Poor performance of bioinformatics programs for genotypic prediction of coreceptor usage of HIV-1 group o isolates

Journal of Acquired Immune Deficiency Syndromes

Volumn 53, Issue 3, 2010, Pages 412-413

  Rupp, Daniel ^a   Geuenich, Silvia ^a   Keppler, Oliver T ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CXCR4; MARAVIROC; VIRUS GLYCOPROTEIN;

BIOINFORMATICS; CAMEROON; DRUG EFFICACY; EQUATORIAL GUINEA; GABON; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; LETTER; PREDICTION; PRIORITY JOURNAL; SEROPREVALENCE; SUPPORT VECTOR MACHINE;

AMINO ACID SEQUENCE; ANTI-HIV AGENTS; COMPUTATIONAL BIOLOGY; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; RECEPTORS, HIV; SEQUENCE ALIGNMENT; VIRUS ATTACHMENT;

EID: 77649229288     PISSN: 15254135     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAI.0b013e3181c9f53f     Document Type: Letter

References (16)

1. Dorr P, Westby M, Dobbs S, et al. Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of che-mokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob Agents Chemother. 2005; 49:4721-4732.
2. Fatkenheuer G, Nelson M, Lazzarin A, et al. Subgroup analyses of maraviroc in previously treated R5 HIV-1 infection. N Engl J Med. 2008;359:1442-1455.
3. Moore JP, Kuritzkes DR. A piece de resistance: how HIV-1 escapes small molecule CCR5 inhibitors. Curr Opin HIV AIDS. 2009;4: 118-124.
4. Archer J, Braverman MS, Taillon BE, et al. Detection of low-frequency pretherapy chemo-kine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. Aids. 2009,23:1209-1218.
5. Lengauer T, Sander O, Sierra S, et al. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol. 2007,25:1407-1410.
6. Boisvert S, Marchand M, Laviolette F, et al. HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology. 2008;5:110.
7. Jensen MA, Coetzer M, van 't Wout AB, et al. A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. J Virol. 2006; 80:4698-4704.
8. Low AJ, Dong W, Chan D, Sing T, et al. Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. Aids. 2007;21:F17-F24.
9. Coakley E, Petropoulos CJ, Whitcomb JM. Assessing chemokine co-receptor usage in HIV. Curr Opin Infect Dis. 2005;18:9-15.
10. Skrabal K, Low AJ, Dong W, et al. Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model. J Clin Microbiol. 2007; 45:279-284.
11. Brennan CA, Bodelle P, Coffey R, et al. The prevalence of diverse HIV-1 strains was stable in Cameroonian blood donors from 1996 to 2004. J Acquir Immune Defic Syndr. 2008;49: 432-439.
12. Zekeng L, Obiang Sima J, Hampl H, et al. Update on HIV-1 group O infection in Equatorial Guinea, Central Africa. Aids. 1997;11:1410-1412.
13. Janssens W, Heyndrickx L, Van der Auwera G, et al. Interpatient genetic variability of HIV-1 group O. Aids. 1999;13:41-48.
14. Gurtler LG, Hauser PH, Eberle J, et al. A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon. J Virol. 1994;68:1581-1585.
15. Vergne L, Bourgeois A, Mpoudi-Ngole E, et al. Biological and genetic characteristics of HIV infections in Cameroon reveals dual group M and O infections and a correlation between SI-inducing phenotype of the predominant CRF02-AG variant and disease stage. Virology. 2003;310:254-266.
16. Geuenich S, Kaderali L, Allespach I, et al. Biological signature characteristics of primary isolates from human immunodeficiency virus type 1 group O in ex vivo human tonsil histocultures. J Virol. 2009;83:10494-10503.