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1.
PLoS One ; 10(8): e0135124, 2015.
Article in English | MEDLINE | ID: mdl-26287814

ABSTRACT

Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999-2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of gag, pol, and envelope), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.


Subject(s)
AIDS Vaccines/immunology , DNA, Viral/genetics , HIV Infections/epidemiology , HIV-1/classification , HIV-1/genetics , Base Sequence , Cohort Studies , Epitopes, T-Lymphocyte/immunology , HIV Infections/complications , HIV Infections/virology , HIV-1/immunology , Humans , Kenya/epidemiology , Malaria/complications , Malaria/epidemiology , Malaria/parasitology , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Recombination, Genetic , Sequence Analysis, DNA , env Gene Products, Human Immunodeficiency Virus/immunology , gag Gene Products, Human Immunodeficiency Virus/immunology , pol Gene Products, Human Immunodeficiency Virus/immunology
2.
Curr HIV Res ; 13(4): 292-9, 2015.
Article in English | MEDLINE | ID: mdl-25613131

ABSTRACT

BACKGROUND: Hepatitis B (HBV) and Human Immunodeficiency virus (HIV) are both bloodborne viruses. Markers of either active or past HBV infection are present in many HIV infected patients. Worldwide, HBV prevalence varies geographically and endemicity is classified as low (<2%) or high (>8%). Genotypically, prevalence varies among different populations, with genotype A having a wide distribution. In Kenya, the prevalence of HIV-1/HBV co-infection ranges from 6-53% depending on the sub-population, with genotype A as the most common. OBJECTIVE: To determine the prevalence and characterize HBV in HBV/HIV co-infected injecting drug users (IDUs) from Mombasa, Kenya. METHODS: Blood samples were collected from HIV-infected IDUs in Mombasa, Kenya. Hepatitis B surface antigen (HBsAg) was tested by enzyme immunoassay (EIA). HBV DNA was extracted by SMITEST R&D kit. Polymerase chain reaction (PCR) was done; followed by population sequencing of HBV preS, core and full genome using specific primers. Analysis was done phylogenetically with reference sequences from the Genbank. RESULTS: Seventy two HIV-positive samples were collected from IDUs in Mombasa in February and March 2010. Of these, 10 (13.89%) were HBsAg-positive by EIA. Nine of the 10 samples (12.5%) were PCR positive for HBV in the preS region; from these, four HBV full length sequences were obtained. Phylogenetic analysis showed that all belonged to genotype A1. CONCLUSION: The prevalence of HBV co-infection among HIV-infected IDUs in Mombasa, Kenya was 12.5%. Phylogenetically, sequences obtained from this study showed clusters that were distinct from reported Kenyan reference sequences from the Genbank. The findings point to an existence of a transmission network among IDUs in Mombasa. This further suggests that HBV genotypes in Kenya may be regionally diverse.


Subject(s)
HIV Infections/epidemiology , Hepatitis B/epidemiology , Substance Abuse, Intravenous/virology , Adult , Coinfection/epidemiology , Coinfection/virology , Female , Genotype , HIV Infections/virology , HIV-1 , Hepatitis B/immunology , Hepatitis B Surface Antigens/blood , Hepatitis B virus/genetics , Humans , Kenya/epidemiology , Male , Middle Aged , Molecular Sequence Data , Polymerase Chain Reaction , Prevalence
3.
AIDS Res Hum Retroviruses ; 29(1): 187-90, 2013 Jan.
Article in English | MEDLINE | ID: mdl-22856626

ABSTRACT

Drug use in Kenya dates back to the precolonial period but research among drug users in relation to human immunodeficiency virus (HIV)-associated risk and intervention strategies has been low. To evaluate HIV-1 diversity and drug resistance among injecting drug users (IDUs), a cross-sectional study involving 58 patients was carried out in Mombasa between February and March 2010. HIV-1 RNA was extracted from plasma and polymerase chain reaction using specific primers for HIV-1 reverse transcriptase was done. Population sequencing was done and subtypes were determined phylogenetically. The prevalent HIV-1 subtypes were A1 (52/58), D (5/58), and C (2/58). The prevalence of drug resistance was 13.8% (8/58) with detection of nucleoside reverse transcriptase inhibitor (NRTI) mutations, T215F (n=5), K219Q (n=3), M184V (n=1), and nonnucleoside RTI mutation, K103N (n=1). Antiretroviral therapy (ART) and its monitoring among infected Kenyan IDUs is feasible. Policymakers and service providers in HIV prevention initiatives should improve service delivery so as to measure ART coverage among IDUs to prevent further transmission of drug-resistant variants.


Subject(s)
Anti-HIV Agents/therapeutic use , HIV Infections/virology , HIV-1/genetics , Substance Abuse, Intravenous/complications , Adult , Base Sequence , Cross-Sectional Studies , Drug Resistance, Viral/genetics , Female , HIV Infections/drug therapy , HIV Infections/genetics , HIV-1/drug effects , Humans , Kenya/epidemiology , Male , Molecular Sequence Data , Mutation/genetics , Phylogeny , Substance Abuse, Intravenous/virology
4.
J Infect Dis ; 201(4): 600-7, 2010 Feb 15.
Article in English | MEDLINE | ID: mdl-20078213

ABSTRACT

BACKGROUND: Human immunodeficiency virus (HIV) vaccine development remains a global priority. We describe the safety and immunogenicity of a multiclade DNA vaccine prime with a replication-defective recombinant adenovirus serotype 5 (rAd5) boost. METHODS: The vaccine is a 6-plasmid mixture encoding HIV envelope (env) subtypes A, B, and C and subtype B gag, pol, and nef, and an rAd5 expressing identical genes, with the exception of nef. Three hundred and twenty-four participants were randomized to receive placebo (n=138), a single dose of rAd5 at 10(10) (n = 24) or 10(11) particle units (n = 24), or DNA at 0, 1, and 2 months, followed by rAd5 at either 10(10) (n= 114) or 10(11) particle units (n = 24) boosting at 6 months. Participants were followed up for 24 weeks after the final vaccination. RESULTS: The vaccine was safe and well tolerated. HIV-specific T cell responses were detected in 63% of vaccinees. Titers of preexisting Ad5 neutralizing antibody did not affect the frequency and magnitude of T cell responses in prime-boost recipients but did affect the response rates in participants that received rAd5 alone (P = .037). CONCLUSION: The DNA/rAd5 vaccination regimen was safe and induced HIV type 1 multi-clade T cell responses, which were not significantly affected by titers of preexisting rAd5 neutralizing antibody. Trial Registration. ClinicalTrials.gov identifier: NCT00123968 .


Subject(s)
AIDS Vaccines/administration & dosage , Adenoviridae/immunology , DNA, Viral/immunology , HIV Infections/prevention & control , HIV-1/immunology , Plasmids/immunology , Vaccines, DNA/administration & dosage , AIDS Vaccines/adverse effects , AIDS Vaccines/genetics , AIDS Vaccines/immunology , Adenoviridae/genetics , Adolescent , Adult , Africa, Eastern , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Antigens, Viral/immunology , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Cells, Cultured , DNA, Viral/genetics , Double-Blind Method , Enzyme-Linked Immunosorbent Assay , Female , HIV Infections/immunology , HIV-1/genetics , Human Immunodeficiency Virus Proteins/genetics , Human Immunodeficiency Virus Proteins/immunology , Humans , Interferon-gamma/metabolism , Leukocytes, Mononuclear/immunology , Male , Middle Aged , Plasmids/genetics , Vaccines, DNA/adverse effects , Vaccines, DNA/genetics , Vaccines, DNA/immunology , Young Adult
5.
J Acquir Immune Defic Syndr ; 53(4): 514-21, 2010 Apr 01.
Article in English | MEDLINE | ID: mdl-19855286

ABSTRACT

BACKGROUND: Incidence data from prospective cohort studies using rigorous laboratory methods are important in designing and evaluating HIV vaccine and therapeutic clinical trials and health care programs. We report 36-month HIV-1 incidence rates and demographic and psychosocial risks from the Kericho cohort in rural Kenya's southern Rift Valley Province. METHODS: Thirty-six month, prospective, closed, observational cohort study of adult plantation workers and dependents followed biannually. HIV-1 incidence rates per 100 person-years (py) were calculated, and Cox regression analyses were used to estimate hazards ratios (HR) associated with seroconversion. RESULTS: Two thousand four hundred volunteers (mean age +/- SD = 30.1 +/- 8.5 years; 36.5% women) participated. Twenty-nine new HIV cases were identified in year 1 of follow-up, which increased to cumulative totals of 49 and 63 cases in years 2 and 3, respectively. The corresponding 1-, 2-, and 3-year incidence rates were 1.41 [95% confidence interval (CI) = 0.95-2.02], 1.16 (95% CI = 0.86-1.54), and 1.00 (95% CI = 0.77-1.28) per 100 py. Risk factors associated with HIV seroconversion included the following: of the Luo tribe (HR = 3.31; 95% CI = 1.65-6.63), marriage more than once (HR = 2.83; 95% CI = 1.20-6.69), self-reported male circumcision (HR = 0.32; 95% CI = 0.17-0.60), history of sexually transmitted infection (HR = 2.40; 95% CI = 1.09-5.26), history of substance abuse during sex (HR = 2.44; 95% CI = 1.16-5.13), and history of transactional sex (HR = 3.30; 95% CI = 1.79-6.09). CONCLUSIONS: HIV-1 incidence rates were relatively low in adult plantation workers and dependents in rural Kenya. Cohorts including higher risk populations (eg, commercial sex workers) warrant consideration for regional HIV preventive vaccine trials. Even low incidence, well-described cohorts generate valuable epidemiological clinical trial data.


Subject(s)
HIV Infections/epidemiology , HIV-1/isolation & purification , Adolescent , Adult , Agriculture , Cohort Studies , Family Health , HIV Infections/virology , Humans , Incidence , Kenya , Male , Middle Aged , Prospective Studies , Risk Factors , Rural Population , Young Adult
6.
AIDS Res Hum Retroviruses ; 25(11): 1061-4, 2009 Nov.
Article in English | MEDLINE | ID: mdl-19943788

ABSTRACT

In preparation for HIV-1 vaccine trials in Kenya, 2801 study volunteers, from a tea plantation in Kericho, were recruited as part of a prospective vaccine cohort development study. Cryopreserved plasma was available from 401 HIV-positive volunteers, and was the source of viral RNA for genotyping by the multiregion hybridization assay (MHA). Logistic regression was performed to determine association of risk factors and HIV-1 recombinant and dual infections. At baseline, HIV-1 subtype A was the dominant circulating pure subtype (56%), followed by subtype D (10%) and C (5%). Recombinant HIV-1 strains accounted for almost one-third of all infections (29%), with 7% infected with a dual strain of the HIV-1 variants described. A higher number of HIV-1 recombinant and dual infections was observed among volunteers who were 18-24 and 25-29 years of age, affiliated with the Luo tribe, had been married two or more times, reported not being circumcised, and had STI symptoms in the past 6 months. Adjusted odds ratios (AOR) significantly associated with HIV-1 recombinant and dual infection were age difference from current spouse (5-9 years; AOR = 2.5, 95% CI = 1.2-5.3 and > or = 10 years; AOR = 3.1, 95% CI = 1.5-6.4) and reported STI symptoms in the past 6 months (AOR = 4.8, 95% CI = 2.0-11.6), respectively. In conclusion, our results suggest that there is considerable heterogeneity with respect to HIV-1 subtype diversity in this population that should be considered in the planning for future vaccine trials in the region.


Subject(s)
Genetic Variation , HIV Infections , HIV-1/genetics , Rural Population , AIDS Vaccines/genetics , Adolescent , Adult , Ethnicity , Female , HIV Infections/epidemiology , HIV Infections/ethnology , HIV Infections/virology , HIV-1/classification , Humans , Kenya/epidemiology , Kenya/ethnology , Male , Molecular Epidemiology , Mutation , Prevalence , Recombination, Genetic , Risk Factors , Young Adult
7.
PLoS One ; 3(10): e3327, 2008 Oct 03.
Article in English | MEDLINE | ID: mdl-18833329

ABSTRACT

The conduct of Phase I/II HIV vaccine trials internationally necessitates the development of region-specific clinical reference ranges for trial enrollment and participant monitoring. A population based cohort of adults in Kericho, Kenya, a potential vaccine trial site, allowed development of clinical laboratory reference ranges. Lymphocyte immunophenotyping was performed on 1293 HIV seronegative study participants. Hematology and clinical chemistry were performed on up to 1541 cohort enrollees. The ratio of males to females was 1.9:1. Means, medians and 95% reference ranges were calculated and compared with those from other nations. The median CD4+ T cell count for the group was 810 cells/microl. There were significant gender differences for both red and white blood cell parameters. Kenyan subjects had lower median hemoglobin concentrations (9.5 g/dL; range 6.7-11.1) and neutrophil counts (1850 cells/microl; range 914-4715) compared to North Americans. Kenyan clinical chemistry reference ranges were comparable to those from the USA, with the exception of the upper limits for bilirubin and blood urea nitrogen, which were 2.3-fold higher and 1.5-fold lower, respectively. This study is the first to assess clinical reference ranges for a highland community in Kenya and highlights the need to define clinical laboratory ranges from the national community not only for clinical research but also care and treatment.


Subject(s)
Laboratories , Reference Values , Rural Population , AIDS Serodiagnosis , Adolescent , Adult , Blood Chemical Analysis , Cohort Studies , Female , Hematologic Tests , Humans , Kenya , Malaria/diagnosis , Male , Middle Aged , Quality Control , Syphilis Serodiagnosis
8.
J Clin Microbiol ; 42(8): 3850-2, 2004 Aug.
Article in English | MEDLINE | ID: mdl-15297547

ABSTRACT

We report a prospective comparison of human immunodeficiency virus type 1 testing by enzyme immunoassay and Western blot with four rapid tests of 486 subjects performed in rural Kenya. Rapid test sensitivity was 100%. Specificity ranged from 99.1 to 100%. Combined use of two Food and Drug Administration-approved rapid tests yielded a single false-positive result.


Subject(s)
Acquired Immunodeficiency Syndrome/diagnosis , HIV Infections/diagnosis , HIV-1/isolation & purification , Acquired Immunodeficiency Syndrome/epidemiology , Blotting, Western/methods , HIV Infections/epidemiology , Humans , Immunoenzyme Techniques/methods , Kenya/epidemiology , Mass Screening/methods , Predictive Value of Tests , Prevalence , Reproducibility of Results , Sensitivity and Specificity
9.
AIDS Res Hum Retroviruses ; 20(2): 255-8, 2004 Feb.
Article in English | MEDLINE | ID: mdl-15018715

ABSTRACT

To investigate the in vivo evolution of recombinant HIV, we followed up on a mother who was initially coinfected with subtypes A and D in Kenya. Blood samples were obtained in 1996 and 2002, and HIV pol and env genes were amplified by PCR, cloned, sequenced, and phylogenetically analyzed. As for the 1996 sample most of the clones generated from the pol and env genes clustered either with subtypes A and D reference strains. However, two clones from the pol gene were found to be independent recombinants between subtypes A and D by RIP analysis, suggesting active generation of recombinant forms. As for the 2002 sample, all the clones from the pol gene clustered only with the subtype A reference strain, while all the env clones clustered only with subtype D, denoting a dominance of an A/D recombinant form. These results indicate that in patients dually infected with subtypes A and D there is an ongoing generation and selection for A/D recombinant forms.


Subject(s)
HIV Infections/virology , HIV-1/classification , HIV-1/genetics , Recombination, Genetic , Adult , Amino Acid Sequence , Base Sequence , DNA, Viral/genetics , Evolution, Molecular , Female , Genes, env , Genes, pol , HIV Envelope Protein gp120/genetics , HIV-1/isolation & purification , Humans , Kenya , Molecular Sequence Data , Peptide Fragments/genetics , Phylogeny , Sequence Homology, Amino Acid , Time Factors
10.
AIDS Res Hum Retroviruses ; 19(2): 161-5, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12643281

ABSTRACT

As part of a program to determine the genetic diversity of human immunodeficiency virus in rural Kenya, we carried out a molecular analysis of the C2-V3 region of HIV-infected blood samples obtained from 30 antenatal clinic attendees of seven health centers in western Kenya. Direct sequencing was carried out on the envelope C2-V3 region of proviral DNA. On phylogenetic analysis with reference strains, 20 were subtype Al, 2 were subtype D, 1 was subtype C, 1 was subtype G, 1 was CRF-10, 2A/D, 2A/C, and 2 were unclassified. The presence of CRF-10 and the great variety of subtypes and recombinants in such a limited sample size suggest that western Kenya may be a potential hotspot for HIV recombination in the country.


Subject(s)
Gene Products, env/genetics , Genetic Variation , HIV Infections/epidemiology , HIV-1/classification , Recombination, Genetic , Rural Population , Adolescent , Adult , Amino Acid Sequence , DNA, Viral/blood , HIV Envelope Protein gp120/genetics , HIV Infections/virology , HIV-1/genetics , Humans , Kenya/epidemiology , Molecular Sequence Data , Peptide Fragments/genetics , Phylogeny , Proviruses , Sequence Analysis, DNA
11.
Afr J Health Sci ; 9(1-2): 81-90, 2002.
Article in English | MEDLINE | ID: mdl-17298148

ABSTRACT

Extracts from twenty two medicinal plants popularly used in preparing traditional remedies in Kenya were screened for activity against the HIV-1 reverse transcriptase. The screening procedure involved the use of tritium labeled thymidine triphosphate as the enzyme substrate and polyadenylic acid.oligodeoxythymidylic acid [poly(rA).p(dT)12-18] as the template primer dimer. Foscarnet was used as a positive control in these experiments. At a concentration of 100 microg/ml, extracts from eight of these plants showed at least 50 per cent reverse transcriptase inhibition. This activity was arbitrarily considered as significant. This indicates that there is the probability that some antiretroviral compounds could be identified and isolated from materials from these plants.


Subject(s)
HIV-1/drug effects , Plant Extracts/chemistry , Plants, Medicinal/chemistry , Reverse Transcriptase Inhibitors/pharmacology , Foscarnet/pharmacology , HIV-1/enzymology , Humans , Kenya , Plant Extracts/pharmacology
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