Near full-length genetic analysis of HIV sequences derived from Cyprus: Evidence of a highly polyphyletic and evolving infection

AIDS Research and Human Retroviruses

Volumn 25, Issue 8, 2009, Pages 727-740

  Kousiappa, Ioanna ^a   Van De Vijver, David A M C ^b   Kostrikis, Leondios G ^a  

^a UNIVERSITY OF CYPRUS   (Cyprus)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; NEF PROTEIN; POL PROTEIN; REV PROTEIN; TRANSACTIVATOR PROTEIN; VIF PROTEIN; VIRUS DNA; VIRUS ENVELOPE PROTEIN; VPR PROTEIN; VPU PROTEIN;

ADULT; ARTICLE; CYPRUS; DEMOCRATIC REPUBLIC CONGO; FEMALE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MAJOR CLINICAL STUDY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYPHYLY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; VIRUS GENE; VIRUS ISOLATION; VIRUS STRAIN;

ADULT; AGED; AGED, 80 AND OVER; CYPRUS; DNA, VIRAL; EVOLUTION, MOLECULAR; FEMALE; GENES, VIRAL; GENETIC VARIATION; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 70349213752     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2008.0239     Document Type: Article

References (51)

1. Ramirez BC, Simon-Loriere E, Galetto R, and Negroni M: Implications of recombination for HIV diversity. Virus Res 2008;134:64-73.
2. Robertson DL, Hahn BH, and Sharp PM: Recombination in AIDS viruses. J Mol Evol 1995;40:249-259.
3. Robertson DL, Sharp PM, McCutchan FE, and Hahn BH: Recombination in HIV-1. Nature 1995;374:124-126.
4. Roberts JD, Bebenek K, and Kunkel TA: The accuracy of reverse transcriptase from HIV-1. Science 1988;242:1171-1173.
5. Leitner T, Korber B, Daniels M, Calef C, and Foley B: HIV-1 Subtype and Circulating Recombinant Form (CRF) Reference Sequences, 2005. Los Alamos National Laboratory, Los Alamos, NM, 2005.
6. Los-Alamos-HIV-sequence-database: HIV-1 Subtype Reference Alignments. Los Alamos National Laboratory, Los Alamos, NM, 2005.
7. Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, et al.: HIV-1 nomenclature proposal. Science 2000;288:55-56.
8. Thomson MM and Najera R: Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: An update. AIDS Rev 2005;7:210-224.
9. Parekh B, Phillips S, Granade TC, Baggs J, Hu DJ, and Respess R: Impact of HIV type 1 subtype variation on viral RNA quantitation. AIDS Res Hum Retroviruses 1999;15:133-142.
10. Gottesman BS, Grossman Z, Lorber M, Levi I, Shitrit P, Katzir M, et al.: Comparative performance of the Amplicor HIV-1 Monitor Assay versus NucliSens EasyQ in HIV subtype C-infected patients. J Med Virol 2006;78:883-887.
11. Gobbers E, Fransen K, Oosterlaken T, Janssens W, Heyndrickx L, Ivens T, et al.: Reactivity and amplification efficiency of the NASBA HIV-1 RNA amplification system with regard to different HIV-1 subtypes. J Virol Methods 1997;66:293-301.
12. Chew CB, Herring BL, Zheng F, Browne C, Saksena NK, Cunningham AL, et al.: Comparison of three commercial assays for the quantification of HIV-1 RNA in plasma from individuals infected with different HIV-1 subtypes. J Clin Virol 1999;14:87-94. (Pubitemid 29512205)
13. Emery S, Bodrug S, Richardson BA, Giachetti C, Bott MA, Panteleeff D, et al.: Evaluation of performance of the Gen-Probe human immunodeficiency virus type 1 viral load assay using primary subtype A, C, and D isolates from Kenya. J Clin Microbiol 2000;38:2688-2695.
14. Jenny-Avital ER and Beatrice ST: Erroneously low or undetectable plasma human immunodeficiency virus type 1 (HIV-1) ribonucleic acid load, determined by polymerase chain reaction, in West African and American patients with non-B subtype HIV-1 infection. Clin Infect Dis 2001;32:1227-1230.
15. Fischer W, Liao HX, Haynes BF, Letvin NL, and Korber B: Coping with viral diversity in HIV vaccine design: A response to Nickle et al. PLoS Comput Biol 2008;4:e15-e25.
16. Nickle DC, Rolland M, Jensen MA, Pond SL, Deng W, Seligman M, et al.: Coping with viral diversity in HIV vaccine design. PLoS Comput Biol 2007;3:e75.
17. Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, et al.: Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med 2007;13:100-106.
18. Rolland M, Nickle DC, and Mullins JI: HIV-1 group M conserved elements vaccine. PLoS Pathog 2007;3:e157.
19. Kostrikis LG, Bagdades E, Cao Y, Zhang L, Dimitriou D, and Ho DD: Genetic analysis of human immunodeficiency virus type 1 strains from patients in Cyprus: Identification of a new subtype designated subtype I. J Virol 1995;69:6122-6130.
20. Gao F, Robertson DL, Carruthers CD, Li YY, Bailes E, Kostrikis LG, et al.: 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). J Virol 1998;72:10234-10241.
21. Kousiappa I, Van de Vijver DAMC, Demetriades I, and LG: K: Genetic analysis of HIV type 1 strains from newly infected untreated patients in Cyprus: High genetic diversity and low prevalence of drug resistance. AIDS Res Hum Retroviruses 2009;25:23-35.
22. Loizidou EZ, Kousiappa I, Zeinalipour-Yazdi CD, Van de Vijver DA, and Kostrikis LG: Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in-silico analyses. Biochemistry 2009;48(1):4-6.
23. Available at www.applied-maths.com=bionumerics=bionumerics.htm; 2008 applied Maths NV.
24. Tamura K, Dudley J, Nei M, and Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-1599.
25. de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, et al.: An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005;21:3797-3800.
26. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, 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;73:152-160.
27. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ: Basic local alignment search tool. J Mol Biol 1990;215:403-410.
28. Available at http:== www.hiv.lanl.gov=content=sequence=HIV=HIVTools.html.
29. Magiorkinis G, Paraskevis D, Vandamme AM, Magiorkinis E, Sypsa V, and Hatzakis A: In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: Determination of hot spots and correlation with sequence similarity. J Gen Virol 2003;84:2715-2722.
30. Fan J, Negroni M, and Robertson DL: The distribution of HIV-1 recombination breakpoints. Infect Genet Evol 2007;7:717-723.
31. Magiorkinis G, Paraskevis D, and Hatzakis A: Comments on "The distribution of HIV-1 recombination breakpoints" by Jun Fan, Matteo Negroni, David L. Robertson. Infect Genet Evol 2008;8:527-528.
32. Vergne L, Peeters M, Mpoudi-Ngole E, Bourgeois A, Liegeois F, Toure-Kane C, et al.: Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: Evidence of many minor drug resistance mutations in treatment-naive patients. J Clin Microbiol 2000;38:3919-3925.
33. Parreira R, Padua E, Piedade J, Venenno T, Paixao MT, and Esteves A: Genetic analysis of human immunodeficiency virus type 1 nef in Portugal: Subtyping, identification of mosaic genes, and amino acid sequence variability. J Med Virol 2005;77:8-16.
34. van der Hoek L, Pollakis G, Lukashov VV, Jebbink MF, Jeeninga RE, Bakker M, et al.: Characterization of an HIV-1 group M variant that is distinct from the known subtypes. AIDS Res Hum Retroviruses 2007;23:466-470.
35. McCutchan FE: Global epidemiology of HIV. J Med Virol 2006;78:S7-S12.
36. Kita K, Ndembi N, Ekwalanga M, Ido E, Kazadi R, Bikandou B, et al.: Genetic diversity of HIV type 1 in Likasi, southeast of the Democratic Republic of Congo. AIDS Res Hum Retroviruses 2004;20:1352-1357. (Pubitemid 40065931)
37. 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 Defisc Syndr 2005;40:456-462.
38. Triques K, Bourgeois A, Vidal N, Mpoudi-Ngole E, Mulanga-Kabeya C, Nzilambi N, et al.: 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. AIDS Res Hum Retroviruses 2000;16:139-151.
39. Janssens W, Buve A, and Nkengasong JN: The puzzle of HIV-1 subtypes in Africa. AIDS 1997;11:705-712.
40. Papathanasopoulos MA, Hunt GM, and Tiemessen CT: Evolution and diversity of HIV-1 in Africa-a review. Virus Genes 2003;26:151-163.
41. Palma AC, Araujo F, Duque V, Borges F, Paixao MT and Camacho R: Molecular epidemiology and prevalence of drug resistance-associated mutations in newly diagnosed HIV-1 patients in Portugal. Infect Genet Evol 2007;7:391-398.
42. Alaeus A, Leitner T, Lidman K, and Albert J: Most HIV-1 genetic subtypes have entered Sweden. AIDS 1997;11:199-202.
43. Chaix ML, Descamps D, Harzic M, Schneider V, Deveau C, Tamalet C, et al.: Stable prevalence of genotypic drug resistance mutations but increase in non-B virus among patients with primary HIV-1 infection in France. AIDS 2003;17:2635-2643.
44. Maljkovic I, Wilbe K, Solver E, Alaeus A, and Leitner T: Limited transmission of drug-resistant HIV type 1 in 100 Swedish newly detected and drug-naive patients infected with subtypes A, B, C, D, G, U, and CRF01-AE. AIDS Res Hum Retroviruses 2003;19:989-997.
45. Deroo S, Robert I, Fontaine E, Lambert C, Plesseria JM, Arendt V, et al.: HIV-1 subtypes in Luxembourg, 1983-2000. AIDS 2002;16:2461-2467.
46. Esteves A, Parreira R, Venenno T, Franco M, Piedade J, De Sousa JG, et al.: Molecular epidemiology of HIV type 1 infection in Portugal: High prevalence of non-B subtypes. AIDS Res Hum Retroviruses 2002;18:313-325.
47. Snoeck J, Van Laethem K, Hermans P, Van Wijngaeden E, Derdelinckx I, Schrooten Y, et al.: Rising prevalence of HIV-1 non-B subtypes in Belgium: 1983-2001. J Acquir Immune Defic Syndr 2004;35:279-285.
48. Grossman Z, Lorber M, Maayan S, Bar-Yacov N, Levy I, Averbuch D, et al.: Drug-resistant HIV infection among drug-naive patients in Israel. Clin Infect Dis 2005;40:294-302.
49. Bouzeghoub S, Jauvin V, Recordon-Pinson P, Garrigue I, Amrane A, Belabbes EH, et al.: High diversity of HIV type 1 in Algeria. AIDS Res Human Retroviruses 2006;22:367-372.
50. Bennett D: HIV-1 genetic diversity surveillance in the United States. J Infect Dis 2005;192:4-9.
51. Salminen MO, Carr JK, Robertson DL, Hegerich P, Gotte D, Koch C, et al.: Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple. J Virol 1997;71:2647-2655.