The genetic determinants of coreceptor usage reside in the HIV envelope, in particular, the V3 loop. Consequently, this region is highly useful for the training and development of computerized genotypic predictors of coreceptor usage, which have the potential to make the screening and testing of HIV-infected patients.
Determination of HIV-1 tropism by bioinformatics-based genotypic rules, such as support vector machines (SVMs) is now available.

The bioinformatic algorithms based using HIV V3 genotype data were able to achieve high concordance with the phenotypic assays, approaching the degree of agreement between phenotype assays themselves. The specificity of tropism genotypic assays is high to detect X4 or R5X4 viruses.
A false positive rate adjusted at 10% with geno2pheno provides the best balance between specificity and sensitivity for predicting the X4 or R5X4 tropism (Recordon-Pinson P et al., 2008; Raymond S et al., 2008)

To go to Geno2Pheno (SVMs) : http://coreceptor.bioinf.mpi-inf.mpg.de/index.php

References 

• Delobel P, Nugeyre MT, Cazabat M, Pasquier C, Marchou B, Massip P, Barre-Sinoussi F, Israël N, Izopet J. Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies. J Clin Microbiol. 2007 May;45(5):1572-80.
• Lengauer T, Sander O, Sierra S, Thielen A, Kaiser R. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol. 2007 Dec;25(12):1407-10.
• Skrabal K, Low AJ, Dong W, Sing T, Cheung PK, Mammano F, Harrigan PR. 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 Feb;45(2):279-84.
• Soulié C, Derache A, Aimé C, Marcelin AG, Carcelain G, Simon A, Katlama C, Calvez V. Comparison of two genotypic algorithms to determine HIV-1 tropism. HIV Med. 2008 Jan;9(1):1-5.
• Moores A et al. Improved detection of X4 virus by V3 genotyping: application to plasma RNA and proviral DNA. XVII International HIV drug resistance workshop: basic principles and clinical implications, 10-14 June 2008, Sitges, Spain, abstract 89.
• Recordon-Pinson P et al. Evaluation of the genotypic prediction of HIV-1 coreceptor tropism in a clinical setting. XVII International HIV drug resistance workshop: basic principles and clinical implications, 10-14 June 2008, Sitges, Spain, abstract 103.
• Raymond S et al. Correlation between genotype prediction based on V3 sequence and phenotypic determination of HIV-1 tropism. AIDS 2008 22:1-6.