Investigation of HIV-1 transmission events by phylogenetic methods: Requirement for scientific rigour [2]

AIDS

Volumn 19, Issue 4, 2005, Pages 449-450

  Hue, Stéphane ^a,b   Clewley, Jonathan P ^b   Cane, Patricia A ^c   Pillay, Deenan ^a,b  

^a ROYAL FREE AND UNIVERSITY COLLEGE MEDICAL SCHOOL   (United Kingdom)

^b PUBLIC HEALTH ENGLAND   (United Kingdom)

^c HPA Porton Down   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; POL PROTEIN; PROTEINASE; RNA DIRECTED DNA POLYMERASE; VIRUS ENVELOPE PROTEIN;

ENVELOPE GENE; EPIDEMIOLOGICAL DATA; EVOLUTION; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; LETTER; METHODOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RELIABILITY; REPRODUCIBILITY; STRUCTURAL GENE; VIRUS TRANSMISSION;

EID: 15944393853     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.aids.0000161778.15568.a1     Document Type: Letter

References (14)

1. Ou CY, Ciesielski CA, Myers G, Bandea CI, Luo CC, Korber BT, et al. Molecular epidemiology of HIV transmission in a dental practice. Science 1992; 256:1165-1171.
2. Smith TF, Waterman MS. The continuing case of the Florida dentist. Science 1992; 256:1155-1156.
3. DeBry RW, Abele LG, Weiss SH, Hill MD, Bouzas M, Lorenzo E, et al. Dental HIV transmission? Nature 1993; 361:691.
4. Crandall KA. Intraspecific phylogenetics: support for dental transmission of human immunodeficiency virus. J Virol 1995; 69:2351-2356.
5. Hue S, Clewley JP, Cane PA, Pillay D. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 2004; 18:719-728.
6. Stürmer M, Preiser W, Gute P, Nisius G, Doerr HW. Phylogenetic analysis of HIV-1 transmission: pol gene sequences are unsufficient to clarify true relationships between patient isolates. AIDS 2004; 18:2109-2113.
7. Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci U S A 1996; 93:10864-10869.
8. Holmes EC, Zhang LQ, Simmonds P, Ludlam CA, Brown AJ. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc Natl Acad Sci U S A 1992; 89:4835-4839.
9. Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Brown AJ, Simmonds P. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol 1993; 67:3345-3356.
10. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999; 73:10489-10502.
11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406-425.
12. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111-120.
13. Yang Z, Goldman N, Friday A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 1994; 11:316-324.
14. Posada D, Crandall KA. Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). Mol Biol Evol 2001; 18:897-906.