The evolution of HIV-1 diversity in rural Cameroon and its implications in vaccine design and trials

Viruses

Volumn 2, Issue 2, 2010, Pages 639-654

  Powell, Rebecca ^a   Barengolts, Denis ^a   Mayr, Luzia ^a   Nyambi, Phillipe ^a,b  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

HIV 1 diversity; Phylogenetics; Rural Cameroon

Indexed keywords

ADOLESCENT; ADULT; AGED; ARTICLE; CAMEROON; CLINICAL STUDY; DRUG DESIGN; ENVELOPE GENE; FEMALE; GENE; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; GROUP SPECIFIC ANTIGEN GENE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MAJOR CLINICAL STUDY; MALE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RURAL AREA; STRUCTURAL GENE; UNINDEXED SEQUENCE; VACCINE PRODUCTION; VIRAL GENETICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79952088324     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v2020639     Document Type: Article

References (26)

1. Nyambi, P.; Zekeng, L.; Kenfack, H.; Tongo, M.; Nanfack, A.; Nkombe, I.; Ndonko, F.; Shang, J.; Burda, S.; Mbah, H.; Agyingi, L.; Zhong, P.; Nadas, A.; Zolla-Pazner, S.; Marmor, M. HIV infection in rural villages of Cameroon. J. Acquir. Immune Defic. Syndr. 2002, 31, 506-513.
2. Zhong, P.; Burda, S.; Urbanski, M.; Kenfack, H.; Tongo, M.; Heyndrickx, L.; Nanfack, A.; Shang, J.; Agyingi, L.; Zolla-Pazner, S.; Zekeng, L.; Nyambi, P. HIV type 1 group M clades infecting subjects from rural villages in equatorial rain forests of Cameroon. J. Acquir. Immune Defic. Syndr. 2002, 31, 495-505.
3. Zhong, P.; Burda, S.; Konings, F.; Urbanski, M.; Ma, L.Y.; Zekeng, L.; Ewane, L.; Agyingi, L.; Agwara, M.; Saa, D.; E., A.Z.; Kinge, T.; Zolla-Pazner, S.; Nyambi, P. Genetic and biological properties of HIV type 1 isolates prevalent in villagers of the Cameroon equatorial rain forests and grass fields: further evidence of broad HIV type 1 genetic diversity. AIDS Res. Hum. Retroviruses 2003, 19, 1167-1178.
4. Konings, F.A.; Nyambi, P.N. V118I substitution in the reverse transcriptase gene of HIV type 1 CRF02_AG strains infecting drug-naive individuals in Cameroon. AIDS Res. Hum. Retroviruses 2004, 20, 673-678.
5. Ndongmo, C.B.; Pieniazek, D.; Holberg-Petersen, M.; Holm-Hansen, C.; Zekeng, L.; Jeansson, S.L.; Kaptue, L.; Kalish, M.L. HIV genetic diversity in Cameroon: possible public health importance. AIDS Res. Hum. Retroviruses 2006, 22, 812-816.
6. Machuca, A.; Tang, S.; Hu, J.; Lee, S.; Wood, O.; Vockley, C.; Vutukuri, S.G.; Deshmukh, R.; Awazi, B.; Hewlett, I. Increased genetic diversity and intersubtype recombinants of HIV-1 in blood donors from urban Cameroon. J. Acquir. Immune Defic. Syndr. 2007, 45, 361-363.
7. Fonjungo, P.N.; Mpoudi, E.N.; Torimiro, J.N.; Alemnji, G.A.; Eno, L.T.; Nkengasong, J.N.; Gao, F.; Rayfield, M.; Folks, T.M.; Pieniazek, D.; Lal, R.B. Presence of diverse human immunodeficiency virus type 1 viral variants in Cameroon. AIDS Res. Hum. Retroviruses 2000, 16, 1319-1324.
8. Heyndrickx, L.; Janssens, W.; Ndumbe, P.M.; Vereecken, K.; Coppens, S.; De Houwer, K.; Fransen, K.; Van der Auwera, G.; van der Groen, G. HIV-1 genetic variability in Cameroon. Aids 2000, 14, 1862-1864.
9. Montavon, C.; Toure-Kane, C.; Nkengasong, J.N.; Vergne, L.; Hertogs, K.; Mboup, S.; Delaporte, E.; Peeters, M. CRF06-cpx: a new circulating recombinant form of HIV-1 in West Africa involving subtypes A, G, K, and J. J. Acquir. Immune Defic. Syndr. 2002, 29, 522-530.
10. Powell, R.L.; Zhao, J.; Konings, F.A.; Tang, S.; Ewane, L.; Burda, S.; Urbanski, M.M.; Saa, D. R.; Hewlett, I.; Nyambi, P.N. Circulating recombinant form (CRF) 37_cpx: an old strain in Cameroon composed of diverse, genetically distant lineages of subtypes A and G. AIDS Res. Hum. Retroviruses 2007, 23, 923-933.
11. Powell, R.L.; Zhao, J.; Konings, F.A.; Tang, S.; Nanfack, A.; Burda, S.; Urbanski, M.M.; Saa, D.R.; Hewlett, I.; Nyambi, P.N. 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, 1008-1019.
12. Wilbe, K.; Casper, C.; Albert, J.; Leitner, T. Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon. AIDS Res. Hum. Retroviruses 2002, 18, 849-856.
13. HIV Immunology and Sequence Databases, Los Alamos, NM, USA [Online]; Los Alamos National Laboratory, Posted 2004. http://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html and http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html (accessed 2009).
14. Brennan, C.A.; Bodelle, P.; Coffey, R.; Devare, S.G.; Golden, A.; Hackett, J., Jr.; Harris, B.; Holzmayer, V.; Luk, K.C.; Schochetman, G.; Swanson, P.; Yamaguchi, J.; Vallari, A.; Ndembi, N.; Ngansop, C.; Makamche, F.; Mbanya, D.; Gurtler, L.G.; Zekeng, L.; Kaptue, L. The Prevalence of Diverse HIV-1 Strains Was Stable in Cameroonian Blood Donors From 1996 to 2004. J. Acquir. Immune Defic. Syndr. 2008, 49, 432-439.
15. Konings, F.A.; Haman, G.R.; Xue, Y.; Urbanski, M.M.; Hertzmark, K.; Nanfack, A.; Achkar, J.M.; Burda, S.T.; Nyambi, P.N. Genetic Analysis of HIV-1 Strains in Rural Eastern Cameroon Indicates the Evolution of Second-Generation Recombinants to Circulating Recombinant Forms. J. Acquir. Immune Defic. Syndr. 2006, 42, 331-341.
16. Nyambi, P.; Heyndrickx, L.; Vereecken, K.; Burda, S.; De Houwer, K.; Coppens, S.; Urbanski, M.; Williams, C.; Ndumbe, P.; Janssens, W. Predominance of infection with HIV-1 circulating recombinant form CRF02_AG in major Cameroonian cities and towns. Aids 2002, 16, 295-296.
17. Powell, R.L.R.; Urbanski, M.M.; Burda, S.; Kinge, T.; Nyambi, P.N. High Frequency of HIV-1 Dual Infections among HIV-Positive Individuals in Cameroon, West-Central Africa. 2009, 50, 84-92.
18. West, B. Cameroon: The Bradt Travel Guide, 2nd ed.; The Globe Pequot Press: Guilford, Connecticut, CT, USA, 2008; p. 248.
19. Konings, F.A.; Zhong, P.; Agwara, M.; Agyingi, L.; Zekeng, L.; Achkar, J.M.; Ewane, L.; Saa; Afane Ze, E.; Kinge, T.; Nyambi, P.N. Protease mutations in HIV-1 non-B strains infecting drug-naive villagers in Cameroon. AIDS Res. Hum. Retroviruses 2004, 20, 105-109.
20. Heyndrickx, L.; Janssens, W.; Zekeng, L.; Musonda, R.; Anagonou, S.; Van der Auwera, G.; Coppens, S.; Vereecken, K.; De Witte, K.; Van Rampelbergh, R.; Kahindo, M.; Morison, L.; McCutchan, F.E.; Carr, J.K.; Albert, J.; Essex, M.; Goudsmit, J.; Asjo, B.; Salminen, M.; Buve, A.; van Der Groen, G. 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.
21. Delwart, E.L.; Shpaer, E.G.; Louwagie, J.; McCutchan, F.E.; Grez, M.; Rubsamen-Waigmann, H.; Mullins, J.I. Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science 1993, 262, 1257-1261.
22. Galtier, N.; Gouy, M.; Gautier, C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 1996, 12, 543-548.
23. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgins, D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876-4882.
24. Kumar, S.; Nei, M.; Dudley, J.; Tamura, K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008, 9, 299-306.
25. Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16, 111-120.
26. Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406-425.