Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples

AIDS Research and Human Retroviruses

Volumn 14, Issue 10, 1998, Pages 869-876

  Günthard, Huldrych F ^a,c   Wong, Joseph K ^a   Ignacio, Caroline C ^a   Havlir, Diane V ^a,b   Richman, Douglas D ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS CHARACTERIZATION; VIRUS GENE; VIRUS MUTATION;

EID: 0032503931     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.1998.14.869     Document Type: Article

References (26)

1. Gulick RM, Mellors JW, Havlir DV, Eron JJ, Gonzalez C, McMahon D, Richman DD, Valentine FT, Jonas L, Deutsch P, Meibohm A, Condra JH, Emini EA, and Chodakewitz JA: Treatment with indinavir, zidovudine, and lamivudine in adults with human immunodeficiency virus infection and prior antiretroviral therapy. N Engl J Med 1997;337:734-739.
2. Mellors JW, Rinaldo CR, Phalguni G, White RM, Todd JA, and Kingsley LA: Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 1996;272:1167-1171.
3. Connor R, Ho D, Kuritzkes D, and Richman DD: Human immunodeficiency virus. In: Clinical Virology. (Richman DD, Whitley RJ, and Hayden FG, eds.), 1st Ed. Churchill Livingstone, New York, 1997, pp. 733-735.
4. D'Aquila RT, Johnson VA, Welles SL, Japour AJ, Kuritzkes DR, DeGruttola V, Reichelderfer PS, Coombs RW, Crumpacker CS, Kahn JO, et al.: Zidovudine resistance and human immunodeficiency virus type 1 disease progression during antiretroviral therapy. Ann Intern Med 1995;122:401-408.
5. Japour AJ, Welles S, D'Aquila RT, Johnson VA, Richman DD, Coombs DW, Reichelderfer PS, Kahn JO, Crumpacker CS, and Kuritzkes DR: Prevalence and clinical significance of zidovudine resistance mutations in human immunodeficiency virus isolated from patients following long-term zidovudine treatment. J Infect Dis 1995;171:1172-1179.
6. Kuritzkes DR: Clinical significance of drug resistance in HIV-1 infection. AIDS 1996;10(Suppl. 5):S27-S31.
7. Montaner JSG, Singer J, Schechter MT, Raboud JM, Tsoukas C, O'Shaughnessy M, Ruedy J, Nagai K, Salomon H, Spira B, et al.: Clinical correlates of in vitro HIV-1 resistance to zidovudine. Results of the multicentre Canadian AZT trial. AIDS 1993;7:189-196.
8. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, and Solas D: Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767-773.
9. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, and Gingeras TR: Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med 1996;2: 753-759.
10. Lipshutz RJ and Fodor SPA: Advanced DNA sequencing technologies. Curr Opin Struct Biol 1994;4:376-380.
11. Lipshutz RJ: Using oligonucleotide probe arrays to assess genetic diversity. BioTechniques 1995;19:442-447.
12. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, and Fodor SPA: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 1991;91:5022-5026.
13. Wong JK, Günthard HF, Havlir DV, Zhang Z, Haase AT, Ignacio CC, Kwok S, Emini E, and Richman DD: Reduction in HIV-1 in blood lymph nodes following potent antiretroviral therapy and the virologie correlates of failure. Proc Natl Acad Sci USA 1997; 95:12574-12579.
14. Deng WP and Nickoloff JA: Site-directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal Biochem 1992; 200:81-88.
15. Wong JK, Ignacio CC, Torriani F, Havlir DV, Fitch NJS, and Richman DD: In vivo compartmentalization of human immunodeficiency virus: Evidence from the examination of pol sequences from autopsy tissues. J Virol 1997;7:2059-2071.
16. Coffin JM: HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy. Science 1995;267: 483-489.
17. Wei X, Ghosh SK, Taylor ME, et al.: Viral dynamics in human immunodeficiency virus type 1 infection. Nature (London) 1995; 373:117-122.
18. Havlir DV, Eastman S, Gamst A, and Richman DD: Nevirapine-resistant human immunodeficiency virus: Kinetics of replication and estimated prevalence in untreated patients. J Virol 1996;79: 7894-7899.
19. Harrigan PR, Bloor S, and Larder B: Quantitation of viral fitness and AZT selection of AZT-resistant HIV-1 variants. In: HIV Drug Resistance, 5th International Workshop, 3-6 July 1996, Whistler, Canada. Antiviral Therapy 1996 (Suppl. 1). International Medical Press, London. Abstract 87, p. 55.
20. Bacheler LT, Paul M, Logue K, Buckery R, Cordova B, and Anton E: Fitness of protease inhibitor-resistant viruses in the presence and absence of drug. In: HIV Drug Resistance, 5th International Workshop, 3-6 July 1996, Whistler, Canada. Antiviral Therapy 1996 (Suppl. 1). International Medical Press, London. Abstract 84, p. 53.
21. Condra JH, Hodler DJ, Graham DJ, Shivaprakash M, Laird DT, Schleif WA, Chodakewitz JA, and Emini EA: Geneotypic or phenotypic susceptibility testing may not predict clinical responses to indinavir. In: International Workshop on HIV Drug Resistance, Treatment Strategies and Eradication, St. Petersburg, Florida, 25-28 June, 1997, Antiviral Therapy 2 (Suppl). International Medical Press, London, 1997, p. 31, Abstract 47.
22. De Antoni A, Foli A, Lisziewicz J, and Lori F: Mutations in the pol gene of human immunodeficiency virus type 1 in infected patients receiving didanosine and hydroxyurea combination therapy. J Infect Dis 1997;176:899-903.
23. Delassus S, Cheynier R, and Wain-Hobson S: Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro. J Virol 1991;65:225-231.
24. Kusumi K, Conway B, Cunninham S, et al.: Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. J Virol 1992;66:875-885.
25. Michael NL, Chang G, Ehrenberg PK, Vahey MT, and Redfield RR: HIV-1 proviral genotypes from the peripheral blood mononuclear cells of an infected patient are differentially represented in expressed sequences. J Acquir Immune Defic Syndr 1993;6: 1073-1085.
26. Günthard HF, Wong JK, Ignacio CC, Guatelli JC, Riggs NL, Havlir DV, and Richman DD: Human immunodeficiency virus replication and genotypic resistance in blood and lymph nodes after a year of potent antiretroviral therapy. J Virol 1998;72:2422-2428.