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Current HIV Research

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ISSN (Print): 1570-162X
ISSN (Online): 1873-4251

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Research Article

Genetic Analysis of HIV-1 vpr Sequences from HIV-Infected Older Patients on Long-Term Antiretroviral Therapy

Author(s): Maria Love, Luiza Samora, Danae Barker, Priya Zukosky, Nathan Kummet, Aasim Ahmad, Dana Bernhardt, Meghna Tripathi, Stephen Klotz and Nafees Ahmad*

Volume 20, Issue 4, 2022

Published on: 09 September, 2022

Page: [309 - 320] Pages: 12

DOI: 10.2174/1570162X20666220705124341

Price: $65

Abstract

Background: Many HIV-infected individuals have achieved undetectable viral load and increased CD4 T cell counts due to the success of Antiretroviral Therapy (ART). However, HIV persists in resting T cells, monocytes/macrophages and other quiescent cells. Furthermore, the HIV- 1 vpr accessory gene may play an important role in the persistence of HIV in these infected patients.

Objectives: Therefore, we characterized the HIV-1 vpr gene from PBMC DNA of 14 HIV-infected older patients on long-term ART with mostly undetectable viral load and increased CD4 T cell counts.

Methods: Peripheral Blood Mononuclear Cells (PBMC) were isolated from 14 HIV-infected individuals, followed by extraction of genomic DNA, amplification of HIV-1 vpr gene by polymerase chain reaction (PCR), cloning of vpr gene in TOPO vector and characterization of correct size recombinant inserts containing vpr genes. An average of 13 clones were sequenced from each patient, followed by sequence analysis by bioinformatic tools.

Results: Phylogenetic analysis of 182 vpr sequences demonstrated that the vpr sequences of each patient were well separated and discriminated from other patients’ sequences and formed distinct clusters. The vpr sequences showed a low degree of viral heterogeneity, lower estimates of genetic diversity and about half of the patients’ sequences were under positive selection pressure. While the majority of the vpr deduced amino acid sequences from most patients contained intact open reading frames, several sequences, mostly from two patients, had stop codons. Numerous patient-specific and common amino acid motifs were found in deduced vpr sequences. The functional domains required for vpr activity, including virion incorporation, nuclear import of pre-integration complex and cell cycle arrest, were generally conserved in most vpr sequences. Several of the known Cytotoxic T-lymphocytes (CTL) epitopes in vpr showed variation in our patients’ sequences.

Conclusion: In summary, a low degree of genetic variability, conservation of functional domains and variations in CTL epitopes were the features of vpr sequences from the 14 HIV-infected older patients with controlled viremia on long-term ART.

Keywords: HIV-infected older individuals, ART, vpr sequences, viral heterogeneity, CTL epitopes, PBMC.

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[1]
Kaplan-Lewis E, Aberg JA, Lee M. Aging with HIV in the ART era. Semin Diagn Pathol 2017; 34(4): 384-97.
[http://dx.doi.org/10.1053/j.semdp.2017.04.002] [PMID: 28552209]
[2]
Lorenzo-Redondo R, Fryer HR, Bedford T, et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature 2016; 530(7588): 51-6.
[http://dx.doi.org/10.1038/nature16933] [PMID: 26814962]
[3]
Effros RB, Fletcher CV, Gebo K, et al. Aging and infectious diseases: Workshop on HIV infection and aging: What is known and future research directions. Clin Infect Dis 2008; 47(4): 542-53.
[http://dx.doi.org/10.1086/590150] [PMID: 18627268]
[4]
Han Y, Lassen K, Monie D, et al. Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J Virol 2004; 78(12): 6122-33.
[http://dx.doi.org/10.1128/JVI.78.12.6122-6133.2004] [PMID: 15163705]
[5]
Equils O, Garratty E, Wei LS, et al. Recovery of replication-competent virus from CD4 T cell reservoirs and change in coreceptor use in human immunodeficiency virus type 1-infected children responding to highly active antiretroviral therapy. J Infect Dis 2000; 182(3): 751-7.
[http://dx.doi.org/10.1086/315758] [PMID: 10950768]
[6]
Behrens NE, Wertheimer A, Klotz SA, Ahmad N. Reduction in terminally differentiated T cells in virologically controlled HIV-infected aging patients on long-term antiretroviral therapy. PLoS One 2018; 13(6): e0199101.
[http://dx.doi.org/10.1371/journal.pone.0199101] [PMID: 29897981]
[7]
Behrens NE, Wertheimer A, Love MB, Klotz SA, Ahmad N. Evaluation of HIV-specific T-cell responses in HIV-infected older patients with controlled viremia on long-term antiretroviral therapy. PLoS One 2020; 15(9): e0236320.
[http://dx.doi.org/10.1371/journal.pone.0236320] [PMID: 32941433]
[8]
Orenstein JM, Feinberg M, Yoder C, et al. Lymph node architecture preceding and following 6 months of potent antiviral therapy: Follicular hyperplasia persists in parallel with p24 antigen restoration after involution and CD4 cell depletion in an AIDS patient. AIDS 1999; 13(16): 2219-29.
[http://dx.doi.org/10.1097/00002030-199911120-00004] [PMID: 10563707]
[9]
Behrens NE, Love M, Bandlamuri M, et al. Characterization of HIV-1 envelope V3 region sequences from virologically controlled HIV-infected older patients on long term antiretroviral therapy. AIDS Res Hum Retroviruses 2021; 37(3): 233-45.
[http://dx.doi.org/10.1089/aid.2020.0139] [PMID: 33287636]
[10]
Connor RI, Chen BK, Choe S, Landau NR. Vpr is required for efficient replication of human immunodeficiency virus type-1 in mononuclear phagocytes. Virology 1995; 206(2): 935-44.
[http://dx.doi.org/10.1006/viro.1995.1016] [PMID: 7531918]
[11]
Wallet C, Rohr O, Schwartz C. Evolution of a concept: From accessory protein to key virulence factor, the case of HIV-1 Vpr. Biochem Pharmacol 2020; 180: 114128.
[http://dx.doi.org/10.1016/j.bcp.2020.114128] [PMID: 32619426]
[12]
Heinzinger NK, Bukrinsky MI, Haggerty SA, et al. The vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in nondividing host cells. Proc Natl Acad Sci USA 1994; 91(15): 7311-5.
[http://dx.doi.org/10.1073/pnas.91.15.7311] [PMID: 8041786]
[13]
Kewalramani VN, Park CS, Gallombardo PA, Emerman M. Protein stability influences human immunodeficiency virus type 2 vpr virion incorporation and cell cycle effect. Virology 1996; 218(2): 326-34.
[http://dx.doi.org/10.1006/viro.1996.0201] [PMID: 8610459]
[14]
Mahalingam S, Ayyavoo V, Patel M, Kieber-Emmons T, Weiner DB. Nuclear import, virion incorporation, and cell cycle arrest/differentiation are mediated by distinct functional domains of human immunodeficiency virus type 1 Vpr. J Virol 1997; 71(9): 6339-47.
[http://dx.doi.org/10.1128/jvi.71.9.6339-6347.1997] [PMID: 9261351]
[15]
Di Marzio P, Choe S, Ebright M, Knoblauch R, Landau NR. Mutational analysis of cell cycle arrest, nuclear localization and virion packaging of human immunodeficiency virus type 1 Vpr. J Virol 1995; 69(12): 7909-16.
[http://dx.doi.org/10.1128/jvi.69.12.7909-7916.1995] [PMID: 7494303]
[16]
Fletcher TM III, Brichacek B, Sharova N, et al. Nuclear import and cell cycle arrest functions of the HIV-1 vpr protein are encoded by two separate genes in HIV-2/SIV(SM). EMBO J 1996; 15(22): 6155-65.
[http://dx.doi.org/10.1002/j.1460-2075.1996.tb01003.x] [PMID: 8947037]
[17]
Ayyavoo V, Mahalingam S, Rafaeli Y, et al. HIV-1 viral protein R (Vpr) regulates viral replication and cellular proliferation in T cells and monocytoid cells in vitro. J Leukoc Biol 1997; 62(1): 93-9.
[http://dx.doi.org/10.1002/jlb.62.1.93] [PMID: 9225999]
[18]
Le Rouzic E, Benichou S. The vpr protein from HIV-1: Distinct roles along the viral life cycle. Retrovirology 2005; 2(1): 11.
[http://dx.doi.org/10.1186/1742-4690-2-11] [PMID: 15725353]
[19]
Nitahara-Kasahara Y, Kamata M, Yamamoto T, et al. Novel nuclear import of vpr promoted by importin alpha is crucial for human immunodeficiency virus type 1 replication in macrophages. J Virol 2007; 81(10): 5284-93.
[http://dx.doi.org/10.1128/JVI.01928-06] [PMID: 17344301]
[20]
Zhang F, Bieniasz PD. HIV-1 vpr induces cell cycle arrest and enhances viral gene expression by depleting CCDC137. eLife 2020; 9: 9.
[http://dx.doi.org/10.7554/eLife.55806] [PMID: 32538781]
[21]
Emerman M. HIV-1, vpr and the cell cycle. Curr Biol 1996; 6(9): 1096-103.
[http://dx.doi.org/10.1016/S0960-9822(02)00676-0] [PMID: 8805364]
[22]
Poon B, Chen IS. Human immunodeficiency virus type 1 (HIV-1) vpr enhances expression from unintegrated HIV-1 DNA. J Virol 2003; 77(7): 3962-72.
[http://dx.doi.org/10.1128/JVI.77.7.3962-3972.2003] [PMID: 12634356]
[23]
Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261]
[24]
Ahmad N, Baroudy BM, Baker RC, Chappey C. Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 1995; 69(2): 1001-12.
[http://dx.doi.org/10.1128/jvi.69.2.1001-1012.1995] [PMID: 7815476]
[25]
Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72(8): 6937-43.
[http://dx.doi.org/10.1128/JVI.72.8.6937-6943.1998] [PMID: 9658150]
[26]
Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677]
[27]
Myers G. Theoretical Biology 1998.
[28]
Jukes TH, Cantor CR. CHAPTER 24 - Evolution of protein molecules. Mammalian Protein Metabolism 1969; pp. 21-132.
[http://dx.doi.org/10.1016/B978-1-4832-3211-9.50009-7]
[29]
Klötzl F, Haubold B. Support values for genome phylogenies. Life (Basel) 2016; 6(1): E11.
[http://dx.doi.org/10.3390/life6010011] [PMID: 26959064]
[30]
Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary? J Comput Biol 2010; 17(3): 337-54.
[http://dx.doi.org/10.1089/cmb.2009.0179] [PMID: 20377449]
[31]
Som A. Theoretical foundation to estimate the relative efficiencies of the Jukes-Cantor+gamma model and the Jukes-Cantor model in obtaining the correct phylogenetic tree. Gene 2006; 385: 103-10.
[http://dx.doi.org/10.1016/j.gene.2006.03.027] [PMID: 16979305]
[32]
Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975; 7(2): 256-76.
[http://dx.doi.org/10.1016/0040-5809(75)90020-9] [PMID: 1145509]
[33]
Posada D. Bioinformatics for DNA sequence analysis. Preface. Methods Mol Biol 2009; 537: vii-viii.
[http://dx.doi.org/10.1007/978-1-59745-251-9] [PMID: 19514139]
[34]
Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3(5): 418-26.
[PMID: 3444411]
[35]
Nei M. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci USA 2007; 104(30): 12235-42.
[http://dx.doi.org/10.1073/pnas.0703349104] [PMID: 17640887]
[36]
Ticher A, Graur D. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J Mol Evol 1989; 28(4): 286-98.
[http://dx.doi.org/10.1007/BF02103424] [PMID: 2499685]
[37]
Plikat U, Nieselt-Struwe K, Meyerhans A. Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. J Virol 1997; 71(6): 4233-40.
[http://dx.doi.org/10.1128/jvi.71.6.4233-4240.1997] [PMID: 9151810]
[38]
Holmes EC. de A Zanotto PM. Genetic drift of human immunodeficiency virus type 1? J Virol 1998; 72(1): 886-7.
[http://dx.doi.org/10.1128/JVI.72.1.886-887.1998] [PMID: 9420306]
[39]
Macreadie IG, Castelli LA, Hewish DR, Kirkpatrick A, Ward AC, Azad AA. A domain of human immunodeficiency virus type 1 vpr containing repeated H(S/F)RIG amino acid motifs causes cell growth arrest and structural defects. Proc Natl Acad Sci USA 1995; 92(7): 2770-4.
[http://dx.doi.org/10.1073/pnas.92.7.2770] [PMID: 7708721]
[40]
Sherman MP, de Noronha CM, Pearce D, Greene WC. Human immunodeficiency virus type 1 vpr contains two leucine-rich helices that mediate glucocorticoid receptor coactivation independently of its effects on G(2) cell cycle arrest. J Virol 2000; 74(17): 8159-65.
[http://dx.doi.org/10.1128/JVI.74.17.8159-8165.2000] [PMID: 10933727]
[41]
Mahalingam S, Khan SA, Jabbar MA, Monken CE, Collman RG, Srinivasan A. Identification of residues in the N-terminal acidic domain of HIV-1 vpr essential for virion incorporation. Virology 1995; 207(1): 297-302.
[http://dx.doi.org/10.1006/viro.1995.1081] [PMID: 7871742]
[42]
Srinivasan A, Ayyavoo V, Mahalingam S, et al. A comprehensive analysis of the naturally occurring polymorphisms in HIV-1 Vpr: Potential impact on CTL epitopes. Virol J 2008; 5(1): 99.
[http://dx.doi.org/10.1186/1743-422X-5-99] [PMID: 18721481]
[43]
Altfeld M, Addo MM, Eldridge RL, et al. Vpr is preferentially targeted by CTL during HIV-1 infection. J Immunol 2001; 167(5): 2743-52.
[http://dx.doi.org/10.4049/jimmunol.167.5.2743] [PMID: 11509618]
[44]
Balamurugan A, Ng HL, Yang OO. Cross-reactivity against multiple HIV-1 epitopes Is characteristic of HIV-1-specific cytotoxic T lymphocyte clones. J Virol 2018; 92(16): e00617-8.
[http://dx.doi.org/10.1128/JVI.00617-18] [PMID: 29899094]
[45]
Bernardin F, Kong D, Peddada L, Baxter-Lowe LA, Delwart E. Human immunodeficiency virus mutations during the first month of infection are preferentially found in known cytotoxic T-lymphocyte epitopes. J Virol 2005; 79(17): 11523-8.
[http://dx.doi.org/10.1128/JVI.79.17.11523-11528.2005] [PMID: 16103205]
[46]
Deng K, Pertea M, Rongvaux A, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature 2015; 517(7534): 381-5.
[http://dx.doi.org/10.1038/nature14053] [PMID: 25561180]
[47]
Marsden MD, Zack JA. Double trouble: HIV latency and CTL escape. Cell Host Microbe 2015; 17(2): 141-2.
[http://dx.doi.org/10.1016/j.chom.2015.01.008] [PMID: 25674977]
[48]
Selby MJ, Doe B, Walker CM. Virus-specific cytotoxic T-lymphocyte activity elicited by coimmunization with human immunodeficiency virus type 1 genes regulated by the bacteriophage T7 promoter and T7 RNA polymerase protein. J Virol 1997; 71(10): 7827-31.
[http://dx.doi.org/10.1128/jvi.71.10.7827-7831.1997] [PMID: 9311870]
[49]
Moir S, Chun TW, Fauci AS. Pathogenic mechanisms of HIV disease. Annu Rev Pathol 2011; 6(1): 223-48.
[http://dx.doi.org/10.1146/annurev-pathol-011110-130254] [PMID: 21034222]
[50]
Preston BD, Poiesz BJ, Loeb LA. Fidelity of HIV-1 reverse transcriptase. Science 1988; 242(4882): 1168-71.
[http://dx.doi.org/10.1126/science.2460924] [PMID: 2460924]
[51]
Dougherty JP, Temin HM. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication. J Virol 1988; 62(8): 2817-22.
[http://dx.doi.org/10.1128/jvi.62.8.2817-2822.1988] [PMID: 2839703]
[52]
Volkov I, Pepin KM, Lloyd-Smith JO, Banavar JR, Grenfell BT. Synthesizing within-host and population-level selective pressures on viral populations: The impact of adaptive immunity on viral immune escape. J R Soc Interface 2010; 7(50): 1311-8.
[http://dx.doi.org/10.1098/rsif.2009.0560] [PMID: 20335194]
[53]
Wolinsky SM, Korber BT, Neumann AU, et al. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996; 272(5261): 537-42.
[http://dx.doi.org/10.1126/science.272.5261.537] [PMID: 8614801]
[54]
Hofhuis J, Schueren F, Nötzel C, et al. The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code. Open Biol 2016; 6(11): 160246.
[http://dx.doi.org/10.1098/rsob.160246] [PMID: 27881739]
[55]
Allec SI, Sun Y, Sun J, Chang CA, Wong BM. Heterogenous CPU+GPU-enabled simulationsfor DFTB molecular dynamics of large chemical and biological systems. J Chem Theory Comput 2019; 15(5): 2807-15.
[http://dx.doi.org/10.1021/acs.jctc.8b01239] [PMID: 30916958]
[56]
Liu J, He X. QM impementation in drug discovery design: Does it really help? Quantum Mech Drug Disco 2020; 2114: 123-42.

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