Genetic analysis of HIV-1 subtypes in Nairobi, Kenya

PLoS ONE

Volumn 3, Issue 9, 2008, Pages

  Khoja, Suhail ^a   Ojwang, Peter ^b   Khan, Saeed ^a   Okinda, Nancy ^b   Harania, Reena ^b   Ali, Syed ^a  

^a AGA KHAN UNIVERSITY HOSPITAL   (Pakistan)

^b AGA KHAN UNIVERSITY   (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; GENOMIC DNA; BETA GLOBIN; VIRUS DNA;

ADOLESCENT; ADULT; ARTICLE; BLOOD SAMPLING; CONTROLLED STUDY; DNA EXTRACTION; FEMALE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; KENYA; MALE; NONHUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; PHYLOGENY; POLYMERASE CHAIN REACTION; SCHOOL CHILD; VIRUS ISOLATION; BLOOD; DNA SEQUENCE; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METABOLISM; MIDDLE AGED; VIROLOGY; VIRUS GENOME;

HUMAN IMMUNODEFICIENCY VIRUS 1;

ADOLESCENT; ADULT; BETA-GLOBINS; DNA, VIRAL; FEMALE; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; KENYA; MALE; MIDDLE AGED; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 52649173845     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003191     Document Type: Article

References (48)

1. Ho DD (1995) HIV-1 dynamics in vivo. J Biol Regul Homeost Agents 9:76-77.
2. Roberts JD, Bebenek K, Kunkel TA (1988) The accuracy of reverse transcriptase from HIV-1. Science 242: 1171-1173.
3. Spica S, Wainberg MA, Loemba H, Turner D, Brenner BG (2003) Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J Antimicrob Chemother 51: 229-2440.
4. Tatt ID, Barlow KL, Nicoll A, Clewley JP (2001) The public health significance of HIV-1 subtypes. Aids 15 Suppl 5: S59-71.
5. Temin HM (1993) A proposal for a new approach to a preventive vaccine against human immunodeficiency virus type 1. Proc Natl Acad Sci U S A 90: 4419-4420.
6. Gao F, Yuc L, Robertson DL, Hill SC, Hui H, et al. (1994) Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. J Virol 68: 7433-7447.
7. Gao F, Yue L, White AT, Pappas PG, Barchue J, et al. (1992) Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature 358: 495-499.
8. Hahn BH, Shaw GM, De Cock KM, Sharp PM (2000) AIDS as a zoonosis: scientific and public health implications. Science 287: 607-614.
9. Osmanov S, Pattou C, Walker N, Schwardlander B, Esparza J (2002) Estimated global distribution and regional spread of HIV-1 genetic subtypes in the year 2000. J Acquir Immune Defic Syndr 29: 184-190.
10. Sharp PM, Robertson DL, Hahn BH (1995) Cross-species transmission and recombination of 'AIDS' viruses. Philos Trans R Soc Lond B Biol Sci 349: 41-47.
11. Thomson MM, Perez-Alvarez L, Najera R (2002) Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect Dis 2: 461-471.
12. Malim MH, Emerman M (2001) HIV-1 sequence variation: drift, shift, and attenuation. Cell 104: 469-472.
13. Peeters M, Sharp PM (2000) Genetic diversity of HIV-1: the moving target. Aids 14 Suppl 3: S129-140.
14. Robertson DL, Anderson JP, Bradae JA, Carr JK, Foley B, et al. (2000) HIV-1 nomenclature proposal. Science 288: 55-56.
15. Tee KK, Li XJ, Nohtomi K, Ng KP, Kamarulzaman A, et al. (2006) Identification of a novel circulating recombinant form (CRF33_01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia. J Acquir Immune Defic Syndr 43: 523-529.
16. Essex M (1999) Human immunodeficiency viruses in the developing world. Adv Virus Res 53: 71-88.
17. Kuiken C, Thakallapalli R, Esklid A, de Ronde A (2000) Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus. Am J Epidemiol 152: 814-822.
18. Kandathil AJ, Ramalingam S, Kannangai R, David S, Sridharan G (2005) Molecular epidemiology of HIV. Indian J Med Res 121: 333-344.
19. Holmes EC (2001) On the origin and evolution of the human immunodeficiency virus (HIV). Biol Rev Camb Philos Soc 76: 239-254.
20. Brennan CA, Bodelle P, Coffey R, Harris B, Holzmayer V, et al. (2006) HIV global surveillance: foundation for retroviral discovery and assay development. J Med Virol 78 Suppl 1: S24-29.
21. Kato S, Saito R, Hiraishi Y, Kitamura N, Matsumoto T, et al. (2003) Differential prevalence of HIV type 1 subtype B and CRF01Æ among different sexual transmission groups in Tokyo, Japan, as revealed by subtype-specific PCR. AIDS Res Hum Retroviruses 19: 1057-1063.
22. McCutchan FE (2000) Understanding the genetic diversity of HIV-1. Aids 14 Suppl 3: S31-44.
23. UNAIDS/WHO (2006) 2006 Report on the global AIDS epidemic.
24. Dowling WE, Kim B, Mason CJ, Wasunna KM, Alain U, et al. (2002) Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants. Aids 16: 1809-1820.
25. Songok EM, Lihana RW, Kiptoo MK, Genga IO, Kibaya R, et al. (2003) Identification of env CRF-10 among HIV variants circulating in rural western Kenya. AIDS Res Hum Retroviruses 19: 161-165.
26. Robbins KE, Kostrikis LG, Brown TM, Anzala O, Shin S, et al. (1999) Genetic analysis of human immunodeficiency virus type 1 strains in Kenya: a comparison using phylogenetic analysis and a combinatorial melting assay. AIDS Res Hum Retroviruses 15: 329-335.
27. Poss M, Gosink J, Thomas E, Kreiss JK, Ndinya-Achola J, et al. (1997) Phylogenetic evaluation of Kenyan HIV type 1 isolates. AIDS Res Hum Retroviruses 13: 493-499.
28. Lihana RW, Khamadi SA, Kiptoo MK, Kinyua JG, Lagat N, et al. (2006) HIV type 1 subtypes among STI patients in Nairobi: a genotypic study based on partial pol gene sequencing. AIDS Res Hum Retroviruses 22: 1172-1177.
29. Khan S, Rai MA, Khanani MR, Khan MN, Ali SH (2006) HIV-1 subtype A infection in a community of intravenous drug users in Pakistan. BMC Infect Dis 6: 164.
30. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
31. Heyndrickx L, Janssens W, Zekeng L, Musonda R, Anagonou S, et al. (2000) Simplified strategy for detection of recombinant human immunodeficiency virus type 1 group M isolates by gag/env heteroduplex mobility assay. Study Group on Heterogeneity of HIV Epidemics in African Cities. J Virol 74: 363-370.
32. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23: 403-405.
33. Maddison DR, Maddison WP (2000) MacClade version 4 Analysis of phylogeny and character evolution. Sunderland, Massachusetts: Sinauer Associates.
34. Swofford DL (2001) PAUP*: Phylogenetic analysis using parsimony (*and other methods) beta version 4.0b8. Sunderland, Massachusetts: Sinauer Associates.
35. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
36. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, et al. (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73: 152-160.
37. Janssens W, Heyndrickx L, Fransen K, Temmerman M, Leonaers A, et al. (1994) Genetic variability of HIV type 1 in Kenya. AIDS Res Hum Retroviruses 10: 1577-1579.
38. Morison L, Buve A, Zekeng L, Heyndrickx L, Anagonou S, et al. (2001) HIV-1 subtypes and the HIV epidemics in four cities in sub-Saharan Africa. Aids 15 Suppl 4: S109-116.
39. Neilson JR, John GC, Carr JK, Lewis P, Kreiss JK, et al. (1999) Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya. J Virol 73: 4393-4403.
40. Zachar V, Goustin AS, Zacharova V, Hager H, Koppelhus U, et al. (1996) Genetic polymorphism of envelope V3 region of HIV type 1 subtypes A, C, and D from Nairobi, Kenya. AIDS Res Hum Retroviruses 12: 75-78.
41. Yang C, Li M, Newman RD, Shi YP, Ayisi J, et al. (2003) Genetic diversity of HIV-1 in western Kenya: subtype-specific differences in mother-to-child transmission. Aids 17: 1667-1674.
42. Bailey RC, Moses S, Parker CB, Agot K, Maclean I, et al. (2007) Male circumcision for HIV prevention in young men in Kisumu, Kenya: a randomised controlled trial. Lancet 369: 643-656.
43. Auvert B, Bove A, Lagarde E, Kahindo, M, Chege J, et al. (2001) Male circumcision and HIV infection in four cities in sub-Saharan Africa. Aids 15 Suppl 4: S31-40.
44. Luginaah I, Elkins D, Maticka-Tyndale E, Landry T, Mathui M (2005) Challenges of a pandemic: HIV/AIDS-related problems affecting Kenyan widows. Soc Sci Med 60: 1219-1228.
45. Mertens TE, Belsey E, Stoneburner RL, Beer DL, SaLo P, et al. (1995) Global estimates and epidemiology of HIV-1 infections and AIDS: further heterogeneity in spread and impact. Aids 9 Suppl A: S259-272.
46. Belda FJ, Mwchari C, Hawken M, Barlow KL, Clewley JP (1997) HIV-1 subtypes in Nairobi, Kenya. J Acquir Immune Defic Syndr Hum Retrovirol 16: 63-64.
47. Hanke T, McMichael AJ (2000) Design and construction of an experimental HIV-1 vaccine for a year-2000 clinical trial in Kenya. Nat Med 6: 951 955.
48. Mwau M, Cebere I, Sutton J, Chikoti P, Winstone N, et al. (2004) A human immunodeficiency virus I (HIV-1) clade A vaccine in clinical trials: stimulation of HIV-specific T-cell responses by DNA and recombinant modified vaccinia virus Ankara (MVA) vaccines in humans. J Gen Virol 85: 911-919.