Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia

AIDS

Volumn 24, Issue 10, 2010, Pages 1577-1582

  Tully, Damien C ^a   Wood, Charles ^a  

^a UNIVERSITY OF NEBRASKA   (United States)

Author keywords

coalescent; Ethiopia; evolution; HIV 1; subtype C

Indexed keywords

ARTICLE; CHRONOLOGY; DEMOGRAPHY; EPIDEMIC; ETHIOPIA; EVOLUTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1C; PRIORITY JOURNAL;

BAYES THEOREM; EPIDEMICS; ETHIOPIA; EVOLUTION, MOLECULAR; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; HIV INFECTIONS; HIV-1; HUMANS; PHYLOGENY;

EID: 77953913628     PISSN: 02699370     EISSN: 14735571     Source Type: Journal    
DOI: 10.1097/QAD.0b013e32833999e1     Document Type: Article

References (38)

1. Tsega E, Mengesha B, Nordenfelt E, Hansson BG, Lindberg J. Serological survey of human immunodeficiency virus infection in Ethiopia. Ethiop Med J 1988; 26:179-184.
2. Lester FT, Ayehunie S, Zewdie D. Acquired immunodeficiency syndrome: seven cases in an Addis Ababa hospital. Ethiop Med J 1988; 26:139-145.
3. Mehret M, Khodakevich L, Zewdie D, Gizaw G, Seyoum A, Shanko B, et al. HIV-1 infection and related risk factors among female sex workers in urban areas of Ethiopia. Ethiop J Health Dev 1990; 4: 163-170.
4. Mehret M, Khodakevich L, Zewdie D, Gizaw G, Seyoum A, Shanko B, et al. HIV-1 infection among employees of the Ethiopian Freight Transport Corporation. Ethiop J Health Dev 1990; 4:177-182.
5. Abebe A, Pollakis G, Fontanet AL, Fisseha B, Tegbaru B, Kliphuis A, et al. Identification of a genetic subcluster of HIV type 1 subtype C (C) widespread in Ethiopia. AIDS Res Hum Retroviruses 2000; 16:1909-1914.
6. Abebe A, Kuiken CL, Goudsmit J, Valk M, Messele T, Sahlu T, et al. HIV type 1 subtype C in Addis Ababa, Ethiopia. AIDS Res Hum Retroviruses 1997; 13:1071-1075.
7. Abebe A, Lukashov VV, Pollakis G, Kliphuis A, Fontanet AL, Goudsmit J, de WitTF. Timing of the HIV-1 subtype C epidemic in Ethiopia based on early virus strains and subsequent virus diversification. AIDS 2001; 15:1555-1561.
8. Abebe A, Lukashov VV, Rinke De Wit TF, Fisseha B, Tegbaru B, Kliphuis A, et al. Timing of the introduction into Ethiopia of subcluster C of HIV type 1 subtype C. AIDS Res Hum Retroviruses 2001; 17:657-661.
9. Worobey M, Gemmel M, Teuwen DE, Haselkorn T, Kunstman K, BunceM, etal. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 2008; 455:661-664.
10. Gilbert MT, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE, Worobey M. The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci USA 2007; 104:18566-18570.
11. Travers SA, Clewley JP, Glynn JR, Fine PE, Crampin AC, Sibande F, et al. Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1. J Virol 2004; 78:10501-10506.
12. Kuiken C, Korber B, Shafer RW. HIV sequence databases. AIDS Rev 2003; 5:52-61.
13. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876-4882.
14. Abecasis AB, Wang Y, Libin P, Imbrechts S, de Oliveira T, Camacho RJ, Vandamme AM. Comparative performance of the REGA subtyping tool version 2 versus version 1. Infect Genet Evol 2010; 10: 380-385.
15. BruenTC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 2006; 172:2665-2681.
16. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006; 23:254-267.
17. Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, et al. The molecular population genetics of HIV-1 group O. Genetics 2004; 167:1059-1068.
18. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214.
19. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005; 22:1185-1192.
20. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006; 4:e88.
21. Shapiro B, Rambaut A, Drummond AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 2006; 23:7-9.
22. Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 2001; 18:1001-1013.
23. Kass RaR AE. Bayes Factor.JAm Stat Assoc 1995; 90:773-795.
24. Rambaut A. Estimating the rate of molecular evolution: incorporating noncontemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 2000; 16:395-399.
25. Swofford D. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). 4 edition: Sinauer Associates, Sunderland, Massachusetts; 2003.
26. Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, etal. Different epidemic potentials of the HIV-1B and C subtypes. J Mol Evol 2005; 60:598-605.
27. Bello G, Guimaraes ML, Passaes CP, Almeida SE, Veloso VG, Morgado MG. Short Communication: evidences of recent decline in the expansion rate of the HIV type 1 subtype C and CRF31-BC epidemics in Southern Brazil. AIDS Res Hum Retroviruses 2009; 25: 1065-1069.
28. Walker PR, Pybus OG, Rambaut A, Holmes EC. Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infect Genet Evol 2005; 5:199-208.
29. McCormack GP, Glynn JR, Crampin AC, Sibande F, Mulawa D, Bliss L, et al. Early evolution of the human immunodeficiency virus type 1 subtype C epidemic in rural Malawi. J Virol 2002; 76:12890-12899.
30. Gray RR, Tatem AJ, Lamers S, Hou W, Laeyendecker O, Serwadda D, et al. Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 2009; 23:F9-F17.
31. NIAID: how HIV causes AIDS. National Institutes of Health, USA; 2004.
32. Morgan D, Malamba SS, Orem J, Mayanja B, Okongo M, Whitworth JA. Survival by AIDS defining condition in rural Uganda. Sex Transm Infect 2000; 76:193-197.
33. Morgan D, Mahe C, Mayanja B, Whitworth JA. Progression to symptomatic disease in people infected with HIV-1 in rural Uganda: prospective cohort study. BMJ 2002; 324:193-196.
34. Anzala OA, Nagelkerke NJ, Bwayo JJ, Holton D,Moses S, Ngugi EN, et al. Rapid progression to disease in African sex workers with human immunodeficiency virus type 1 infection. J Infect Dis 1995; 171:686-689.
35. Vasan A, Renjifo B, Hertzmark E, Chaplin B, Msamanga G, Essex M, et al. Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype. Clin Infect Dis 2006; 42:843-852.
36. Jaffar S, Grant AD, Whitworth J, Smith PG, Whittle H. The natural history of HIV-1 and HIV-2 infections in adults in Africa: a literature review. Bull World Health Organ 2004; 82:462-469.
37. Rinke de Wit TF, Tsegaye A, Wolday D, Hailu B, Aklilu M, Sanders E, et al. Primary HIV-1 subtype C infection in Ethiopia. J Acquir Immune Defic Syndr 2002; 30:463-470.
38. Tesfaghiorghis H. The growth of urbanization in Ethiopia, 1966-1984. East Afr Econ Rev 1986; 2:157-167.