Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E

Journal of Virology

Volumn 74, Issue 22, 2000, Pages 10752-10765

  Anderson, J P ^a   Rodrigo, A G ^a   Learn, G H ^a   Madan, A ^a   Delahunty, C ^a   Coon, M ^a   Girard, M ^a   Osmanov, S ^a   Hood, L ^a   Mullins, J I ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE SEQUENCE; GENETIC DISTANCE; GENETIC RECOMBINATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SIMULATION; VIRUS GENOME;

EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; TERMINOLOGY;

EID: 0033766134     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.74.22.10752-10765.2000     Document Type: Article

References (65)

1. Recombination in HIV: An important viral evolutionary strategy
2. Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants
3. Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand
4. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes
5. Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient
6. Confidence limits on phylogenies: An approach using the bootstrap
7. Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G
8. An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I)
9. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1
10. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin
11. Likelihood-based tests of topologies in phylogenetics
12. A likelihood method for the detection of selection and recombination using nucleotide sequences
13. Correlation of functional domains and rates of nucleotide substitution in cytochrome b
14. Signal, noise, and reliability in molecular phylogenetic analyses
15. In vivo sequence variation of the human immunodeficiency virus type 1 env gene: Evidence for recombination among variants found in a single individual
16. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
17. Biological, serological, and genetic characterization of HIV-1 subtype E isolates from northern Thailand
18. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
19. Primary infections with HIV-1 of women and their offspring in Rwanda: Findings of heterogeneity at seroconversion, coinfection, and recombinants of HIV-1 subtypes A and C
20. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea
21. Infection with HIV-1 subtypes B and E in injecting drug users screened for enrollment into a prospective cohort in Bangkok, Thailand
22. Genetic analysis of human immunodeficiency virus type 1 strains from patients in Cyprus: Identification of a new subtype designated subtype I
23. The rapid spread of recombinants during a natural in vitro infection with two human immunodeficiency virus type 1 strains
24. A new method for calculating evolutionary substitution rates
25. Evolution of the structural proteins of Human immunodeficiency virus: Selective constraints on nucleotide substitution
26. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden
27. HIV-1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad
28. The epidemiological evolution of HIV-1 subtypes B and E among heterosexuals and injecting drug users in Thailand, 1992-1997
29. Phylogenetic analysis of gag genes from seventy international HIV-1 isolates provides evidence for multiple genotypes
30. Two antigenetically distinct subtypes of HIV-1: Viral genotype predicts neutralization serotype
31. Diversity of the envelope glycoprotein among human immunodeficiency virus type 1 isolates of clade E from Asia and Africa
32. Subtype G and multiple forms of A/G intersubtype recombinant human immunodeficiency virus type 1 in Nigeria
33. HIV-1 genetic diversity
34. Diversity of V3 region sequences of human immunodeficiency viruses type 1 from the central african republic
35. Genotypic subtypes of HIV-1 in Cameroon
36. MODELTEST: Testing the model of DNA substitution
37. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
38. Recombination in AIDS viruses
39. Recombination in HIV-1
40. Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays
41. HIV-1 molecular evolution and the measure of selection
42. Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals in Brazil
43. Coinfection and genetic recombination between HIV-1 strains: Possible biological implications in Australia and South East Asia
44. Identification of breakpoints in intergenotypic recombinants of HIV-1 by bootscanning
45. Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple
46. Statistical tests for detecting gene conversion
47. Genetic recombination of HIV-1 strains identified in China
48. The identification of recombinant HIV-1 strains in IDUs in Southwest and Northwest China
49. Multiple comparisons of log-likelihoods with applications to phylogenetic inference
50. A computer program designed to rapidly screen for HIV-1 intersubtype recombinant sequences
51. Analyzing the mosaic structure of genes
52. Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion
53. HIV type 1 in Thailand, 1994-1995: Persistence of two subtypes with low genetic diversity
54. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
55. Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K
56. Determination of HIV-1 subtypes in injecting drug users in Bangkok, Thailand, using peptide binding enzyme immunoassay and the heteroduplex mobility assay: Evidence of increasing infection with HIV-1 subtype E
57. Phylogenetic profiles: A graphical method for detecting genetic recombinations in homologous sequences
58. Experience from HIV incidence cohorts in Thailand: Implications for HIV vaccine efficacy trials