Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

Journal of Virology

Volumn 84, Issue 22, 2010, Pages 12087-12092

  Bimber, Benjamin N ^a   Dudley, Dawn M ^b   Lauck, Michael ^b   Becker, Ericka A ^a   Chin, Emily N ^b   Lank, Simon M ^a   Grunenwald, Haiying L ^e   Caruccio, Nicholas C ^e   Maffitt, Mark ^e   Wilson, Nancy A ^a   Reed, Jason S ^a   Sosman, James M ^f   Tarosso, Leandro F ^d   Sanabani, Sabri ^d   Kallas, Esper G ^d   Hughes, Austin L ^c   O'Connor, David H ^a,b  

^a UNIVERSITY OF WISCONSIN   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^c UNIVERSITY OF SOUTH CAROLINA   (United States)

^d UNIVERSITY OF SÃO PAULO   (Brazil)

^e ILLUMINA INC   (United States)

^f UNIVERSITY OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CYTOTOXIC T LYMPHOCYTE; GENE MUTATION; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS; PRIORITY JOURNAL; PYROSEQUENCING; SIMIAN IMMUNODEFICIENCY VIRUS; TRANSPOSON; ULTRADEEP PYROSEQUENCING; VIRUS GENOME;

AMINO ACID SEQUENCE; ANIMALS; GENETIC VARIATION; GENOME, VIRAL; HIV; HIV INFECTIONS; HUMANS; MACACA MULATTA; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; SPECIES SPECIFICITY; VIRAL PROTEINS;

SIMIAE; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 78049524598     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01378-10     Document Type: Article

References (15)

1. Abegaz, W. E., Z. Grossman, D. Wolday, et al. 2008. Threshold survey evaluating transmitted HIV drug resistance among public antenatal clinic clients in Addis Ababa, Ethiopia. Antivir. Ther. 13(Suppl. 2):89-94.
2. Allen, T. M., D. H. O'Connor, P. Jing, et al. 2000. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407:386-390.
3. Barouch, D. H., and N. L. Letvin. 2004. HIV escape from cytotoxic T lymphocytes: a potential hurdle for vaccines? Lancet 364:10-11.
4. Bimber, B. N., B. J. Burwitz, S. O'Connor, et al. 2009. Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J. Virol. 83:8247-8253.
5. Bordería, A. V., R. Lorenzo-Redondo, M. Pernas, et al. 2010. Initial fitness recovery of HIV-1 is associated with quasispecies heterogeneity and can occur without modifications in the consensus sequence. PLoS One 5:e10319.
6. de Oliveira, T., K. Deforche, S. Cassol, et al. 2005. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 21:3797-3800.
7. Halvas, E. K., A. Wiegand, V. F. Boltz, et al. 2010. Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment-experienced patients. J. Infect. Dis. 201:672-680.
8. Keele, B. F., E. E. Georgi, J. F. Salazar-Gonzalez, et al. 2008. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl. Acad. Sci. U. S. A. 105:7552-7557.
9. Lengauer, T., O. Sander, S. Sierra, et al. 2007. Bioinformatics prediction of HIV coreceptor usage. Nat. Biotechnol. 25:1407-1410.
10. Li, W. H. 1978. Maintenance of genetic variability under the joint effect of mutation, selection and random drift. Genetics 90:349-382.
11. Loh, L., and S. J. Kent. 2008. Quantification of simian immunodeficiency virus cytotoxic T lymphocyte escape mutant viruses. AIDS Res. Hum. Retroviruses 24:1067-1072.
12. Loh, L., J. Petravic, C. J. Batten, et al. 2008. Vaccination and timing influence SIV immune escape viral dynamics in vivo. PLoS Pathog. 4:e12.
13. Macleod, I. J., C. F. Rowley, I. Thior, et al. 2010. Minor resistant variants in nevirapine-exposed infants may predict virologic failure on nevirapine-containing ART. J. Clin. Virol. 48:162-167.
14. Peyerl, F. W., D. H. Barouche, H. S. Bazick, et al. 2005. Use of molecular beacons for rapid, real-time, quantitative monitoring of cytotoxic T-lymphocyte epitope mutations in simian immunodeficiency virus. J. Clin. Microbiol. 43:4773-4779.
15. Simen, B. B., J. F. Simons, K. H. Hullsiek, et al. 2009. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis. 199:693-701.