Chapter 15 : The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder

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The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder, Page 1 of 2

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This chapter talks about the neuro-AIDS epidemic. Recent decreases in the heterogeneity of HIV sequences for many strains that have occurred in several places in the world including Southeast Asia are described, and their possible association with human behaviors such as drug abuse is considered. Genetic variability and sequence heterogeneity are key features of HIV. Its enzyme, reverse transcriptase (RT), exhibits the ability to jump between nucleic acid strands during replication, resulting in recombination of different types of HIV that infect the same cell. The basic risks for HIV infection are no mystery. Sexual activity, drug abuse (injection), transfusion, needle-sticks, and transplacental transmission are primary risks. It has been hypothesized that there are long-term viral reservoirs of HIV-1. These can exist in the context of T-cell latency as well as highly active antiretroviral therapy (HAART). HIV-associated neurocognitive disorders (HAND) recognized a spectrum of neurocognitive impairments ranging from asymptomatic neurocognitive impairment to HIV-1- associated mild neurocognitive disorder to full-blown HAD. HIV viral isolates and strains with different sequences appear to be important for the pathogenesis of brain disease in neuro-AIDS, and early studies identified HIV-1 isolates related to neuro-AIDS. Genetic recombination is a highly significant and effective mechanism associated with this genetic hypervariability that protects HIV-1 from immunity and eventually leads to profound immunosuppression and demise of AIDS patients.

Citation: Shapshak P, Minagar A, Kangueane P, Frost S, Kosakovsky Pond S, Zarate S, Singer E, Commins D, Groot A, Quinones-Mateu M, Terwilliger E. 2009. The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder, p 201-218. In Goodkin K, Shapshak P, Verma A (ed), The Spectrum of Neuro-AIDS Disorders. ASM Press, Washington, DC. doi: 10.1128/9781555815691.ch15

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Maximum likelihood phylogenetic trees for env sequences from different brain regions. MG94 x TrN93 codon model was used to infer the trees, scaled on the expected number of nucleotide substitutions per site per unit time. Bootstrap support values for clade-separating branches were obtained via 1,000 neighbor-joining bootstrap trees.

Citation: Shapshak P, Minagar A, Kangueane P, Frost S, Kosakovsky Pond S, Zarate S, Singer E, Commins D, Groot A, Quinones-Mateu M, Terwilliger E. 2009. The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder, p 201-218. In Goodkin K, Shapshak P, Verma A (ed), The Spectrum of Neuro-AIDS Disorders. ASM Press, Washington, DC. doi: 10.1128/9781555815691.ch15
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1. Abdulle, S.,, L. Hagberg, and, M. Gisslén. 2005. Effects of antiretroviral treatment on blood-brain barrier integrity and intrathecal immunoglobulin production in neuroasymptomatic HIV-1-infected patients. HIV Med. 6:164169.
2. Abebe, A.,, V. V. Lukashov,, T. F. Rinke de Wit,, B. Fisseha,, B. Tegbaru, and, A. Kliphuis. 2001. Timing of the introduction into Ethiopia of subcluster C9 of HIV-1 subtype C. AIDS Res. Hum. Retrovir. 17:657661.
3. Alaeus, A.,, E. Lilja,, S. Herman,, J. Spadoro,, J. Wang, and, J. Albert. 1999. Assay of plasma samples representing different HIV-1 genetic subtypes: an evaluation of new versions of the Amplicor HIV-1 Monitor assay. AIDS Res. Hum. Retrovir. 15:889894.
4. Alisky, J. 2007. The coming problem of HIV-associated Alzheimer’s disease. Med. Hypotheses 69:11401143.
5. Allen, T. M.,, X. G. Yu,, E. T. Kalife,, L. L. Reyor,, M. Licherfeld,, M. John, and, M. Cheng. 2005. De novo generation of escape variant-specific CD81 T-cell responses following CTL escape in chronic HIV-1 infection. J. Virol. 79:1295212960.
6. Altfeld, M.,, T. M. Allen,, X. G. Yu,, M. N. Johnston,, D. Agrawal,, B. T. Korber,, D. C. Montefiori,, D. H. O’Connor,, B. T. Davis,, P. K. Lee,, E. L. Maier,, J. Harlow,, P. J. Goulder,, C. Brander,, E. S. Rosenberg, and, B. D. Walker. 2002. HIV-1 superinfection despite broad CD81 T-cell responses containing replication of the primary virus. Nature 420:434439.
7. American Academy of Neurology AIDS Task Force. 1991. Nomenclature and research case definitions for neurologic manifestations of human immunodeficiency virus-type 1 (HIV-1) infection. Report of a Working Group of the American Academy of Neurology AIDS Task Force. Neurology 41:778785.
8. Andersson, S.,, H. Norrgren,, F. Dias,, G. Biberfeld, and, J. Albert. 1999. Molecular characterization of HIV-1 and HIV-2 in individuals from Guinea-Bissau with single or dual infections: predominance of a distinct HIV-1 subtype A/G recombinant in West Africa. Virology 262:312320.
9. Anthony, I. C.,, S. N. Ramage,, F. W. Carnie,, P. Simmonds, and, J. E. Bell. 2005. Influence of HAART on HIV-related CNS disease and neuroinflammation. J. Neuropathol. Exp. Neurol. 64:529536.
10. Antinori, A.,, G. Arendt,, J. T. Becker,, B. J. Brew,, D. A. Byrd,, M. Cherner,, D. B. Clifford,, P. Cinque,, L. G. Epstein,, K. Goodkin,, M. Gisslen,, I. Grant,, R. K. Heaton,, J. Joseph,, K. Marder,, C. M. Marra,, J. C. McArthur,, M. Nunn,, R. W. Price,, L. Pulliam,, K. R. Robertson,, N. Sacktor,, V. Valcour, and, V. E. Wojna. 2007. Updated research nosology for HIV-associated neurocognitive disorders. Neurology 69:17891799.
11. Babu, P. G.,, A. Pramilabai,, G. Sripriya,, S. Damodharan, and, J. T. Jacob. 1997. Immunologic profiles of HIV-infected and uninfected commercial sex workers in the Vellore region of Southern India. J. AIDS Hum. Retrovir. 16:357361.
12. Bakhanashvili, T. 2001. P53 enhances the fidelity of DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase. Oncogene 20:76357644.
13. Bell, J.,, J. C. Arango, and, I. Anthony. 2006. Neurobiology of multiple insults: HIV-1-associated brain disorders in those who use illicit drugs. J. Neuroimmune Pharmacol. 1:182191.
14. Bell, J. E. 1998. The neuropathology of adult HIV infection. Rev. Neurol. (Paris) 154:816829.
15. Bell, J. E. 2004. An update on the neuropathology of HIV in the HAART era. Histopathology 45:549559.
16. Bell, J. E.,, R. P. Brettle,, A. Chiswick, and, P. Simmonds. 1998. HIV encephalitis, proviral load and dementia in drug users and homosexuals with AIDS. Effect of neocortical involvement. Brain 121:20432052.
17. Bhaskaran, K.,, C. Mussini,, A. Antinori,, A. S. Walker,, M. Dorrucci,, C. Sabin,, A. Phillips,, K. Porter, et al. 2008. Changes in the incidence and predictors of human immunodeficiency virus-associated dementia in the era of highly active antiretroviral therapy. Ann. Neurol. 63:213221.
18. Boccara, F.,, and A. Cohen. 2003. Coronary artery disease and stroke in HIV-infected patients: prevention and pharmacological therapy. Adv. Cardiol. 40:163184.
19. Borthwick, N. J.,, M. Bofill,, W. M. Gombert,, A. N. Akbar,, E. Medina,, K. Sagawa,, M. C. Lipman,, M. A. Johnson, and, G. Janossy. 1994. Lymphocyte activation in HIV-1 infection. II. Functional defects of CD28-T cells. AIDS 8:431441.
20. Brew, B. J. 2004. Evidence for a change in AIDS dementia complex in the era of highly active antiretroviral therapy and the possibility of new forms of AIDS dementia complex. AIDS 1:7578.
21. Budka, H. 1986. Multinucleated giant cells in brain: a hallmark of the acquired immune deficiency syndrome (AIDS). Acta Neuropathol. (Berlin) 69:253258.
22. Chang, J.,, R. Joswiak,, B. Wang,, T. Ng,, Y. C. Ge, and, W. Bolton. 1998. Unique HIV type 1 V3 region sequences derived from 6 different regions of brain: region-specific evolution within host-determined quasispecies. AIDS Res. Hum. Retrovir. 14:2530.
23. Chang, S. Y.,, C. Apichartpiyakul,, C. L. Kuiken,, M. Essex, and, T. H. Lee. 1999. Sequence features downstream of the primer binding site of HIV-1 subtype E shared by subtype G and a subset of subtype A. AIDS Res. Hum. Retrovir. 15:17031706.
24. Chang, S. Y.,, B. H. Bowman,, J. B. Weiss,, R. E. Garcia, and, T. White. 1993. The origin of HIV-1 isolate HTLV-IIIB. Nature 363:466469.
25. Cheng-Mayer, C.,, D. Seto, and, J. A. Levy. 1991a. Altered host range of HIV-1 after passage through various human cell types. Virology 181:288294.
26. Cheng-Mayer, C.,, T. Shioda, and, J. A. Levy. 1991b. Host range, replicative, and cytopathic properties of human immunodeficiency virus type 1 are determined by very few amino acid changes in tat and gp120. J. Virol. 65:69316941.
27. Clapham, P. R.,, and A. McKnight. 2001. HIV-1 receptors and cell tropism. Br. Med. Bull. 58:4359.
28. Clark, S. J.,, M. S. Saag,, W. D. Decker,, S. Campbell-Hill,, J. L. Roberson,, P. J. Veldkamp,, J. C. Kappes,, B. H. Hahn, and, G. M. Shaw. 1991. High titers of cytopathic virus in plasma of patients with symptomatic primary HIV-1 infection. N. Engl. J. Med. 32:954960.
29. Clarke, J. R.,, S. Galpin,, R. Braganza,, A. Ashraf,, R. Russell,, D. R. Churchill,, J. N. Weber, and, M. O. McClure. 2000. Comparative quantification of diverse serotypes of HIV-1 in plasma from a diverse population of patients. J. Med. Virol. 62:445449.
30. Clements, J. E.,, M. Li,, L. Gama,, B. Bullock,, L. M. Carruth,, J. L. Mankowski, and, M. C. Zink. 2005. The CNS is a viral reservoir in SIV-infected macaques on combined antiretroviral therapy: a model for HIV patients on HAART. J. Neurovirol. 11:180189.
31. Coffin, J. M. 1995. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267:483489.
32. Constantine, N. T.,, J. D. Callahan, and, D. M. Watts. 1992. Retroviral Testing, Essentials for Quality Control and Laboratory Diagnosis, p. 89102. CRC Press, Ann Arbor, MI.
33. Crandall, K. 1996. Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type 1 sequences. Mol. Biol. Evol. 13:115131.
34. Cunningham, A. L.,, H. Naif,, N. Saksena,, G. Lynch,, J. Chang,, S. Li,, R. Jozwiak,, M. Alali,, B. Wang,, W. Fear,, A. Sloane,, L. Pemberton, and, B. J. Brew. 1997. HIV infection of macrophages and pathogenesis of AIDS dementia complex: interaction of the host cell and viral genotypes. J. Leukoc. Biol. 62:117125.
35. Cysique, L. A.,, B. J. Brew,, M. Halman,, J. Catalan,, N. Sacktor,, R. W. Price,, S. Brown,, J. H. Atkinson,, D. B. Clifford,, D. Simpson,, G. Torres,, C. Hall,, C. Power,, K. Marder,, J. C. McArthur,, W. Symonds, and, C. Romero. 2005. Undetectable cerebrospinal fluid HIV RNA and beta-2 microglobulin do not indicate inactive AIDS dementia complex in highly active antiretroviral therapy-treated patients. J. Acquir. Immune Defic. Syndr. 39:426429.
36. Cysique, L. A.,, P. Maruff, and, B. J. Brew. 2004. Prevalence and pattern of neuropsychological impairment in human immunodeficiency virus-infected/acquired immunodeficiency syndrome (HIV/AIDS) patients across pre- and post-highly active antiretroviral therapy eras: a combined study of two cohorts. J. Neurovirol. 10:350357.
37. Daar, E. S.,, T. Moudgil,, R. D. Meyer, and, D. D. Ho. 1991. Transient high levels of viremia in patients with primary human immunodeficiency virus type 1 infection. N. Engl. J. Med. 324:961964.
38. De Groot, A. S.,, H. Sbai,, J. Frost, and, C. Saint-Aubin. 2001. Designing HIV-1 vaccines to reflect viral diversity and the global context of HIV/AIDS. Science 1:116.
39. Dern, K.,, H. Rubsamen-Waigmann, and, R. E. Unger. 2001. Inhibition of HIV-1 replication by simultaneous infection of PBLs with HIV-1 and HIV-2. AIDS Res. Hum. Retrovir. 17:295309.
40. DeStefano, J. J.,, L. M. Mallaber,, L. Rodriguez,, P. J. Fay, and, R. A. Bambara. 1992. Requirements for strand transfer between internal regions of heteropolymer templates by human immunodeficiency virus reverse transcriptase. J. Virol. 66:63706380.
41. Dilley, J. W.,, S. Schwarcz,, L. Loeb,, L. Hsu,, K. Nelson, and, S. Scheer. 2005. The decline of incident cases of HIV-associated neurological disorders in San Francisco, 1991-2003. AIDS 19:634635.
42. Dore, G. J.,, P. K. Correll,, Y. Li,, J. M. Kaldor,, D. A. Cooper, and, B. J. Brew. 1999. Changes to AIDS dementia complex in the era of highly active antiretroviral therapy. AIDS 13:12491253.
43. Dore, G. J.,, A. McDonald,, Y. Li,, J. M. Kaldor, and, B. J. Brew. 2003. Marked improvement in survival following AIDS dementia complex in the era of highly active antiretroviral therapy. AIDS 17:15391545.
44. Dunfee, R.,, E. R. Thomas,, P. R. Gorry,, J. Wang,, J. Taylor,, K. Kunstman,, S. M. Wolinsky, and, D. Gabuzda. 2006a. The HIV env variant N283 enhances macrophage tropism and is associated with brain infection and dementia. Proc. Natl. Acad. Sci. USA 103:1516015165.
45. Dunfee, R.,, E. R. Thomas,, P. R. Gorry,, J. Wang,, P. Ancuta, and, D. Gabuzda. 2006b. Mechanisms of HIV-1 neurotropism. Curr. HIV Res. 4:267278.
46. Du Pasquier, R.,, M. Kuroda,, Y. Zheng,, J. Jean-Jacques,, N. Letvin, and, I. Koralnik. 2004. A prospective study demonstrates an association between JC virus-specific cytotoxic T lymphocytes and the early control of progressive multifocal leukoencephalopathy. Brain 127:19701978.
47. Edlin, B. R.,, K. L. Irwin,, S. Faruque,, C. B. McCoy,, C. Word,, Y. Serrano,, J. A. Inciardi,, B. P. Bowser,, R. F. Schilling, and, S. D. Holmberg. 1994. Intersecting epidemics--crack cocaine use and HIV infection among inner-city young adults. N. Engl. J. Med. 331:14221427.
48. Eisen, L. N.,, T. M. Field,, E. S. Bandstra,, J. P. Roberts,, C. Morrow,, S. K. Larson, and, B. M. Steele. 1991. Perinatal cocaine effects on neonatal stress behavior and performance on the Brazelton Scale. Pediatrics 88:477480.
49. Erdmann, N.,, Y. Huang, and, J. Zheng. 2006. The relevance of chemokines and cytokines to the pathogenesis of HIV-1 associated dementia, p. 41–80. In A. Minagar and, P. Shapshak (ed.), Neuro-AIDS. Nova Biomedical Books, New York, NY.
50. Essex, M. E. 1997. Origin of AIDS, p. 3–14. In V. T. de Vita, Jr.,, S. Hellman, and, S. A. Rosenberg (ed.), AIDS: Biology, Diagnosis, Treatment, and Prevention, 4th ed. Lippincott-Raven Publishers, Philadelphia, PA.
51. Esteves, A.,, J. Piedade,, C. Santos,, T. Venenno,, W. F. Canas-Ferreira, and, R. Parreira. 2001. Follow-up study of intra-host HIV-2 variability reveals discontinuous evolution of C2V3 sequences. AIDS Res. Hum. Retrovir. 17:253256.
52. Fellay, J.,, K. V. Shianna,, D. Ge,, S. Colombo,, B. Ledergerber,, M. Weale,, K. Zhang,, C. Gumbs, et al. 19 July 2007, posting date. Identification of major determinants of the host control of HIV-1 through a whole-genome association study. Science Express doi:10.1126/science.1143767.
53. Fernandez, F.,and, P. Ruiz (ed.). 2006. Psychiatric Aspects of HIV/AIDS, p. 69–146. Lippincott Williams & Wilkins, Philadelphia, PA.
54. Ferrando, S. J.,, and C. G. Lyketsos. 2006. Psychiatric comorbidities in medically ill patients with HIV/AIDS, p. 198–211. In F. Fernandez and, P. Ruiz (ed.), Psychiatric Aspects of HIV/AIDS. Lippincott Williams & Wilkins, Philadelphia, PA.
55. Finzi, D.,, J. Bankson,, J. D. Siliciano,, J. B. Margolick,, K. Chadwisk, and, T. Pierson. 1999. Latent infection of CD41 T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5:512517.
56. Forton, D. M.,, S. D. Taylor-Robinson, and, H. C. Thomas. 2003. Cerebral dysfunction in chronic hepatitis C infection. J. Viral Hepatol. 10:8186.
57. Frost, S. D.,, S. J. Little,, S. L. Pond,, C. Chappey,, Y. Liu,, T. Wrin,, C. J. Petropoulos, and, D. D. Richman. 2005. Characterization of HIV-1 envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J. Virol. 79:65236527.
58. Fujimura, R. K. 2006. Viral load on HIV-1 associated dementia: neuropathology and drug efficacy, p. 101–119. In A. Minagar and, P. Shapshak (ed.), Neuro-AIDS. Nova Biomedical Books, New York, NY.
59. Fujimura, R. K.,, K. Goodkin,, C. Petito,, R. Douyon,, D. Feaster,, M. Concha, and, P. Shapshak. 1997a. HIV-1 proviral DNA load across neuroanatomic regions of individuals with evidence for HIV-1-associated dementia. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 16:146152.
60. Fujimura, R. K.,, I. Khamis,, P. Shapshak, and, K. Goodkin. 2005. Regional quantitative comparison of multispliced to unspliced ratios of HIV-1 RNA copy number in infected human brain. J. Neuro-AIDS 2:4560.
61. Fujimura, R. K.,, P. Shapshak,, D. Feaster,, M. Epler, and, K. Goodkin. 1997b. A rapid method for comparative quantitative PCR of HIV-1 proviral DNA extracted from cryopreserved brain tissues. J. Virol. Methods 67:177187.
62. Garcia, J. V.,, and A. D. Miller. 1991. Serine phosphorylation-independent downregulation of cell-surface CD4 by nef. Nature 350:508511.
63. Gartner, S. 2000. HIV infection and dementia. Science 287:602604.
64. Gartner, S. 2006. Mechanism of HIV entry into the CNS, p. 15–40. In A. Minagar and, P. Shapshak (ed.), Neuro-AIDS. Nova Biomedical Books, New York, NY.
65. Gaschen, B.,, J. Taylor,, K. Yusim,, B. Foley,, F. Gao,, D. Lang,, V. Novitsky,, B. Haynes,, B. H. Hahn,, T. Bhattacharya, and, B. Korber. 2002. Diversity considerations in HIV-1 vaccine selection. Science 296:23542360.
66. Gendelman, H. E. 2002. Neural immunity: friend or foe? J. Neurovirol. 8:474479.
67. Gilbert, M. T. P.,, A. Rambaut,, G. Wlasiuk,, T. J. Spira,, A. E. Pitchenik, and, M. Worobey. 2007. The emergence of HIV/AIDS in the Americas and beyond. Proc. Natl. Acad. Sci. USA. http://www.pnas.org/cgi/reprint/0705329104v2.
68. Gilizia, R. J.,, J. A. Levy, and, D. E. Mosier. 1996. The envelope gp120 gene of human immunodeficiency virus type 1 determines the rate of cd4-positive t-cell depletion in scid mice engrafted with human peripheral blood leukocytes. J. Virol. 70:41844187.
69. Glass, J. D.,, H. Fedor,, S. L. Wesselingh, and, J. C. McArthur. 1995. Immunocytochemical quantitation of human immunodeficiency virus in the brain: correlations with dementia. Ann. Neurol. 38:755762.
70. Gonzalez, E.,, H. Kulkarni,, H. Bolivar,, A. Mangano,, R. Sanchez,, G. Catano, et al. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307:14341439.
71. Goodkin, K. 2006. Virology, immunology, transmission, and disease stage, p. 11–22. In F. Fernandez and, P. Ruiz (ed.), Psychiatric Aspects of HIV/AIDS. Lippincott Williams & Wilkins, Philadelphia, PA.
72. Goudsmit, J.,, C. Debouck, and, R. H. Moloen. 1988. Human immunodeficiency virus type 1 neutralization epitope with conserved architecture elicits early type-specific antibodies in experimentally infected chimpanzees. Proc. Natl. Acad. Sci. USA 85:44784482.
73. Goulder, P. J.,, R. E. Phillips, and, R. A. Colbert. 1997. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat. Med. 3:212217.
74. Graham, B. S. 2002. Clinical trials of HIV vaccines. Annu. Rev. Med. 53:207221.
75. Gray, F.,, F. Chretien,, A. V. Vallat-Decouvelaere, and, F. Scaravilli. 2003. The changing pattern of HIV neuropathology in the HAART era. J. Neuropathol. Exp. Neurol. 62:429440.
76. Greenough, T. C.,, D. B. Brettler,, M. Somasundaran,, D. L. Panicali, and, J. L. Sullivan. 1997. Human immunodeficiency virus type 1-specific cytotoxic T lymphocytes (CTL), virus load, and CD4 T cell loss: evidence supporting a protective role for CTlL in vivo. J. Infect. Dis. 176:118125.
77. Grez, N.,, U. Dietrich,, P. Balfe,, H. von Briesen,, J. K. Maniar,, G. Mhambre,, E. L. Delwar,, J. I. Mullins, and, H. Rubsamen-Waigmann. 1994. Genetic analysis of HIV1 and HIV-2 mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses. J. Virol. 68:21612168.
78. Gunthard, H.,, S. Frost,, A. Leigh-Brown,, C. Ignacio,, K. Kee,, A. Perelson,, C. Spina,, D. Havlir,, M. Hezareh,, D. Looney,, D. Richman, and, J. Wong. 1999. Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy. J. Virol. 73:94049412.
79. Herbeck, J. T.,, D. C. Nickle,, G. H. Learn,, G. S. Gottlieb,, M. E. Curlin,, L. Heath, and, J. I. Mullins. 2006. HIV-1 env evolves towards ancestral states upon transmission to a new host. J. Virol. 80:16371644.
80. Hizi, A.,, A. S. Kamath-Loeb,, K. D. Rose, and, L. A. Loeb. 1997. Mutagenesis by human immunodeficiency virus reverse transcriptase: incorporation of O6-methyldeoxyguanosine triphosphate. Mutat. Res. 374:4150.
81. Hoxie, J. A.,, J. D. Alpers, and, J. L. Rackowski. 1986. Alterations in T4 (CD4) protein and mRNA synthesis in cells infected with HIV. Science 234:11231127.
82. Hu, W. S.,, T. Rhodes,, T. Q. Dang, and, V. Pathak. 2003. Retroviral recombination: review of genetic analyses. Front. Biosci. 8:D143D155.
83. Hudson, R. R.,, M. Slatkin, and, W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583589.
84. Jurado, A.,, P. Rahimi-Moghaddam,, S. Bar-Jurado,, J. S. Richardson,, M. Jurado, and, A. Shuaib. 1999. Genetic markers on HIV-1 gp120 C2-V3 region associated with the expression or absence of cognitive motor complex in HIV/AIDS. J. NeuroAIDS 2:1528.
85. Kageyama, S.,, J. K. Maniar,, M. Iwasaki,, J. Zhang,, D. G. Saple,, H. Tsuchie,, A. Tanabe-Tochikura,, K. Taniguchi,, K. Shiraki, and, T. Kurimura. 2000. Seronegative HIV-2 carriers in India. Int. J. STD AIDS 11:3137.
86. Kannangai, R.,, S. Ramalingam,, R. C. Castillo,, P. G. Babu,, T. J. John,, G. Sridharan, and, D. H. Schwartz. 1999. HIV-2 status in Southern India. Trans. R. Soc. Trop. Med. Hyg. 93:3031.
87. King, J. E.,, E. A. Eugenin,, C. M. Buckner, and, J. W. Berman. 2006. HIV tat and neurotoxicity. Microbes Infect. 8:13471357.
88. Kong, L. I.,, S. W. Lee,, J. C. Kappes,, J. S. Parkin,, D. Decker,, J. A. Hoxie,, B. H. Hahn, and, G. M. Shaw. 1988. West African HIV-2-related human retrovirus with attenuated cytopathicity. Science 240:15251529.
89. Kopnisky, K. L.,, J. Bao, and, Y. W. Lin. 2007. Neurobiology of HIV, psychiatric and substance abuse comorbidity research: workshop report. Brain Behav. Immun. 21:428441.
90. Korber, B.,, M. Muldoon,, J. Theiler,, F. Gao,, R. Gupta,, A. Lapedes,, B. H. Hahn,, S. Wolinsky, and, T. Bhattacharya. 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288:17891796.
91. Korber, B. T. M.,, K. J. Kunstman,, B. K. Patterson,, M. Furtado,, M. M. McEvilly,, R. Levy, and, S. M. Wolinsky. 1994. Genetic differences between blood- and brain-derived viral sequences from HIV-1 infected patients: evidence of conserved elements in the V3 region of the env protein of brain-derived sequences. J. Virol. 68:74677481.
92. Korber, B. T. M.,, G. Learn,, J. I. Mullins,, B. H. Hahn, and, S. Wolinsky. 1995. Protecting HIV sequence databases. Nature (London) 378:242243.
93. Kosakovsky Pond, S. L.,, D. Posada,, M. B. Gravenor,, C. H. Woelk, and, S. D. W. Frost. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23:18911901.
94. Koup, R.,, J. Safrit, and, Y. Cao. 1994. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J. Virol. 68:46504655.
95. Kulkarni, S. S.,, S. Tripathy,, R. S. Paranjape,, N. S. Mani,, D. R. Joshi,, U. Patil, and, D. A. Gadkari. 1999. Isolation and preliminary characterization of two HIV-2 strains from Pune, India. Indian J. Med. Res. 109:123130.
96. Kumar, A. M.,, I. Borodowsky,, B. J. Fernandez,, L. Gonzalez, and, M. Kumar. 2007. Human immunodeficiency virus type 1 RNA levels in different regions of human brain: quantification using real-time reverse transcriptase–polymerase chain reaction. J. Neurovirol. 13:210224.
97. Kuroda, M. J.,, J. E. Schmitz,, W. A. Charini,, C. E. Nickerson,, M. A. Lifton,, C. I. Lord,, M. A. Forman, and, N. L. Letvin. 1999. Emergence of CTL coincides with clearance of virus during primary simian immunodeficiency virus infection in rhesus monkeys. J. Immunol. 162:51275133.
98. Kurosu, T.,, T. Mukai,, W. Auwanit,, P. I. N. Ayuthaya,, S. Saeng-Aroon, and, K. Ikuta. 2001. Variable sequences in the LTR and its downstream region of some of HIV-1 CRF01_AE recently distributing among Thai carriers. AIDS Res. Hum. Retrovir. 17:863866.
99. Langford, T. D.,, A. Adame,, A. Grigorian,, I. Grant,, J. A. McCutchan,, R. J. Ellis,, T. D. Marcotte, and, E. Masliah. 2003. Changing patterns in the neuropathogenesis of HIV during the HAART era. Brain Pathol. 13:195210.
100. Learn, G. H., Jr.,, B. T. M. Korber,, B. Foley,, B. H. Hahn,, S. M. Wolinsky, and, J. I. Mullins. 1996. Maintaining the integrity of human immunodeficiency virus sequence databases. J. Virol. 70:57205730.
101. Letendre, S.,, A. D. Paulino,, E. Rockenstein,, A. Adame,, L. Crews,, M. Cherner,, R. Heaton,, R. Ellis,, I. P. Everall,, I. Grant, and, E. Masliah. 2007. Pathogenesis of hepatitis C virus coinfection in the brains of patients infected with HIV. J. Infect. Dis. 196:361370.
102. Levine, A. J.,, E. J. Singer, and, P. Shapshak. 9 February 2008. The role of host genetics in the susceptibility for HIV-1-associated neurocognitive disorders. AIDS Behav. [Epub ahead of print.] doi: 10.1007/s 10461-008-3254.
103. Lima, M.,, R. Katz-Brull,, R. Lenkinski,, R. Nunez,, D. Feinrider, and, I. Koralnik. 2007. Remission of progressive multifocal leukoencephalopathy and primary central nervous system lymphoma in an HIV-infected patient. Eur. J. Neurol. 14:598602.
104. Liu, L.,, B. Su, and, K. Zhuang. 2005. Genetic characterization of full-length HIV-1 genomes from 3 infected paid blood donors in Henan, China. J. Acquir. Immune Defic. Syndr. 40:501502.
105. Liu, Z. Q.,, C. Wood,, J. A. Levy, and, C. Cheng-Mayer. 1990. The viral envelope gene is involved in macrophage tropism of a human immunodeficiency virus type 1 strain isolated from brain tissue. J. Virol. 64:61486153.
106. Lopalco, L. 2004. Humoral immunity in HIV-1 exposure: cause or effect of HIV resistance? Curr. HIV Res. 2:127139.
107. Luo, G.,, and J. Taylor. 1990. Template switching by reverse transcriptase during DNA synthesis. J. Virol. 64:43214328.
108. Mahadevan, A.,, S. Shankar,, P. Satishchandra,, U. Ranga,, Y. Chickabasaviah,, V. Santosh,, R. Vasanthapuram,, C. Pardo,, A. Nath, and, M. Zink. 2007. Characterization of human immunodeficiency virus (HIV)-infected cells in infiltrates associated with CNS opportunistic infections in patients with HIV clade C infection. J. Neuropathol. Exp. Neurol. 66:799808.
109. Masliah, E.,, R. M. DeTeresa,, M. E. Mallory, and, L. A. Hansen. 2000. Changes in pathological findings at autopsy in AIDS cases for the last 15 years. AIDS 14:6974.
110. Masliah, E.,, R. K. Heaton,, T. D. Marcotte,, R. J. Ellis,, C. A. Wiley,, M. Mallory,, C. L. Achim,, J. A. McCutchan,, J. A. Nelson,, J. H. Atkinson, and, I. Grant. 1997. Dendritic injury is a pathological substrate for human immunodeficiency virus-related cognitive disorders. Ann. Neurol. 42:963972.
111. Masliah, E.,, E. S. Roberts,, D. Langford,, I. Everall,, L. Crews,, A. Adame,, E. Rockenstein, and, H. S. Fox. 2004. Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. J. Neuroimmunol. 157:163175.
112. McArthur, J. C. 2004. HIV dementia: an evolving disease. J. Neuroimmunol. 157:310.
113. McArthur, J. C.,, M. P. McDermott,, D. McClernon,, C. St Hillaire,, K. Conant,, K. Marder,, G. Schifitto,, O. A. Selnes,, N. Sacktor,, Y. Stern,, S. M. Albert,, K. Kieburtz,, J. A. deMarcaida,, B. Cohen, and, L. G. Epstein. 2004. Attenuated central nervous system infection in advanced HIV/AIDS with combination antiretroviral therapy. Arch. Neurol. 61:16871696.
114. McCoy, C. B.,, and E. L. Khoury. 1990. Drug use and the risk of AIDS. Am. Behav. Sci. 33:419431.
115. McCoy, C. B.,, P. Shapshak,, J. E. Rivers,, H. V. McCoy,, N. L. Weatherby,, D. D. Chitwood,, S. M. Shah,, J. A. Inciardi,, D. C. McBride, and, J. K. Watters. 1994. The risks of injection practices and compliance to risk reduction protocols in the prevention of HIV-1 among injecting drug users. J. Acquir. Immune Defic. Syndr. 7:773776.
116. McCutchan, F. E. 1999. Global diversity in human immunodeficiency viruses, p. 41–101. In K. A. Crandall (ed.), The Evolution of HIV. Johns Hopkins University Press, Baltimore, MD.
117. Mellgran, A.,, R. W. Price,, L. Hagberg,, L. Rosengren,, B. J. Brew, and, M. Gisslen. 2007. Antiretroviral treatment reduces increased CSF neurofilament protein (NFL) in HIV-1 infection. Neurology 69:15361541.
118. Minagar, A.,, D. Commins,, J. S. Alexander,, R. Hoque,, F. Chiappelli,, E. J. Singer,, B. Nikbin, and, P. Shapshak. 2008. NeuroAIDS: characteristics and diagnosis of the neurological complications of AIDS. 12:2543.
119. Minagar, A.,, and P. Shapshak. 2006. HIV-associated dementia: clinical features and pathogenesis, p. 1–14. In A. Minagar and, P. Shapshak (ed.), Neuro-AIDS. Nova Biomedical Books, New York, NY.
120. Minagar, A.,, P. Shapshak,, E. M. Duran,, A. S. Kablinger,, J. A. Alexander,, R. E. Kelley,, R. Seth, and, T. Kazic. 2004. Gene expression in HIV-associated dementia, Alzheimer’s disease, multiple sclerosis, and schizophrenia. J. Neurosci. Res. 224:317.
121. Minagar, A.,, P. Shapshak,, R. Fujimura,, R. Ownby,, M. Heyes, and, C. Eisdorfer. 2002. The role of macrophage/microglia and astrocytes in the pathogenesis of three neurologic disorders: HIV-associated dementia, Alzheimer disease, and multiple sclerosis. J. Neurol. Sci. 202:1323.
122. Moore, J. P.,, Y. Cao,, D. D. Ho, and, R. A. Koup. 1994. Development of the anti-gp120 antibody response during seroconversion to human immunodeficiency virus type 1. J. Virol. 68:51425155.
123. Morgello, S.,, R. Mahboob,, T. Yakoushina,, S. Khan, and, K. Hague. 2002. Autopsy finding in a HIV-infected population over 2 decades. Arch. Pathol. Lab. Med. 126:182190.
124. Musey, L.,, J. Hughes, and, T. Schacker. 1997. Cytotoxic-T-cell responses, viral load, and disease progression in early human immunodeficiency virus type 1 infection. N. Engl. J. Med. 337:12671274.
125. Nath, A.,, N. J. Haughey,, M. Jones,, J. E. Anderson,, C. Bell, and, J. D. Geiger. 2000. Synergistic neurotoxicity by HIV proteins tat and gp120: protection by memantine. Ann. Neurol. 7:186194.
126. Nath, A.,, K. F. Hauser,, M. Prendergast, and, J. Berger. 2006. Drug abuse and neuro-AIDS, p. 81–100. In A. Minagar and, P. Shapshak (ed.), Neuro-AIDS. Nova Biomedical Books, New York, NY.
127. Navia, B. A.,, E. S. Cho,, C. K. Petito, and, R. W. Price. 1986a. The AIDS dementia complex. II. Neuropathology. Ann. Neurol. 19:525535.
128. Navia, B. A.,, B. D. Jordan, and, R. W. Price. 1986b. The AIDS dementia complex. I. Clinical features. Ann. Neurol. 19:517524.
129. Negroni, M.,, and H. Buc. 2001. Mechanisms of retroviral recombination. Annu. Rev. Genet. 35:275302.
130. Nickle, D. C.,, M. A. Jensen,, G. S. Gottlieb,, D. Shriner,, G. H. Learn,, A. G. Rodrigo, and, J. I. Mullins. 2003a. Consensus and ancestral state HIV vaccines. Science 299:15151518.
131. Nickle, D. C.,, M. A. Jensen,, D. Shriner, et al. 2003b. Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. J. Virol. 77:55405546.
132. Nickle, D. C.,, D. Shriner,, J. E. Mittler,, L. M. Frenkel, and, J. I. Mullins. 2003c. Importance and detection of virus reservoirs and compartments of HIV infection 1. Curr. Opin. Microbiol. 6:410416.
133. Nkengasong, J. N.,, C. Bile,, M. Kalou,, C. Maurice,, E. Boateng,, M. Sassan-Morokro,, M. Rayfield,, D. Coulibaly,, A. E. Greenberg, and, S. Z. Wiktor. 1999. Quantification of RNA in HIV type 1 subtypes D and G by NucliSens and Amplicor assays in Abidjan, Ivory Coast. AIDS Res. Hum. Retrovir. 15:495498.
134. Nuttall, J. J.,, J. M. Wilmshurst,, A. P. Ndondo,, J. Yeats,, C. Corcoran,, G. D. Hussey, and, B. S. Eley. 2004. Progressive multifocal leukoencephalopathy after initiation of highly active antiretroviral therapy in a child with advanced human immunodeficiency virus infection: a case of immune reconstitution inflammatory syndrome. Pediatr. Infect. Dis. J. 23:683685.
135. Ogg, G. S.,, X. Jin,, S. Bonhoeffer,, P. R. Dunbar,, M. A. Nowak, and, S. Monard. 1998. Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. Science 279:21032106.
136. Ohagen, A.,, A. Devitt,, K. J. Kunstman,, P. R. Gorry,, P. P. Rose,, B. Korber,, J. Taylor,, R. Levy,, R. L. Murphy,, S. M. Wolinsky, and, D. Gabuzda. 2003. Genetic and functional analysis of full-length HIV-1 env genes derived from brain and blood of patients with AIDS. J. Virol. 77:1233612345.
137. Palker, T. J.,, M. E. Clark,, A. J. Langlois,, T. J. Matthews,, K. J. Weinhold,, R. R. Randall,, D. P. Bolognesi, and, B. F. Haynes. 1988. Type-specific neutralization of the human immunodeficiency virus with antibodies to env-encoded synthetic peptides. Proc. Natl. Acad. Sci. USA 85:19321936.
138. Pantaleo, G.,, J. F. Demarest,, H. Soudeyns,, C. Graziosi,, F. Denis,, J. W. Adelsberger,, P. Borrow,, M. S. Saag,, G. M. Shaw, and, R. P. Sekaly. 1994. Major expansion of CD81 T cells with a predominant V beta usage during the primary immune response to HIV. Nature 370:463467.
139. Pasquier, C.,, K. Sandres,, G. Salama,, J. Puel, and, J. Izopet. 1999. Using RT-PCR and bDNA assays to measure non-clade B HIV-1 subtype RNA. J. Virol. Methods 81:123129.
140. Peeters, M.,, and P. M. Sharp. 2000. Genetic diversity of HIV-1: the moving target. AIDS 14:129140.
141. Perelson, A. S.,, A. U. Neumann,, M. Markowitz,, J. M. Leonard, and, D. D. Ho. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271:15821586.
142. Petito, C. K.,, E. S. Cho,, W. Lemann,, B. A. Navia, and, R. W. Price. 1986. Neuropathology of acquired immunodeficiency syndrome (AIDS): an autopsy review. J. Neuropathol. Exp. Neurol. 45:635646.
143. Pillai, S. K.,, S. L. Pond,, Y. Liu,, B. M. Good,, M. C. Strain,, R. J. Ellis,, S. Letendre,, D. M. Smith,, H. F. Günthard,, I. Grant,, T. D. Marcotte,, J. A. McCutchan,, D. D. Richman, and, J. K. Wong. 2006. Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain 129(Pt. 7):18721883.
144. Poluektova, L. Y.,, D. H. Munn,, Y. Persidsky, and, H. E. Gendelman. 2002. Generation of CTL against virus-infected human brain macrophages in a murine model for HIV-1 encephalitis. J. Immunol. 168:39413949.
145. Power, C.,, J. C. McArthur,, A. Nath,, K. Wehrly,, M. Mayne,, J. Nishio,, T. Langelier,, R. T. Johnson, and, B. Chesebro. 1998. Neuronal death induced by brain-derived HIV-1 env genes differs between demented and nondemented AIDS patients. J. Virol. 72:90459053.
146. Power, C.,, J. C. McArthur,, R. T. Johnson,, D. E. Griffin,, J. D. Glass,, S. Perryman, and, B. Chesebro. 1994. Demented and non-demented patients with aids differ in brain-derived human immunodeficiency virus type 1 envelope sequences. J. Virol. 68:46434649.
147. Ranga, U.,, R. Shankarappa,, N. B. Siddappa,, L. Ramakrishna,, R. Nagendran, et al. 2004. Tat protein of HIV-1 subtype C strains is a defective chemokine. J. Virol. 78:25862590.
148. Resnick, L.,, J. R. Berger,, P. Shapshak, and, W. W. Tourtellotte. 1988. Early penetration of the blood-brain-barrier by HTLV-III/LAV. Neurology 38:915.
149. Roberts, E. S.,, M. A. Zandonatti,, D. D. Watry,, L. J. Madden,, S. J. Henriksen,, M. A. Taffe, and, H. S. Fox. 2003. Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am. J. Pathol. 162:20412057.
150. Roberts, J. D.,, B. D. Preston,, L. A. Johnston,, A. Soni,, L. A. Loeb, and, T. A. Kunkel. 1989. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol. Cell. Biol. 9:469476.
151. Robertson, K. R.,, M. Smurzynski,, T. D. Parsons,, K. Wu,, R. J. Bosch,, J. Wu,, J. C. McArthur,, A. C. Collier,, S. R. Evans, and, R. J. Ellis. 2007. The prevalence and incidence of neurocognitive impairment in the HAART era. AIDS 21:19151921.
152. Sacktor, N.,, M. P. McDermott,, K. Marder,, G. Schifitto,, O. A. Selnes,, J. C. McArthur,, Y. Stern,, S. Albert,, D. Palumbo,, K. Kieburtz,, J. A. De Marcaida,, B. Cohen, and, L. Epstein. 2002. HIV-associated cognitive impairment before and after the advent of combination therapy. J. Neurovirol. 8:136142.
153. Salemi, M.,, S. L. Lamers,, S. Yu,, T. de Oliveira,, W. M. Fitch, and, M. S. McGrath. 2005. Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J. Virol. 79:1134311352.
154. Sankale, J. L.,, R. S. de la Tour, and, B. Renjifo. 1995. Intrapatient variability of HIV-2 envelope V3 loop. AIDS Res. Hum. Retrovir. 11:617623.
155. Sarr, A. D.,, J. L. Sankale,, D. L. Hamel,, K. U. Travers,, A. Gueye-Ndiaye,, M. Essex,, S. Mboup, and, P. J. Kanki. 2000. Interaction with HIV-2 predicts HIV-1 genotypes. Virology 268:402410.
156. Schultz, A. M.,, and J. A. Bradac. 2001. The HIV vaccine pipeline, from preclinical to phase III. AIDS 5:147158.
157. Sei, Y.,, P. H. Tsang,, F. N. Chu,, I. Wallace,, J. P. Roboz,, P. S. Sarin, and, J. G. Bekesi. 1989. Inverse relationship between HIV-1 p24 antigenemia, anti-p24 antibody and neutralizing antibody response in all stages of HIV-1 infection. Immunol. Lett. 20:223230.
158. Sewell, A. K.,, D. A. Price,, A. Oxenius,, A. D. Kelleher, and, R. E. Phillips. 2000. Cytotoxic T lymphocyte responses to human immunodeficiency virus: control and escape. Stem Cells 18:230244.
159. Shah, S. M.,, P. Shapshak,, J. E. Rivers,, N. L. Weatherby,, K. Q. Xin,, R. V. Stewart,, D. D. Chitwood,, B. Page,, D. C. Mash,, D. Vlahov, and, C. B. McCoy. 1996. Detection of HIV-1 DNA in needle/syringes, paraphernalia, and washes from shooting galleries in Miami: preliminary laboratory results. J. Acquir. Immune Defic. Syndr. 11:301306.
160. Shapshak, P.,, M. Alireza,, M. Duran,, F. Ziegler,, W. Davis,, R. Seth, and, T. Kazic. 2005a. Gene expression in HIV associated dementia, p. 305–318. In A. Minagar and, J. S. Alexander (ed.), Inflammatory Disorders of the Nervous System, Clinical Aspects, Pathogenesis, and Management. Humana Press, Totowa, NJ.
161. Shapshak, P.,, K. A. Crandall,, K. Goodkin, et al. 1996. HIV-1. Neuropathogenesis and abused drugs. Current views: problems and solutions. Adv. Exp. Med. Biol. 23:171186.
162. Shapshak, P.,, R. Duncan,, C. B. McCoy, and, J. B. Page. 2005b. Real time reverse transcriptase PCR method for quantification of HIV gag RNA. Front. Biosci. 10:135142.
163. Shapshak, P.,, R. Duncan,, A. Nath,, J. Turchan,, P. Kangueane,, S. Shapshak,, H. Rodriguez,, E. M. Duran,, F. Ziegler,, E. Amaro,, A. Lewis,, A. Rodriguez,, A. Minagar,, W. Davis,, R. Seth,, F. Chiappelli, and, T. Kazic. 2006. Gene chromosomal organization and expression in cultured human neurons exposed to cocaine and HIV-1 proteins gp120 and tat: drug abuse and NeuroAIDS. Front. Biosci. 11:17741793.
164. Shapshak, P.,, R. Duncan,, J. Torres-Munoz,, M. Duran,, A. Minagar, and, C. Petito. 2004. Analytic approaches to differential gene expression in AIDS vs. control brains. Front. Biosci. 9:29352946.
165. Shapshak, P.,, R. Duncan,, J. E. Torres-Munoz,, A. Minagar, and, C. K. Petito. 2002. Preliminary gene expression studies in AIDS: problems and solutions. Proceedings of the 2nd Virtual Conference on Genomics and Bioinformatics. North Dakota State University, Fargo. http://www.ndsu.edu/virtual-genomics.
166. Shapshak, P.,, R. Fujimura,, B. Page,, D. Segal,, J. Yang,, S. Shah,, G. Graham,, J. Rivers,, D. Chitwood, and, C. McCoy. 2000. HIV-1 RNA load in needle/syringes from shooting galleries in Miami: a preliminary laboratory report. Drug Alcohol Depend. 58:153157.
167. Shapshak, P.,, C. McCoy,, S. Shah,, B. Page,, J. Rivers,, N. Weatherby,, D. Chitwood, and, D. Mash. 1994. Preliminary laboratory studies on inactivation of HIV-1 in needles and syringes containing infected blood using undiluted household bleach. J. Acquir. Immune Defic. Syndr. 7:754759.
168. Shapshak, P.,, I. Nagano,, K. Q. Xin,, W. Bradley, et al. 1995. HIV-1 heterogeneity and cytokines: neuropathogenesis. Adv. Exp. Med. Biol. 373:225238.
169. Shapshak, P.,, D. Segal,, K. Crandall,, R. Fujimura,, B. Zhang,, K. Xin,, K. Okuda,, C. Petito,, C. Eisdorfer, and, K. Goodkin. 1999. Independent evolution of HIV-1 in different brain regions. AIDS Res. Hum. Retrovir. 15:811820.
170. Shapshak, P.,, and R. Stengel. 2002. Discovering brain mechanisms and the rules of molecular biology. 6th World Multiconference on Systemics, Cybernetics and Informatics, Orlando, FL, July 14–18. http://www.iiis.org/sci2002/.
171. Shapshak, P.,, J. Torres-Munos, and, C. Petito. 2001. Bioinformatics in neurodegenerative diseases. Proceedings of Virtual Conference on Genomics and Bioinformatics. North Dakota State University, Fargo. http://www.ndsu/virtual-genomics.
172. Shioda, T.,, J. A. Levy, and, C. Cheng-Mayer. 1992. Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc. Natl. Acad. Sci. USA 89:94349438.
173. Singer, E. J.,, K. Syndulko,, P. Shapshak,, L. Resnick, and, W. W. Tourtellotte. 1994. Cerebrospinal fluid p24 antigen levels and intrathecal immunoglobulin G synthesis are associated with cognitive disease severity in HIV-1. AIDS 8:197204.
174. Singh, S.,, S. N. Dwivedi,, R. Sood, and, J. P. Wali. 2000. Hepatitis B, C, and HIV infections in multiply-injected Kalaazar patients in Delhi. Scand. J. Infect. Dis. 32:36.
175. Smit, T. K.,, B. J. Brew,, W. W. Tourtellotte,, S. Morgello,, B. B. Gelman, and, N. K. Saksena. 2004. Independent evolution of HIV drug resistance mutations in diverse areas of the brain in HIV-infected patients, with and without dementia, on antiretroviral treatment. J. Virol. 78:100133100148.
176. Smith, K. A. 2005. The continuing HIV vaccine saga: naked emperors alongside fairy godmothers. Med. Immun. 4:15.
177. Snider, W. D.,, D. M. Simpson,, S. Nielsen,, J. Gold,, C. Metroka, and, J. Posner. 1983. Neurological complications of acquired immune deficiency syndrome: analysis of 50 patients. Ann. Neurol. 14:403418.
178. Solomon, S.,, N. Kumarasamy,, A. K. Ganesh, and, R. E. Amalraj. 1998. Prevalence and risk factors of HIV-1 and HIV-2 infection in urban and rural areas in Tamil Nadu, India. Int. J. STD AIDS 9:98103.
179. Strain, M. C.,, S. Letendre,, S. K. Pillai,, T. Russell,, C. C. Ignacio,, H. F. Günthard,, B. Good,, D. M. Smith,, S. M. Wolinsky,, M. Furtado,, J. Marquie-Beck,, J. Durelle,, I. Grant,, D. D. Richman,, T. Marcotte,, J. A. McCutchan,, R. J. Ellis, and, J. K. Wong. 2005. Genetic composition of human immunodeficiency virus type 1 in cerebrospinal fluid and blood without treatment and during failing antiretroviral therapy. J. Virol. 79:17721788.
180. Torre, D.,, F. Speranza, and, R. Martegani. 2005. Impact of highly active antiretroviral therapy on organ-specific manifestations of HIV-1 infection. HIV Med. 6:6678.
181. Tozzi, V.,, P. Balestra,, P. Lorenzini,, R. Bellagamba,, S. Galgani,, A. Corpolongo,, C. Vlassi,, D. Larussa,, M. Zaccarelli,, P. Noto,, U. Visco-Comandini,, M. Giulianelli,, G. Ippolito,, A. Antinori, and, P. Narciso. 2005a. Prevalence and risk factors for human immunodeficiency virus-associated neurocognitive impairment, 1996 to 2002: results from an urban observational cohort. J. Neurovirol. 11:265273.
182. Tozzi, V.,, P. Balestra,, D. Serraino,, R. Bellagamba,, A. Corpolongo,, P. Piselli,, P. Lorenzini,, U. Visco-Comandini,, C. Vlassi,, M. E. Quartuccio,, M. Giulianelli,, P. Noto,, S. Galgani,, G. Ippolito,, A. Antinori, and, P. Narciso. 2005b. Neurocognitive impairment and survival in a cohort of HIV-infected patients treated with HAART. AIDS Res. Hum. Retrovir. 21:706713.
183. Triques, K.,, J. Coste,, J. L. Perret,, T. Segarra,, E. Mpoudi,, J. Reynes,, E. Delaporte,, A. Butcher,, K. Dreyer,, S. Herman,, J. Spadoro, and, M. Peeters. 1999. Efficiencies of four versions of the amplicor HIV-1 monitor test for quantification of different subtypes of human immunodeficiency virus type 1. J. Clin. Microbiol. 37:110116.
184. Vahey, M. T.,, M. E. Nau,, M. Taubman,, J. Yalley-Ogunro,, P. Silvera, and, M. G. Lewis. 2003. Patterns of gene expression in PBMNCs of Rhesus macaques infected with SIVmac251 and exhibiting differential rates of disease progression. AIDS Res. Hum. Retrovir. 19:369387.
185. Vallat-Decouvelaere, A. V.,, F. Chretien,, G. Lorin de la Grandmaison,, R. Carlier,, G. Force, and, F. Gray. 2003. The neuropathology of HIV infection in the era of highly active antiretroviral therapy. Ann. Pathol. 23:408423.
186. van Marle, G.,, and C. Power. 2005. HIV-1 genetic diversity in the nervous system: evolutionary epiphenomenon or disease determinant. J. Neurovirol. 11:107128.
187. Vendrely, A.,, B. Bienvenu,, J. Gasnault,, J. B. Thiebault,, D. Salmon, and, F. Gray. 2005. Fulminant inflammatory leukoencephalopathy associated with HAART-induced immune restoration in AIDS-related progressive multifocal leukoencephalopathy. Acta Neuropathol. (Berlin) 109:449455.
188. Venkataramana, A.,, C. A. Pardo,, J. C. McArthur,, D. A. Kerr,, D. N. Irani,, J. W. Griffin,, P. Burger,, D. S. Reich,, P. A. Calabresi, and, A. Nath. 2006. Immune reconstitution inflammatory syndrome in the CNS of HIV-infected patients. Neurology 67:383388.
189. Wang, F. X.,, Y. Xu,, J. Sullivan,, E. Souder,, E. G. Argyris,, E. A. Acheampong, et al. 2005. IL-7 is a potent and proviral strain-specific inducer of latent HIV-1 cellular reservoirs of infected individuals on virally suppressive HAART. J. Clin. Investig. 115:128137.
190. Weber, J. N.,, P. R. Clapham, and, R. A. Weiss. 1987. Human immunodeficiency virus infection in two cohorts of homosexual men: neutralizing sera and association of anti-gag antibody with prognosis. Lancet i:119122.
191. Wiley, R. L.,, F. Maldarelli,, M. A. Martin, and, K. Strebel. 1992. Human immunodeficiency virus type 1 Vpu protein regulates the formation of intracellular gp160-CD4 complexes. J. Virol. 66:226234.
192. Williams, K. J.,, and L. A. Loeb. 1992. Retroviral reverse transcriptases: error frequencies and mutagenesis. Curr. Top. Microbiol. Immunol. 176:165180.
193. Wilson, J. D.,, G. S. Ogg,, R. L. Allen,, C. Davis,, S. Shaunak,, J. Downie,, W. Dyer,, C. Workman,, S. Sullivan,, A. J. McMichael, and, S. L. Rowland-Jones. 2000. Direct visualization of HIV-1-specific cytotoxic T lymphocytes during primary infection. AIDS 14:225233.
194. Wolthers, K. C.,, S. A. Otto,, S. M. Lens,, R. A. Van Lier,, F. Miedema, and, L. Meyaard. 1997. Functional B cell abnormalities in HIV type 1 infection: role of CD40L and CD70. AIDS Res. Hum. Retrovir. 13:10231029.
195. Wong, J. K.,, C. C. Ignacio,, F. Torriani,, D. Havlir,, N. J. Fitch, and, D. D. Richman. 1997. In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J. Virol. 71:20592071.
196. Xin, K. Q.,, K. Hamajima,, S. Sasaki,, A. Honsho,, T. Tsuji,, N. Ishii,, X. R. Cao,, Y. Lu,, P. Shapshak, and, K. Okuda. 1998. Intranasal administration of HIV-1 DNA vaccine with IL-2 expression plasmid enhances cell-mediated immunity against HIV. Immunology 94:438444.
197. Yilmaz, A.,, R. W. Price,, S. Spudich,, D. Fuchs,, L. Hagberg, and, M. Gisslén. 2008. Persistent intrathecal immune activation in HIV-1-infected individuals on antiretroviral therapy. J. Acquir. Immune Defic. Syndr. 47:168173.
198. Yu, X. F.,, W. Liu,, J. Chen,, W. Kong,, B. Liu,, Q. Zhu,, F. Liang,, F. McCutchan,, S. Piyasirisilp, and, S. Lai. 2002. Maintaining low HIV type 1 env genetic diversity among injection drug users infected with a B/C recombinant and CRF01_AE HIV type 1 in southern China. AIDS Res. Hum. Retrovir. 18:167170.
199. Zárate, S.,, S. L. Kosakovsky-Pond,, P. Shapshak, and, S. D. W. Frost. 2007. A comparative study of methods for detecting sequence compartmentalization in HIV-1. J. Virol. 81:66436651.
200. Zhang, K.,, F. Rana,, C. Silva,, J. Ethier,, K. Ehrly,, B. Chesebro, and, C. Power. 2003. HIV-1 envelope-mediated neuronal death: uncoupling of viral replication and neurotoxicity. J. Virol. 77:68992003.


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Distance-based tests for viral population division

Citation: Shapshak P, Minagar A, Kangueane P, Frost S, Kosakovsky Pond S, Zarate S, Singer E, Commins D, Groot A, Quinones-Mateu M, Terwilliger E. 2009. The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder, p 201-218. In Goodkin K, Shapshak P, Verma A (ed), The Spectrum of Neuro-AIDS Disorders. ASM Press, Washington, DC. doi: 10.1128/9781555815691.ch15
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Selective pressure on sequences by brain region

Citation: Shapshak P, Minagar A, Kangueane P, Frost S, Kosakovsky Pond S, Zarate S, Singer E, Commins D, Groot A, Quinones-Mateu M, Terwilliger E. 2009. The Role of Viral Genetic Variability in HIV-Associated Neurocognitive Disorder, p 201-218. In Goodkin K, Shapshak P, Verma A (ed), The Spectrum of Neuro-AIDS Disorders. ASM Press, Washington, DC. doi: 10.1128/9781555815691.ch15

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