Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks

Virology

Volumn 288, Issue 1, 2001, Pages 51-62

  Resch, Wolfgang ^a   Hoffman, Noah ^a   Swanstrom, Ronald ^a,b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Coreceptor; Env; HIV 1; MT 2 cell tropism; Neural network; Phenotype; V3

Indexed keywords

ENVELOPE PROTEIN; VIRUS RECEPTOR;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; ARTIFICIAL NEURAL NETWORK; CLASSIFICATION; GENOTYPE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERMETHOD COMPARISON; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RELIABILITY; REPRODUCIBILITY; VIRUS CELL INTERACTION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0035884899     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.2001.1087     Document Type: Article

References (48)

1. CC CKR5: A RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophagetropic HIV-1
2. Both the V2 and V3 regions of the human immunodeficiency virus type 1 surface glycoprotein functionally interact with other envelope regions in syncytium formation
3. Positioning of positively charged residues in the V3 loop correlates with HIV type 1 syncytium-inducing phenotype
4. Coreceptor usage of primary human immunodeficiency virus type
5. Human immunodeficiency virus type 1 tropism for T-lymphoid cell lines: Role of the V3 loop and C4 envelope determinants
6. V3 recombinants indicate a central role for CCR5 as a coreceptor in tissue infection by human immunodeficiency virus type 1
7. Identification of human immunodeficiency virus envelope gene sequences influencing viral entry into CD4-positive HeLa cells, T-leukemia cells, and macrophages
8. Macrophage-tropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: Definition of critical amino acids involved in cell tropism
9. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates
10. The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for chemokine-mediated blockade of infection
11. Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a non-syncytium-inducing/Sl phenotypically mixed human immunodeficiency virus population
12. Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity
13. Identification of a major co-receptor for primary isolates of HIV-1
14. A dual-tropic primary HIV-1 isolate that uses fusin and the beta-chemokine receptors CKR-5, CKR-3, and CKR-2b as fusion cofactors
15. HW-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5
16. HIV-1 entry cofactor: Functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor
17. Simple determination of human immunodeficiency virus type 1 syncytium-inducing V3 genotype by PCR
18. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule
19. Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: Evidence for in vivo recombination and determinants of cytotropism outside the V3 domain
20. Relation of phenotype evolution of HIV-1 to envelope V2 configuration
21. Analysis of the critical domain in the V3 loop of human immunodeficiency virus type 1 gp120 involved in CCR5 utilization
22. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1
23. Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDS
24. Co-receptor usage was more predictive than NSI/SI phenotype for HIV replication in macrophages: Is NSI/SI phenotyping sufficient?
25. Persistent CCR5 utilization and enhanced macrophage tropism by primary blood human immunodeficiency virus type 1 isolates from advanced stages of disease and comparison to tissue-derived isolates
26. V2 loop glycosylation of the human immunodeficiency virus type 1 SF162 envelope facilitates interaction of this protein with CD4 and CCR5 receptors and protects the virus from neutralization by anti-V3 loop and anti-CD4 binding site antibodies
27. Bayesian Interpolation
28. Exclusive and persistent use of the entry coreceptor CXCR4 by human immunodeficiency virus type 1 from a subject homozygous for CCR5 delta32
29. V3 loop of the human immunodeficiency virus type 1 Env protein: Interpreting sequence variability
30. Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein
31. A general method applicable to the search for similarities in the amino acid sequence of two proteins
32. Patterns of changes in human immunodeficiency virus type 1 V3 sequence populations late in infection
33. The impact of the syncytium-inducing phenotype of human immunodeficiency virus on disease progression
34. Viral phenotype and immune response in primary human immunodeficiency virus type 1 infection
35. Biphasic rate of CD4+ cell count decline during progression to AIDS correlates with HW-1 phenotype
36. A mathematical theory of communication
37. Determinants of syncytium formation in microglia by human immunodeficiency virus type 1: Role of the V1/V2 domains
38. Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1
39. Patterns of chemokine receptor fusion cofactor utilization by human immunodeficiency virus type 1 variants from the lungs and blood
40. Heterogeneous spectrum of coreceptor usage among variants within a dualtropic human immunodeficiency virus type 1 primary-isolate quasispecies
41. Effect of amino acid changes in the V1/V2 region of the human immunodeficiency virus type 1 gp120 glycoprotein on subunit association, syncytium formation, and recognition by a neutralizing antibody
42. Host range mutant of human immunodeficiency virus type 1: Modification of cell tropism by a single point mutation at the neutralization epitope in the env gene
43. Differential syncytium-inducing capacity of human immunodeficiency virus isolates: Frequent detection of syncytium-inducing isolates in patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex
44. Association between biological properties of human immunodeficiency virus variants and risk for AIDS and AIDS mortality
45. CCR5 coreceptor usage of non-syncytium-inducing primary HIV-1 is independent of phylogenetically distinct global HIV-1 isolates: Delineation of consensus motif in the V3 domain that predicts CCR-5 usage
46. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and new discontinuous epitopes
47. Chemokine coreceptor usage by diverse primary isolates of human immunodeficiency virus type 1
48. Genotypic and phenotypic characterization of HIV-1 patients with primary infection