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Galvez NMS, Sheehan ML, Lin AZ, Cao Y, Lam EC, Jackson AM, Balazs AB. QuickFit: A High-Throughput RT-qPCR-Based Assay to Quantify Viral Growth and Fitness In Vitro. Viruses 2024; 16:1320. [PMID: 39205294 PMCID: PMC11360610 DOI: 10.3390/v16081320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Quantifying viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method termed QuickFit that enables the quantification of viral fitness by employing large numbers of parallel viral cultures to measure growth rates accurately. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches, but with significantly higher throughput and lower rates of error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.
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Affiliation(s)
| | | | | | | | | | | | - Alejandro B. Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
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2
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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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3
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Trompet E, Topalis D, Gillemot S, Snoeck R, Andrei G. Viral fitness of MHV-68 viruses harboring drug resistance mutations in the protein kinase or thymidine kinase. Antiviral Res 2020; 182:104901. [PMID: 32763314 DOI: 10.1016/j.antiviral.2020.104901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Murine γ-herpesvirus-68 (MHV-68), genetically and biologically related to human γ-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, can be easily propagated in vitro allowing drug resistance studies. Previously, we described specific changes in MHV-68 protein kinase (PK) or thymidine kinase (TK) associated with resistance to various purine or pyrimidine nucleoside analogues, respectively. To investigate how specific TK and PK mutations affect viral replication capacity, we performed dual infection competition assays in which wild-type and drug-resistant virus compete in absence or presence of antivirals in Vero cells. The composition of the mixed viral population was analyzed using next-generation sequencing and relative fitness of seven MHV-68 PK or TK mutants was calculated based on the frequency of viral variants at the time of infection and after 5-days growth. A MHV-68 mutant losing the PK function due to a 2-nucleotide deletion was less fit than the wild-type virus in absence of antivirals, consistent with the essential role of viral PKs during lytic replication, but overgrew the wild-type virus under pressure of purine nucleosides. TK mutant viruses, with frameshift or missense mutations, grew equal to wild-type virus in absence of antivirals, in accordance with the viral TK function only being essential in non-replicating or in TK-deficient cells, but were more fit when treated with pyrimidine nucleosides. Moreover, TK missense mutant viruses also increased fitness under pressure of antivirals other than pyrimidine nucleosides, indicating that MHV-68 TK mutations might influence viral fitness by acting on cellular and/or viral functions that are unrelated to nucleoside activation.
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Affiliation(s)
- Erika Trompet
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sarah Gillemot
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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4
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Guerrero-Beltran C, Rodriguez-Izquierdo I, Serramia MJ, Araya-Durán I, Márquez-Miranda V, Gomez R, de la Mata FJ, Leal M, González-Nilo F, Muñoz-Fernández MA. Anionic Carbosilane Dendrimers Destabilize the GP120-CD4 Complex Blocking HIV-1 Entry and Cell to Cell Fusion. Bioconjug Chem 2018; 29:1584-1594. [PMID: 29570280 DOI: 10.1021/acs.bioconjchem.8b00106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cell-to-cell transmission is the most effective pathway for the spread of human immunodeficiency virus (HIV-1). Infected cells expose virus-encoded fusion proteins on their surface as a consequence of HIV-1 replicative cycle that interacts with noninfected cells through CD4 receptor and CXCR4 coreceptor leading to the formation of giant multinucleated cells known as syncytia. Our group previously described the potent activity of dendrimers against CCR5-tropic viruses. Nevertheless, the study of G1-S4, G2-S16, and G3-S16 dendrimers in the context of X4-HIV-1 tropic cell-cell fusion referred to syncytium formation remains still unknown. These dendrimers showed a suitable biocompatibility in all cell lines studied and our results demonstrated that anionic carbosilane dendrimers G1-S4, G2-S16, and G3-S16 significantly inhibit the X4-HIV-1 infection, as well as syncytia formation, in a dose dependent manner. We also demonstrated that G2-S16 and G1-S4 significantly reduced syncytia formation in HIV-1 Env-mediated cell-to-cell fusion model. Molecular modeling and in silico models showed that G2-S16 dendrimer interfered with gp120-CD4 complex and demonstrated its potential use for a treatment.
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Affiliation(s)
- Carlos Guerrero-Beltran
- Laboratorio InmunoBiología Molecular , Hospital General Universitario Gregorio Marañón and Instituto de Investigación Sanitaria Gregorio Marañón (IISGM) , 28007 Madrid , Spain.,Spanish HIV HGM BioBank , 28009 Madrid , Spain.,Plataforma de Laboratorio , Hospital General Universitario Gregorio Marañón , 28007 Madrid , Spain
| | - Ignacio Rodriguez-Izquierdo
- Laboratorio InmunoBiología Molecular , Hospital General Universitario Gregorio Marañón and Instituto de Investigación Sanitaria Gregorio Marañón (IISGM) , 28007 Madrid , Spain.,Spanish HIV HGM BioBank , 28009 Madrid , Spain
| | - Ma Jesus Serramia
- Laboratorio InmunoBiología Molecular , Hospital General Universitario Gregorio Marañón and Instituto de Investigación Sanitaria Gregorio Marañón (IISGM) , 28007 Madrid , Spain.,Spanish HIV HGM BioBank , 28009 Madrid , Spain
| | - Ingrid Araya-Durán
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas , Universidad Andres Bello , Av. República 239 , Santiago , Chile , 8370146.,Fundación Fraunhofer Chile Research , Las Condes , Chile , 7550296.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias , Universidad de Valparaíso , Valparaíso , Chile , 2360102
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas , Universidad Andres Bello , Av. República 239 , Santiago , Chile , 8370146.,Fundación Fraunhofer Chile Research , Las Condes , Chile , 7550296.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias , Universidad de Valparaíso , Valparaíso , Chile , 2360102
| | - Rafael Gomez
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Instituto de Salud Carlos III , Av. de Monforte de Lemos, 5 , 28029 Madrid , Spain
| | - Francisco Javier de la Mata
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Instituto de Salud Carlos III , Av. de Monforte de Lemos, 5 , 28029 Madrid , Spain
| | - Manuel Leal
- Instituto de Biomedicina de Sevilla (IBiS) . Hospital Universitario Virgen del Rocio , Av. Manuel Siurot, s/n , 41013 Sevilla , Spain.,Servicio de Medicina Interna . Hospital Viamed Santa Ángela , Av. de Jerez, 59 , 41014 Sevilla , Spain
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas , Universidad Andres Bello , Av. República 239 , Santiago , Chile , 8370146.,Fundación Fraunhofer Chile Research , Las Condes , Chile , 7550296.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias , Universidad de Valparaíso , Valparaíso , Chile , 2360102
| | - M Angeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular , Hospital General Universitario Gregorio Marañón and Instituto de Investigación Sanitaria Gregorio Marañón (IISGM) , 28007 Madrid , Spain.,Spanish HIV HGM BioBank , 28009 Madrid , Spain.,Plataforma de Laboratorio , Hospital General Universitario Gregorio Marañón , 28007 Madrid , Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Instituto de Salud Carlos III , Av. de Monforte de Lemos, 5 , 28029 Madrid , Spain
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5
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Pankrac J, Klein K, McKay PF, King DFL, Bain K, Knapp J, Biru T, Wijewardhana CN, Pawa R, Canaday DH, Gao Y, Fidler S, Shattock RJ, Arts EJ, Mann JFS. A heterogeneous human immunodeficiency virus-like particle (VLP) formulation produced by a novel vector system. NPJ Vaccines 2018; 3:2. [PMID: 29367885 PMCID: PMC5775397 DOI: 10.1038/s41541-017-0040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 01/12/2023] Open
Abstract
First identified as the etiological agent behind Acquired Immunodeficiency Syndrome (AIDS) in the early 1980s, HIV-1 has continued to spread into a global pandemic and major public health concern. Despite the success of antiretroviral therapy at reducing HIV-1 viremia and preventing the dramatic CD4+ T-cell collapse, infected individuals remain HIV positive for life. Unfortunately, it is increasingly clear that natural immunity is not, and may never be, protective against this pathogen. Therefore, efficacious vaccine interventions, which can either prevent infection or eradicate the latent viral reservoir and effect cure, are a major medical priority. Here we describe the development of a safe vaccine platform, currently being utilized in on-going prophylactic and therapeutic preclinical studies and consisting of highly heterogeneous virus-like particle formulations that represent the virus diversity within infected individuals. These VLPs contain no 5'LTR, no functional integrase, and have a severely mutated stem loop 1-thereby preventing any potential reverse transcription, integration, and RNA packaging. Furthermore, we demonstrate that these VLPs are morphologically identical to wild-type virus with polyvalent Env in a functional form. Finally, we show that the VLPs are antigenic and capable of generating strong immune recall responses.
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Affiliation(s)
- Joshua Pankrac
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Katja Klein
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Paul F. McKay
- Division of Medicine, Department of Infectious Diseases, Imperial College London, Norfolk Place, London, W2 1PG UK
| | - Deborah F. L. King
- Division of Medicine, Department of Infectious Diseases, Imperial College London, Norfolk Place, London, W2 1PG UK
| | - Katie Bain
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Jason Knapp
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Tsigereda Biru
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Chanuka N. Wijewardhana
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Rahul Pawa
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
| | - David H. Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Yong Gao
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Sarah Fidler
- Department of Medicine, Imperial College London, London, UK
| | - Robin J. Shattock
- Division of Medicine, Department of Infectious Diseases, Imperial College London, Norfolk Place, London, W2 1PG UK
| | - Eric J. Arts
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Jamie F. S. Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1 Canada
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
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6
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Klein K, Nickel G, Nankya I, Kyeyune F, Demers K, Ndashimye E, Kwok C, Chen PL, Rwambuya S, Poon A, Munjoma M, Chipato T, Byamugisha J, Mugyenyi P, Salata RA, Morrison CS, Arts EJ. Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection. PLoS Pathog 2018; 14:e1006754. [PMID: 29346424 PMCID: PMC5773221 DOI: 10.1371/journal.ppat.1006754] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/16/2017] [Indexed: 02/07/2023] Open
Abstract
In the majority of cases, human immunodeficiency virus type 1 (HIV-1) infection is transmitted through sexual intercourse. A single founder virus in the blood of the newly infected donor emerges from a genetic bottleneck, while in rarer instances multiple viruses are responsible for systemic infection. We sought to characterize the sequence diversity at early infection, between two distinct anatomical sites; the female reproductive tract vs. systemic compartment. We recruited 72 women from Uganda and Zimbabwe within seven months of HIV-1 infection. Using next generation deep sequencing, we analyzed the total genetic diversity within the C2-V3-C3 envelope region of HIV-1 isolated from the female genital tract at early infection and compared this to the diversity of HIV-1 in plasma. We then compared intra-patient viral diversity in matched cervical and blood samples with three or seven months post infection. Genetic analysis of the C2-V3-C3 region of HIV-1 env revealed that early HIV-1 isolates within blood displayed a more homogeneous genotype (mean 1.67 clones, range 1–5 clones) than clones in the female genital tract (mean 5.7 clones, range 3–10 clones) (p<0.0001). The higher env diversity observed within the genital tract compared to plasma was independent of HIV-1 subtype (A, C and D). Our analysis of early mucosal infections in women revealed high HIV-1 diversity in the vaginal tract but few transmitted clones in the blood. These novel in vivo finding suggest a possible mucosal sieve effect, leading to the establishment of a homogenous systemic infection. During chronic HIV-1 infection, high viral diversity can be found in the blood and semen of donors. However, a single HIV-1 clone establishes productive infection in the recipient following heterosexual transmission. To investigate the genetic bottleneck occurring at the earliest stages of heterosexual HIV-1 transmission, we characterized the HIV-1 envelope sequence diversity at very early and early stages of infection in the female reproductive tract and matched plasma samples from a cohort of Ugandan and Zimbabwean women. A more diverse viral population was observed in the endocervical swab samples compared to plasma. Endocervical samples harbored a larger number of viral clones, while in the majority of plasma samples only a single clone was present early in infection. Interestingly, these observations were independent of HIV-1 subtype, hormonal contraceptive use or the number of sex acts and partners. Furthermore, in the cases of higher HIV-1 diversity in the blood during early infection, faster CD4 T cell decline were observed during chronic disease suggesting faster disease progression. Our findings provide novel in vivo evidence for the existence of an intra-patient genetic bottleneck restricting the HIV-1 from the vaginal tract to the blood during early heterosexual HIV-1 transmission.
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Affiliation(s)
- Katja Klein
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gabrielle Nickel
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | | | - Korey Demers
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Joint Clinical Research Centre, Kampala, Uganda
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Joint Clinical Research Centre, Kampala, Uganda
| | - Cynthia Kwok
- FHI 360, Durham, North Carolina, United States of America
| | - Pai-Lien Chen
- FHI 360, Durham, North Carolina, United States of America
| | - Sandra Rwambuya
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Joint Clinical Research Centre, Kampala, Uganda
| | - Art Poon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Marshall Munjoma
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | - Tsungai Chipato
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | | | | | - Robert A. Salata
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | - Eric J. Arts
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Joint Clinical Research Centre, Kampala, Uganda
- * E-mail:
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7
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Gonzalez-Serna A, Genebat M, Ruiz-Mateos E, Leal M. Short-term maraviroc exposure, a clinical approach to decide on maraviroc prescription in HIV-1-infected treatment-naïve patients. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:353-4. [PMID: 26848259 PMCID: PMC4723024 DOI: 10.2147/dddt.s100639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Alejandro Gonzalez-Serna
- Laboratory of Molecular Immunobiology, Hospital General Universitario Gregorio Maranon, Madrid, Spain
| | - Miguel Genebat
- Laboratory of Immunovirology, Institute of Biomedicine of Seville, Seville, Spain
| | - Ezequiel Ruiz-Mateos
- Laboratory of Immunovirology, Institute of Biomedicine of Seville, Seville, Spain
| | - Manuel Leal
- Laboratory of Immunovirology, Institute of Biomedicine of Seville, Seville, Spain
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