, Rugeles MT. Increased levels of human beta-defensins mRNA in sexually HIV-1 exposed but uninfected individuals. Curr HIV Res 2008; 6:531-8. [PMID: 18991618 DOI: 10.2174/157016208786501463] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protection against HIV-1 infection in exposed seronegative (ESN) individuals likely involves natural resistance mechanisms that have not been fully elucidated. Human beta defensins (HBD) are antimicrobial peptides found primarily in mucosae, the main ports of HIV entry. HBD-2 and 3 mRNA are induced by HIV-1 in human oral epithelial cells and exhibit strong anti-HIV-1 activity; in addition, polymorphisms in the DEFB1 gene, which encodes HBD-1, have been associated with resistance/susceptibility to different infections, including HIV-1. Here, we have assessed the association of HBD expression with the ESN phenotype. Peripheral blood and vaginal/endocervical and oral mucosal samples were taken from 47 ESN, 44 seropositive (SP) and 39 healthy controls (HC). HBD-1, 2 and 3 mRNA copy numbers were quantified by real time RT-PCR and A692G/G1654A/A1836G polymorphisms in the DEFB1 gene were detected by restriction fragment length polymorphisms and confirmed by nucleotide sequencing. ESN expressed significantly greater mRNA copy numbers of HBD-2 and 3 in oral mucosa than HC; p=0.0002 and p=0.007, respectively. mRNA copy numbers of HBD-1, 2 and 3 in vaginal/endocervical mucosa from ESN and HC were similar. Homozygosity for the A692G polymorphism was significantly more frequent in ESN (0.39) than in SP (0.05) (p=0.0002). In summary, ESN exhibited enhanced mucosal expression of the innate defense genes HBD-2 and 3; however, additional studies are required to verify these results and the potential association of the A692G polymorphism to the relative resistance of ESN to HIV-1 infection.
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Affiliation(s)
- Wildeman Zapata
- Group of Immunovirology, School of Medicine, University of Antioquia, Medellín, Colombia
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Abstract
Twenty-five years after the emergence of HIV onto the global scene, multiple advancements have been made in the understanding of HIV pathology. Thanks to the development of antiretroviral therapies, growing numbers of individuals with HIV infection experience slowed or halted acceleration to AIDS. Despite this, new HIV infections and AIDS-related morbidity and mortality are still common in the highly active antiretroviral therapy era. Recently, we and others have identified viral replicative fitness as a major determinant of HIV disease progression, which could have a major impact in the clinical setting. Therefore, in this review, we will discuss host and viral factors that affect viral fitness and its relationship on HIV pathogenesis.
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Affiliation(s)
- Kenneth R Henry
- Division of Infectious Diseases, BRB 1029, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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Weber J, Weberova J, Carobene M, Mirza M, Martinez-Picado J, Kazanjian P, Quiñones-Mateu ME. Use of a novel assay based on intact recombinant viruses expressing green (EGFP) or red (DsRed2) fluorescent proteins to examine the contribution of pol and env genes to overall HIV-1 replicative fitness. J Virol Methods 2006; 136:102-17. [PMID: 16690137 DOI: 10.1016/j.jviromet.2006.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/31/2006] [Accepted: 04/04/2006] [Indexed: 12/21/2022]
Abstract
Multiple studies have described a reduction in the replicative fitness of HIV-1 isolates harboring mutations that confer resistance to antiretroviral drugs. Contradictory results, however, have been obtained depending on the methodology used in each study (Quinones-Mateu, M.E., Arts, E.J., 2002. Fitness of drug resistant HIV-I: methodology and clinical implications. Drug Resist. Update 5, 224-233), affecting our understanding of the potential relationship of viral replicative fitness with HIV-1 disease. It has been demonstrated previously that both pol and env genes play a major role in HIV-1 replicative fitness of clinical isolates. Therefore, measuring clinically relevant replicative fitness using recombinant viruses where a single mutation and/or viral gene have been introduced does not seem like a reasonable approach in this era of multi-target antiretroviral therapy. A novel method was developed to measure HIV-1 replicative fitness based on recombinant viruses expressing the enhanced green fluorescent (EGFP) or the Discosoma sp. red fluorescent (DsRed2) proteins in a HIV-1NL4-3 backbone. Contrary to previous designs to analyze HIV-1 fitness, these replication competent viruses were created in an intact viral genetic background (without deleting or affecting the expression of any viral gene). This new system was used to evaluate the contribution of drug-resistance mutations in the pol and env genes to overall viral replicative fitness (in the presence and absence of drug pressure) using direct growth competition experiments. Mutations in pol showed a stronger effect on HIV-1 replicative fitness than mutations in the env gene associated with resistance to enfuvirtide, corroborating the plasticity of the later gene to accept mutations and the sensibility of the protease and reverse transcriptase enzymes to drug-associated primary mutations. In conclusion, a new protocol was used to measure HIV-1 replicative fitness in either the presence or absence of antiretroviral drugs, which may be used as a high-throughput assay to help us understand the clinical significance of viral fitness.
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Affiliation(s)
- Jan Weber
- Department of Molecular Genetics, Section of Virology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Abstract
Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.
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Affiliation(s)
- M E Quiñones-Mateu
- Department of Molecular Genetics, Section Virology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue/NN10, Cleveland, OH 44195, USA.
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Weber J, Piontkivska H, Quiñones-Mateu ME. HIV type 1 tropism and inhibitors of viral entry: clinical implications. AIDS Rev 2006; 8:60-77. [PMID: 16848274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Since their discovery in 1996, the two main coreceptors used by human immunodeficiency virus type 1 (HIV-1) to enter human cells (CCR5 and CXCR4) have been the subject of numerous scientific articles. A recent search in PubMed (www.pubmed.gov) using "HIV coreceptor" as keywords led to more than 1100 original research publications and 90 review articles. This number skyrocketed to more than double if we used "HIV CCR5". Most of the reviews described in detail several aspects of HIV tropism, viral entry mechanism, coreceptor usage and its implication on disease progression, antiretroviral therapy, and vaccine development. A few others centered on the tools utilized to measure the ability of HIV to use these coreceptors to infect target cells. On the other hand, identification of the HIV coreceptors renewed the effort and expectation to block HIV replication by targeting viral entry into the target cells. As with HIV tropism, hundreds of articles have been published addressing this topic (more than 350 original publications and 50 review articles when using "HIV entry inhibitor" as a descriptive word). Therefore, in addition to providing a brief update of the most important aspects described above, we discuss here how an accurate quantification of HIV coreceptor usage is essential for the successful management of HIV-infected individuals in this new era of entry inhibitors, mainly CCR5- or CXCR4-antagonists.
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Affiliation(s)
- Jan Weber
- Department of Molecular Genetics, Section of Virology, Lerner Research Institute, Cleveland Clinic Foundation, Ohio 44195, USA
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Abstract
Mechanisms of resistance to HIV-1 infection in the human oral cavity are incompletely understood. While salivary components have been implicated in protection, there is growing evidence that human beta-defensins (hBDs), originating in oral epithelial cells, may be playing an important role in the prevention of HIV infection. New antiviral, chemotactic, and immunosurveillance properties are being attributed to hBDs, which are small cationic antimicrobial innate response molecules expressed in mucosal epithelium. Inducible hBDs are always expressed in normal oral epithelium, a property not shared by other mucosal barriers. Data reviewed in this paper demonstrate that: (1) HIV-1 X4 and R5 phenotypes induce hBD-2 and -3 mRNA in normal human oral epithelial cells; (2) hBD-2 and -3 inhibit HIV-1 infection by both viral strains, with greater activity against X4 viruses; and (3) this inhibition is due to a direct interaction with virions and through modulation of the CXCR4 co-receptor. These properties may be exploited as strategies for mucosal protection against HIV-1 transmission.
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Affiliation(s)
- A Weinberg
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University (CWRU), 10900 Euclid Ave., Cleveland, OH 44106, USA.
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Ariën KK, Abraha A, Quiñones-Mateu ME, Kestens L, Vanham G, Arts EJ. The replicative fitness of primary human immunodeficiency virus type 1 (HIV-1) group M, HIV-1 group O, and HIV-2 isolates. J Virol 2005; 79:8979-90. [PMID: 15994792 PMCID: PMC1168791 DOI: 10.1128/jvi.79.14.8979-8990.2005] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main (M) group of human immunodeficiency virus type 1 (HIV-1) is responsible for the global AIDS epidemic while HIV-1 group O (outlier) and HIV type 2 are endemic only in west and central Africa. The failure of HIV-2 and especially HIV-1 group O to spread following the initial zoonotic jumps is not well understood. This study was designed to examine the relative replicative capacities between these human lentiviruses. A pairwise competition experiment was performed with peripheral blood mononuclear cells with eight HIV-2 isolates, 6 group O viruses, and 15 group M viruses of subtype A (2 viruses), B (5 viruses), C (4 viruses), D (2 viruses) and CRF01_AE (2 viruses). HIV-1 group M isolates of any subtype were typically 100-fold-more fit than group O or HIV-2 strains when competed in peripheral blood mononuclear cells from various humans. This order in replicative fitness was also observed when virus pairs were added to human dendritic cells and then cocultured with primary, quiescent T cells, which is the model for HIV-1 transmission. These results suggest that reduced replicative and transmission fitness may be contributing to the low prevalence and limited geographical spread of HIV-2 and group O HIV-1 in the human population.
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Affiliation(s)
- Kevin K Ariën
- Centre for AIDS Research, Case Western Reserve University, Cleveland, OH, USA
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Weber J, Chakraborty B, Weberova J, Miller MD, Quiñones-Mateu ME. Diminished replicative fitness of primary human immunodeficiency virus type 1 isolates harboring the K65R mutation. J Clin Microbiol 2005; 43:1395-400. [PMID: 15750116 PMCID: PMC1081293 DOI: 10.1128/jcm.43.3.1395-1400.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) resistance mutation K65R confers intermediate levels of resistance to several RT inhibitors, including a three- to fourfold reduction of tenofovir susceptibility. Here, we have used for the first time primary HIV-1 isolates from individuals who developed the K65R mutation while enrolled in a clinical trial of tenofovir to analyze the impact of this mutation on HIV-1 replicative fitness. A marked impairment in replicative fitness was observed in association with the selection of viruses carrying the K65R mutation in all patients. The mean replicative fitness among these viruses was 20% relative to the corresponding baseline wild-type virus, ranging from 10 to 32% depending on the accompanying RT mutations. These results support a reduction in in vivo replication for K65R mutant viruses.
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Affiliation(s)
- Jan Weber
- Cleveland Clinic Foundation, Lerner Research Institute, Department of Molecular Genetics, Section Virology/NN10, 9500 Euclid Ave., Cleveland, OH 44195, USA
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