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Khan NH, Kohli M, Gupta K, Das BK, Pandey RM, Sinha S. HIV Drug Resistance Mutations in Patients with HIV and HIV-TB Coinfection After Failure of First-Line Therapy: A Prevalence Study in a Resource-Limited Setting. J Int Assoc Provid AIDS Care 2020; 18:2325958219849061. [PMID: 31117863 PMCID: PMC6748516 DOI: 10.1177/2325958219849061] [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] [Indexed: 11/17/2022] Open
Abstract
Introduction: The present study aimed to report the prevalent HIV-1 drug-resistant mutations in
patients with HIV-1 alone and tuberculosis (TB) coinfection alone to improve our
understanding of the mutation patterns and aid treatment decisions. Methods: Patients with HIV-1 and HIV-TB on treatment for more than 1 year with suspected failure
were recruited. Sequencing of protease and two-thirds of the region of reverse
transcriptase gene was done for drug-resistant mutations. Results: In the HIV-TB group (n = 25), 88%, 92%, and 12% had mutations to nucleoside reverse
transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors
(NNRTIs), and protease inhibitors (PIs), respectively. In the HIV-alone group (n = 25),
84%, 100%, and 4% had mutations to NRTIs, NNRTIs, and PIs, respectively. M184V, M41L,
D67N, G190A, A98G, and K103N were the most common mutations seen. Conclusion: There is a high prevalence of drug-resistant mutations in HIV and HIV-TB coinfected
patients.
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Affiliation(s)
- Nawaid Hussain Khan
- 1 Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Mikashmi Kohli
- 1 Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Kartik Gupta
- 1 Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Kumar Das
- 2 Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ravindra Mohan Pandey
- 3 Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjeev Sinha
- 1 Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
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2
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Mefford ME, Kunstman K, Wolinsky SM, Gabuzda D. Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5. Virology 2015; 481:210-22. [PMID: 25797607 DOI: 10.1016/j.virol.2015.01.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 12/17/2013] [Accepted: 01/28/2015] [Indexed: 10/23/2022]
Abstract
Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120-CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues.
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Affiliation(s)
- Megan E Mefford
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Kevin Kunstman
- Northwestern University Medical School, Chicago, IL, USA.
| | | | - Dana Gabuzda
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurology (Microbiology and Immunobiology), Harvard Medical School, Boston, MA, USA.
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3
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Dahiya S, Irish BP, Nonnemacher MR, Wigdahl B. Genetic variation and HIV-associated neurologic disease. Adv Virus Res 2013; 87:183-240. [PMID: 23809924 DOI: 10.1016/b978-0-12-407698-3.00006-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-associated neurologic disease continues to be a significant complication in the era of highly active antiretroviral therapy. A substantial subset of the HIV-infected population shows impaired neuropsychological performance as a result of HIV-mediated neuroinflammation and eventual central nervous system (CNS) injury. CNS compartmentalization of HIV, coupled with the evolution of genetically isolated populations in the CNS, is responsible for poor prognosis in patients with AIDS, warranting further investigation and possible additions to the current therapeutic strategy. This chapter reviews key advances in the field of neuropathogenesis and studies that have highlighted how molecular diversity within the HIV genome may impact HIV-associated neurologic disease. We also discuss the possible functional implications of genetic variation within the viral promoter and possibly other regions of the viral genome, especially in the cells of monocyte-macrophage lineage, which are arguably key cellular players in HIV-associated CNS disease.
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Affiliation(s)
- Satinder Dahiya
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Bryan P Irish
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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4
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Kuo SM, Kao HW, Hou MH, Wang CH, Lin SH, Su HL. Evolution of infectious bronchitis virus in Taiwan: positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity. Vet Microbiol 2012; 162:408-418. [PMID: 23159091 PMCID: PMC7117379 DOI: 10.1016/j.vetmic.2012.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 10/15/2012] [Accepted: 10/17/2012] [Indexed: 12/04/2022]
Abstract
RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5’ end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA–N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein.
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Affiliation(s)
- Shu-Ming Kuo
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hsiao-Wei Kao
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Ho Wang
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Siou-Hong Lin
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hong-Lin Su
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Department of Physical Therapy, Graduate Institute of Rehabilitation Science, China Medical University, Taichung, Taiwan.
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5
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Spudich S, González-Scarano F. HIV-1-related central nervous system disease: current issues in pathogenesis, diagnosis, and treatment. Cold Spring Harb Perspect Med 2012; 2:a007120. [PMID: 22675662 PMCID: PMC3367536 DOI: 10.1101/cshperspect.a007120] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
HIV-associated central nervous system (CNS) injury continues to be clinically significant in the modern era of HIV infection and therapy. A substantial proportion of patients with suppressed HIV infection on optimal antiretroviral therapy have impaired performance on neuropsychological testing, suggesting persistence of neurological abnormalities despite treatment and projected long-term survival. In the underresourced setting, limited accessibility to antiretroviral medications means that CNS complications of later-stage HIV infection continue to be a major concern. This article reviews key recent advances in our understanding of the neuropathogenesis of HIV, focusing on basic and clinical studies that reveal viral and host features associated with viral neuroinvasion, persistence, and immunopathogenesis in the CNS, as well as issues related to monitoring and treatment of HIV-associated CNS injury in the current era.
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Affiliation(s)
- Serena Spudich
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
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6
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Cinque P, Brew BJ, Gisslen M, Hagberg L, Price RW. Cerebrospinal fluid markers in central nervous system HIV infection and AIDS dementia complex. HANDBOOK OF CLINICAL NEUROLOGY 2007; 85:261-300. [PMID: 18808988 DOI: 10.1016/s0072-9752(07)85017-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Paola Cinque
- Clinic of Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
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7
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van Marle G, Power C. Human immunodeficiency virus type 1 genetic diversity in the nervous system: Evolutionary epiphenomenon or disease determinant? J Neurovirol 2005; 11:107-28. [PMID: 16036790 DOI: 10.1080/13550280590922838] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Over the past decade there has been a revolution in the understanding and care of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-associated disease. Much of this progress stems from a broader recognition of the importance of differences in viral types, including receptor preference(s), replication properties, and reservoirs, as contributing factors to immunosuppresion and disease progression. In contrast, there is limited conceptualizatin of viral diversity and turnover in the brain and circulation in relation to neurocognitive impairments. Herein, the authors review current concepts regarding viral molecular diversity and phenotypes together with features of HIV-1 neuroinvasion, neurotropism, neurovirulence and neurosusceptiblity. Viral genetic and antigenic diversity is reduced within the brain compared to blood or other systemic organs within individuals. Conversely, viral molecular heterogeneity is greater in patients with HIV-associated dementia compared to nondemented patients, depending on the viral gene examined. Individual viral proteins exert multiple neuropathogenic effects, although the neurological consequences of different viral polymorphisms remain uncertain. Nonetheless, host genetic polymorphisms clearly influence neurological disease outcomes and likely dictate both acquired and innate immune responses, which in turn shape viral evolution within the host. Emerging issues include widespread antiretroviral therapy resistance and increasing awareness of viral superinfections together with viral recombination, all of which are likely to impact on both HIV genetic variation and neuropathogenesis. With the persisting prevalence of HIV-induced neurocognitive disabilities, despite marked improvements in managing immunosuppression, it remains imperative to fully define and understand the mechanisms by which viral dynamics and diversity contribute to neurological disease, permitting the development of new therapeutic strategies.
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Affiliation(s)
- Guido van Marle
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
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Tirado G, Jove G, Kumar R, Noel RJ, Reyes E, Sepulveda G, Yamamura Y, Kumar A. Differential virus evolution in blood and genital tract of HIV-infected females: evidence for the involvement of drug and non-drug resistance-associated mutations. Virology 2004; 324:577-86. [PMID: 15207642 DOI: 10.1016/j.virol.2004.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 01/30/2004] [Accepted: 04/09/2004] [Indexed: 11/19/2022]
Abstract
There is increasing evidence that male or female genital tract represent a distinct replication compartment for human immunodeficiency virus type 1 (HIV-1) and that such compartments may serve as a virus reservoir. Forty-four paired plasma and vaginal samples from HIV-infected females undergoing HAART were collected to examine the viral responses to antiretroviral therapy and to assess the possible role of the vaginal tract as a reservoir for drug-resistant variants. Twenty-one females had detectable viral RNA both in plasma and vaginal fluid, whereas 14 females had detectable virus only in plasma. Twelve paired samples were used to analyze HIV-1 pol sequences for the presence of drug resistance-associated mutations. Nine of the twelve paired samples exhibited discordant drug resistance mutation patterns. The other three females showed identical drug resistance-associated mutations. However, further examination of protease and RT showed numerous non-drug-associated mutations that corresponded to predefined CTL epitopes. These non-drug-associated mutations were different between plasma and vaginal viruses, suggesting that evolution of HIV-1 was independent in these two compartments.
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Affiliation(s)
- Grissell Tirado
- Laboratory of Viral Immunology, Ponce School of Medicine, Ponce 00732, Puerto Rico
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9
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Potter SJ, Lemey P, Achaz G, Chew CB, Vandamme AM, Dwyer DE, Saksena NK. HIV-1 compartmentalization in diverse leukocyte populations during antiretroviral therapy. J Leukoc Biol 2004; 76:562-70. [PMID: 15218056 DOI: 10.1189/jlb.0404234] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
CD4+ T lymphocytes are the primary target of human immunodeficiency virus type 1 (HIV-1), but there is increasing evidence that other immune cells in the blood, including CD8+ T lymphocytes and monocytes, are also productively infected. The extent to which these additional cellular reservoirs contribute to ongoing immunodeficiency and viral persistence during therapy remains unclear. In this study, we conducted a detailed investigation of HIV-1 diversity and genetic structure in CD4+ T cells, CD8+ T cells, and monocytes of 13 patients receiving highly active antiretroviral therapy (HAART). Analysis of molecular variance and nonparametric tests performed on HIV-1 envelope sequences provided statistically significant evidence of viral compartmentalization in different leukocyte populations. Signature pattern analysis and predictions of coreceptor use provided no evidence that selection arising from viral tropism was responsible for the genetic structure observed. Analysis of viral genetic variation in different leukocyte populations demonstrated the action of founder effects as well as significant variation in the extent of genetic differentiation between subpopulations among patients. In the absence of evidence for leukocyte-specific selection, these features were supportive of a metapopulation model of HIV-1 replication as described previously among HIV-1 populations in the spleen. Compartmentalization of the virus in different leukocytes may have significant implications for current models of HIV-1 population genetics and contribute to the highly variable way in which drug resistance evolves in different individuals during HAART.
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Affiliation(s)
- Simon J Potter
- Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Darcy Road, Westmead, Sydney NSW 2145, Australia
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