Genetic analysis of human immunodeficiency virus type 1 strains in Kenya: A comparison using phylogenetic analysis and a combinatorial melting assay

AIDS Research and Human Retroviruses

Volumn 15, Issue 4, 1999, Pages 329-335

  Robbins, Kenneth E ^a,d   Kostrikis, Leondios G ^b   Brown, Teresa M ^a   Anzala, Omu ^c   Shin, Sunny ^b   Plummer, Francis A ^c   Kalish, Marcia L ^a  

^a NATL CENTER FOR INFECTIOUS DISEASES   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c UNIVERSITY OF MANITOBA   (Canada)

^d CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA; VIRUS DNA;

AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STRAIN DIFFERENCE; VIRUS INFECTION;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, VIRAL; FEMALE; HIV INFECTIONS; HIV-1; HUMANS; KENYA; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0032971117     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/088922299311295     Document Type: Article

References (43)

1. De Leys R, Van der Borght B, Vanden Haesevelde M, Heyndrickx L, VanGeel A, Wauters C, Bernaerts R, Saman E, Nijs P, Willems B, Taelman H, van der Goen G, Piot P, Tersmette T, Huisman JG, and Van Heuverswyn H: Isolation and partial characterization of an unusual human immunodeficiency retrovirus from 2 persons of West-Central African origin. J Virol 1990;64:1207-1216.
2. 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.
3. Louwagie J, McCutchan F, Peeters M, Brennan T, Sanders-Buell E, Eddy G, van der Groen G, Fransen K, Gershy-Damet G, Deleys R and Burke D: Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 1993;7:769-780.
4. Myers G, Korber B, Hahn BH, Jeang K-T, Mellors JW, McCutchan FE, Henderson LE, and Pavlakis GN: Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos National Laboratory, Los Alamos, New Mexico, 1995.
5. Bruce C, Clegg C, Featherstone A, Smith J, Biryahawaho B, Downing R, and Oram J: Presence of multiple genetic subtypes of human immunodeficiency virus type 1 proviruses in Uganda. AIDS Res Hum Retroviruses 1994;10;1543-1550.
6. Janssens W, Heyndrickx L, Fransen K, Temmerman M, Leonaers A, Ivens T, Motte J, Piot P, and Van Der Groen G: Genetic variability of HIV type 1 in Kenya. AIDS Res Hum Retroviruses 1994;10:1577-1579,
7. Hu DJ, Dondero TJ, Rayfield MA, George JR, Schochetman G, Jaffe HW, Luo C-C, Kalish ML, Weniger BG, Pau C-P, Schabte CA, and Curran JW: The emerging genetic diversity of HIV. JAMA 1996;275:210-216.
8. Cheingsong-Popov R, Lister S, Callow D, Kaleebu P, Weber S, and the WHO Network for HIV Isolation and Characterization: Serotyping HIV type 1 by antibody binding to the V3 loop: Relationship to viral genotype. AIDS Res Hum Retroviruses 1994;10: 1379-1386.
9. Pau C-P, Lee-Thomas S, Auwanit W, George JR, Ou C-Y, Parekh BS, Granade TS, Holloman DL, Phillips S, Schochetman G, Young NL, Takebe Y, Gayle HD, and Weniger BG: Highly specific V3 peptide enzyme immunoassay for serotyping HIV-1 specimens from Thailand. AIDS 1993;7:337-340.
10. Wasi C, Herring B, Raktham S, Vanichseni S, Mastro TD, Young NL, Rübsamen-Waigmann H, von Briesen H, Kalish ML, Luo C-C, Pau C-P, Baldwin A, Mullins JI, Delwart EL, Esparza J, Heyward WL, and Osmanov S: Determination of HIV-1 subtypes in injecting drug users in Bangkok, Thailand, using peptide binding enzyme immunoassay and the heteroduplex mobility assay: evidence of increasing infection with HIV-1 subtype E. AIDS 1995;9:843-849.
11. Delwart EL, Shpaer EG, Louwagie J, McCutchen FE, Grez M, Rübsamen-Waigmann H, and Mullins JI: Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes. Science 1993;262:1257-1261.
12. Osmanov S, Belsey L, Heyward W, Esparza J, Bradac B, Galvao-Castro P, Van de Peere P, Karita E, Sempala S, Tugume B, Biryanwaho B, Wasi C, Rübsamen-Waigmann H, von Briesen H, Esser U, Grez H, Holmes H, McCutchan FE, Louwagie J, Hegerich P, Lopez-Galindez C, Mullins JI, Delwart EL, Bachman MH, and Goudsmit J: HIV variation in WHO-sponsored vaccine evaluation sites: Genetic screening, sequence analyses and preliminary biological characterization of representative strains. AIDS Res Hum Retroviruses 1994;10:1327-1343.
13. McCutchan FE, Sanders-Buell E, Oster CW, Redfield RR, Hira SK, Perine PL, Ungar BL, and Burke DS: Genetic comparison of human immunodeficiency virus (HIV-1) isolates by polymerase chain reaction. J Acquir Immune Defic Syndr 1991;4:1241-1250.
14. WHO Network for HIV Isolation and Characterization: HIV type 1 variation in World Health Organization-sponsored vaccine evaluation sites: Genetic screening, sequence analysis, and preliminary biological characterization of selected viral strains. AIDS Res Hum Retroviruses 1994;10:1327-1343.
15. DeJong JJ, Goudsmit J, Keulen W, Klaver B, Krone W, Tersmette M, and deRonde A: Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. J Virol 1992;66:757-765.
16. Goudsmit J, Back NK, and Nara PL: Genomic diversity and anti-genic variation of HIV-1: Links between pathogenesis, epidemiology and vaccine development. FASEB J 1991;5:2427-2436
17. Hwang SS, Boyle TJ, Lyerly HK, and Cullen BR: Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 1991;253:71-74.
18. Ivanhoff LA, Dubay JW, Morris JF, Roberts SJ, Gutshall L, Sternberg EJ, Hunter, Matthews TJ, and Petteway SR Jr: V3 loop region of the HIV-1 gp 120 envelope protein is essential for virus infectivity. Virology 1992;187:423-432.
19. Javaherian K, Langlois AJ, LaRosa GJ, Profy AT, Bolognesi DP, Herlihy WC, Putney SD, and Matthews TJ: Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant in HIV-1. Science 1990;250:1590-1593.
20. Hillis DM, Huelsenbeck JP, and Cunningham CW: Application and accuracy of molecular phylogenies. Science 1994;264:671-677.
21. Leitner T, Kescanilla D, Franzen C, Uhlen M, and Albert J: Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci USA 1996;93: 19864-10869.
22. Kostrikis LG, Shin S, and Ho DD: Genotyping HIV-1 and HCV strains by a combinatorial DNA melting assay (COMA). Mol Med 1998;4:443-453.
23. Potts KE, Kalish ML, Bandea C, Orloff G, St Louis M, Brown C, Malanda N, Kavuka M, Schochetman G, Ou C-Y, and Heyward WL: Genetic diversity of human immunodeficiency virus type 1 (HIV-1) strains in Kinshasa, Zaire. AIDS Res Hum Retroviruses 1993;9:613-618.
24. Smith S: GDE: Genetic Data Environment, version 2.2. Millipore Imaging Systems, Ann Arbor, Michigan, 1992.
25. Kumar S, Tamura K, and Nei M: MEGA: Molecular Evolutionary Genetic Analysis, version 1.01. Pennsylvania State University, University Park, Pennsylvania, 1993.
26. Felsenstein J: PHYLIP: Phylogeny Inference Package, versions 3.5c and 4.0. University of Washington, Seattle, Washington, 1993.
27. Poss M, Gosink J, Thomas E, Kreiss JK, Ndinya-Achola J, Mandaliya K, Bwayo J, and Overbaugh J: Phylogenetic evaluation of Kenyan HIV type 1 isolates. AIDS Res Hum Retroviruses 1997;13: 493-499.
28. Zachar V, Goustin AS, Zacharova V, Hager H, Koppelhus U, Womble DD, Liu X, Bambra C, Nyongo A, and Ebbesen P: 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.
29. Milich L, Margolin B, and Swanstrom R: V3 Loop of the human immunodeficiency virus type 1 Env protein: Interpreting sequence variability. J Virol 1993;67:5623-5634.
30. Robbins KE, Bandea CI, Levin A, Goedert JJ, Blattner WA, Brubaker G, Brown TM, Schochetman G, Kalish ML, Shao J, and O'Brien TR: Genetic variability of human immunodeficiency virus type 1 in rural northwest Tanzania. AIDS Res Hum Retroviruss 1996;12:1389-1391.
31. Asjo BL, Morfeldt-Manson J, Biberfeld AG, Karlsson K, Lidman K, and Fenyö E-M: Replicative properties of human immunodeficiency virus from patients with varying severity of HIV infection. Lancet 1986;ii:660-662.
32. Tersmette M, De Goede R, Al BJM, Winkel I, Coutinho RA, Cuypers H, Huisman GJ, and Miedema F: Differential syncytium-inducing capacity of HIV isolates. Frequent detection of syncytium-inducing isolates in patients with AIDS and ARC. J Virol 1988;62:2026-2032.
33. Louwagie J, Janssens W, Mascola J, Heyndrickx L, Hegerich P, van der Groen G, McCutchan FE, and Burke DS: Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolais of African origin. J Virol 1995;69:263-271.
34. Murphy E, Korber B, Georges-Courbot MC, You B, Pinter A, Cook D, Kieny MP, Georges A, Mathiot C, and Barré-Sinoussi F: Diversity of the V3 region sequences of human immunodeficiency virus type 1 from the Central African Republic. AIDS Res Hum Retroviruses 1993;9:997-1006.
35. Orloff GM, Kalish ML, Chiphangwi J, Potts KE, Ou C-Y, Schochetman G, Dallabetta G, Saah A, and Miotti PG: V3 Loops of HIV-1 specimens from pregnant women in Malawi uniformly lack a potential N-linked glycosylation site. AIDS Res Hum Retroviruses 1993;9:705-706.
36. Jameel S, Zafrullah M, Ahmad M, Kapoor GS, and Sehgal S: A genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants. AIDS 1995;9:685-690.
37. Luo CC, Tian C, Hu DJ, Kai M, Dondero T, and Zheng X: HIV subtype in China. Lancet 1995;345:1051-1052.
38. Brown TM, Robbins KE, Sinniah M, Saraswathy TS, Lee V, Hooi LS, Vijayamalar B, Luo C-C, Ou C-Y, Rapier J, Schochetman G, and Kalish ML: HIV type 1 subtypes in Malaysia include B, C, and E. AIDS Res Hum Retroviruses 1996;12:1655-1657.
39. Lukashov VV, Cornelissen MTE, Goudsmit J, Papuashvilli MN, Rytik PG, Khaitov RM, Karamov EV, and de Wolf F: Simultaneous introduction of distinct HIV-1 subtypes into different risk groups in Russia, Byelorussia and Lithuania. AIDS 1995;9: 435-439.
40. Arnold C, Barlow KL, Parry JV, and Clewey JP: At least five HIV-1 sequence subtypes (A, B, C, D, A/E) occur in England. AIDS Res Hum Retroviruses 1995;11:427-429.
41. European Commission (DG XII, INCO-DC) and the Joint United Nations Programme on HIV/AIDS: HIV-1 Subtypes: Implications for epidemiology, pathogenicity, vaccines and diagnostics. AIDS 1997;11:17-36. [Workshop report]
42. Muller O, Ungchusak K, Leng HB, Chung A, and Tadiar F: HIV and AIDS in southeast Asia. Lancet 1997;350:288.
43. Bwayo J, Plummer F, Omari M, Mutere A, Moses S, Ndinya-Achola J, Velentgas P, and Kreiss J: Human immunodeficiency virus infection in long-distance truck drivers in East Africa. Arch Intern Med 1994;154:1391-1396.