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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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Kimulwo MJ, Okendo J, Aman RA, Ogutu BR, Kokwaro GO, Ochieng DJ, Muigai AWT, Oloo FA, Ochieng W. Plasma nevirapine concentrations predict virological and adherence failure in Kenyan HIV-1 infected patients with extensive antiretroviral treatment exposure. PLoS One 2017; 12:e0172960. [PMID: 28235021 PMCID: PMC5325546 DOI: 10.1371/journal.pone.0172960] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/13/2017] [Indexed: 11/19/2022] Open
Abstract
Treatment failure is a key challenge in the management of HIV-1 infection. We conducted a mixed-model survey of plasma nevirapine (NVP) concentrations (cNVP) and viral load in order to examine associations with treatment and adherence outcomes among Kenyan patients on prolonged antiretroviral therapy (ART). Blood plasma was collected at 1, 4 and 24 hours post-ART dosing from 58 subjects receiving NVP-containing ART and used to determine cNVP and viral load (VL). Median duration of treatment was 42 (range, 12–156) months, and 25 (43.1%) of the patients had virologic failure (VF). cNVP was significantly lower for VF than non- VF at 1hr (mean, 2,111ng/ml vs. 3,432ng/ml, p = 0.003) and at 4hr (mean 1,625ng/ml vs. 3,999ng/ml, p = 0.001) but not at 24hr post-ART dosing. Up to 53.4%, 24.1% and 22.4% of the subjects had good, fair and poor adherence respectively. cNVP levels peaked and were > = 3μg.ml at 4 hours in a majority of patients with good adherence and those without VF. Using a threshold of 3μg/ml for optimal therapeutic nevirapine level, 74% (43/58), 65.5% (38/58) and 86% (50/58) of all patients had sub-therapeutic cNVP at 1, 4 and 24 hours respectively. cNVP at 4 hours was associated with adherence (p = 0.05) and virologic VF (p = 0.002) in a chi-square test. These mean cNVP levels differed significantly in non-parametric tests between adherence categories at 1hr (p = 0.005) and 4hrs (p = 0.01) and between ART regimen categories at 1hr (p = 0.004) and 4hrs (p<0.0001). Moreover, cNVP levels correlated inversely with VL (p< = 0.006) and positively with adherence behavior. In multivariate tests, increased early peak NVP (cNVP4) was independently predictive of lower VL (p = 0.002), while delayed high NVP peak (cNVP24) was consistent with increased VL (p = 0.033). These data strongly assert the need to integrate plasma concentrations of NVP and that of other ART drugs into routine ART management of HIV-1 patients.
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Affiliation(s)
- Maureen J. Kimulwo
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- ITROMID, Jomo Kenyatta University of Science and Technology, Nairobi, Kenya
| | - Javan Okendo
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
| | - Rashid A. Aman
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- African Centre for Clinical Trials, Nairobi, Kenya
| | - Bernhards R. Ogutu
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Gilbert O. Kokwaro
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
| | - Dorothy J. Ochieng
- School of Pharmacy, MCPHS University, Worcester, Massachusetts, United States of America
| | - Anne W. T. Muigai
- ITROMID, Jomo Kenyatta University of Science and Technology, Nairobi, Kenya
| | - Florence A. Oloo
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Department of Chemical Science and Technology, Technical University of Kenya, Nairobi, Kenya
| | - Washingtone Ochieng
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
- Immunology and Infectious Diseases Department, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Kitawi RC, Hunja CW, Aman R, Ogutu BR, Muigai AWT, Kokwaro GO, Ochieng W. Partial HIV C2V3 envelope sequence analysis reveals association of coreceptor tropism, envelope glycosylation and viral genotypic variability among Kenyan patients on HAART. Virol J 2017; 14:29. [PMID: 28196510 PMCID: PMC5310022 DOI: 10.1186/s12985-017-0703-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/08/2017] [Indexed: 01/18/2023] Open
Abstract
Background HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antiviral immunity and treatment. The aim of this study was to assess if HIV subtype differences were associated with variations in glycosylation patterns and co-receptor tropism among HAART patients experiencing different virologic treatment outcomes. Methods A total of 118 HIV env C2V3 sequence isolates generated previously from 59 Kenyan patients receiving highly active antiretroviral therapy (HAART) were examined for tropism and glycosylation patterns. For analysis of Potential N-linked glycosylation sites (PNGs), amino acid sequences generated by the NCBI’s Translate tool were applied to the HIVAlign and the N-glycosite tool within the Los Alamos Database. Viral tropism was assessed using Geno2Pheno (G2P), WebPSSM and Phenoseq platforms as well as using Raymond’s and Esbjörnsson’s rules. Chi square test was used to determine independent variables association and ANOVA applied on scale variables. Results At respective False Positive Rate (FPR) cut-offs of 5% (p = 0.045), 10% (p = 0.016) and 20% (p = 0.005) for CXCR4 usage within the Geno2Pheno platform, HIV-1 subtype and viral tropism were significantly associated in a chi square test. Raymond’s rule (p = 0.024) and WebPSSM (p = 0.05), but not Phenoseq or Esbjörnsson showed significant associations between subtype and tropism. Relative to other platforms used, Raymond’s and Esbjörnsson’s rules showed higher proportions of X4 variants, while WebPSSM resulted in lower proportions of X4 variants across subtypes. The mean glycosylation density differed significantly between subtypes at positions, N277 (p = 0.034), N296 (p = 0.036), N302 (p = 0.034) and N366 (p = 0.004), with HIV-1D most heavily glycosylated of the subtypes. R5 isolates had fewer PNGs than X4 isolates, but these differences were not significant except at position N262 (p = 0.040). Cell-associated isolates from virologic treatment success subjects were more glycosylated than cell-free isolates from virologic treatment failures both for the NXT (p = 0.016), and for all the patterns (p = 0.011). Conclusion These data reveal significant associations of HIV-1 subtype diversity, viral co-receptor tropism, viral suppression and envelope glycosylation. These associations have important implications for designing therapy and vaccines against HIV. Heavy glycosylation and preference for CXCR4 usage of HIV-1D may explain rapid disease progression in patients infected with these strains.
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Affiliation(s)
- Rose C Kitawi
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya
| | - Carol W Hunja
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,South Eastern Kenya University, P.O Box 170-90200, Kitui, Kenya
| | - Rashid Aman
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,African Center for Clinical Trials, P.O. Box 2288-00202, Nairobi, Kenya.,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Bernhards R Ogutu
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Anne W T Muigai
- Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya
| | - Gilbert O Kokwaro
- Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Washingtone Ochieng
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. .,Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. .,Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya. .,Immunology and Infectious Diseases Dept, Harvard School of Public Health, Boston, MA, USA.
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Mwatelah RS, Lwembe RM, Osman S, Ogutu BR, Aman R, Kitawi RC, Wangai LN, Oloo FA, Kokwaro GO, Ochieng W. Co-Infection Burden of Hepatitis C Virus and Human Immunodeficiency Virus among Injecting Heroin Users at the Kenyan Coast. PLoS One 2015. [PMID: 26208212 PMCID: PMC4514798 DOI: 10.1371/journal.pone.0132287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Injection drug use is steadily rising in Kenya. We assessed the prevalence of both human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections among injecting heroin users (IHUs) at the Kenyan Coast. METHODS A total of 186 IHUs (mean age, 33 years) from the Omari rehabilitation center program in Malindi were consented and screened for HIV-1 and HCV by serology and PCR and their CD4 T-cells enumerated by FACS. RESULTS Prevalence of HIV-1 was 87.5%, that of HCV was 16.4%, co-infection was 17.9% and 18/152 (11.8%) were uninfected. Only 5.26% of the HIV-1 negative injectors were HCV positive. Co-infection was higher among injectors aged 30 to 40 years (20.7%) and among males (22.1%) than comparable groups. About 35% of the injectors were receiving antiretroviral treatment (ART). Co-infection was highest among injectors receiving D4T (75%) compared to those receiving AZT (21.6%) or TDF (10.5%) or those not on ART (10.5%). Mean CD4 T-cells were 404 (95% CI, 365 - 443) cells/mm3 overall, significantly lower for co-infected (mean, 146; 95% CI 114 - 179 cells/mm3) than HIV mono infected (mean, 437, 95% CI 386 - 487 cells/mm3, p<0.001) or uninfected (mean, 618, 95% CI 549 - 687 cells/mm3, p<0.001) injectors and lower for HIV mono-infected than uninfected injectors (p=0.002). By treatment arm, CD4 T-cells were lower for injectors receiving D4T (mean, 78; 95% CI, 0.4 - 156 cells/mm3) than TDF (mean 607, 95% CI, 196 - 1018 cells/mm3, p=0.005) or AZT (mean 474, 95% CI -377 - 571 cells/mm3, p=0.004). CONCLUSION Mono and dual infections with HIV-1 and HCV is high among IHUs in Malindi, but ART coverage is low. The co-infected IHUs have elevated risk of immunodeficiency due to significantly depressed CD4 T-cell numbers. Coinfection screening, treatment-as-prevention for both HIV and HCV and harm reduction should be scaled up to alleviate infection burden.
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Affiliation(s)
- Ruth S. Mwatelah
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Raphael M. Lwembe
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Saida Osman
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Bernhards R. Ogutu
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
| | - Rashid Aman
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- African Center for Clinical Trials, Nairobi, Kenya
| | - Rose C. Kitawi
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Institute of Tropical Medicine and Infectious Diseases, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Laura N. Wangai
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Florence A. Oloo
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Technical University of Kenya, Nairobi, Kenya
| | - Gilbert O. Kokwaro
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
| | - Washingtone Ochieng
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- * E-mail:
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