Understanding the diversification of HIV-1 groups M and O

AIDS

Volumn 21, Issue 13, 2007, Pages 1693-1700

  Archer, John ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

AIDS; Diversity; Evolution; HIV; Phylogenetics; Subtypes

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; STATISTICAL ANALYSIS; VIRUS MORPHOLOGY; VIRUS STRAIN;

EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; MODELS, GENETIC; PHYLOGENY; VARIATION (GENETICS);

EID: 34547750546     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAD.0b013e32825eabd0     Document Type: Article

References (35)

1. Van Heuverswyn F, Li Y, Neel C, Bailes E, Keele BF, Liu W, et al. Human immunodeficiency viruses: SIV infection in wild gorillas. Nature 2006; 444:164.
2. Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, et al. HIV-1 nomenclature proposal. Science 2000; 288:55-57.
3. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, et al. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 1999; 397:336-441.
4. Bibollet-Ruche F, Gao F, Bailes E, Saragosti S, Delaporte E, Peeters M, et al. Complete genome analysis of one of the earliest SIVcpzPtt strains from Gabon (SIVcpzGAB2). AIDS Res Hum Retroviruses 2004; 20:1377-1381.
5. Keele BF, Van Heuverswyn F, Li Y, Bailes E, Takehisa J, Santiago ML, et al. Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science 2006; 313:523-526.
6. Yamaguchi J, Coffey R, Vallari A, Ngansop C, Mbanya D, Ndembi N, et al. Identification of HIV type 1 group N infections in a husband and wife in Cameroon: viral genome sequences provide evidence for horizontal transmission. AIDS Res Hum Retroviruses 2006; 22:83-92.
7. Takebe y, Kusagawa S, Motomura K. Molecular epidemiology of HIV: tracking AIDS pandemic. Pediatr Int 2004; 46:236-244.
8. Korber B, Muldoon M, Theiler J, Gao G, Gupta R, Lapedes A, et al. Timing the ancestor of the HIV-1 pandemic strains. Science 2000; 288:1789-1796.
9. Vidal N, Peeters M, Mulanga-Kabeya C, Nzilambi N, Robertson D, Ilunga W, et al. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J Virol 2000; 74: 10498-10507.
10. Rambaut A, Robertson DL, Pybus OG, Peeters M, Holmes C. Phylogeny and the origin of HIV-1. Nature 2001; 410:1047-1048.
11. Mauclere P, Loussert-Ajaka I, Damond F, Fagot P, Souquieres S, Monny Lobe M, et al. Serological and virological characterization of HIV-1 group O infection in Cameroon. AIDS 1997; 11:445-453.
12. Yamaguchi J, Bodelle P, Vallari AS, Coffey R, McArthur CP, Schochetman G, et al. HIV infections in northwestern Cameroon: identification of HIV type 1 group O and dual HIV type 1 group M and group O infections. AIDS Res Hum Retroviruses 2004; 20:944-957.
13. Quinones-Mateu ME, Ball SC, Arts EJ. Role of human immunodeficiency virus type 1 group O in the AIDS pandemic. AIDS Rev 2000; 2:190-202.
14. Roques P, Robertson DL, Souquiere S, Damond F, Ayouba A, Farfara I, et al. Phylogenetic analysis of 49 newley derived HIV-1 group O strains: High viral diversity but no group M-like subtype structure. Virology 2002; 302:259-273.
15. 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.
16. Yamaguchi J, Bodelle P, Kaptue L, Zekeng L, Gurtler LG, Devare SG, et al. Near full-length genomes of 15 HIV type 1 group O isolates. AIDS Res and Hum Retroviruses 2003; 19:979-988.
17. Yamaguchi J, Vallari AS, Swanson P, Bodelle P, Kaptue L, Ngansop C, et al. Evaluation of HIV type 1 group O isolates: identification of five phylogenetic clusters. AIDS Res Hum Retroviruses 2002; 18:269-282.
18. Loussert-Ajaka I, Chaix ML, Korber B, Letourneur F, Gomas E, Allen E, et al. Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France. J Virol 1995; 69:5640-5649.
19. Heeney JL, Dalgleish AG, Weiss RA. Origins of HIV and the evolution of resistance to AIDS. Science 2006; 313:462-546.
20. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673-4680.
21. Kalish ML, Robbins KE, Pieniazek D, Schaefer A, Nzilambi N, Quinn TC, et al. Recombinant viruses and early global HIV-1 epidemic. J Emerg Infectious Dis 2004; 10:1227-1234.
22. Vidal N, Mulanga C, Bazepeo SE, Mwamba JK, Tshimpaka JW, Kashi M, et al. Distribution of HIV-1 variants in the Democratic Republic of Congo suggests increase of subtype C in Kinshasa between 1997 and 2002. J Acquir Immune Defic Syndr 2005; 40:456-462.
23. Mokili JL, Rogers M, Carr JK, Simmonds P, Bopopi JM, Foley BT, et al. Identification of a novel clade of human immunodefi-ciency virus type 1 in Democratic Republic of Congo. AIDS Res Hum Retroviruses 2002; 18:817-823.
24. Drummond A, Strimmer K. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001; 17:662-663.
25. Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland, Massachusetts: Sinauer Associates; 2003.
26. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 2004; 303:327-332.
27. Worobey M. The origins and diversification of HIV (2007). In: Global HIV/AIDS Medicine. Edited by Sande M, Lange J, Volberding P, Greene WC. Philadelphia: Elsevier; 2006. pp. 13-21.
28. Taylor JE, Korber BT. HIV-1 intra-subtype superinfection rates: estimates using a structured coalescent with recombination. Infect Genet Evol 2005; 5:85-95.
29. Fang G, Weiser B, Kuiken C, Philpott SM, Rowland-Jones S, et al. Recombination following superinfection by HIV-1. AIDS 2004; 18:153-159.
30. Pernas M, Casado C, Fuentes R, Perez-Elias MJ, Lopez-Galindez C. A dual superinfection and recombination within HIV-1 subtype B 12 years after primoinfection. J Acquir Immune Defic Syndr 2006; 42:12-18.
31. Shriner D, Rodrigo AG, Nickle DC, Mullins JI. Pervasive genomic recombination of HIV-1 in vivo. Genetics 2004; 167:1573-1583.
32. Robertson DL, Sharp PM, McCutchan FE, Hahn BH. Recombination in HIV-1. Nature 1995; 374:124-126.
33. Baird HA, Galetto R, Gao Y, Simon-Loriere E, Abreha M, Archer J, et al. Sequence determinants of breakpoint location during HIV-1 intersubtype recombination. Nucleic Acids Res 2006; 34:5203-5216.
34. Choisy M, Woelk CH, Guegan JF, Robertson DL. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol 2004; 78:1962-1970.
35. Yang W, Bielawski JP, Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol 2003; 57:212-221.