Diversity of Human Immunodeficiency Virus Type-1 Subtypes in Western Kenya


Background: HIV/AIDS is the principal pandemic in the world today. Two viral types (HIV-1 and HIV-2), with numerous groups (M, N and O for HIV-1 and A through H for HIV-2) have emerged. These have further proliferated into numerous subtypes, sub-subtypes and circulating recombinant forms (CRF) over the last 30 years. HIV-1 variants circulate together within a geographical region providing an opportunity for recombination of viral strains within infected individuals. In Kenya, at least nine different genetic HIV-1 subtypes and several recombinant forms have been defined within group M, which accounts for the majority of cases in the AIDS pandemic. Objective: To determine the genetic diversity of HIV-1 in the western region of Kenya bordering Uganda. Methodology: A cross sectional study was carried out at Busia District Hospital between 2007 and 2009. A total of 75 patients were sampled randomly from a cohort of 1000 clients on antiretroviral therapy. Blood samples were analysed at the HIV Laboratory, Kenya Medical Research Institute, Nairobi, Kenya. PCR was carried out on the Pol region of HIV, sequenced and analysed by BLAST for subtypes. Results: BLAST analysis revealed the following circulating subtypes: 40/75 (53.30%) were HIV-1 group M subtype A1; 21/75 (28.0%) were subtype D; 5/75 (6.7%) were subtype G; 4/75 (5.30%) were subtype C; and 2/75 (2.70%) were subtype A2. Only one isolate was identified for the other subtypes viz: 1/75 (1.30%) resembled subtype B; 1/75 (1.30%) was A1/C, and 1/75 (1.30%) was A1/D. Conclusion: The study showed increasing HIV-1 diversity along the Kenya-Uganda border with the emergence of A1/C and A1/D recombinants. Such HIV-1 diversityvis a vis the recent expanded access to antiretroviral therapy in resource limited settings calls for continuous evaluation of anti-HIV regimens. There is need therefore, for regular surveillance and monitoring for mutations that are likely to lead to drug resistance if we have to achieve successful treatment outcomes.

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Adungo, F. , Gicheru, M. , Adungo, N. , Matilu, M. , Lihana, R. and Khamadi, S. (2014) Diversity of Human Immunodeficiency Virus Type-1 Subtypes in Western Kenya. World Journal of AIDS, 4, 365-372. doi: 10.4236/wja.2014.44043.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Robertson, D.L., Anderson, J.P., Bradac, J.A., Carr, J.K., Foley, B., Funkhouser, R.K., Gao, F., Hahn, B.H., Kalish, M.L., Kuiken, C., Learn, G.H., Leitner, T., McCutchan, F., Osmanov, S., Peeters, M., Pieniazek, D., Salminen, M., Sharp, P.M., Wolinsky, S. and Korber, B. (2000) HIV-1 Nomenclature Proposal. Science, 288, 55-56. http://dx.doi.org/10.1126/science.288.5463.55d
[2] Hemelaar, J., Gouws, E., Ghys, P.D. and Osmanov, S. (2006) Global and Regional Distribution of HIV-1 Genetic Subtypes and Recombinants in 2004. AIDS, 20, W13-W23.
[3] Eholie, S. and Anglaret, X. (2006) Commentary: Decline of HIV-2 Prevalence in West Africa: Good News or Bad News? International Journal of Epidemiology, 35, 1329-1330.
[4] Achkar, J.M., Burda, S.T., Konings, F.A., Urbanski, M.M., Williams, C.A., Seifen, D., Kahirimbanyi, M.N., Vogler, M., Parta, M., Lupatkin, H.C., Zolla-Pazner, S. and Nyambi, P.N. (2004) Infection with HIV Type 1 Group M Non-B Subtypes in Individuals Living in New York City. Journal of Acquired Immune Deficiency Syndromes, 36, 835-844. http://dx.doi.org/10.1097/00126334-200407010-00011
[5] Triques, K., Bourgeois, A., Vidal, N., Mpoudi-Ngole, E., Mulanga-Kabeya, C., Nzilambi, N., Torimiro, N., Saman, E., Delaporte, E. and Peeters, M. (2000) 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 Research and Human Retroviruses, 16, 139-151.
[6] Burke, D.S. (1997) Recombination in HIV: An Important Viral Evolutionary Strategy. Emerging Infectious Diseases, 3, 253-259. http://dx.doi.org/10.3201/eid0303.970301
[7] Peeters, M. and Sharp, P.M. (2000) Genetic Diversity of HIV-1: The Moving Target. AIDS, 14, S129-S140.
[8] Nasioulas, G., Paraskevis, D., Magiorkinis, E., Theodoridou, M. and Hatzakis, A. (1999) Molecular Analysis of the Full-Length Genome of HIV Type 1 Subtype I: Evidence of A/G/I Recombination. AIDS Research and Human Retroviruses, 15, 745-758. http://dx.doi.org/10.1089/088922299310836
[9] Hu, D.J., Baggs, J., Downing, R.G., Pieniazek, D., Dorn, J., Fridlund, C., Biryahwaho, B., Sempala, S.D., Rayfield, M.A., Dondero, T.J. and Lal, R. (2000) Predominance of HIV-1 Subtype A and D Infections in Uganda. Emerging Infectious Diseases, 6, 609-615. http://dx.doi.org/10.3201/eid0606.000609
[10] Blackard, J.T., Renjifo, B.R., Mwakagile, D., Montano, M.A., Fawzi, W.W. and Essex, M. (1999) Transmission of Human Immunodeficiency Type 1 Viruses with Intersubtype Recombinant Long Terminal Repeat Sequences. Virology, 254, 220-225. http://dx.doi.org/10.1006/viro.1998.9504
[11] Hoelscher, M., Kim, B., Maboko, L., Mhalu, F., von Sonnenburg, F., Birx, D.L. and McCutchan, F.E. (2001) High Proportion of Unrelated HIV-1 Intersubtype Recombinants in the Mbeya Region of Southwest Tanzania. AIDS, 15, 1461-1470. http://dx.doi.org/10.1097/00002030-200108170-00002
[12] De Baar, M.P., De Ronde, A., Berkhout, B., Cornelissen, M., Van Der Horn, K.H.M., Van Der Schoot, A.M., De Wolf, F., Lukashov, V.V. and Goudsmit, J. (2000) Subtype-Specific Sequence Variation of the HIV Type 1 Long Terminal Repeat and Primer-Binding Site. AIDS Research and Human Retroviruses, 16, 499-504. http://dx.doi.org/10.1089/088922200309160
[13] Khamadi, S.A., Ochieng, W., Lihana, R.W., Kinyua, J., Muriuki, J., Mwangi, J., Lwembe, R., Kiptoo, M., Osman, S., Lagat, N., Pelle, R., Muigai, A., Carter, J.Y., Oishi, I., Ichimura, H., Mwaniki, D.L., Okoth, F.A., Mpoke, S. and Songok, E.M. (2005) HIV Type 1 Subtypes in Circulation in Northern Kenya. AIDS Research and Human Retroviruses, 21, 810-814. http://dx.doi.org/10.1089/aid.2005.21.810
[14] Carr, J.K., Nadai, Y., Eyzaguirre, L., Saad, M.D., Khakimov, M.M., Yakubov, S.K., Birx, D.L., Graham, R.R., Wolfe, N.D., Earhart, K.C. and Sanchez, J.L. (2005) Outbreak of a West African Recombinant of HIV-1 in Tashkent, Uzbekistan. Journal of Acquired Immune Deficiency Syndromes, 39, 570-575.
[15] Lihana, R.W., Khamadi, S.A., Kiptoo, M.K., Kinyua, J.G., Lagat, N., Magoma, G.N., Mwau, M.M., Makokha, E.P., Onyango, V., Osman, S., Okoth, F.A. and Songok, E.M. (2006) HIV Type 1 Subtypes among STI Patients in Nairobi: A Genotypic Study Based on Partial pol Gene Sequencing. AIDS Research and Human Retroviruses, 22, 1172-1177. http://dx.doi.org/10.1089/aid.2006.22.1172
[16] Kumar, S., Tamura, K., Jakobsen, I.B. and Nei, M. (2001) MEGA2: Molecular Evolutionary Genetics Analysis Software. Bioinformatics, 17, 1244-1245.
[17] Rhee, S.Y., Gonzales, M.J., Kantor, R., Betts, B.J., Ravela, J. and Shafer, R.W. (2003) Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. Nucleic Acids Research, 31, 298-303. http://dx.doi.org/10.1093/nar/gkg100
[18] Neilson, J.R., John, G.C., Carr, J.K., Lewis, P., Kreiss, J.K., Jackson, S., Nduati, R.W., Mbori-Ngacha, D., Panteleeff, D.D., Bodrug, S., Giachetti, C., Bott, M.A., Richardson, B.A., Bwayo, J., Ndinya-Achola, J. and Overbaugh, J. (1999) Subtypes of Human Immunodeficiency Virus Type 1 and Disease Stage among Women in Nairobi, Kenya. Journal of Virology, 73, 4393-4403.
[19] Ortiz, M., Munoz, L., Bernal, A., Rodriguez, A., Zorraquino, A., Vadillo, J., Salas, A., Moreno, A. and García-Sáiz, A. (2000) Molecular Characterization of Non-B HIV Type 1 Subtypes from Africa in Spain. AIDS Research and Human Retroviruses, 16, 1967-1971.

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