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Miscellaneous Article

PCR Detection of Host and HIV-1 Sequences from Archival Brain Tissue

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Pages 164-171 | Received 30 Jul 1999, Accepted 14 Dec 1999, Published online: 10 Jul 2009

References

  • Albright A. V., Shieh J. T C, Itoh Y., Lee B., Pleasure D., O'Connor M. J., Doms R. W., González-Scarano. Microglia express CCR5, CXCR4, CCR3, but of these, CCR5 is the principal coreceptor for human immunodeficiency virus type 1 dementia isolates. J Virol 1999; 73: 205–213
  • An S. F., Ciardi A., Scaravilli. PCR detection of HIV pruviral DNA (gag) in the brains of patients with AIDS: comparison between results using fresh frozen and paraffin wax embedded specimens. J Clin Pathol 1994; 47: 990–994
  • Barroga C. F., Ellis R., Nelson J., Heaton R. K., Atkinson J. H., McCutchan J. A., Grant I., Spector S. A. HIV-1 neurocognitive disorders and chemokine receptors. AIDS 1997; 11: 1651–1664
  • Brew B., Rosenblum M., Cronin K., Price R. AIDS dementia complex and HIV-1 brain infection: clinical correlations. Ann Neurol 1995; 38: 563–570
  • Chang I., Jozwiak R., Wang B., Ng T., Ge Y. C., Bolton W., Dweyer D. E., Randle C., Osborn R., Cunningham A. L., Saksena N. K. Unique HIV type 1 V3 region sequences derived from six different regions of brain: region specific evolution within host determined quasispecies. AIDS Research and Human Retroviruses 1998; 14: 25–30
  • Crandall K. A. Intraspecific cladogram estimation: accuracy at higher levels of divergence. Systemic Biology 1994; 43: 222–235
  • Crandall K. A., Templeton A. R., Sing C. F. Intraspecific phylogenetics: problems and solutions. Models in Phylogeny Reconstruction, D. J. Seilbert, D. M. Williams. Clarendon Press, Scotland 1994; 273–297
  • Crandall K. A. Intraspecific phylogenetics: supp ort for dental transmission of human immunodeficiency virus. J Virol 1995; 69: 2351–2356
  • Crandall K. A. Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus Type I sequences. Mol Biol Evol 1996; 13: 115–131
  • Crandall K. A., Kelsey C. R., Imamichi H., Salzman N. P. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Molecular Biology and Evolution 1999a; 16: 372–382
  • Crandall K. A., Vasco D. A., Posada D., Imamichi H. Advances in understanding the evolution of HIV. AIDS 1999b; 13: 539–547
  • Dean M., Carrington M., Winkler C., Huttley G. A., Smith M. W., Allikmets R., Goedert J. J., Buchbinder S. P., Vittinghoff E., Gomperts E., Donfield S., Vlahov D., Kaslow R., Saah A., Rinaldo C., Detels R., O'Brien S. J. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 1996; 273: 1856–1862
  • Di Stefano M., Wilt S., Gray F., Dubois-Dalcq M., Chiodi F. HIV type 1 V3 sequences and the development of dementia during AIDS. AIDS Research and Human Retroviruses 1996; 12: 471–476
  • Epstein L. G., Kuiken C., Blumberg B. M., Hartman S., Sharer L. R., Clement M., Goudsmit J. V3 domain variation in brain and spleen of children with AIDS: Tissue-specific evolution within host-determined quasispecies. Virology 1991; 180: 583–590
  • Gartner S., McDonald R. A., Hunter E. A., Bouwman F., Liu Y., Popovic M. Gp120 sequence variation in brain and in T-lymphocyte human immunodeficiency virus type 1 primary isolates. J Human Virol 1997; 1: 3–18
  • Ghorpade A., Xia M. Q., Hyman B. T., Persidsky Y., Nukuna A., Bock P., Che M., Limoges J., Gendelman H. E., Mackay C. R. Role of the β-chemokine receptors CCR3 and CCR5 in human immunodeficiency virus type 1 infection of monocytes and microglia. J Virol 1998; 72: 3351–3361
  • He J., Chen Y., Farzan M., Choe H., Ohagen A., Gartner S., Busciglio J., Yang X., Hofmann W., Newman W., Mackay C. R., Sodroski J., Gabuzda D. CCR3 and CCR5 are co-receptors for HIV-1 infection of microglia. Nature 1997; 385: 645–649
  • Huang Y., Paxton W. A., Wolinsky S. M., Neumann A. U., Zhang L., He T., Kang S., Ceradini D., Jin Z., Yazdanbakhst K., Kunstman K., Erickson D., Dragon E., Landau N. R., Phair J., Ho D. D., Koup R. A. The role of mutant CCR5 allele in HIV-1 transmission and Disease Progression. Nature Medicine 1996; 2: 1240–1243
  • Korber B. T M, Kunstman K. J., Patterson B. K., Furtado M., McEvilly M. M., Levy R., Wolinsky S. M. Genetic Differences between blood-derived and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: Evidence of Conserved Elements in the V3 region of the envelope protein of brain-derived sequences. J Virol 1994; 68: 7467–7481
  • Kostrikis L. G., Huang Y., Moore J. P., Wolinsky S. M., Zhang L., Guo Y., Deutsch L., Phair J., Neumann A. U., Ho D. D. A chemokine receptor CCR2 allele delays HIV-1 disease Progression and is Associated with a CCR5 Promoter Mutation. Nature Medicine 1998; 4: 350–353
  • LaRosa G. J., Davide J. P., Weinhold K., Waterbury J. A., Profy A. T., Lewis J. A., Langlois A. J., Dreesman G. R., Boswell R. N., Shadduck P., et al. Conserved sequence and structural elements in the HIV-1 principal neutralizing determinant. Science 1990; 249: 932–935
  • Lavi E., Strizki J. M., Ulrich A. M., Zhang W., Fu L., Wang Q., O'Connor M., Hoxie J. A., González-Scarano F. CXCR-4 (fusin), a co-receptor for the type-1 human immunodeficiency virus (HIV-1), is expressed in the human brain in a variety of cell types, including microglia and neurons. Am J Pathol 1997; 151: 1035–1041
  • Lavi E., Kolson D. L., Ulrich A. M., Fu L., Gonzalez-Scarano F. Chemokine receptors in the human brain and their relationship to HIV infection. J Neurovirol 1998; 4: 301–311
  • Li Y., Kapp es J. C., Conway J. A., Price R. W., Shaw G. M., Hahn B. H. Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and -defective viral genomes. J Virol 1991; 65: 3973–3985
  • Liu R., Paxton W. A., Choe S., Ceradini D., Martin S. R., Horuk R., MacDonald M. E., Stuhlmann H., Koup R. A., Landau N. R. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 1996; 86: 367–377
  • Martin M. P., Dean M., Smith M. W., Winkler C., Gerrard B., Michael N. L., Lee B., Doms R. W., Margolick J., Buchbinder S., Goedert J. J., O'Brien T. R., Hilgartner M. W., Vlahov D., O'Brien S. J., Carrington M. Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science 1998; 282: 1907–1911
  • Messier W., Stewart C. B. Episodic adaptive evolution of primate lysozymes. Nature 1997; 385: 151–154
  • Navia B. A., Jordan B., Price R. W. The AIDS dementia complex: I. Clinical features. Ann Neurol 1986a; 19: 517–524
  • Navia B. A., Cho E., Petito C., Price R. W. The AIDS dementia complex: II. Neuropathology. Ann Neurol 1986b; 19: 525–535
  • Nicoll J. A R, Maitland N. J., Love S. Use of the polymerase chain reaction to detect herpes simplex virus DNA in paraffin sections of human brain at necropsy. J Neurol Neurosurg Psychiatry 1991; 54: 168–169
  • Ohagen A., Ghosh S., He J., Huang K., Chen Y., Yuan M., Osathanondh R., Gartner S., Shi B., Shaw G., Gabuzda D. Apoptosis induced by infection of primary brain cultures with diverse human immunodeficiency virus type 1 isolates: evidence for a role of the envelope. J Virol 1999; 73: 897–906
  • Power C., McArthur J. C., Johnson R. T., Griffin D. E., Glass J. D., Perryman S., Chesebro B. Demented and nondemented patients with AIDS differ in brain-derived human immunodeficiency virus type 1 envelope sequences. J Virol 1994; 68: 4643–4649
  • Power C., McArthur J. C., Nath A., Wehrly K., Mayne M., Nishio J., Langelier T., Johnson R. T., Chesebro B. Neuronal death induced by brain-derived immunodeficiency virus type 1 envelope genes differs between demented and nondemented AIDS patients. J Virol 1998; 72: 9045–9053
  • Price R. W. Understanding the AIDS dementia complex. HIV, AIDS and the Brain, R. W. Price, S. W I I I Perry. Raven Press, New York 1995; 1–45
  • Redely R. T., Achim C. L., Sirko D. A., Tehranchi S., Kraus F. G., Wong-Staal F., Wiley C. A. Sequence analysis of the V3 loop in brain and spleen of patients with HIV encephalitis. AIDS Research and Human Retroviruses 1996; 12: 477–482
  • Rizzardi G. P., Morawetz R. A., Vicenzi E., Ghezzi S., Poli G., Lazzarin A. Pantaleo G and the Swiss HIV Cohort. CCR2 polymorphism and HIV disease. Nature Medicine 1998; 4: 252–253
  • Rogers B. B., Alpert L. C., Hine E. A S, Buffone G. J. Analysis of DNA in fresh and fixed tissue by the Polymerase Chain Reaction. Am J Pathol 1990; 136: 541–548
  • Samson M., Libert F., Doranz B. J., Rucker J., Liesnard C., Farber C. M., Saragosti S., Lapoumeroulie C., Cognaux J., Forceille C., Muyldermans G., Verhofstede C., Burton-Boy G., Georges M., Imai T., Rana S., Yi Y., Smyth R. J., Collman R. G., Doms R. W., Vassart G., Parmentier M. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 1996; 382: 722–725
  • Sanders V. J., Pittman C. A., White M. G., Wang G., Wiley C. A., Achim C. L. Chemokines and receptors in HIV encephalitis. AIDS 1998; 12: 1021–1026
  • Shapshak P., Segal D. M., Crandall K. A., Fujimura R. K., Zhang B.-T, Xin K.-Q., Okuda K., Petito C. K., Eisdorfer C., Goodkin K. Independent evolution of HIV-1 in different brain regions. AIDS Research and Hainan Retroviruses 1999; 15: 811–820
  • Sharp P. M. In search of molecular dwarfism. Nature 1997; 385: 111–112
  • Sheih J. T C, Albright A. V., Sharron M., Gartner S., Stizki J., Doms R. W., González-Scarano F. Chemokine receptor utilization by human immunodeficiency virus type 1 isolates that replicate in microglia. J Virol 1998; 72: 4243–4249
  • Smith M. W., Dean M., Carrington M., Winkler C., Huttley G. A., Lomb D. A., Goedert J. J., O'Brien T. R., Jacobson L. P., Kaslow R., Buchbinder S., Vittinghoff E., Vlahov D., Hoots K., Hilgartner M. W. Hemophilia Growth and Development Study, Multicenter Aids Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study, O'Brien S. J. Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Science 1997; 277: 959–965
  • Swofford D. L. PAUP* phylogenetic analysis using parsimony and other methods4.0 Obeta ed. Sinaiier Associates, Sunderland, MA 1998
  • Taouik Y., Boutet A., Lannuzel A., Salim H., Azzarone B., Dussaix E., Vincent J. D., Tardieu M., Delfraissy J. F. Expression of CD4 and chemokine receptors in human brain cells: astrocyte entry by HIV-1 T and M tropic strains is blocked by SDF-1 and Rantes. Abstracts of the 5th Conference on Retroviruses and Opp ortunistic Infections. 1998, #448
  • Taubenberger J. K., Reid A. H., Krafft A. E., Bijwaard K. E., Fanning T. G. Initial genetic characterization of the ‘Spanish’ influenza virus. Science 1997; 275: 1793–1796
  • Templeton A. R., Crandall K. A., Sing C. F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapp ing anil DNA sequence data. III Cladogram estimation. Genetics 1992; 132: 619–633
  • Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. The ClustalX Windows Interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997; 24: 4876–4882
  • Vago L., Nebuloni M., Sala E., Cinque P., Bonetto S., Isella A., Ottoni L., Crociati A., Costanzi G. Coinfection of the central nervous system by cytomegalovirus and herpes simplex virus type 1 or 2 in AIDS patients: Autopsy study on 82 cases by immunohistochemistry and polymerase chain reaction. Acta Neuropathologica 1996; 92: 404–408
  • Vallat A. V., De Girolami U., He J., Mhashilkar A., Marasco W., Shi B., Gray F., Bell J., Keohane C., Smith T. W., Gabuzda D. Localization of HIV-1 co-receptors CCR5 and CXCR4 in the brain of children with AIDS. Am J Pathol 1998; 152: 167–178
  • van Rij R. P., van Wout A. B., Portegies P., Halaby T., Ran L., de Roda Husman A. M., Lange J. M A, Schuitemaker H. Absence of NSI HIV-1 in tissues of CCR-Δ32 heterozygotes as explanation for reduced incidence of AIDS dementia complex. Abstracts of the 5th Conference on Retroviruses and Opp ortunistic Infections. 1998, #449
  • Vesy C. J., Greenson J. K., Papp A. C., Snyder P. J., Qualman S. J., Prior T. W. Evaluation of Celiac Disease Biopsies for Adenovirus 12 DNA Using Multiplex PCR. Modern Pathology 1993; 6: 62–64
  • Winkler C., Modi W., Smith M. W., Nelson G. W., Carrington M., Dean M., Honjo T., Tashiro K., Yabe D., Buchbinder S., Vittinghoff E., Goedert J. J., O'Brien T. R., Jacobson L. P., Detels R., Donfield S., Willoughby A., Gomperts E., Vlabov D., Phair J., O'Brien S. J. Genetic restriction of AIDS pathogenesis by an SDS-1 chemokine gene variant. ALIVE Study, Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort. Science 1998; 279: 389–393
  • Wright D. K., Manos M. M. Sample Preparation from Paraffin-Embedded Tissues. PCR Protocols: a Guide to Methods and App lications, M. A. Innis, D. H. Gelfand, J. J. Sninsky, T. J. White. Academic Press, San Diego, California 1990; 153–158

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