The reverse transcriptase sequence of human immunodeficiency virus type 1 is under positive evolutionary selection within the central nervous system

References

• An SF, Groves M, Gray F, Scaravilli F (1999). Early en-try and widespread cellular involvement of HIV-1 DNA in brains of HIV-1 positive asymptomatic individuals. J Neuropathol Exp Neurol 58: 1156–1162.
   PubMed Web of Science ®Google Scholar
• Ball JK, Holmes EC, Whitwell H, Desselberger U (1994). Genomic variation of human immunodeficiency virus type 1 (HIV-1): Molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy. J Gen Virol 75: 67–79.
   PubMed Web of Science ®Google Scholar
• Boyer PL, Hughes SH (2000). Effects of amino acid substi-tutions at position 115 on the fidelity of human immu-nodeficiency virus type 1 reverse transcriptase. I Virol 74: 6494–6500.
   Google Scholar
• Bratanich AC, Liu C, McArthur JC, Fudyk T, Glass JD, Mittoo S, Klassen GA, Power C (1998). Brain-derived HIV-1 tat sequences from AIDS patients with dementia show increased molecular heterogeneity. I NeuroVirol 4: 387–393.
   PubMed Web of Science ®Google Scholar
• Carr J, Avila M, Gomez-Carrillo M, Salomon H, Hierholzer J, Watanaveeradej V, Pando M, Negrete M, Russell K, Russell KL, Sanchez, J, Birx D, Birx DL, Andrade R, Vinoles J, McCutchan F, McCutchan FE (2001). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• Cases-Gonzalez CE, Gutierrez-Rivas M, Menendez-Arias L (2000). Coupling ribose selection to fidelity of DNA synthesis. The role of Tyr-115 of human immunodefi-ciency virus type 1 reverse transcriptase. I Biol Chem 275: 19759–19767.
   Google Scholar
• Corboy JR, Garl PJ (1997). HIV-1 LTR DNA sequence varia-tion in brain-derived isolates. J NeuroVirol 5: 331–341.
   Google Scholar
• Cunningham PH, Smith DG, Satchell C, Cooper DA, Brew B (2000). Evidence for independent development of re-sistance to HIV-1 reverse transcriptase inhibitors in the cerebrospinal fluid. AIDS 14: 1949–1954.
   Google Scholar
• Ding J, Hughes SH, Arnold E (1997). Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse tran-scriptase with a double-stranded DNA template-primer. Biopolymers 44: 125–138.
   Google Scholar
• Di Stefano M, Gray F, Leitner T, Chiodi F (1996). Analysis of ENV V3 sequences from HIV-1-infected brain indi-cates restrained virus expression throughout the disease. J Med Virol 49: 41–48.
   Google Scholar
• Ellis RJ, Gamst AC, Capparelli E, Spector SA, Hsia K, Wolfson T, Abramson I, Grant I, McCutchan JA (2000). Cerebrospinal fluid HIV RNA originates from both lo-cal CNS and systemic sources. Neurology 54: 927–936.
   PubMed Web of Science ®Google Scholar
• Epstein LG, Kuiken C, Blumberg BM, Hartman S, Sharer LR, Clement M, Goudsmit J (1991). HIV-1 V3 domain varia-tion in brain and spleen of children with AIDS: Tissue-specific evolution within host-determined quasispecies. Virology 180: 583–590.
   Google Scholar
• Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM (1997). Human immunodeficiency virus type 1 ge-netic evolution in children with different rates of devel-opment of disease. I Virol 71: 663–677.
   Google Scholar
• Gatanaga H, Oka S, Ida S, Wakabayashi T, Shioda T, Iwamoto A (1999). Active HIV-1 redistribution and repli-cation in the brain with HIV encephalitis. Arch Virol 144: 29–43.
   PubMed Web of Science ®Google Scholar
• Gisslen M, Hagberg L, Norkrans G, Lekman A, Fredman P (1997). Increased cerebrospinal fluid ganglioside GM1 concentrations indicating neuronal involvement in all stages of HIV-1 infection. J NeuroVirol 3: 148–152.
   Web of Science ®Google Scholar
• Glass JD, Wesselingh SL, Selnes OA, McArthur JC (1993). Clinical-neuropathologic correlation in HIV-associated dementia. Neurology 43: 2230–2237.
   PubMedGoogle Scholar
• Guillon C, Bedin F, Fouchier RAM, van't Wout AB, Guters RA (1995). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• Haas DW, Clough LA, Johnson BW, Harris VL, Spearman P, Wilkinson GR, Fletcher CV, Fiscus S, Raffanti S, Donlon R, McKinsey J, Nicotera J, Schmidt D, Shoup RE, Kates RE, Lloyd RM, Jr, Larder B (2000). Evidence of a source of HIV type 1 within the central nervous system by ul-traintensive sampling of cerebrospinal fluid and plasma. AIDS Res Hum Retroviruses 16: 1491–1502.
   PubMed Web of Science ®Google Scholar
• Haas J (1993). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• Halvas EK, Svarovskaia ES, Pathak VK (2000). Role of murine leukemia virus reverse transcriptase deoxyri-bonucleoside triphosphate-binding site in retroviral replication and in vivo fidelity. I Virol 74: 10349–10358.
   Google Scholar
• Huang H, Chopra R, Verdine GL, Harrison SC (1998). Struc-ture of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance. Science 282: 1669–1675.
   PubMed Web of Science ®Google Scholar
• Iftimovici E, Rabian C, Burgard M, Peytavin G, Rouzioux C, Viard JP (1998). Longitudinal comparison of HIV-1 RNA burden in plasma and cerebrospinal fluid in two patients starting triple combination antiretroviral therapy. AIDS 12: 535–537.
   Google Scholar
• Jearunougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998). Multiple sequence alignment with Clustal X. Trends Biochem Sci 23: 403–405.
   Google Scholar
• Jonckheere H, De Clercq E, Anne J (2000). Fidelity analysis of HIV-1 reverse transcriptase mutants with an altered amino-acid sequence at residues Leu74, G1u89, Tyr115, Tyr183 and Met184. Eur J. Biochem 267: 2658–2665.
   Google Scholar
• Julias JG, Pathak VK (1998). Deoxyribonucleoside triphos-phate pool imbalances in vivo are associated with an increased retroviral mutation rate. I Virol 72: 7941–7949.
   PubMedGoogle Scholar
• Kaushik N, Talele TT, Pandey PK, Harris D, Yadav PN, Pandey VN (2000). Role of glutamine 151 of human immunodeficiency virus type-1 reverse transcriptase in substrate selection as assessed by site-directed mutage-nesis. Biochemistry 39: 2912–2920.
   Google Scholar
• Kim B, Ayran JC, Sagar SG, Adman ET, Fuller SM, Tran NH, Horrigan J (1999). New human immunodeficiency virus, type 1 reverse transcriptase (HIV-1 RT) mutants with increased fidelity of DNA synthesis. Accuracy, tem-plate binding, and processivity. J Biol Chem 274: 27666–27673.
   Google Scholar
• Kohlstaedt LA, Wang J, Friedman JM, Rice PA, and Steitz TA (1992). Crystal structures at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256: 1783–1790.
   Google Scholar
• Korber B (1994a). Computational analysis of HIV molecu-lar sequences. In HIV signature and sequence variation analysis. Rodrigo AG, Learn GH (eds). Kluwer Academic Publishers: Dordrecht, Netherlands, pp 55–72.
   Google Scholar
• Korber BT, Kunstman KJ, Patterson BK, Furtado M, McEvilly MM, Levy R, Wolinsky SM (1994b). Genetic differences between blood- and brain-derived viral se-quences from human immunodeficiency virus type 1-infected patients: Evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. I Virol 68: 7467–7481.
   PubMed Web of Science ®Google Scholar
• Krebs FC, Mehrens D, Pomeroy S, Goodenow MM, Wigdahl B (1998). Human immunodeficiency virus type 1 long terminal repeat quasispecies differ in basal transcription and nuclear factor recruitment in human glial cells and lymphocytes. J Biomed Sci 5: 31–44.
   Google Scholar
• Lewis DA, Bebenek K, Beard WA, Wilson SH, Kunkel TA (1999). Uniquely altered DNA replication fidelity con-ferred by an amino acid change in the nucleotide binding pocket of human immunodeficiency virus type 1 reverse transcriptase. J Biol Chem 274: 32924–32930.
   Google Scholar
• Li Y, Kappes JC, Conway JA, Price RW, Shaw GM (1992). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• Liu C, Power C (1996). [online] (http://hiv-web.lanl.gov/) Lukashov VV (2000). [online] (http://hiv-web.lanl.gov/) Mansky LM, Temin HM (1995). Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 69: 5087–5094.
   Google Scholar
• Masliah E, DeTeresa RM, Mallory ME, Hansen LA (2000). Changes in pathological findings at autopsy in AIDS cases for the last 15 years. AIDS 14: 69–74.
   PubMed Web of Science ®Google Scholar
• Matala E (1996). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• McArthur JC (1987). Neurologic manifestations of AIDS. Medicine 66: 407–437.
   PubMed Web of Science ®Google Scholar
• McArthur JC, Becker PS, Parisi JE, Trapp B, Selnes OA, Cornblath DR, Balakrishnan J, Griffin JW, Price D (1989). Neuropathological changes in early HIV-1 dementia. Ann Neurol 26: 681–684.
   Google Scholar
• Morris A, Marsden M, Halcrow K, Hughes ES, Brettle RP, Bell JE, Simmonds P (1999). Mosaic structure of the hu-man immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: Evidence for frequent in vivo recombination events in the evolution of regional populations. I Virol 73: 8720–8731.
   PubMed Web of Science ®Google Scholar
• Najera I, Holguin A, Quinones-Mateu ME, Munoz-Fernandez MA, Najera R, Lopez Galindez C, Domingo E (1995). Pol gene quasispecies of human immuno-deficiency virus: Mutations associated with drug resis-tance in virus from patients undergoing no drug therapy. J Virol 69: 23–31.
   PubMed Web of Science ®Google Scholar
• Nei M, Gojobori T (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nu-cleotide substitutions. Mol Biol Evol 3: 418–426.
   PubMed Web of Science ®Google Scholar
• O'Brien WA, Koyanagi Y, Namazie A, Zhao JQ, Diagne A, Idler K, Zack JA, Chen ISY (1991). [online] (http://hiv-web. lanl.gov/)
   Google Scholar
• Oelrichs RB, Mcphee DA, Deacon NJ (1998). [online] (http://hiv-web.lanl.gov/)
   Google Scholar
• Ota T, Nei M (1994). Variance and covariances of the num-bers of synonymous and nonsynonymous substitutions per site. Mol Biol Evol 11: 613–619.
   PubMed Web of Science ®Google Scholar
• Pang S, Vinters HV, Akashi T, O'Brien WA, Chen IS (1991). HIV-1 env sequence variation in brain tissue of patients with AIDS-related neurologic disease. J Acquir Immune Defic Syndr 4: 1082–1092.
   Google Scholar
• Power C, McArthur JC, Johnson RT, Griffin DE, Glass JD, Dewey R, Chesebro B (1995). Distinct HIV-1 env se-quences are associated with neurotropism and neurovir-ulence. Curr Top Microbiol Immunol 202: 89–104.
   Google Scholar
• Sarafianos SG, Das K, Ding J, Boyer PL, Hughes SH, Arnold E (1999). Touching the heart of HIV-1 drug resistance: The fingers close down on the dNTP at the polymerase active site. Chem Biol 6: R137–146.
   Google Scholar
• Shafer RW, Stevenson D, Chan B (1999). Human immu-nodeficiency virus reverse transcriptase and protease se-quence database. Nucleic Acids Res 27: 348–352.
   PubMed Web of Science ®Google Scholar
• Shah FS, Curr KA, Hamburgh ME, Parniak M, Mitsuya H, Arnez JG, Prasad VR (2000). Differential influence of nu-cleoside analog-resistance mutations K65R and L74V on the overall mutation rate and error specificity of human immunodeficiency virus type 1 reverse transcriptase. J Biol Chem 275: 27037–27044.
   PubMed Web of Science ®Google Scholar
• Shaw GM, Harper ME, Hahn BH, Epstein LG, Gajdusek DC, Price RW, Navia BA, Petito CK, O'Hara CJ, Groopman JE (1985). HTLV-III infection in brains of children and adults with AIDS encephalopathy. Science 227: 177–182.
   PubMed Web of Science ®Google Scholar
• Stankoff B, Calvez V, Suarez S, Bossi P, Rosenblum O, Conquy L, Turell E, Dubard T, Coutellier A, Baril L, Bricaire F, Lacomblez L, Lubetzki C (1999). Plasma and cerebrospinal fluid human immunodeficiency virus type-1 (HIV-1) RNA levels in HIV-related cognitive im-pairment. Eur J Neurol 6: 669–675.
   Google Scholar
• Strizki JM, Albright AV, Sheng H, O'Connor M, Perrin L, Gonzalez-Scaran o F (1996). Infection of primary human microglia and monocyte-derived macrophages with hu-man immunodeficiency virus type 1 isolates: Evidence of differential tropism. I Virol 70: 7654–7662.
   PubMedGoogle Scholar
• van't Wout AB, Ran LJ, Kuiken CL, Kootstra NA, Pals ST, Schuitemaker H (1998). Analysis of the temporal relationship between human immunodeficiency virus type 1 quasispecies in sequential blood samples and various organs obtained at autopsy. I Virol 72: 488–496.
   Google Scholar
• Venturi G, Catucci M, Romano L, Corsi P, Leoncini F, Valensin PE, Zazzi M (2000). Antiretroviral resistance mutations in human immunodeficiency virus type 1 reverse transcriptase and protease from paired cere-brospinal fluid and plasma samples. I Infect Dis 181: 740–745.
   Google Scholar
• Weiss KK, Isaacs SJ, Tran NH, Adman ET, Kim B (2000). Molecular architecture of the mutagenic active site of human immunodeficiency virus type 1 reverse tran-scriptase: Roles of the beta 8-alpha E loop in fidelity, pro-cessivity, and substrate interactions. Biochemistry 39: 10684–10694.
   Google Scholar
• Wildemann B, Haas J, Ehrhart K, Wagner H, Lynen N, Storch-Hagenlocher B (1993). In vivo compari-son of zidovudine resistance mutations in blood and CSF of HIV-1-infected patients. Neurology 43: 2659–2663.
   PubMed Web of Science ®Google Scholar
• Wong JK, Ignacio CC, Torriani F, Havlir D, Fitch NJ, Richman DD (1997). In vivo compartmentalization of human immunodeficiency virus: Evidence from the ex-amination of pol sequences from autopsy tissues. I Virol 71: 2059–2071.
   Google Scholar
• Wrobel JA, Chao SF, Conrad MJ, Merker JD, Swanstrom R, Pielak GJ, Hutchison CA (1998). A genetic approach for identifying critical residues in the fingers and palm sub-domains of HIV-1 reverse transcriptase. Proc Nat] Acad Sci USA 95: 638–645.
   Google Scholar