In-depth analysis of the origins of HIV type 1 subtype C in South America

AIDS Research and Human Retroviruses

Volumn 25, Issue 10, 2009, Pages 951-959

  Jones, Leandro R ^a,b   Dilernia, Darío A ^a   Manrique, Julieta M ^a   Moretti, Franco ^a   Salomón, Horacio ^a   Gomez Carrillo, Manuel ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^b Estacion de Fotobiologia Playa Union   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLADISTICS; EPIDEMIOLOGICAL DATA; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOUTH AMERICA; VIRUS STRAIN;

CLUSTER ANALYSIS; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SOUTH AMERICA;

EID: 70449505305     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2008.0293     Document Type: Article

References (62)

1. Rambaut A, Posada D, Crandall KA, and Holmes EC: The causes and consequences of HIV evolution. Nat Rev Genet 2004;5(1):52-61.
2. Hahn BH, Shaw GM, Arya SK, Popovic M, Gallo RC, and Wong-Staal F: Molecular cloning and characterization of the HTLV-III virus associated with AIDS. Nature 1984;312(5990): 166-169.
3. Seillier-Moiseiwitsch F, Margolin BH, and Swanstrom R: Genetic variability of the human immunodeficiency virus: Statistical and biological issues. Annu Rev Genet 1994;28: 559-596.
4. Peeters M and Sharp PM: Genetic diversity of HIV-1: The moving target. AIDS 2000;14(Suppl. 3):S129-140.
5. UNAIDS: 08 Report on the global AIDS epidemic. http:==www.unaids.org=.
6. Buonaguro L, Tornesello ML, and Buonaguro FM: Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: Pathogenetic and therapeutic implications. J Virol 2007;81(19):10209-10219.
7. Robertson DL, Anderson JP, Bradac JA, et al.: HIV-1 nomenclature proposal. Science 2000;288(5463):55-56.
8. Ramirez BC, Simon-Loriere E, Galetto R, and Negroni M: Implications of recombination for HIV diversity. Virus Res 2008;134(1-2):64-73.
9. Hemelaar J, Gouws E, Ghys PD, and Osmanov S: Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 2006;20(16):W13-23.
10. Gomez-Carrillo M, Pampuro S, Duran A, et al.: Analysis of HIV type 1 diversity in pregnant women from four Latin American and Caribbean countries. AIDS Res Hum Retroviruses 2006;22(11):1186-1191.
11. Bello G, Passaes CP, Guimaraes ML, et al.: Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 2008; 22(15):1993-2000.
12. Carr JK, Avila M, Gomez Carrillo M, et al.: Diverse BF recombinants have spread widely since the introduction of HIV-1 into South America. AIDS 2001;15(15):F41-47.
13. Carrion G, Eyzaguirre L, Montano SM, et al.: Documentation of subtype C HIV Type 1 strains in Argentina, Paraguay, and Uruguay. AIDS Res Hum Retroviruses 2004;20(9):1022-1025.
14. Carrion G, Hierholzer J, Montano S, et al.: Circulating recombinant form CRF02-AG in South America. AIDS Res Hum Retroviruses 2003;19(4):329-332.
15. Gomez Carrillo M, Avila M, Hierholzer J, et al.: Motherto-child HIV type 1 transmission in Argentina: BF recombinants have predominated in infected children since the mid-1980s. AIDS Res Hum Retroviruses 2002;18(7):477-483.
16. Carobene MG, Rubio AE, Carrillo MG, et al.: Differences in frequencies of drug resistance-associated mutations in the HIV-1 pol gene of B subtype and BF intersubtype recombinant samples. J Acquir Immune Defic Syndr 2004;35(2):207-209.
17. Dilernia DA, Gomez AM, Lourtau L, et al.: HIV type 1 genetic diversity surveillance among newly diagnosed individuals from 2003 to 2005 in Buenos Aires, Argentina. AIDS Res Hum Retroviruses 2007;23(10):1201-1207. (Pubitemid 350017602)
18. Gomez-Carrillo M, Quarleri JF, Rubio AE, et al.: Drug resistance testing provides evidence of the globalization of HIV type 1: A new circulating recombinant form. AIDS Res Hum Retroviruses 2004;20(8):885-888.
19. Quarleri JF, Rubio A, Carobene M, et al.: HIV type 1 BF recombinant strains exhibit different pol gene mosaic patterns: Descriptive analysis from 284 patients under treatment failure. AIDS Res Hum Retroviruses 2004;20(10): 1100-1107.
20. Castro E, Moreno M, Deibis L, de Perez G, Salmen S, and Berrueta L: Trends of HIV-1 molecular epidemiology in Venezuela: Introduction of subtype C and identification of a novel B=C mosaic genome. J Clin Virol 2005;32(3):257-258.
21. Fontella R, Soares MA, and Schrago CG: On the origin of HIV-1 subtype C in South America. AIDS 2008;22(15):2001-2011.
22. Farris J: The logical basis of phylogenetic analysis. In: Advances in Cladistics (Platnick NI and Funk VA, eds.). Columbia University Press, New York, 1983.
23. Cavalli-Sforza LL and Edwards AW: Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet 1967; 19(3Pt. 1):233-257.
24. Felsenstein J: The number of evolutionary trees. Syst Zool 1978;27(1):7.
25. Swofford D: Phylogenetic inference. In: Molecular Systematics (Hillis D, Moriz C, and Mable B, eds.). Sinauer Associates, Sunderland, MA, 1996, pp. 407-514.
26. Goloboff P: Analysing large data sets in reasonable times: Solutions for composite optima. Cladistics 1999;15:14.
27. Nixon K: The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999;15:8.
28. T.N.T.: Tree Analysis Using New Technology [computer program]. Version: Program and documentations are available from the authors, and at http:==www.zmuc.dk=public=phylogeny; 2003.
29. Goloboff PA and Pol D: On divide-and-conquer strategies for parsimony analysis of large data sets: Rec-I-DCM3 versus TNT. Syst Biol 2007;56(3):485-495.
30. Guindon S and Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52(5):696-704.
31. Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22(21):2688-2690.
32. Katoh K, Kuma K, Miyata T, and Toh H: Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inform 2005;16(1):22-33.
33. Katoh K and Toh H: Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008; 9(4):286-298.
34. Smith SW, Overbeek R, Woese CR, Gilbert W, and Gillevet PM: The genetic data environment: An expandable GUI for multiple sequence analysis. Comput Appl Biosci 1994;10(6): 671-675.
35. Camin JS and Sokal RR: A method for deducing branching sequences in phylogeny. Evolution 1967;19:311-326.
36. Saitou N and Nei M: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4(4):406-425.
37. Felsenstein J: Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981;17(6):368-376.
38. Stamatakis A: A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008;57(5):758-771.
39. MrAIC.pl. Program distributed by the author [computer program]. Version: Evolutionary Biology Centre, Uppsala University, 2004.
40. McMahon MM and Sanderson MJ: Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst Biol 2006;55(5):818-836.
41. Smith SA and Donoghue MJ: Rates of molecular evolution are linked to life history in flowering plants. Science 2008;322(5898):86-89.
42. Goloboff PAF, Farris JS, Kallersjo M, Oxelman B, Ramirez MJ, and Szumuk CA: Improvements to resampling reassures group support. Cladistics 2003;19:324-332.
43. Farris JA, Albert VA, Kallersjo M, Lipscomb D, and Kluge A: Parsimony jackknifing outperforms neighbor-joining. Cladistics 1996;12:99-124.
44. Anisimova MG and Gascuel O: Approximate likelihoodratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006;55:539-552.
45. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). [computer program]. Version still beta. Sinauer Associates, Sunderland, MA, 1998.
46. Salminen MO, Carr JK, Burke DS, and McCutchan FE: Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 1995;11(11):1423-1425.
47. Lole KS, Bollinger RC, Paranjape RS, et al.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999;73(1):152-160.
48. Zhuang J, Jetzt AE, Sun G, et al.: Human immunodeficiency virus type 1 recombination: Rate, fidelity, and putative hot spots. J Virol 2002;76(22):11273-11282.
49. Moumen A, Polomack L, Unge T, Veron M, Buc H, and Negroni M: Evidence for a mechanism of recombination during reverse transcription dependent on the structure of the acceptor RNA. J Biol Chem 2003;278(18):15973-15982.
50. Galetto R, Moumen A, Giacomoni V, Veron M, Charneau P, and Negroni M: The structure of HIV-1 genomic RNA inthe gp120 gene determines a recombination hot spot in vivo. J Biol Chem 2004;279(35):36625-36632.
51. Aulicino PC, Kopka J, Rocco C, Mangano A, and Sen L: Sequence analysis of a South American HIV type 1 BC recombinant. AIDS Res Hum Retroviruses 2005;21(10):894-896.
52. Galetto R, Giacomoni V, Veron M, and Negroni M: Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J Biol Chem 2006;281(5):2711-2720.
53. Neogi U, Sood V, Goel N, Wanchu A, and Banerjea AC: Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B=C recombinants in North India. Arch Virol 2008;153(10):1961-1966.
54. Dietrich U, Grez M, von Briesen H, et al.: HIV-1 strains from India are highly divergent from prototypic African and US=European strains, but are linked to a South African isolate. AIDS 1993;7(1):23-27.
55. Khan IF, Vajpayee M, Prasad VV, and Seth P: Genetic diversity of HIV type 1 subtype C env gene sequences from India. AIDS Res Hum Retroviruses 2007;23(7):934-940.
56. Shankarappa R, Chatterjee R, Learn GH, et al.: Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: Identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virol 2001;75(21):10479-10487.
57. Hue S, Clewley JP, Cane PA, and Pillay D: HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 2004;18(5): 719-728.
58. Grenfell BT, Pybus OG, Gog JR, et al.: Unifying the epidemiological and evolutionary dynamics of pathogens. Science 2004;303(5656):327-332.
59. Pando MA, Eyzaguirre LM, Carrion G, et al.: High genetic variability of HIV-1 in female sex workers from Argentina. Retrovirology 2007;4:58.
60. Salemi M, de Oliveira T, Ciccozzi M, Rezza G, and Goodenow MM: High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS ONE 2008;3(1):e1390.
61. Fitch W: Toward defining the course of evolution: Minimum change for a specific tree topology. Syst Zool 1971;20:406-416.
62. Yabar CA, Salvatierra J, and Quijano E: Polymorphism, recombination, and mutations in HIV type 1 gag-infecting Peruvian male sex workers. AIDS Res Hum Retroviruses 2008;24(11):1405-1413.