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Viral and Host Characteristics of Recent and Established HIV-1 Infections in Kisumu based on a Multiassay Approach. Sci Rep 2016; 6:37964. [PMID: 27897226 PMCID: PMC5126579 DOI: 10.1038/srep37964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022] Open
Abstract
Integrated approaches provide better understanding of HIV/AIDS epidemics. We optimised a multiassay algorithm (MAA) and assessed HIV incidence, correlates of recent infections, viral diversity, plus transmission clusters among participants screened for Kisumu Incidence Cohort Study (KICoS1) (2007–2009). We performed BED-CEIA, Limiting antigen (LAg) avidity, Biorad avidity, and viral load (VL) tests on HIV-positive samples. Genotypic analyses focused on HIV-1 pol gene. Correlates of testing recent by MAA were assessed using logistic regression model. Overall, 133 (12%, 95% CI: 10.2–14.1) participants were HIV-positive, of whom 11 tested recent by MAA (BED-CEIA OD-n < 0.8 + LAg avidity OD-n < 1.5 + VL > 1000 copies/mL), giving an incidence of 1.46% (95% CI: 0.58–2.35) per year. This MAA-based incidence was similar to longitudinal KICoS1 incidence. Correlates of testing recent included sexually transmitted infection (STI) treatment history (OR = 3.94, 95% CI: 1.03–15.07) and syphilis seropositivity (OR = 10.15, 95% CI: 1.51–68.22). Overall, HIV-1 subtype A (63%), D (15%), C (3%), G (1%) and recombinants (18%), two monophyletic dyads and intrinsic viral mutations (V81I, V81I/V, V108I/V and K101Q) were observed. Viral diversity mirrored known patterns in this region, while resistance mutations reflected likely non-exposure to antiretroviral drugs. Management of STIs may help address ongoing HIV transmission in this region.
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Onsongo S, Abidi SH, Khamadi S, Shah R, Kageha S, Ojwang P, Ali S, Okinda N. Prevalence of Transmitted Drug Resistance Mutations in HIV-1-Infected Drug-Naive Patients from Urban and Suburban Regions of Kenya. AIDS Res Hum Retroviruses 2016; 32:220-5. [PMID: 26401720 DOI: 10.1089/aid.2015.0026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HIV was first described in Kenya in 1984-1985. Currently, Kenya has an estimated HIV-1 prevalence of 6.2%. With the introduction of antiretroviral drugs, the survival of most HIV patients has been prolonged markedly. However, this is greatly threatened by increasing rates of antiretroviral dug resistance, which may eventually lead to suboptimal treatment outcomes. The objective of this study was to characterize currently occurring antiretroviral drug resistance mutations among drug-naive patients visiting two referral hospitals in Kenya. Using polymerase chain reaction, the HIV protease gene was amplified from blood samples of 63 study participants. The sequences were used to determine HIV-1 subtype and presence/prevalence of mutations associated with resistance to protease inhibitors. Finally, the protease gene was variably measured using Shannon entropy analysis. Analysis of frequency of HIV-1 subtypes revealed subtype A to be the predominant subtype, while the analysis of drug resistance mutations revealed the presence of four minor drug resistance mutations associated weakly with resistance to protease inhibitors. Among these mutations, L33I was the most prevalent mutation. Shannon entropy analysis revealed high genomic variability, especially in region spanning nucleotides 1-55, 113-170, and 205-240. This study warrants the need for dedicated efforts to improve compliance to antiretroviral therapy and reduce transmitted resistance rates, which will greatly ensure the therapeutic efficacy of antiretroviral drugs.
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Affiliation(s)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Samoel Khamadi
- U.S. Military HIV Research Program, Henry M. Jackson Foundation Medical Research International, Mbeya, Tanzania
| | - Reena Shah
- Aga Khan University Hospital, Nairobi, Kenya
| | | | | | - Syed Ali
- Department of Biomedical Sciences, Nazarbayer School of Medicine, Nazarbayer University, Astana, Kazakstan
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Kitawi RC, Nzomo T, Mwatelah RS, Aman R, Kimulwo MJ, Masankwa G, Lwembe RM, Okendo J, Ogutu B, Ochieng W. HIV-1 subtype diversity based on envelope C2V3 sequences from Kenyan patients on highly active antiretroviral therapy. AIDS Res Hum Retroviruses 2015; 31:452-5. [PMID: 25423998 DOI: 10.1089/aid.2014.0306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is a continuous need to genetically characterize the HIV strains in circulation in order to assess interventions and inform vaccine discovery. We partially sequenced the envelope C2V3 gene from a total of 59 Kenyan patients on highly active antiretroviral treatment (HAART) and determined HIV subtypes using both the JPHMM subtyping tool and the phylogenetic method. HIV-1 subtype A1 was the predominant strain in circulation, representing 65.5% and 74.5% of all isolates as determined by JPHMM and phylogenetic methods, respectively. Subtypes C and D were the next most prevalent pure strains at 9.1% each by both methods. JPHMM identified 9.1% of the isolates as recombinant. Four isolates had short sequences not covering the entire C2V3 region and were thus not subtyped. From this study, subtype A viruses are still the predominant HIV-1 strains in local circulation in Kenya. Constant surveillance is needed to update molecular trends under continuing HAART scale-up.
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Affiliation(s)
- Rose C. Kitawi
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
| | - Timothy Nzomo
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
| | - Ruth S. Mwatelah
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
| | - Rashid Aman
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- African Center for Clinical Trials, Nairobi, Kenya
| | - Maureen J. Kimulwo
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
| | - Geoffrey Masankwa
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- African Center for Clinical Trials, Nairobi, Kenya
| | | | | | - Bernhards Ogutu
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Washingtone Ochieng
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
- Immunology and Infectious Disease Department, Harvard School of Public Health, Boston, Massachusetts
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Nyamache AK, Muigai AW, Khamadi SA. Circulating trends of non-B HIV type 1 subtypes among Kenyan individuals. AIDS Res Hum Retroviruses 2013; 29:400-3. [PMID: 22916803 DOI: 10.1089/aid.2012.0213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As the AIDS pandemic progresses, an increasingly broad range of genetic diversity continues to be reported within the main (M) group of HIV-1 viruses with viral subtype predominating in specific geographic areas. To determine the genetic diversity of HIV-1 subtypes among Kenyan individuals, the env-C2-V3 gene was successfully sequenced in samples from 176 patients. Analysis of the sequences showed that a majority of them belonged to subtype A1: 73.9% (130/176), followed by C: 10.8% (19/176), D: 10.2% (18/176), and 0.6% (1/176) for G and A2 as pure subtypes while the rest were recombinants of A1/U: 2.3% (4/176) and 0.6% (1/176) each for D/U, A/C/U, and AC. Similar to previous studies conducted in other parts of Kenya, HIV-1 subtype A1 still remains the most predominant subtype while subtype C continues to show an increasing prevalence. Continued surveillance of circulating subtypes of HIV-1 in Kenya is important in determining the evolution of the HIV/AIDS epidemic in Kenya.
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Affiliation(s)
- Anthony Kebira Nyamache
- Department of Plant and Microbial Sciences, Kenyatta University, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Anne W.T. Muigai
- Department of Botany and Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Samoel A. Khamadi
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
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Hassan AS, Mwaringa SM, Obonyo CA, Nabwera HM, Sanders EJ, Rinke de Wit TF, Cane PA, Berkley JA. Low prevalence of transmitted HIV type 1 drug resistance among antiretroviral-naive adults in a rural HIV clinic in Kenya. AIDS Res Hum Retroviruses 2013; 29:129-35. [PMID: 22900472 DOI: 10.1089/aid.2012.0167] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Low levels of HIV-1 transmitted drug resistance (TDR) have previously been reported from many parts of sub-Saharan Africa (sSA). However, recent data, mostly from urban settings, suggest an increase in the prevalence of HIV-1 TDR. Our objective was to determine the prevalence of TDR mutations among HIV-1-infected, antiretroviral (ARV)-naive adults enrolling for care in a rural HIV clinic in Kenya. Two cross-sectional studies were carried out between July 2008 and June 2010. Plasma samples from ARV-naive adults (>15 years old) at the time of registering for care after HIV diagnosis and before starting ARVs were used. A portion of the pol subgenomic region of the virus containing the protease and part of the reverse transcriptase genes was amplified and sequenced. TDR mutations were identified and interpreted using the Stanford HIV drug resistance database and the WHO list for surveillance of drug resistance strains. Overall, samples from 182 ARV-naive adults [mean age (95% CI): 34.9 (33.3-36.4) years] were successfully amplified and sequenced. Two TDR mutations to nucleoside reverse transcriptase inhibitors [n=1 (T215D)] and protease inhibitors [n=1 (M46L)] were identified, giving an overall TDR prevalence of 1.1% (95% CI: 0.1-3.9). Despite reports of an increase in the prevalence of HIV-1 TDR in some urban settings in sSA, we report a prevalence of HIV-1 TDR of less than 5% at a rural HIV clinic in coastal Kenya. Continued broader surveillance is needed to monitor the extent of TDR in sSA.
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Affiliation(s)
| | | | | | | | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Amsterdam, The Netherlands
- Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - James A. Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
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Hué S, Hassan AS, Nabwera H, Sanders EJ, Pillay D, Berkley JA, Cane PA. HIV type 1 in a rural coastal town in Kenya shows multiple introductions with many subtypes and much recombination. AIDS Res Hum Retroviruses 2012; 28:220-4. [PMID: 21770741 DOI: 10.1089/aid.2011.0048] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extent of HIV-1 diversity was examined among patients attending a rural district hospital in a coastal area of Kenya. The pol gene was sequenced in samples from 153 patients. Subtypes were designated using the REGA, SCUEAL, and jpHMM programs. The most common subtype was A1, followed by C and D; A2 and G were also detected. However, a large proportion of the samples was found to be recombinants, which clustered within the pure subtype branches. Phylogeographic analysis of Kilifi sequences compared with those from other regions of Africa showed that while many sequences were closely related to sequences from Kenya, others were most closely related to known sequences from other parts of Africa, including West Africa. Overall, these data indicate that there have been multiple introductions of HIV-1 into this small rural town and surroundings with ongoing diversity being generated by recombination.
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Affiliation(s)
- Stéphane Hué
- Centre for Medical Molecular Virology, University College, London, United Kingdom
| | - Amin S. Hassan
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Helen Nabwera
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Eduard J. Sanders
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Deenan Pillay
- Centre for Medical Molecular Virology, University College, London, United Kingdom
- Health Protection Agency, London, United Kingdom
| | - James A. Berkley
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
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Oyaro M, Mbithi J, Oyugi F, Laten A, Anzala O, Engelbrecht S. Molecular characterization of HIV type 1 among HIV-infected respondents in a cohort being prepared for HIV Phase III vaccine clinical trials, Western Kenya. AIDS Res Hum Retroviruses 2011; 27:257-64. [PMID: 20950148 DOI: 10.1089/aid.2010.0061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Kenya is one of the sub-Saharan African countries affected by HIV-1 infection and AIDS. We investigated HIV-1 genetic diversity in 130 individuals from Busia, Bungoma, and Kakamega in western Kenya as part of an HIV-1 vaccine feasibility study in preparation for Phase III efficacy clinical trials. After RNA extraction the partial gag (484 bp) and env (1297 bp) regions were amplified and directly sequenced. Phylogenetic analysis was done using MEGA version 4 and recombinants were identified using the jpHMM tool and phylogenetic analysis. HIV-1 sequences were amplified from 122 of the 130 samples, 118 (90.8%) from the gag region and 78 (60 %) from the env region and 74 samples (56.9%) from both the gag and env regions. Of these sequenced on both regions, 51.4% were subtype A, 9.4% subtype D, 1.4% subtype C, 4.1% subtype G, and 33.7% were discordant and thus possible recombinants, including A1/C, A1/D, A1/A2, and A2/C. The jpHMM tool indicated a further two samples with CD and BD breakpoints within the env gene and one within the gag gene (A1C). An additional sample had an A1D breakpoint in the gag gene, but the envelope was not amplified. HIV-1 subtype diversity in western Kenya should be considered in vaccines designed for clinical trials in this region and this genetic diversity should be continuously monitored.
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Affiliation(s)
- Micah Oyaro
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - John Mbithi
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
| | - Fred Oyugi
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Annette Laten
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
| | - Omu Anzala
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Susan Engelbrecht
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
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Conroy SA, Laeyendecker O, Redd AD, Collinson-Streng A, Kong X, Makumbi F, Lutalo T, Sewankambo N, Kiwanuka N, Gray RH, Wawer MJ, Serwadda D, Quinn TC. Changes in the distribution of HIV type 1 subtypes D and A in Rakai District, Uganda between 1994 and 2002. AIDS Res Hum Retroviruses 2010; 26:1087-91. [PMID: 20925575 DOI: 10.1089/aid.2010.0054] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 subtype D (HIV-1D) progresses to disease faster and has lower transmissibility than subtype A (HIV-1A). We examined whether these differences could lead to a population level change in the distribution of these subtypes over time. HIV-1 viral RNA was extracted from stored serum samples from HIV-positive subjects participating in a population-based cohort study in Rakai, Uganda in 1994 and 2002. Portions of the viral proteins gag and gp41 were sequenced and subtyped. HIV-1 subtype assignments were generated for 773 subjects in 1994 and 812 subjects in 2002. The change in subtype distribution of the population as a whole as well as quartile age groups were examined for significant changes using a linear model. There was a significant decrease in the proportion of subjects infected with HIV-1D from 70.2% to 62.4% and a significant increase in subjects infected with HIV-1A from 16.7% to 23.3% over the 8-year period (p = 0.005). The most marked changes in proportion of HIV-1D and A were seen in the younger individuals (<25 and 25-30 years; p < 0.05). The percentages of subjects infected with HIV-1C and recombinant subtypes did not change significantly. Over this 8-year period, the overall viral population in this region evolved toward the less virulent HIV-1A strain, most likely as a consequence of the faster disease progression and lower transmissibility of HIV-1D.
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Affiliation(s)
- Samantha A. Conroy
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland
| | - Aleisha Collinson-Streng
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland
| | - Xiangrong Kong
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Tom Lutalo
- Rakai Health Sciences Program, Rakai, Uganda
| | | | - Noah Kiwanuka
- Rakai Health Sciences Program, Rakai, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Maria J. Wawer
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - David Serwadda
- Makerere University School of Public Health, Kampala, Uganda
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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Lihana RW, Khamadi SA, Lubano K, Mwangi J, Kinyua JG, Okoth VO, Lagat NJ, Okoth FA, Songok EM, Makokha EP. Genetic characterization of HIV type 1 among patients with suspected immune reconstitution inflammatory syndrome after initiation of antiretroviral therapy in Kenya. AIDS Res Hum Retroviruses 2010; 26:833-8. [PMID: 20624074 DOI: 10.1089/aid.2009.0229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy (ART) has improved the survival of HIV patients but is also associated with unique manifestations of disease in some subjects during the initial months of therapy. Immune reconstitution inflammatory syndrome (IRIS) is a disorder among individuals starting ART, with no evidence-based treatment and management guidelines. We characterized HIV-1 and determined drug resistance among 14 Kenyan patients with suspected IRIS after ART initiation in 2005. Polymerase chain reaction, sequencing, and phylogenetic analysis of viral pol and env showed the following HIV-1 subtypes: A1/A1/A1 (pol-RT/gp41/C2V3), 5; A1/C/A1, 1; A1/D/A1, 2; D/A1/A1, 1; D/C/A1, 1; D/D/A1, 2; D/D/D, 1; and D/A1/A2, 1. Three patients had viruses with major drug resistance-associated mutations. These included nucleoside reverse transcriptase inhibitor (RTI) mutations: M41L, K65R, D67N, K70R, M184V, and K219Q, and nonnucleoside RTI mutations: K101P, L100I, K103N, and Y181C. Twelve patients harbored viruses that are predicted to use chemokine coreceptor 5 (CCR5) whereas two had variant viruses predicted to use the CXCR4 coreceptor. Drug resistance may not be the only cause of ART adverse events. HIV-1 characterization would be important before and during HIV therapy to avoid treatment failure.
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Affiliation(s)
- Raphael W. Lihana
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samoel A. Khamadi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kizito Lubano
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joseph Mwangi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Vincent O. Okoth
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Nancy J. Lagat
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Fredrick A. Okoth
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Elijah M. Songok
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ernest P. Makokha
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
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Lihana RW, Khamadi SA, Lubano K, Lwembe R, Kiptoo MK, Lagat N, Kinyua JG, Okoth FA, Songok EM, Makokha EP, Ichimura H. HIV type 1 subtype diversity and drug resistance among HIV type 1-infected Kenyan patients initiating antiretroviral therapy. AIDS Res Hum Retroviruses 2009; 25:1211-7. [PMID: 19954302 DOI: 10.1089/aid.2009.0007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The treatment of HIV-1 infection with antiretroviral drugs has greatly improved the survival of those who are infected. However, HIV-1 diversity and drug resistance are major challenges in patient management, especially in resource-poor countries. To evaluate HIV-1 genetic diversity and drug resistance-associated mutations among drug-naive patients in Kenya prior to antiretroviral therapy (ART), a genetic analysis of HIV-1 pol-RT and env-gp41 was performed on samples collected from 53 (18 males and 35 females) consenting patients between April and June 2005. The average age, baseline CD4(+) T cell counts, and viral loads were 38 (range, 24-62) years, 475 (range, 203-799) cells/mm(3), and 4.7 (range, 3.4-5.9) log(10) copies/ml, respectively. Phylogenetic analysis revealed that 40 samples (75.5%) were concordant subtypes for the two genes and 13 (24.5%) were discordant, suggesting possible recombination and/or dual infections. Prevalent subtypes included A1/A1(pol-RT/env-gp41), 31 (58.5%); D/D, 9 (16.9%); A1/C, 2 (3.8%); A1/D, 4 (7.5%); G/A1, 2 (3.8%); A1/A2, 1 (1.9%); C/A1, 2 (3.8%); D/A1, 1(1.9%); and D/A2, 1 (1.9%). Major reverse transcriptase inhibitor (RTI) resistance-associated mutations were found in four patients (7.5%). Of these patients, three had nucleoside RTI resistance mutations, such as M184V, K65R, D67N, K70R, and K219Q. Nonnucleoside RTI resistance-associated mutations K103N and Y181C were detected in three patients and one patient, respectively. Multiple drug resistance mutations were observed in this drug-naive population. With increasing numbers of patients that require treatment and the rapid upscaling of ART in Kenya, HIV-1 drug resistance testing is recommended before starting treatment in order to achieve better clinical outcomes.
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Affiliation(s)
- Raphael W. Lihana
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Kanazawa University, Graduate School of Medical Sciences, Department of Viral Infection and International Health, Kanazawa, Ishikawa, Japan
| | - Samoel A. Khamadi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kizito Lubano
- Reproductive Health Research Unit, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Raphael Lwembe
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Michael K. Kiptoo
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Nancy Lagat
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Fredrick A. Okoth
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Elijah M. Songok
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Ernest P. Makokha
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Hiroshi Ichimura
- Kanazawa University, Graduate School of Medical Sciences, Department of Viral Infection and International Health, Kanazawa, Ishikawa, Japan
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