1
|
Fortner A, Bucur O. mRNA-based vaccine technology for HIV. Discoveries (Craiova) 2022; 10:e150. [PMID: 36438441 PMCID: PMC9683993 DOI: 10.15190/d.2022.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) poses a major health problem around the globe, resulting in hundred-thousands of deaths from AIDS and over a million new infections annually. Although the standard treatment of HIV infection, antiretroviral therapy, has proven effective in preventing HIV transmission, it is unsuitable for worldwide use due to its substantial costs and frequent adverse effects. Besides promoting HIV/AIDS awareness through education, there is hardly an alternative for inhibiting the spread of the disease. One promising approach is the development of an HIV vaccine. Unfortunately, the high variability of envelope proteins from HIV subtypes, their frequency of mutation and the lack of fully understanding the mechanisms of protection against the virus constitute an obstacle for vaccine development. Efforts for developing successful anti-HIV vaccines have been underway for decades now, with little success. Lately, significant progress has been made in adopting the novel mRNA vaccine approach as an anti-HIV strategy. mRNA vaccines received a great thrust during the COVID-19 pandemic. Now, several mRNA-based HIV vaccines are undergoing clinical trials to evaluate their safety and efficacy. This review offers an overview of the pathogenesis and treatment of HIV / AIDS, previous efforts of HIV vaccine development and introduces mRNA vaccines as a promising and potential game changing platform for HIV vaccination.
Collapse
Affiliation(s)
- Andra Fortner
- Albert-Ludwigs-Universitat Freiburg, Germany,Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Octavian Bucur
- Victor Babes National Institute of Pathology, Bucharest, Romania,Viron Molecular Medicine Institute, Boston, MA 02108, USA,* Corresponding authors: Octavian Bucur, MD, PhD, Next Generation Pathology Group, Victor Babes National Institute of Pathology, Bucharest, Romania and Viron Molecular Medicine Institute, Boston, MA 02108, USA; ;
| |
Collapse
|
2
|
Khanaliha K, Bokharaei-Salim F, Donyavi T, Nahand JS, Marjani A, Jamshidi S, Khatami A, Moghaddas M, Esghaei M, Fakhim A. Evaluation of CCR5-Δ32 mutation and HIV-1 surveillance drug-resistance mutations in peripheral blood mononuclear cells of long-term non progressors of HIV-1-infected individuals. Future Virol 2022. [DOI: 10.2217/fvl-2021-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: This study aimed to evaluate chemokine receptor 5 delta 32 (CCR5-Δ32) mutation and HIV-1 surveillance drug-resistance mutations (SDRMs) in peripheral blood mononuclear cells of long-term non progressors (LTNPs) of HIV-1-infected individuals. Materials and methods: This research was performed on 197 treatment-naive HIV-1-infected patients. After follow-up, it was determined that 15 (7.6%) of these people were LTNPs. The PCR assay was performed to identify the CCR5 genotype and HIV-1 SDRMs. Results: One (6.7%) of the LTNPs was heterozygous (wt/Δ32) for the CCR5 delta 32 (CCR5Δ32). However, none of the individuals was homozygous for this mutation (Δ32/Δ32). Moreover, none of the LTNPs showed HIV-1 SDRMs. The CRF35-AD subtype was the most dominant subtype, with a percentage of 93.3%. Conclusion: Iranian elite controllers are negative for CCR5-delta 32 homozygous genotype and drug resistance against antiretroviral drugs.
Collapse
Affiliation(s)
- Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Tahereh Donyavi
- Medical Biotechnology Department, School of Allied Medical Sciences, Iran University of Medical Sciences
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arezoo Marjani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sogol Jamshidi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - AliReza Khatami
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Moghaddas
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Atousa Fakhim
- Department of Architectural Engineering, Faculty of Engineering, Islamic Azad University, South Tehran Branch, Tehran, Iran
| |
Collapse
|
3
|
Sadri Nahand J, Salmaninejad A, Mollazadeh S, Tamehri Zadeh SS, Rezaee M, Sheida AH, Sadoughi F, Dana PM, Rafiyan M, Zamani M, Taghavi SP, Dashti F, Mirazimi SMA, Bannazadeh Baghi H, Moghoofei M, Karimzadeh M, Vosough M, Mirzaei H. Virus, Exosome, and MicroRNA: New Insights into Autophagy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1401:97-162. [DOI: 10.1007/5584_2022_715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
4
|
Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
Collapse
Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| |
Collapse
|
5
|
Hao X, Eskridge KM, Wang D. Variational Bayesian inference for association over phylogenetic trees for microorganisms. J Appl Stat 2020; 49:1140-1153. [PMID: 35707516 PMCID: PMC9041926 DOI: 10.1080/02664763.2020.1854200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
With the advance of next generation sequencing technologies, researchers now routinely obtain a collection of microbial sequences with complex phylogenetic relationships. It is often of interest to analyze the association between certain environmental factors and characteristics of the microbial collection. Though methods have been developed to test for association between the microbial composition with environmental factors as well as between coevolving traits, a flexible model that can provide a comprehensive picture of the relationship between microbial community characteristics and environmental variables will be tremendously beneficial. We developed a Bayesian approach for association analysis while incorporating the phylogenetic structure to account for the dependence between observations. To overcome the computational difficulty related to the phylogenetic tree, a variational algorithm was developed to evaluate the posterior distribution. As the posterior distribution can be readily obtained for parameters of interest and any derived variables, the association relationship can be examined comprehensively. With two application examples, we demonstrated that the Bayesian approach can uncover nuanced details of the microbial assemblage with regard to the environmental factor. The proposed Bayesian approach and variational algorithm can be extended for other problems involving dependence over tree-like structures.
Collapse
Affiliation(s)
- Xiaojuan Hao
- Department of Statistics, University of Nebraska, Lincoln, NE, USA
| | - Kent M. Eskridge
- Department of Statistics, University of Nebraska, Lincoln, NE, USA
| | - Dong Wang
- Division of Bioinformatics and Biostatistics, FDA National Center for Toxicological Research, Jefferson, AR, USA
| |
Collapse
|
6
|
Macharia GN, Yue L, Staller E, Dilernia D, Wilkins D, Song H, McGowan E, King D, Fast P, Imami N, Price MA, Sanders EJ, Hunter E, Gilmour J. Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection. PLoS Pathog 2020; 16:e1008853. [PMID: 32886726 PMCID: PMC7498102 DOI: 10.1371/journal.ppat.1008853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from a pool of genetically diverse quasispecies establishes infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and represent a unique opportunity to characterize transmitted/founder viruses (TF) where disease outcome is known. To identify the TF, the HIV-1 repertoire of 38 MSM participants' samples was sequenced close to transmission (median 21 days post infection, IQR 18-41) and assessment of multivariant infection done. Patient derived gag genes were cloned into an NL4.3 provirus to generate chimeric viruses which were characterized for replicative capacity (RC). Finally, an evaluation of how the TF virus predicted disease progression and modified the immune response at both acute and chronic HIV-1 infection was done. There was higher prevalence of multivariant infection compared with previously described heterosexual cohorts. A link was identified between multivariant infection and replicative capacity conferred by gag, whereby TF gag tended to be of lower replicative capacity in multivariant infection (p = 0.02) suggesting an overall lowering of fitness requirements during infection with multiple variants. Notwithstanding, multivariant infection was associated with rapid CD4+ T cell decline and perturbances in the CD4+ T cell and B cell compartments compared to single variant infection, which were reversible upon control of viremia. Strategies aimed at identifying and mitigating multivariant infection could contribute toward improving HIV-1 prognosis and this may involve strategies that tighten the stringency of the transmission bottleneck such as treatment of STI. Furthermore, the sequences and chimeric viruses help with TF based experimental vaccine immunogen design and can be used in functional assays to probe effective immune responses against TF.
Collapse
Affiliation(s)
- Gladys N. Macharia
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Ling Yue
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Ecco Staller
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Dario Dilernia
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Daniel Wilkins
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Heeyah Song
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Edward McGowan
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Deborah King
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Pat Fast
- IAVI, New York, NY, United States of America
| | - Nesrina Imami
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Matthew A. Price
- IAVI, New York, NY, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States of America
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, United Kingdom
| | - Eric Hunter
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States of America
| | - Jill Gilmour
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| |
Collapse
|
7
|
Tarasova O, Ivanov S, Filimonov DA, Poroikov V. Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1. Molecules 2020; 25:E2944. [PMID: 32604797 PMCID: PMC7357070 DOI: 10.3390/molecules25122944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/11/2022] Open
Abstract
Viruses can be spread from one person to another; therefore, they may cause disorders in many people, sometimes leading to epidemics and even pandemics. New, previously unstudied viruses and some specific mutant or recombinant variants of known viruses constantly appear. An example is a variant of coronaviruses (CoV) causing severe acute respiratory syndrome (SARS), named SARS-CoV-2. Some antiviral drugs, such as remdesivir as well as antiretroviral drugs including darunavir, lopinavir, and ritonavir are suggested to be effective in treating disorders caused by SARS-CoV-2. There are data on the utilization of antiretroviral drugs against SARS-CoV-2. Since there are many studies aimed at the identification of the molecular mechanisms of human immunodeficiency virus type 1 (HIV-1) infection and the development of novel therapeutic approaches against HIV-1, we used HIV-1 for our case study to identify possible molecular pathways shared by SARS-CoV-2 and HIV-1. We applied a text and data mining workflow and identified a list of 46 targets, which can be essential for the development of infections caused by SARS-CoV-2 and HIV-1. We show that SARS-CoV-2 and HIV-1 share some molecular pathways involved in inflammation, immune response, cell cycle regulation.
Collapse
Affiliation(s)
- Olga Tarasova
- Department for Bioinformatics, Institute of Biomedical Chemistry, 107076 Moscow, Russia; (S.I.); (D.A.F.); (V.P.)
| | - Sergey Ivanov
- Department for Bioinformatics, Institute of Biomedical Chemistry, 107076 Moscow, Russia; (S.I.); (D.A.F.); (V.P.)
- Department of Bioinformatics of Pirogov Russian National Research Medical University, 107076 Moscow, Russia
| | - Dmitry A. Filimonov
- Department for Bioinformatics, Institute of Biomedical Chemistry, 107076 Moscow, Russia; (S.I.); (D.A.F.); (V.P.)
| | - Vladimir Poroikov
- Department for Bioinformatics, Institute of Biomedical Chemistry, 107076 Moscow, Russia; (S.I.); (D.A.F.); (V.P.)
| |
Collapse
|
8
|
Boucau J, Le Gall S. Antigen processing and presentation in HIV infection. Mol Immunol 2019; 113:67-74. [PMID: 29636181 PMCID: PMC6174111 DOI: 10.1016/j.molimm.2018.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/09/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]
Abstract
The presentation of virus-derived peptides by MHC molecules constitutes the earliest signals for immune recognition by T cells. In HIV infection, immune responses elicited during infection do not enable to clear infection and correlates of immune protection are not well defined. Here we review features of antigen processing and presentation specific to HIV, analyze how HIV has adapted to the antigen processing machinery and discuss how advances in biochemical and computational protein degradation analyses and in immunopeptidome definition may help identify targets for efficient immune clearance and vaccine immunogen design.
Collapse
Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States.
| |
Collapse
|