Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing

Journal of Clinical Microbiology

Volumn 51, Issue 2, 2013, Pages 444-451

  Knapp, David J H F ^a   Mcgovern, Rachel A ^a   Dong, Winnie ^a   Poon, Art F Y ^a   Swenson, Luke C ^a   Zhong, Xiaoyin ^a   Woods, Conan K ^a   Richard Harrigan, P ^a,b  

^a BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MARAVIROC;

AMPLICON; ARTICLE; CHROMATOGRAPHY; COHORT ANALYSIS; CONTROLLED STUDY; GENE DOSAGE; HIV TEST; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MAJOR CLINICAL STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREVALENCE; PRIORITY JOURNAL; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; VIRAL TROPISM; VIRUS LOAD; VIRUS REPLICATION;

BASE SEQUENCE; GENETIC ASSOCIATION STUDIES; GENOME, VIRAL; GENOTYPE; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV INFECTIONS; HIV-1; HUMANS; PHENOTYPE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; VIRAL LOAD; VIRAL TROPISM; VIRUS REPLICATION;

EID: 84873025235     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00739-12     Document Type: Article

References (31)

1. Este JA, Telenti A. 2007. HIV entry inhibitors. Lancet 370:81- 88.
2. Berger EA, Doms RW, Fenyo EM, Korber BT, Littman DR, Moore JP, Sattentau QJ, Schuitemaker H, Sodroski J, Weiss RA. 1998. A new classification for HIV-1. Nature 391:240. doi:10.1038/34571.
3. Connor RI, Sheridan KE, Ceradini D, Choe S, Landau NR. 1997. Change in coreceptor use correlates with disease progression in HIV-1- infected individuals. J. Exp. Med. 185:621- 628.
4. Delobel P, Sandres-Saune K, Cazabat M, Pasquier C, Marchou B, Massip P, Izopet J. 2005. R5 to X4 switch of the predominant HIV-1 population in cellular reservoirs during effective highly active antiretroviral therapy. J. Acquir. Immune Defic. Syndr. 38:382-392.
5. Lifson JD, Feinberg MB, Reyes GR, Rabin L, Banapour B, Chakrabarti S, Moss B, Wong-Staal F, Steimer KS, Engleman EG. 1986. Induction of CD4-dependent cell fusion by the HTLV-III/LAV envelope glycoprotein. Nature 323:725-728.
6. Dorr P, Westby M, Dobbs S, Griffin P, Irvine B, Macartney M, Mori J, Rickett G, Smith-Burchnell C, Napier C, Webster R, Armour D, Price D, Stammen B, Wood A, Perros M. 2005. Maraviroc (UK-427, 857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob. Agents Chemother. 49:4721- 4732.
7. Gulick RM, Lalezari J, Goodrich J, Clumeck N, DeJesus E, Horban A, Nadler J, Clotet B, Karlsson A, Wohlfeiler M, Montana JB, McHale M, Sullivan J, Ridgway C, Felstead S, Dunne MW, van der Ryst E, Mayer H, Study Teams MOTIVATE. 2008. Maraviroc for previously treated patients with R5 HIV-1 infection. N. Engl. J. Med. 359:1429 -1441.
8. Poveda E, Alcami J, Paredes R, Cordoba J, Gutierrez F, Llibre JM, Delgado R, Pulido F, Iribarren JA, Garcia Deltoro M, Hernandez Quero J, Moreno S, Garcia F. 2010. Genotypic determination of HIV tropism- clinical and methodological recommendations to guide the therapeutic use of CCR5 antagonists. AIDS Rev. 12:135-148.
9. Koot M, Vos AH, Keet RP, de Goede RE, Dercksen MW, Terpstra FG, Coutinho RA, Miedema F, Tersmette M. 1992. HIV-1 biological phenotype in long-term infected individuals evaluated with an MT-2 cocultivation assay. AIDS. 6:49 -54.
10. Rose JD, Rhea AM, Weber J, Quinones-Mateu ME. 2009. Current tests to evaluate HIV-1 coreceptor tropism. Curr. Opin. HIV. AIDS. 4:136- 142.
11. Chueca N, Garrido C, Alvarez M, Poveda E, de Dios Luna J, Zahonero N, Hernandez-Quero J, Soriano V, Maroto C, de Mendoza C, Garcia F. 2009. Improvement in the determination of HIV-1 tropism using the V3 gene sequence and a combination of bioinformatic tools. J. Med. Virol. 81:763-767. doi:10.1002/jmv.21425.
12. Hwang SS, Boyle TJ, Lyerly HK, Cullen BR. 1991. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253:71-74.
13. Lengauer T, Sander O, Sierra S, Thielen A, Kaiser R. 2007. Bioinformatics prediction of HIV coreceptor usage. Nat. Biotechnol. 25:1407- 1410.
14. Sander O, Sing T, Sommer I, Low AJ, Cheung PK, Harrigan PR, Lengauer T, Domingues FS. 2007. Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput. Biol. 3:e58. doi:10.1371/journal.pcbi. 0030058.
15. Seclen E, Garrido C, Gonzalez Mdel M, Gonzalez-Lahoz J, de Mendoza C, Soriano V, Poveda E. 2010. High sensitivity of specific genotypic tools for detection of X4 variants in antiretroviral-experienced patients suitable to be treated with CCR5 antagonists. J. Antimicrob. Chemother. 65:1486- 1492.
16. Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues FS, Buch J, Daumer M, Kaiser R, Lengauer T, Harrigan PR. 2007. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir. Ther. 12:1097-1106.
17. Kagan RM, Johnson EP, Siaw M, Biswas P, Chapman DS, Su Z, Platt JL, Pesano RL. 2012. A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment- experienced patients. PLoS One 7:e46334. doi:10.1371/journal .pone.0046334.
18. McGovern RA, Thielen A, Mo T, Dong W, Woods CK, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. 2010. Populationbased V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS 24:2517- 2525.
19. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376 -380.
20. Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJ, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR. 2011. Deep third variable sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin. Infect. Dis. 53:732-742.
21. Eckert KA, Kunkel TA. 1991. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1:17-24.
22. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186 -194.
23. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185.
24. Richterich P. 1998. Estimation of errors in "raw" DNA sequences: a validation study. Genome Res. 8:251-259.
25. Saag M, Goodrich J, Fatkenheuer G, Clotet B, Clumeck N, Sullivan J, Westby M, van der Ryst E, Mayer H, A4001029 Study Group. 2009. A double-blind, placebo-controlled trial of maraviroc in treatment-experienced patients infected with non-R5 HIV-1. J. Infect. Dis. 199:1638-1647.
26. Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. 2010. Improved detection of CXCR4-using HIV by V3 genotyping: application of population- based and "deep" sequencing to plasma RNA and proviral DNA. J. Acquir. Immune Defic. Syndr. 54:506 -510.
27. Brooks JI, Woods CK, Merks H, Wynhoven B, Hall TA, Sandstrom PA, Harrigan PR. 2009. Evaluation of an automated sequence analysis tool to standardize HIV genotyping results, abstr O061. Abstr. Can. Conf. HIV/AIDS Res., Vancouver, British Columbia, Canada.
28. Harrigan PR, Dong W, Wynhoven B, Mo T, Hall T, Galli RA. 2002. Performance of ReCall basecalling software for high-throughput HIV drug resistance basecalling using "in-house" methods, abstr TuPeB4598. Abstr. XIV Int. AIDS Conf., Barcelona, Spain, 7 to 12 July, 2002.
29. Jensen MA, Li FS, van't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI. 2003. Improved coreceptor usage prediction and genotypic monitoring of R5- to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J. Virol. 77:13376 -13388.
30. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
31. Harrington DP, Fleming TR. 1982. A class of rank test procedures for censored survival-data. Biometrika 69:553-566.