Analysis of V3 loop sequences using various bioinformatic tools designed for genotypic HIV-1 tropism testing

HIV and AIDS Review

Volumn 9, Issue 3, 2010, Pages 65-71

  Parczewski, Miłosz ^a   Leszczyszyn Pynka, Magdalena ^a   Urbańska, Anna ^a   Bander, Dorota ^a   Boroń Kaczmarska, Anna ^a  

^a POMERANIAN MEDICAL UNIVERSITY   (Poland)

Author keywords

CCR5 inhibitors; Genotyping; HIV 1; Tropism

Indexed keywords

ALGORITHM; ALLELE; ARTICLE; BIOINFORMATICS; C4 5 ALGORITHM; CHARGE RULE ALGORITHM; COMPUTER PREDICTION; CONTROLLED STUDY; DECISION TREE; GENO2PHENO ALGORITHM; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PART ALGORITHM; PHYLOGENETIC TREE; POSITION SPECIFIC SCORING MATRIX SINSI; POSITION WEIGHT MATRIX; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE; VIRAL TROPISM;

EID: 80053969320     PISSN: 17301270     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1730-1270(10)60098-7     Document Type: Article

References (21)

1. Berger EA, Doms RW, Fenyo EM, Korber BT, Littman DR, et al. A new classification for HIV-1. Nature 1998; 391:240
2. Huang W, Eshleman SH, Toma J, Fransen S, Stawiski E, Paxinos EE et al. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents chemother 2007; 51:566-75. (Pubitemid 46185274)
3. Fouchier RA, Brouwer M, Broersen SM, Schuitemaker H. Simple determination of human immunodeficiency virus type 1 syncytium-inducing V3 genotype by PCR. J Clin Microbiol 1995; 33: 906-11.
4. Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, et al. 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 2003; 77:13376-88. (Pubitemid 37494331)
5. Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001; 288:51-62. (Pubitemid 32846473)
6. Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues F et al. Predicting HIV co-receptor usage based on genetic and clinical covariates. Antiviral Therapy 2007; 12:1097-106. (Pubitemid 350114990)
7. Low AJ, Dong W, Chan D, Sing T, Swanstrom R, et al. Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. AIDS 2007;21:F17-24. (Pubitemid 47329758)
8. 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.
9. Raymond S, Delobel P, Mavigner M, Cazabat M, Souyris C, Sandres-Sauné K, et al. Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism. AIDS. 2008; 22: F11-6.
10. Soulié C, Derache A, Aimé C, Marcelin AG, Carcelain G, Simon A, et al. Comparison of two genotypic algorithms to determine HIV-1 tropism. HIV Med 2008; 9:1-5.
11. Geretti AM, Mackie N. Determining HIV-1 tropism in routine clinical practice. Available on-line www.bhiva.org/documents/Guidelines/Tropism/HIV- 1Tropism.doc
12. Recommendations for determining hiv-1 coreceptor usage. Available on-line http://www.genafor.org/arevir2008/presentation/11-04-2008/Recommendations- tropismus.pdf
13. Harrigan PR, Dong W, Wynhoven B, Mo T, Hall T, Galli R. Performance of ReCall basecalling soft ware for highthroughput HIV drug resistance basecalling using "inhouse"methods. The XIV International AIDS Conference. Abstract #TuPeB4598. Spain, Barcelona, July 7-12, 2002.
14. Rector A, Vermeire S, Thoelen I, Keyaerts E, Struyf F, Vlietinck R, et al. Analysis of the CC chemokine receptor 5 (CCR5) delta-32 polymorphism in inflammatory bowel disease. Hum Genet 2001; 108: 190-3. (Pubitemid 32293663)
15. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) soft ware version 4.0. Mol Biol Evol 2007; 24: 1596-9. (Pubitemid 47236692)
16. Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland, Massachusetts. Sinauer Associates; 1998.
17. Parczewski M, Leszczyszyn-Pynka M, Urbanska A, Bander D, Boron-Kaczmarska A. Genotypic tropism among treatment-experienced patients with drug resistant HIV-1. In press.
18. McGovern R, Dong W, Zhong W, D Knapp, A Thielen, et al. Population-based Sequencing of the V3-loop Is Comparable to the Enhanced Sensitivity Trofile Assay in Predicting Virologic Response to Maraviroc of Treatment-naïve Patients in the MERIT Trial. 17th Conference on retroviruses and Opportunistic Infections San Francisco, USA, 16-19 Feb 2010.
19. Garrido C, Roulet V, Chueca N, Poveda E, Aguilera A, Skrabal K, et al. Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes. J Clin Microbiol 2008; 46:887-91 (Pubitemid 351379974)
20. Poveda E, Briz V, Roulet V, Del Mar González M, Faudon JL, Skrabal K, Soriano V. Correlation between a phenotypic assay and three bioinformatic tools for determining HIV coreceptor use. AIDS 2007; 21: 1487-90. (Pubitemid 46988013)
21. Recordon-Pinson P, Soulié C, Anies G, Flandre P, Descamps D, Cottalorda J et al. The genotypic prediction of HIV-1 coreceptor tropism in a clinical setting. 17th International HIV Drug Resistance Workshop 10-14 June 2008, Sitges, Spain Antivir Ther 2008; 13(Suppl. 3):A113 (abstract no. 103).