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Kuznetsova A, Kim K, Tumanov A, Munchak I, Antonova A, Lebedev A, Ozhmegova E, Orlova-Morozova E, Drobyshevskaya E, Pronin A, Prilipov A, Kazennova E. Features of Tat Protein in HIV-1 Sub-Subtype A6 Variants Circulating in the Moscow Region, Russia. Viruses 2023; 15:2212. [PMID: 38005889 PMCID: PMC10675479 DOI: 10.3390/v15112212] [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: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Tat, the trans-activator of transcription, is a multifunctional HIV-1 protein that can induce chronic inflammation and the development of somatic diseases in HIV-infected patients. Natural polymorphisms in Tat can impact the propagation of the inflammatory signal. Currently, Tat is considered an object for creating new therapeutic agents. Therefore, the identification of Tat protein features in various HIV-1 variants is a relevant task. The purpose of the study was to characterize the genetic variations of Tat-A6 in virus variants circulating in the Moscow Region. The authors analyzed 252 clinical samples from people living with HIV (PLWH) with different stages of HIV infection. Nested PCR for two fragments (tat1, tat2) with subsequent sequencing, subtyping, and statistical analysis was conducted. The authors received 252 sequences for tat1 and 189 for tat2. HIV-1 sub-subtype A6 was identified in 250 samples. The received results indicated the features of Tat1-A6 in variants of viruses circulating in the Moscow Region. In PLWH with different stages of HIV infection, C31S in Tat1-A6 was detected with different occurrence rates. It was demonstrated that Tat2-A6, instead of a functional significant 78RGD80 motif, had a 78QRD80 motif. Herewith, G79R in Tat2-A6 was defined as characteristic amino acid substitution for sub-subtype A6. Tat2-A6 in variants of viruses circulating in the Moscow Region demonstrated high conservatism.
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Affiliation(s)
- Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Alexander Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Iana Munchak
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
- Mechnikov Scientific Research Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Elena Orlova-Morozova
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases, 129110 Moscow, Russia; (E.O.-M.); (E.D.); (A.P.)
| | - Elena Drobyshevskaya
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases, 129110 Moscow, Russia; (E.O.-M.); (E.D.); (A.P.)
| | - Alexander Pronin
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases, 129110 Moscow, Russia; (E.O.-M.); (E.D.); (A.P.)
| | - Aleksey Prilipov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (A.T.); (I.M.); (A.A.); (A.L.); (E.O.); (A.P.); (E.K.)
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Ruhanya V, Jacobs GB, Paul RH, Joska JA, Seedat S, Nyandoro G, Glashoff RH, Engelbrecht S. HIV-1 subtype C Tat exon-1 amino acid residue 24K is a signature for neurocognitive impairment. J Neurovirol 2022; 28:392-403. [PMID: 35394614 DOI: 10.1007/s13365-022-01073-4] [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: 09/27/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
Variation and differential selection pressures on Tat genes have been shown to alter the biological function of the protein, resulting in pathological consequences in a number of organs including the brain. We evaluated the impact of genetic variation and selection pressure on 147 HIV-1 subtype C Tat exon 1 sequences from monocyte-depleted peripheral lymphocytes on clinical diagnosis of neurocognitive impairment. Genetic analyses identified two signature amino acid residues, lysine at codon 24 (24K) with a frequency of 43.4% and arginine at codon 29 (29R) with a frequency of 34.0% in individuals with HIV-associated neurocognitive impairment. The analyses also revealed two signature residues, asparagine, 24 N (31.9%), and histidine, 29H (21.3%), in individuals without neurocognitive impairment. Both codons, 24 and 29, were associated with high entropy but only codon 29 was under positive selection. The presence of signature K24 increased by 2.08 times the risk of neurocognitive impairment, 3.15 times higher proviral load, and 69% lower absolute CD4 T-cell count compared to those without the signature. The results support a linkage between HIV-1 C Tat N24K polymorphism, proviral load, immunosuppression, and neurocognitive impairment. The signature may induce more neurotoxic effects, which contributes to establishment and severity of HIV-associated neurocognitive impairment.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa. .,Department of Medical Microbiology, Harare, Zimbabwe.
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa
| | - Robert H Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, University Boulevard, St Louis, USA
| | - John A Joska
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | | | - Richard H Glashoff
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
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Singh J, Ronsard L, Pandey M, Kapoor R, Ramachandran VG, Banerjea AC. Molecular and Genetic Characterization of Natural Variants of HIV-1 Nef Gene from North India and its Functional Implication in Down-Regulation of MHC-I and CD-4. Curr HIV Res 2021; 19:172-187. [PMID: 32981506 DOI: 10.2174/1570162x18666200925160755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 Nef is an important accessory protein with multiple effector functions. Genetic studies of the HIV-1 Nef gene show extensive genetic diversity and the functional studies have been carried out mostly with Nef derived from regions dominated by subtype B (North America & Europe). OBJECTIVE This study was carried out to characterize genetic variations of the Nef gene from HIV-1 infected individuals from North India and to find out their functional implications. METHODS The unique representative variants were sub-cloned in a eukaryotic expression vector and further characterized with respect to their ability to downregulate cell surface expression of CD4 and MHC-1 molecules. RESULTS The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying the importance of mutations in Nef variants. Intracellular stability of Nef variants differed greatly when compared with wild type Nef B and C. There were some variants that possessed mutations in the functional domains of Nef and responsible for its differential CD4 and MHC-1 downregulation activity. CONCLUSION We observed enhanced biological activities in some of the variants, perhaps arising from amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a population to become the most abundant after a single selection event.
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Affiliation(s)
- J Singh
- National Institute of Immunology, New Delhi, India
| | - L Ronsard
- National Institute of Immunology, New Delhi, India
| | - M Pandey
- King George`s Medical University, India
| | - R Kapoor
- National Institute of Immunology, New Delhi, India
| | - V G Ramachandran
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
| | - A C Banerjea
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
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de Almeida SM, Rotta I, Vidal LRR, Dos Santos JS, Nath A, Johnson K, Letendre S, Ellis RJ. HIV-1C and HIV-1B Tat protein polymorphism in Southern Brazil. J Neurovirol 2021; 27:126-136. [PMID: 33462791 PMCID: PMC8510567 DOI: 10.1007/s13365-020-00935-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 11/19/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023]
Abstract
The transactivator of transcription (Tat) is a key HIV regulatory protein. We aimed to identify the frequency of key polymorphisms in HIV-1C compared with HIV-1B Tat protein, chiefly in the cysteine-, arginine-, and glutamine-rich domains and identify novel point mutations in HIV-1B and C sequences from Southern Brazil. This study was the first to investigate the genetic diversity and point mutations within HIV-1 Tat C in a Brazilian cohort. This was an observational, cross-sectional study, which included sequences of HIV-1B (n = 20) and HIV-1C (n = 21) from Southern Brazil. Additionally, 344 HIV-1C sequences were obtained from the Los Alamos database: 29 from Brazil and 315 from Africa, Asia, and Europe. The frequency of C31S substitution on HIV-1 Tat C in Brazil was 82% vs. 10% in the HIV-1B group (p < 0.0001). The frequency of the R57S substitution among the HIV-1C sequences from Brazil was 74% vs. 20% in HIV-1B (p = 0.004), and that of substitution Q63E in HIV-1C was 80% and 20% in HIV-1B (p < 0.0001). The mutation P60Q was more frequent in HIV-1B than in HIV-1C (55% and 6.12%, respectively, p < 0.0001)). Novel point mutations in the HIV-1C and B Tat functional domains were described. The frequency of C31S and other key point mutations in HIV-1 Tat C in Brazil were similar to those described in Africa, although lower than those in India. The Tat-B and C sequences found in Southern Brazil are consistent with biological differences and have potential implications for HIV-1 subtype pathogenesis.
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Affiliation(s)
| | | | | | | | - Avindra Nath
- National Institute of Neurological Disorders and Stroke, NIH/NINDS, Bethesda, USA
| | - Kory Johnson
- National Institute of Neurological Disorders and Stroke, NIH/NINDS, Bethesda, USA
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Balance between Retroviral Latency and Transcription: Based on HIV Model. Pathogens 2020; 10:pathogens10010016. [PMID: 33383617 PMCID: PMC7824405 DOI: 10.3390/pathogens10010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/04/2023] Open
Abstract
The representative of the Lentivirus genus is the human immunodeficiency virus type 1 (HIV-1), the causative agent of acquired immunodeficiency syndrome (AIDS). To date, there is no cure for AIDS because of the existence of the HIV-1 reservoir. HIV-1 infection can persist for decades despite effective antiretroviral therapy (ART), due to the persistence of infectious latent viruses in long-lived resting memory CD4+ T cells, macrophages, monocytes, microglial cells, and other cell types. However, the biology of HIV-1 latency remains incompletely understood. Retroviral long terminal repeat region (LTR) plays an indispensable role in controlling viral gene expression. Regulation of the transcription initiation plays a crucial role in establishing and maintaining a retrovirus latency. Whether and how retroviruses establish latency and reactivate remains unclear. In this article, we describe what is known about the regulation of LTR-driven transcription in HIV-1, that is, the cis-elements present in the LTR, the role of LTR transcription factor binding sites in LTR-driven transcription, the role of HIV-1-encoded transactivator protein, hormonal effects on virus transcription, impact of LTR variability on transcription, and epigenetic control of retrovirus LTR. Finally, we focus on a novel clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/dCas9)-based strategy for HIV-1 reservoir purging.
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In-Vitro Subtype-Specific Modulation of HIV-1 Trans-Activator of Transcription (Tat) on RNAi Silencing Suppressor Activity and Cell Death. Viruses 2019; 11:v11110976. [PMID: 31652847 PMCID: PMC6893708 DOI: 10.3390/v11110976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 01/22/2023] Open
Abstract
Human immunodeficiency virus (HIV) is a global health concern affecting millions of individuals with a wide variety of currently circulating subtypes affecting various regions of the globe. HIV relies on multiple regulatory proteins to modify the host cell to promote replication in infected T cells, and these regulatory proteins can have subtle phenotypic differences between subtypes. One of these proteins, HIV-1 Trans-Activator of Transcription (Tat), is capable of RNA interference (RNAi) Silencing Suppressor (RSS) activity and induction of cell death in T cells. However, the subtype-specific RSS activity and induction of cell death have not been explored. We investigated the ability of Tat subtypes and variants to induce RSS activity and cell death. TatB, from HIV-1 subtype B, was found to be a potent RSS activator by 40% whereas TatC, from HIV-1 subtype C, showed 15% RSS activity while subtype TatC variants exhibited varying levels. A high level of cell death (50–53%) was induced by subtype TatB when compared to subtype TatC (25–28%) and varying levels were observed with subtype TatC variants. These differential activities could be due to variations in the functional domains of Tat. These observations further our understanding of subtype-specific augmentation of Tat in HIV-1 replication and pathogenesis.
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Ronsard L, Sood V, Yousif AS, Ramesh J, Shankar V, Das J, Sumi N, Rai T, Mohankumar K, Sridharan S, Dorschel A, Ramachandran VG, Banerjea AC. Genetic Polymorphisms in the Open Reading Frame of the CCR5 gene From HIV-1 Seronegative and Seropositive Individuals From National Capital Regions of India. Sci Rep 2019; 9:7594. [PMID: 31110236 PMCID: PMC6527560 DOI: 10.1038/s41598-019-44136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/10/2019] [Indexed: 11/19/2022] Open
Abstract
C-C chemokine receptor type 5 (CCR5) serves as a co-receptor for Human immunodeficiency virus (HIV), enabling the virus to enter human CD4 T cells and macrophages. In the absence of CCR5, HIV strains that require CCR5 (R5 or M-tropic HIV) fail to successfully initiate infection. Various natural mutations of the CCR5 gene have been reported to interfere with the HIV-CCR5 interaction, which influences the rate of AIDS progression. Genetic characterization of the CCR5 gene in individuals from the National Capital Regions (NCRs) of India revealed several natural point mutations in HIV seropositive/negative individuals. Furthermore, we identified novel frame-shifts mutations in the CCR5 gene in HIV seronegative individuals, as well as the well reported CCR5Δ32 mutation. Additionally, we observed a number of mutations present only in HIV seropositive individuals. This is the first report to describe the genetic variations of CCR5 in individuals from the NCRs of India and demonstrates the utility of investigating understudied populations to identify novel CCR5 polymorphisms.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of Immunology, New Delhi, India. .,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India. .,Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA.
| | - Vikas Sood
- Laboratory of Virology, National Institute of Immunology, New Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA
| | - Janani Ramesh
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vijay Shankar
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA
| | - N Sumi
- Endocrinology & Toxicology Lab, Department of Zoology, University of Calicut, Kerala, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Delhi, India
| | | | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
| | | | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India.
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Ramesh J, Ronsard L, Gao A, Venugopal B. Autophagy Intertwines with Different Diseases-Recent Strategies for Therapeutic Approaches. Diseases 2019; 7:diseases7010015. [PMID: 30717078 PMCID: PMC6473623 DOI: 10.3390/diseases7010015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a regular and substantial “clear-out process” that occurs within the cell and that gets rid of debris that accumulates in membrane-enclosed vacuoles by using enzyme-rich lysosomes, which are filled with acids that degrade the contents of the vacuoles. This machinery is well-connected with many prevalent diseases, including cancer, HIV, and Parkinson’s disease. Considering that autophagy is well-known for its significant connections with a number of well-known fatal diseases, a thorough knowledge of the current findings in the field is essential in developing therapies to control the progression rate of diseases. Thus, this review summarizes the critical events comprising autophagy in the cellular system and the significance of its key molecules in manifesting this pathway in various diseases for down- or upregulation. We collectively reviewed the role of autophagy in various diseases, mainly neurodegenerative diseases, cancer, inflammatory diseases, and renal disorders. Here, some collective reports on autophagy showed that this process might serve as a dual performer: either protector or contributor to certain diseases. The aim of this review is to help researchers to understand the role of autophagy-regulating genes encoding functional open reading frames (ORFs) and its connection with diseases, which will eventually drive better understanding of both the progression and suppression of different diseases at various stages. This review also focuses on certain novel therapeutic strategies which have been published in the recent years based on targeting autophagy key proteins and its interconnecting signaling cascades.
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Affiliation(s)
- Janani Ramesh
- Department of Medical Biochemistry, Dr. A.L.M. Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai 600113, India.
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02140, USA.
| | - Anthony Gao
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Bhuvarahamurthy Venugopal
- Department of Medical Biochemistry, Dr. A.L.M. Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai 600113, India.
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Liu T, Xiao P, Li R, She R, Tian J, Wang J, Mao J, Yin J, Shi R. Increased Mast Cell Activation in Mongolian Gerbils Infected by Hepatitis E Virus. Front Microbiol 2018; 9:2226. [PMID: 30333798 PMCID: PMC6175998 DOI: 10.3389/fmicb.2018.02226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/31/2018] [Indexed: 12/21/2022] Open
Abstract
Recently, mechanism study of hepatitis E virus (HEV) infection has attracted an increasing attention because of the growing rate of the acute hepatitis caused by the virus over the world. As an important initiate in the inflammation, mast cells (MCs) play a critical role in maintaining a healthy physiology. However, the function of the MCs in the acute hepatitis caused by HEV is still unclear. In the present study, mongolian gerbils infected by HEV were used as an animal model to evaluate the role of MCs in the HEV infection. The positive ELISA and RT-PCR results showed the gerbils was successfully infected with HEV. The number of mast cell in the liver and the small intestine in the infected animals were growing higher significantly than the control group. In addition, higher expression of the tryptase and 5-HT in the liver and the intestine detected by immunohistochemical method and western blot also indicate the activation of MCs in the infection. These results suggest that MCs play an important role in the hepatitis E.
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Affiliation(s)
- Tianlong Liu
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Peng Xiao
- Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Ruiwen Li
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Dingzhou, China
| | - Ruiping She
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jijing Tian
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingyuan Wang
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingjing Mao
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jun Yin
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruihan Shi
- Laboratory of Veterinary Pathology and Public Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Zitzmann C, Kaderali L. Mathematical Analysis of Viral Replication Dynamics and Antiviral Treatment Strategies: From Basic Models to Age-Based Multi-Scale Modeling. Front Microbiol 2018; 9:1546. [PMID: 30050523 PMCID: PMC6050366 DOI: 10.3389/fmicb.2018.01546] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/21/2018] [Indexed: 12/14/2022] Open
Abstract
Viral infectious diseases are a global health concern, as is evident by recent outbreaks of the middle east respiratory syndrome, Ebola virus disease, and re-emerging zika, dengue, and chikungunya fevers. Viral epidemics are a socio-economic burden that causes short- and long-term costs for disease diagnosis and treatment as well as a loss in productivity by absenteeism. These outbreaks and their socio-economic costs underline the necessity for a precise analysis of virus-host interactions, which would help to understand disease mechanisms and to develop therapeutic interventions. The combination of quantitative measurements and dynamic mathematical modeling has increased our understanding of the within-host infection dynamics and has led to important insights into viral pathogenesis, transmission, and disease progression. Furthermore, virus-host models helped to identify drug targets, to predict the treatment duration to achieve cure, and to reduce treatment costs. In this article, we review important achievements made by mathematical modeling of viral kinetics on the extracellular, intracellular, and multi-scale level for Human Immunodeficiency Virus, Hepatitis C Virus, Influenza A Virus, Ebola Virus, Dengue Virus, and Zika Virus. Herein, we focus on basic mathematical models on the population scale (so-called target cell-limited models), detailed models regarding the most important steps in the viral life cycle, and the combination of both. For this purpose, we review how mathematical modeling of viral dynamics helped to understand the virus-host interactions and disease progression or clearance. Additionally, we review different types and effects of therapeutic strategies and how mathematical modeling has been used to predict new treatment regimens.
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Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
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van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C, Cornelissen M. The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012. Virus Res 2018; 250:51-64. [PMID: 29654800 DOI: 10.1016/j.virusres.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/18/2022]
Abstract
For the production of viral genomic RNA, HIV-1 is dependent on an early viral protein, Tat, which is required for high-level transcription. The quantity of viral RNA detectable in blood of HIV-1 infected individuals varies dramatically, and a factor involved could be the efficiency of Tat protein variants to stimulate RNA transcription. HIV-1 virulence, measured by set-point viral load, has been observed to increase over time in the Netherlands and elsewhere. Investigation of tat gene evolution in clinical isolates could discover a role of Tat in this changing virulence. A dataset of 291 Dutch HIV-1 subtype B tat genes, derived from full-length HIV-1 genome sequences from samples obtained between 1985-2012, was used to analyse the evolution of Tat. Twenty-two patient-derived tat genes, and the control TatHXB2 were analysed for their capacity to stimulate expression of an LTR-luciferase reporter gene construct in diverse cell lines, as well as for their ability to complement a tat-defective HIV-1LAI clone. Analysis of 291 historical tat sequences from the Netherlands showed ample amino acid (aa) variation between isolates, although no specific mutations were selected for over time. Of note, however, the encoded protein varied its length over the years through the loss or gain of stop codons in the second exon. In transmission clusters, a selection against the shorter Tat86 ORF was apparent in favour of the more common Tat101 version, likely due to negative selection against Tat86 itself, although random drift, transmission bottlenecks, or linkage to other variants could also explain the observation. There was no correlation between Tat length and set-point viral load; however, the number of non-intermediate variants in our study was small. In addition, variation in the length of Tat did not significantly change its capacity to stimulate transcription. From 1985 till 2012, variation in the length of the HIV-1 subtype B tat gene is increasingly found in the Dutch epidemic. However, as Tat proteins did not differ significantly in their capacity to stimulate transcription elongation in vitro, the increased HIV-1 virulence seen in recent years could not be linked to an evolving viral Tat protein.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Monique Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Fokla Zorgdrager
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Chris Wymant
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - François Blanquart
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Christophe Fraser
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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12
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Ronsard L, Rai T, Rai D, Ramachandran VG, Banerjea AC. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity. Front Microbiol 2017; 8:1467. [PMID: 28848502 PMCID: PMC5550727 DOI: 10.3389/fmicb.2017.01467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC) is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues) of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesNew Delhi, India
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesNew Delhi, India
| | - Vishnampettai G Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India
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13
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Ronsard L, Ganguli N, Singh VK, Mohankumar K, Rai T, Sridharan S, Pajaniradje S, Kumar B, Rai D, Chaudhuri S, Coumar MS, Ramachandran VG, Banerjea AC. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol 2017; 8:706. [PMID: 28484443 PMCID: PMC5399533 DOI: 10.3389/fmicb.2017.00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyDelhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalDelhi, India
| | - Nilanjana Ganguli
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
| | - Vivek K Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | - Kumaravel Mohankumar
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Veterinary Physiology and Pharmacology, Texas A&M University, College StationTX, USA
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesDelhi, India
| | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Symptom Research, The University of Texas MD Anderson Cancer Center, HoustonTX, USA
| | - Sankar Pajaniradje
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India
| | - Binod Kumar
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, ChicagoIL, USA
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesDelhi, India
| | - Suhnrita Chaudhuri
- Department of Neurological Surgery, Northwestern University, ChicagoIL, USA
| | - Mohane S Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
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14
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Aralaguppe SPG, Sharma S, Menon M, Prasad VR, Saravanan S, Murugavel KG, Solomon S, Ranga U. The Evolving Profile of the Signature Amino Acid Residues in HIV-1 Subtype C Tat. AIDS Res Hum Retroviruses 2016; 32:503-14. [PMID: 26678403 DOI: 10.1089/aid.2015.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Using several HIV-1 tat exon 1 amino acid sequences available from public databases and additional sequences derived from a southern Indian clinical cohort, we compared the profile of the signature amino acid residues (SAR) between two different time periods, 1986-2004 and 2005-2014. The analysis identified eight positions as signature residues in subtype C Tat and demonstrated a changing pattern at four of these positions between the two periods. At three locations (histidine 29, serine 57, and proline 60), there appears to be a nonuniform negative selection against the SAR. The negative selection appears to be severe, especially against histidine 29 (p < .0001) and moderate against proline 60 (p < .0001). The negative selection against serine 57 is statistically insignificant and appears to have begun recently. At position 63, the frequency of signature residue glutamic acid increased over the past decade, although the difference was not significant. Importantly, at the three locations where the negative selection is in progress, the substitute amino acids are the generic residues present in most of the other HIV-1 subtypes. Our data demonstrate that viral evolution can subject specific amino acid residues to subtle and progressive selection pressures without affecting the prevalence of other amino acid residues.
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Affiliation(s)
- Shambhu Prasad G. Aralaguppe
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Shilpee Sharma
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Malini Menon
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Vinayaka R. Prasad
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, New York
| | | | | | - Suniti Solomon
- YRG Centre for AIDS Research and Education, Chennai, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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15
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Hser YI, Liang D, Lan YC, Vicknasingam BK, Chakrabarti A. Drug Abuse, HIV, and HCV in Asian Countries. J Neuroimmune Pharmacol 2016; 11:383-93. [PMID: 27000123 DOI: 10.1007/s11481-016-9665-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/10/2016] [Indexed: 02/07/2023]
Abstract
Drug abuse and co-occurring infections are associated with significant morbidity and mortality. Asian countries are particularly vulnerable to the deleterious consequences of these risks/problems, as they have some of the highest rates of these diseases. This review describes drug abuse, HIV, and hepatitis C (HCV) in Asian countries. The most commonly used illicit drugs include opioids, amphetamine-type stimulants (ATS), cannabis, and ketamine. Among people who inject drugs, HIV rates range from 6.3 % in China to 19 % in Malaysia, and HCV ranges from 41 % in India and Taiwan to 74 % in Vietnam. In the face of the HIV epidemics, drug policies in these countries are slowly changing from the traditional punitive approach (e.g., incarcerating drug users or requiring registration as a drug user) to embrace public health approaches, including, for example, community-based treatment options as well as harm reduction approaches to reduce needle sharing and thus HIV transmission. HIV and HCV molecular epidemiology indicates limited geographic diffusion. While the HIV prevalence is declining in all five countries, use of new drugs (e.g., ATS, ketamine) continues to increase, as well as high-risk sexual behaviors associated with drug use-increasing the risk of sexual transmission of HIV, particularly among men who have sex with men. Screening, early intervention, and continued scaling up of therapeutic options (drug treatment and recovery support, ART, long-term HIV and HCV care for drug users) are critical for effective control or continued reduction of drug abuse and co-infections.
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Affiliation(s)
- Yih-Ing Hser
- University of California, Los Angeles, Los Angeles, CA, USA. .,China Medical University, Taichung City, Taiwan.
| | - Di Liang
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Amit Chakrabarti
- Regional Occupational Health Centre (ROHC), Eastern, National Institute of Occupational Health, Ahmedabad, Gujarat, India
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16
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Genetic and functional characterization of HIV-1 Vif on APOBEC3G degradation: First report of emergence of B/C recombinants from North India. Sci Rep 2015; 5:15438. [PMID: 26494109 PMCID: PMC4616021 DOI: 10.1038/srep15438] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 07/02/2015] [Indexed: 12/12/2022] Open
Abstract
HIV-1 is characterized by high genetic heterogeneity which is a challenge for developing therapeutics. Therefore, it is necessary to understand the extent of genetic variations that HIV is undergoing in North India. The objective of this study was to determine the role of genetic and functional role of Vif on APOBEC3G degradation. Vif is an accessory protein involved in counteracting APOBEC3/F proteins. Genetic analysis of Vif variants revealed that Vif C variants were closely related to South African Vif C whereas Vif B variants and Vif B/C showed distinct geographic locations. This is the first report to show the emergence of Vif B/C in our population. The functional domains, motifs and phosphorylation sites were well conserved. Vif C variants differed in APOBEC3G degradation from Vif B variants. Vif B/C revealed similar levels of APOBEC3G degradation to Vif C confirming the presence of genetic determinants in C-terminal region. High genetic diversity was observed in Vif variants which may cause the emergence of more complex and divergent strains. These results reveal the genetic determinants of Vif in mediating APOBEC3G degradation and highlight the genetic information for the development of anti-viral drugs against HIV. Importance: Vif is an accessory HIV-1 protein which plays significant role in the degradation of human DNA-editing factor APOBEC3G, thereby impeding the antiretroviral activity of APOBEC3G. It is known that certain natural polymorphisms in Vif could degrade APOBEC3G relatively higher rate, suggesting its role in HIV-1 pathogenesis. This is the first report from North India showcasing genetic variations and novel polymorphisms in Vif gene. Subtype C is prevalent in India, but for the first time we observed putative B/C recombinants with a little high ability to degrade APOBEC3G indicating adaptation and evolving nature of virus in our population. Indian Vif C variants were able to degrade APOBEC3G well in comparison to Vif B variants. These genetic changes were most likely selected during adaptation of HIV to our population. These results elucidate that the genetic determinants of Vif and highlights the potential targets for therapeutics.
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17
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Aggarwal S, Phadke SR. Medical genetics and genomic medicine in India: current status and opportunities ahead. Mol Genet Genomic Med 2015; 3:160-71. [PMID: 26029702 PMCID: PMC4444157 DOI: 10.1002/mgg3.150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, India ; Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India
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