title: Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks.
abstract: The HIV-1 genome is highly heterogeneous. This variation affords the virus a wide range of molecular properties, including the ability to infect cell types, such as macrophages and lymphocytes, expressing different chemokine receptors on the cell surface. In particular, R5 HIV-1 viruses use CCR5 as co-receptor for viral entry, X4 viruses use CXCR4, whereas some viral strains, known as R5X4 or D-tropic, have the ability to utilize both co-receptors. X4 and R5X4 viruses are associated with rapid disease progression to AIDS. R5X4 viruses differ in that they have yet to be characterized by the examination of the genetic sequence of HIV-1 alone. In this study, a series of experiments was performed to evaluate different strategies of feature selection and neural network optimization. We demonstrate the use of artificial neural networks trained via evolutionary computation to predict viral co-receptor usage. The results indicate identification of R5X4 viruses with predictive accuracy of 75.5%.
authors.affiliation: BioInfoExperts, Gainesville, FL 32606, USA. Susanna@HIVanalysis.net
authors.forename: Susanna L
authors.initials: SL
authors.lastname: Lamers
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.forename: Michael S
authors.initials: MS
authors.lastname: McGrath
authors.forename: Gary B
authors.initials: GB
authors.lastname: Fogel
mesh_terms: D005075:Biological Evolution; D019295:Computational Biology; D015658:HIV Infections / Q000209:etiology / Q000821:virology; D015497:HIV-1 / Q000235:genetics* / Q000472:pathogenicity*; D006801:Humans; D008954:Models, Biological; D016571:Neural Networks, Computer; D010641:Phenotype; D019713:Receptors, CCR5 / Q000502:physiology*; D019718:Receptors, CXCR4 / Q000502:physiology*; D015728:Receptors, HIV / Q000235:genetics*
chemical_list: C527276:CXCR4 protein, human; D019713:Receptors, CCR5; D019718:Receptors, CXCR4; D015728:Receptors, HIV