HIV type 1 genetic diversity in Moyale, Mandera, and Turkana based on env-C2-V3 sequences

AIDS Research and Human Retroviruses

Volumn 24, Issue 12, 2008, Pages 1561-1564

  Khamadi, Samoel A ^a,c   Lihana, Raphael W ^a   Mwaniki, D L ^a   Kinyua, Joyceline ^a   Lagat, Nancy ^a   Carter, Jane Y ^b   Ichimura, Hiroshi ^a   Oishi, Isao ^a   Okoth, Fredrick A ^a   Ochieng, Washington ^a  

^a KENYA MEDICAL RESEARCH INSTITUTE   (Kenya)

^b AMREF HEALTH AFRICA   (Kenya)

^c KEMRI JICA Project ^*  (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; ENVELOPE GENE; GENE AMPLIFICATION; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; KENYA; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION;

CHILD; CLUSTER ANALYSIS; DNA, VIRAL; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; EPIDEMIOLOGY, MOLECULAR; FEMALE; GENETIC VARIATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; KENYA; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROVIRUSES; SEQUENCE ANALYSIS, DNA;

EID: 58149125276     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2008.0085     Document Type: Article

References (15)

1. McCutchan FE: Understanding the genetic diversity of HIV-1. AIDS 2000;14:S31-S34.
2. Powell RL, Zhao J, Konings FA, Tang S, Nanfack A, Burda S, Urbanski MM, Saa DR, Hewlett I, and Nyambi PN: Identification of a novel circulating recombinant form (CRF) 36_cpx in Cameroon that combines two CRFs (01_AE and 02_AG) with ancestral lineages of subtypes A and G. AIDS Res Hum Retroviruses 2007;23(8):1008-1019.
3. Robertson DL, Anderson JP, Bradac J, et al.: HIV-1 nomenclature proposal. Human Retroviruses and AIDS. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 1999.
4. Esteves A, Parreira R, Venenno T, Franco M, Piedade J, Germano De Sousa J, and Canas-Ferreira WF: Molecular epidemiology of HIV type 1 infection in Portugal: High prevalence of non-B subtypes. AIDS Res Hum Retroviruses 2002;18(5):313-325.
5. Arens M: Methods for subtyping and molecular comparison of human viral genomes. Clin Microbiol Rev 1999;12(4):612-626.
6. 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, NM, 1995.
7. Ivanoff LA, Dubay JW, Morris JF, Roberts SJ, Gutshall L, Sternberg EJ, Hunter E, Matthews TJ, and Petteway SR Jr: V3 loop region of the HIV-1 gp120 envelope protein is essential for virus infectivity. Virology 1992;187(2):423-432.
8. Hillis DM, Huelsenbeck JP, and Cunningham CW: Application and accuracy of molecular phylogenies. Science. 1994;264(5159):671-677.
9. Leitner T, Escanilla D, Franzén C, Uhlén M, and Albert J: Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci USA 1996;93(20):10864-10869.
10. Dowling WE, Kim B, Mason CJ, Wasunna KM, Alam U, Elson L, Birx DL, Robb ML, McCutchan FE, and Carr JK: Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants. AIDS 2002;16(13):1809-1820. Erratum in AIDS 2002;16(15):2104.
11. 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.
12. Thomson JD, Higgins DG, and Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
13. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotides sequences. J Mol Evol 1980;16:111-120.
14. Page RD: TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996;12:357-358.
15. Khamadi AS, Ochieng W, Lihana RW, Lwembe R, Kiptoo MK, Kinyua J, Lagat N, Muriuki J, Mwangi J, Oishi I, Ichimura H, Mpoke S, and Songok EM: HIV type 1 subtypes in circulation in northern Kenya. AIDS Res Hum Retroviruses 2005;21(9):810-814.