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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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Nzomo TJ, Kitawi RC, Mwatelah RS, Aman R, Kimulwo MJ, Masankwa G, Okendo J, Lwembe RM, Ogutu B, Muigai A, Ochieng W. Genotypic Variability of HIV-1 Reverse Transcriptase Gene from Long-Term Antiretroviral-Experienced Patients in Kenya. AIDS Res Hum Retroviruses 2015; 31:550-3. [PMID: 25748548 DOI: 10.1089/aid.2015.0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is continuous need to track genetic profiles of HIV strains circulating in different geographic settings to hasten vaccine discovery and inform public health and intervention policies. We partially sequenced the reverse transcriptase region of the HIV-1 pol gene from a total of 54 Kenyan patients aged 18-56 years who continued highly active antiretroviral treatment (HAART) for between 8 and 102 months. Subtyping was done using both the JPHMM tool and phylogenetic method. HIV-1 subtype A1 was the predominant strain in circulation, representing 57.4% and 70.4% of all isolates as determined by JPHMM and phylogenetic methods, respectively. Subtypes D (14.8%, 7.4%), C (5.6%, 9.3%), and A2 (0%, 5.6%) were determined at respective prevalence by both methods. JPHMM identified 22.2% of the isolates as recombinants. This surveillance focused on the RT gene and reaffirms the predominance of subtype A and an increasing proportion of recombinant strains in the Kenyan epidemic.
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Affiliation(s)
- Timothy J. Nzomo
- Center 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
| | - Rose C. Kitawi
- Center 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
| | - Ruth S. Mwatelah
- Center 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
| | - Rashid Aman
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- African Center for Clinical Trials, Nairobi, Kenya
- Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
| | - Maureen J. Kimulwo
- Center 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
| | - Geoffrey Masankwa
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Bernhards 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
| | - Anne Muigai
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Washingtone Ochieng
- Center for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
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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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Delatorre EO, Bello G. Phylodynamics of HIV-1 subtype C epidemic in east Africa. PLoS One 2012; 7:e41904. [PMID: 22848653 PMCID: PMC3407063 DOI: 10.1371/journal.pone.0041904] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/27/2012] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east Africa. A large number (n = 1,981) of subtype C pol sequences were retrieved from public databases to explore relationships between strains from the east, southern and central African regions. Maximum-likelihood phylogenetic analysis of those sequences revealed that most (>70%) strains from east Africa segregated in a single regional-specific monophyletic group, here called CEA. A second major Ethiopian subtype C lineage and a large collection of minor Kenyan and Tanzanian subtype C clades of southern African origin were also detected. A Bayesian coalescent-based method was then used to reconstruct evolutionary parameters and migration pathways of the CEA African lineage. This analysis indicates that the CEA clade most probably originated in Burundi around the early 1960s, and later spread to Ethiopia, Kenya, Tanzania and Uganda, giving rise to major country-specific monophyletic sub-clusters between the early 1970s and early 1980s. The results presented here demonstrate that a substantial proportion of subtype C infections in east Africa resulted from dissemination of a single HIV local variant, probably originated in Burundi during the 1960s. Burundi was the most important hub of dissemination of that subtype C clade in east Africa, fueling the origin of new local epidemics in Ethiopia, Kenya, Tanzania and Uganda. Subtype C lineages of southern African origin have also been introduced in east Africa, but seem to have had a much more restricted spread.
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Affiliation(s)
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail:
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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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Khamadi SA, Lihana RW, Osman S, Mwangi J, Muriuki J, Lagat N, Kinyua J, Mwau M, Kageha S, Okoth V, Ochieng W, Okoth FA. Genetic diversity of HIV type 1 along the coastal strip of Kenya. AIDS Res Hum Retroviruses 2009; 25:919-23. [PMID: 19751145 DOI: 10.1089/aid.2009.0005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A study on the genetic diversity of HIV-1 subtypes present along the coastal strip of Kenya, i.e., Kilifi, Mombasa, Msambweni, and Malindi districts, was carried out. DNA sequences for regions encoding a portion of the env-gp41 region of the virus were generated by PCR and sequenced directly. Eighty six samples that were successfully sequenced were analyzed. From the analysis, 86% (74) were subtype A1, 5% (4) were subtype C, 8% (7) were subtype D, and 1% (1) was subtype G. This study shows that HIV-1 subtype A1 is the most dominant subtype in circulation in this region.
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Affiliation(s)
| | | | - Saida Osman
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | - Nancy Lagat
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Matilu Mwau
- Kenya Medical Research Institute, Nairobi, Kenya
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O'Rourke SM, Schweighardt B, Scott WG, Wrin T, Fonseca DPAJ, Sinangil F, Berman PW. Novel ring structure in the gp41 trimer of human immunodeficiency virus type 1 that modulates sensitivity and resistance to broadly neutralizing antibodies. J Virol 2009; 83:7728-38. [PMID: 19474108 PMCID: PMC2708639 DOI: 10.1128/jvi.00688-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 05/18/2009] [Indexed: 11/20/2022] Open
Abstract
The identification of the determinants of sensitivity and resistance to broadly neutralizing antibodies is a high priority for human immunodeficiency virus (HIV) research. An analysis of the swarm of closely related envelope protein variants in an HIV-infected individual revealed a mutation that markedly affected sensitivity to neutralization by antibodies and antiviral entry inhibitors targeting both gp41 and gp120. This mutation mapped to the C34 helix of gp41 and disrupted an unexplored structural feature consisting of a ring of hydrogen bonds in the gp41 trimer. This mutation appeared to affect the assembly of the six-helix bundle required for virus fusion and to alter the conformational equilibria so as to favor the prehairpin intermediate conformation required for the binding of the membrane proximal external region-specific neutralizing antibodies 2F5 and 4E10 and the antiviral drug enfuvirtide (Fuzeon). The "swarm analysis" method we describe furthers our understanding of the relationships among the structure, function, and antigenicity of the HIV envelope protein and represents a new approach to the identification of vaccine antigens.
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Affiliation(s)
- Sara M O'Rourke
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
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