Rapid full-length genomic sequencing of two cytopathically heterogeneous Australian primary HIV-1 isolates

Journal of Biomedical Science

Volumn 7, Issue 2, 2000, Pages 128-135

  Oelrichs, Robert B ^a,d   Lawson, Victoria A ^b,c   Coates, Karen M ^b,c   Chatfield, Catherine ^b   Deacon, Nicholas J ^a   McPhee, Dale A ^b,c  

^a AIDS Molecular Unit   (Australia)

^b MACFARLANE BURNET INSTITUTE FOR MEDICAL RESEARCH AND PUBLIC HEALTH   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d THAI RED CROSS AIDS RESEARCH CENTRE   (Thailand)

Author keywords

HIV, Australian isolates; HIV, rapid sequencing, full length

Indexed keywords

ARTICLE; HELPER CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRAIN DIFFERENCE; TECHNIQUE; VIRUS GENOME;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0034124341     PISSN: 10217770     EISSN: 14230127     Source Type: Journal    
DOI: 10.1007/BF02256619     Document Type: Article

References (55)

1. Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, Berger EA. CC CKR5: a REANTES, MIP-1α, MIP-1β receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 272:1955-1958;1996.
2. Åsjö B, Morfedt-Månson L, Albert J, Biberfeld G, Karlsson A, Lidman K, Fenyö EM. Replicative capacity of human immunodeficiency virus from patients with varying seventy of HIV infection. Lancet ii:660-662;1986.
3. Chen BK, Gandhi RT, Baltimore D. CD4 down-modulation during infection of human T cells with human immunodeficiency virus type 1 involves independent activities of vpu, env, and nef. J Virol 70:6044-6053;1996.
4. Cheng-Mayer C, Liu R, Landau NR, Stamatatos L. Macrophage tropism of human immunodeficiency virus type 1 and utilization of the CC-CKR5 coreceptor. J Virol 71:1657-1661; 1997.
5. Cho MVW, Lee MK, Carney MC, Berson JF, Doms RW, Martin MA. Identification of determinants on a dualtropic human immunodeficiency virus type 1 envelope glycoproteins that confer usage of CXCR4. J Virol 72;2509-2515; 1998.
6. Collman RJ, Ballict W, Gregory SA, Friedman H, Kolson DL, Nathanson N, Srinivasan A. An infectious molecular clone of an unusual macrophage-tropic and highly cytopathic strain of human immunodeficiency virus type 1. J Virol 66:7517-7521;1992.
7. Cornelissen M, Hogervorst E, Zorgdrager F, Hartman S, Goudsmit J. Maintenance of syncytium-induced phenotype of HIV type 1 is associated with positively charged residues in the HIV type 1 gp120 V2 domain without fixed positions, elongation, or relocated N-linked glycosylation sites. AIDS Res Hum Retroviruses 11:1169-1175;1995.
8. De Jong JJ, De Ronde A, Keulen W, Tersmette M, Goudsmit J. Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: Analysis by single amino acid substitution. J Virol 66:6777-6780;1992.
9. Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR. Identification of a major co-receptor for primary isolates of HIV-1. Nature 381:661-666;1996.
10. Dragic T, Litwin V, Allaway GP, Martin SR, Huang Y, Nagashima KA, Cayanan C, Maddon PJ, Koup RA, Moore JP, Paxton WA. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature 381: 667-673;1996.
11. Fenyö EM, Morfeldt-Månson L, Chiodi F, Lind B, von Gegerfelt A, Albert J, Olausson E, Åsjö B. Distinct replicative and cytopathic characteristics of human immunodeficiency virus isolates. J Virol 62:4414-4419;1988.
12. Fouchier RA, Groenink M, Kootstra NA, Tersmette M, Huisman HG, Miedema F, Schuitemaker H. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 66:3183-3187;1992.
13. Gao F, Robertson DL, Carruthers CD, Morrison SG, Jian B, Chen Y, Barre-Sinoussi F, Girard M, Srinivasan A, Abimiku AG, Sharp PM, Hahn BH. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol 72:5680-5698; 1998.
14. Ghosh SK, Fultz PN, Keddie E, Saag MS, Sharp PM, Hahn BH, Shaw GM. A molecular clone of HIV-1 tropic and cytopathic for human and chimpanzee lymphocytes. Virology 194:858-864;1993.
15. Graf M, Shao Y, Zhao Q, Seidl T, Kestler J, Wolf H, Wagner R. Cloning and characterization of a virtually full-length HIV-1 genome from a subtype B′-Thai strain representing the most prevalent B-clade isolate in China. AIDS Res Hum Retroviruses 14:285-288;1998.
16. Greenway AL, McPhee DA, Grgacic E, Hewish D, Lucantoni A, Macreadie I, Azad AA. Nef 27 but not the Nef 25 isoform of human immunodeficiency virus type 1 pNL4.3 isolate down-regulates surface CD4 and IL-2R expression in peripheral blood mononuclear cells and transformed T-cells. Virology 198:245-256;1994.
17. Groenink M, Fouchier RA, Broersen S, Baker CH, Koot M, van't Wout AB, Huisman HG, Miedema F, Tersmette M, Schuitemaker H. Relation of phenotype evolution of HIV-1 to envelope V2 configuration. Science 260:1513-1516;1993.
18. Guillon C, Bedin F, Fouchier RA, Schuitemaker H, Gruters RA. Completion of nucleotide sequence of non-syncytium-induced and syncytium-inducing HIV type 1 variants isolated from the same patient. AIDS Res Hum Retroviruses 11:1537-1541;1995.
19. Gurgo C, Guo HG, Franchini G, Aldovini A, Collalti E, Farrell K, Wong-Staal F, Gallo RC, Reitz MS. Envelope sequences of two new United States HIV-1 isolates. Virology 164: 531-536;1988.
20. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol 36:365-369;1967.
21. HIV sequence database at the Los Alamos National Laboratory (http://hiv-web.lanl.gov/). These figures are based on data available 30/ 6/99.
22. Huet T, Dazza MC, Brun-Vezinet F, Roelants GE, Wain-Hobson S. A highly defective HIV-1 strain isolated from a healthy Gabonese individual presenting an atypical Western blot. AIDS 3:707-715;1989.
23. Iafrate AJ, Bronson S, Skowronski J. Separable functions of Nef disrupt two aspects of T cell receptor machinery: CD4 expression and CD3 signaling. EMBO J 16:673-684;1997.
24. Kemp DJ, Churchill MJ, Smith DB, Biggs BA, Foote SJ, Peterson MG, Samaras N, Deacon NJ, Doherty R. Simplified colorimetric analysis of polymerase chain reactions: Detection of HIV sequences in AIDS patients. Gene 94: 223-228;1990.
25. Kiernan R, Marshall J, Bowers R, Doherty R, McPhee D. Kinetics of HIV-1 replication and intracellular accumulation of particles in HTLV-I-transformed cells. AIDS Res Hum Retroviruses 6:743-752;1990.
26. Koyanagi Y, Miles S, Mitsuyasu RT, Merrill JE, Vinters HV, Chen IS. Dual infection of the central nervous system by AIDS viruses with distinct cellular tropisms. Science 236:819-822;1987.
27. Laukkanen T, Janssen W, Carr J, Albert J, Leinikki PO, McCutchan FE, Salminen MO. Inter-subtype recombinant strains of HIV-1 are frequently found among new full-length sequences. In: Conference Record of the 12th World AIDS Conference, Geneva 1998; abstr 11170, p 16.
28. Lee TH, Sunzeri FJ, Tobler LH, Williams BG, Busch MP. Quantitative assessment of HIV-1 DNA load by coamplification of NIV-1 gag and HLA-DQ-a genes. AIDS 5:683-691;1990.
29. Li Y, Kappes JC, Conway JA, Price RW, Shaw GW, Hahn BH. 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 65:3973-3985;1991.
30. McPhee D, Greenway A, Holloway G, Smith K, Deacon N, Pemberton L, Brew B. Anomalies in Nef expression within the central nervous system of HIV-1-positive individuals/ AIDS patients with or without AIDS dementia complex. J Neurovirol 4:291-300;1998.
31. Muesing MA, Smith DH, Cabradilla CD, Benton CV, Lasky LA, Capon DJ. Nucleic acid structure and expression of the human AIDS/ lymphadencpathy retrovirus. Nature 313:450-458;1985.
32. Neate EV, Pringle RC, Jowett JBV, Healey DS, Gust ID. Isolation of HIV from Australian patients with AIDS. AIDS-related conditions and healthy antibody-positive individuals. Aust NZ J Med 17:461-466;1987.
33. Neumann M, Felber BK, Kleinschmidt A, Froese B, Erfle V, Pavlakis GN, Brack-Werner R. Restriction of human immunodeficiency virus type 1 production in a human astrocytoma cell line is associated with a cellular block in Rev function. J Virol 69:2159-2167;1995.
34. Oelrichs R, Tsykin A, Rhodes D, Solomon A, Ellett A, McPhee D, Deacon N. Genomic sequence of HIV-1 from four members of the Sydney Blood Bank cohort of long-term non-progressors. AIDS Res Hum Retroviruses 14: 811-814;1998.
35. Oelrichs R, Workman C, Laukkanen T, McCutchan F, Deacon N. A novel subtype A/ G/J recombinant full-length HIV-1 genome from Burkina Faso. AIDS Res Hum Retroviruses 14:1495-1500;1998.
36. Oelrichs R, Juarez J, Alali M, Cunningham A, Stewart G, Naif H. Unpubl data, 1999.
37. Ou CY, Kwok S, Mitchell SW, Mack DH, Sninsky JJ, Krebs JW, Feorino P, Warfield D, Schochetman G. DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239:295-297;1988.
38. Pal A, Greenough TC, Sullivan JL, Somasundaran MJ. In vitro characterization of adult primary human immunodeficiency virus type 1: Demonstration of distinctive single-cell killing phenotypes in spite of similar levels of viral replication. J Infect Dis 176:933-940;1997.
39. Reitz M, Hall L, Robert-Guroff M, Lautenberger J, Hahn B, Shaw G, Kong L, Weiss S, Waters D, Gallo R, Blattner W. Viral variability and serum antibody response in a laboratory worker infected with HIV type 1 (HTLV type IIIB). AIDS Res Hum Retroviruses 10:1143-1155;1994.
40. Rizzuto CD, Wyatt R, Hernandez-Ramos N, Sun Y, Kwong PD, Hendrickson WA, Sodroski J. A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science 280:1949-1953;1998.
41. Robertson D, Gao F, Hahn B, Sharp P. Inter-subtype recombinant HIV-1 sequences. p III: 25-30. In: Korber B, Hahn B, Foley B, Mellors J, Leitner T, Myers G, McCutchan F, Kuiken C, eds. The Human Retroviruses and AIDS 1997 Compendium. Los Alamos National Laboratory, 1997.
42. Salminen MO, Koch C, Sanders-Buell E, Ehrenberg PK, Michael NL, Carr JK, Burke DS, McCutchan FE. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 213:80-86;1995.
43. Sanchez-Pescador R, Power MD, Barr PJ, Steimer KS, Stempien MM, Brown-Shimer SL, Gee WW, Renard A, Randolph A, Levy JA, Dina D, Luciw PA. Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2). Science 227:484-492;1985.
44. Sauermann U, Schneider J, Mous J, Brunckhorst U, Schedel I, Jentsch KD, Hunsmann G. Molecular cloning and characterization of a German HIV-1 isolate. AIDS Res Hum Retroviruses 6:813-823;1990.
45. Shibata R, Hoggan MD, Broscius C, Englund G, Theodore TS, Buckler-White A, Arthur LO, Israel Z, Schultz A, Lane HC, Martin MA. Isolation and characterization of a syncytium-inducing, macrophage/T-cell line-tropic human immunodeficiency virus type 1 isolate that readily infects chimpanzee cells in vitro and in vivo. J Virol 69:4453-4462;1995.
46. Siebenkotten G, Leyendeckers H, Christine R, Radbruch A. Isolation of plasmid DNA from mammalian cells with QIAprep. Qiagen News 2/95:11-12;1995.
47. Starcich BR, Hahn BH, Shaw GM, McNeely PD, Modrow S, Wolf H, Parks ES, Parks WP, Josephs SF, Gallo RC, Wong-Staal F. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retroviruses of AIDS. Cell 45: 637-648;1986.
48. Theodore TS, Englund G, Buckler-White A, Buckler CE, Martin MA, Peden KW. Construction and characterization of a stable full-length macrophage-tropic HIV type 1 molecular clone that directs the production of high titers of progeny virions. AIDS Res Hum Retroviruses 10:191-194;1996.
49. Wain-Hobson S, Sonigo P, Danos O, Cole S, Alizon M. Nucleotide sequence of the AIDS virus, LAV. Cell 40:9-17;1985.
50. Wang WK, Dudek T, Zhao YJ, Brumblay HG, Essex M, Lee TH. CCR5 coreceptor utilization involves a highly conserved arginine residue of HIV type 1 gp120. Proc Natl Acad Sci USA 95: 5740-5745;1998.
51. Willey RL, Rutledge RA, Dias S, Folks T, Theodore T, Buckler CE, Martin MA. Identification of conserved and divergent domains within the envelope gene of the acquired immunodeficiency syndrome retrovirus. Proc Natl Acad Sci USA 83:5038-5042;1986.
52. Wong-Staal F, Gallo RC, Chang NT, Ghrayeb J, Papas TS, Lautenberger JA, Pearson ML, Petteway SR, Ivanoff L, Baumeister K, Whitehorn EA, Rafalski JA, Doran ER, Josephs SJ, Starcich B, Livak KJ, Patarca R, Haseltine WA, Ratner L. Complete nucleotide sequence of the AIDS virus. HTLV-III. Nature 313:277-284;1985.
53. Xiao L, Owen SM, Goldman I, Lal AA, deJong JJ, Goudsmit J, Lal RB. CCR5 coreceptor usage of non-syncytium-inducing primary HIV-1 is independent of phylogenetically distinct global HIV-1 isolates: Delineation of consensus motif in the V3 domain that predicts CCR-5 usage. Virology 240:83-92;1998.
54. Yu X, McLane MF, Ratner L, O'Brien W, Collman R, Essex M, Lee TH. Killing of primary CD4+ T cells by non-syncytium-inducing macrophage-tropic human immunodeficiency virus type 1. Proc Natl Acad Sci USA 91:10237-10241;1994.
55. Zhu T, Ho DD. Was HIV present in 1959? Nature 374:503-504;1995.