Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants

AIDS

Volumn 16, Issue 13, 2002, Pages 1809-1820

  Dowling, William E ^a   Kim, Bohye ^a   Mason, Carl J ^a   Wasunna, K Monique ^a   Alam, Uzma ^a   Elson, Lynne ^a   Birx, Deborah L ^a   Robb, Merlin L ^a   McCutchan, Francine E ^a   Carr, Jean K ^a  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

Author keywords

A2 sub subtype; Full genome sequences; HIV 1 subtypes; Kenya; Recombination

Indexed keywords

CELL DNA; HUMAN IMMUNODEFICIENCY VIRUS VACCINE;

ARTICLE; CONTROLLED STUDY; EPIDEMIC; GENE AMPLIFICATION; GENE ISOLATION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS PREVALENCE; KENYA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS GENE; VIRUS STRAIN;

DISEASE OUTBREAKS; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; KENYA; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 18644375896     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/00002030-200209060-00015     Document Type: Article

References (49)

1. Gao F, Bailes E, Robertson DL, et al. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 1999, 397:436-441.
2. McCutchan FE. Understanding the genetic diversity of HIV-1. AIDS 2000, 14:S31-44.
3. Peeters M, Sharp PM. Genetic diversity of HIV-1: the moving target. AIDS 2000, 14:S129-S140.
4. Robertson DL, Anderson JP, Bradac JA, et al. HIV-1 nomenclature proposal. In Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Edited by Kuiken CL, Foley BT, Hahn BH, et al. Los Alamos, NM: Los Alamos National Laboratory, Theoretical Biology and Biophysics Group; 1999:492-505.
5. Gao F, Vidal N, Li Y, et al. Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Res Hum Retroviruses 2001, 17:675-688.
6. Bebenek K, Abbotts J, Roberts JD, Wilson SH, Kunkel TA. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J Biol Chem 1989, 264:16948-16956.
7. Boyer JC, Bebenek K, Kunkel TA. Unequal human immunodeficiency virus type 1 reverse transcriptase error rates with RNA and DNA templates. Proc Natl Acad Sci USA 1992, 89:6919-6923.
8. Robertson DL, Sharp PM, McCutchan FE, Hahn BH. Recombination in HIV-1. Nature 1995, 374:124-126.
9. Stuhlmann H, Berg P. Homologous recombination of copackaged retrovirus RNAs during reverse transcription. J Virol 1992, 66:2378-2388.
10. Human Retroviruses and AIDS: A Compliation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, NM: Los Alamos National Laboratory, Theoretical Biology and Biophysics Group; 1999.
11. Epidemiological Fact Sheet on HIV/AIDS and sexually transmitted infections: Kenya. 2000 update. In Joint United Nations Programme on HIV/AIDS/World Health Organization. Geneva: UNAIDS/WHO; 2000.
12. Hoelscher M, Kim B, Maboko L, et al. High proportion of unrelated HIV-1 intersubtype recombinants in the Mbeya region of southwest Tanzania. AIDS 2001, 15:1461-1470.
13. Harris M, Serwada D, Sewankambo N, et al. 46 near full-length HIV genome sequences from Rakai District, Uganda show subtype A and D plus 30% unique recombinants. AIDS Vaccine 2001 Conference. Philadelphia, September 2001 [abstract 271].
14. Robb ML, McCutchan FE, Carr JK, et al. Support of HIV-1 vaccine development in East Africa: sequencing of 96 full-genome sequences from Uganda, Kenya and Tanzania. AIDS Vaccine 2001 Philadelphia, September 2001 [abstract 25].
15. Carr JK, Torimiro JN, Wolfe ND, et al. The AG recombinant IbNG and novel strains of group M HIV-1 are common in Cameroon. Virology 2001, 286:168-181.
16. Salminen MO, Koch C, Sanders-Buell E, et al. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 1995, 213:80-86.
17. Carr JK, Foley BT, Leitner T, Salminen M, Korber B, McCutchan FE. Reference sequences representing the principal genetic diversity of HIV-1 in the pandemic. In Human Retroviruses and AIDS. Edited by Korber B, Kuiken CL, Foley BT, et al. Los Alamos, NM: Los Alamos National Laboratory, Theoretical Biology and Biophysics Group; 1998:III-10-III-19.
18. Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
19. Maciukenas S. Tretool; Ribosomal Database Project. http://rdp.cme.msu.edu/download/programs/TreeTool/
20. Hillis D, Bull J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic trees. Syst Biol 1993, 42:182-192.
21. Carr JK, Salminen MO, Koch C, et al. Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand. J Virol 1996, 70:5935-5943.
22. Salminen MO, Carr JK, Burke DS, McCutchan FE. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 1995, 11:1423-1425.
23. Murphy D. Recombinant Breakpoint Analysis (RBA) ver. 1.0. 2001.
24. Rose PP, Korber BT. Detecting hypermutations in viral sequences with an emphasis on G-A hypermutation. Bioinformatics 2000, 16:400-401.
25. Janini M, Rogers M, Birx DR, McCutchan FE. Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4(+) T cells. J Virol 2001, 75:7973-7986.
26. Koulinska IN, Ndung'u T, Mwakagile D, et al. A new human immunodeficiency virus type 1 circulating recombinant form from Tanzania. AIDS Res Hum Retroviruses 2001, 17:423-431.
27. Carr JK, Salminen MO, Albert J, et al. Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology 1998, 247:22-31.
28. Howard TM, Rasheed S. Genomic structure and nucleotide sequence analysis of a new HIV type 1 subtype A strain from Nigeria. AIDS Res Hum Retroviruses 1996, 12:1413-1425.
29. Robertson DL, Anderson JP, Bradac JA, et al. HIV-1 nomenclature proposal. Science 2000, 288:55-56.
30. Janssens W, Heyndrickx L, Fransen K, et al. Genetic variability of HIV type 1 in Kenya. AIDS Res Hum Retroviruses 1994, 10:1577-1579.
31. Robbins KE, Kostrikis LG, Brown TM, et al. 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 1999, 15:329-335.
32. Zachar V, Goustin AS, Zacharova V, et al. Genetic polymorphism of envelope V3 region of HIV type 1 subtypes A, C, and D from Nairobi, Kenya. AIDS Res Hum Retroviruses 1996, 12:75-78.
33. Poss M, Gosink J, Thomas E, et al. Phylogenetic evaluation of Kenyan HIV type 1 isolates. AIDS Res Hum Retroviruses 1997, 13:493-499.
34. Belda FJ, Mwchari C, Hawken M, Barlow KL, Clewley JP. HIV-1 subtypes in Nairobi, Kenya. J Acquir Immune Defic Syndr Hum Retrovirol 1997, 16:63-64.
35. Neilson JR, John GC, Carr JK, et al. Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya. J Virol 1999, 73:4393-4403.
36. Delwart EL, Shpaer EG, Louwagie J, et al. Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science 1993, 262:1257-1261.
37. Delwart EL, Herring B, Rodrigo AG, Mullins JI. Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay. PCR Methods Appl 1995, 4:S202-216.
38. Heyndrickx L, Janssens W, Zekeng L, et al. 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 2000, 74:363-370.
39. Dumitrescu O, Kalish ML, Kliks SC, Bandea CI, Levy JA. Characterization of human immunodeficiency virus type 1 isolates from children in Romania: identification of a new envelope subtype. J Infect Dis 1994, 169:281-288.
40. Morgado MG, Sabino EC, Shpaer EG, et al. V3 region polymorphisms in HIV-1 from Brazil: prevalence of subtype B strains divergent from North American/European prototype and detection of subtype F. AIDS Res Hum Retroviruses 1994, 10:569-576.
41. Triques K, Bourgeois A, Saragosti S, et al. High diversity of HIV-1 subtype F strains in Central Africa. Virology 1999, 259:99-109.
42. Triques K, Bourgeois A, Vidal 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.
43. Carr JK, Laukkanen T, Salminen MO, et al. Characterization of subtype A HIV-1 from Africa by full genome sequencing. AIDS 1999, 13:1819-1826.
44. Bobkov A, Kazennova E, Khanina T, et al. An HIV type 1 subtype A strain of low genetic diversity continues to spread among injecting drug users in Russia: study of the new local outbreaks in Moscow and Irkutsk. AIDS Res Hum Retroviruses 2001, 17:257-261.
45. Salminen MO, Carr JK, Robertson DL, et al. Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple. J Virol 1997, 71:2647-2655.
46. Kostrikis LG, Bagdades E, Cao Y, Zhang L, Dimitriou D, 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.
47. Robbins KE, Bandea CI, Levin A, et al. Genetic variability of human immunodeficiency virus type 1 in rural northwest Tanzania. AIDS Res Hum Retroviruses 1996, 12:1389-1391.
48. Lyamuya E, Olausson-Hansson E, Albert J, Mhalu F, Biberfeld G. Evaluation of a prototype Amplicor PCR assay for detection of human immunodeficiency virus type 1 DNA in blood samples from Tanzanian adults infected with HIV-1 subtypes A, C and D. J Clin Virol 2000, 17:57-63.
49. Hoelscher M, Dowling WE, Sanders-Buell E, et al. Rapid, efficient detection of HIV-1 subtypes, recombinants and dual infections in East Africa by a Multi-Region Hybridization Assay (MHA) (in press).