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Eight genotypes of hepatitis B virus (A-H) and subgenotypes have been recognized worldwide. However, there is limited information on prevalent genotypes in many countries in Africa. This study was undertaken to determine the hepatitis B virus (HBV) genotypes in Kenya. Seropositive HBV blood samples from a blood donor setting were used in the study. HBV genotypes were determined in 52 nucleic acid-positive samples using specific primer in a nested PCR and sequencing employed in the HBV genotyping. This study shows presence of HBV variants with genotypes A (88%), E (8%) and D (4%). In conclusion, we found that HBV genotype A is the most predominant genotype in Kenya with both subgenotype A1 and A2 present. Genotype D and E are also present in our population. This demonstrates that there could be a high genetic diversity of HBV in Kenya. Copyright © 2009 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

It has been reported that HIV infection is not a risk factor for Entamoeba species infection but is for Giardia intestinalis assemblage B in children living in Western Kenya. This study aimed to investigate the prevalence of and the risk factors for Entamoeba spp. and G. intestinalis infection in children living in Nairobi, Kenya. This cross-sectional study included 87 children with HIV [HIV(+)] and 85 without HIV [HIV(−)]. Stool and blood samples were collected for the detection of the parasites by PCR and immunological analyses using flow cytometry. Sociobehavioral and hygienic data were collected using questionnaires and analyzed statistically. The prevalence of Entamoeba spp. infection was significantly lower in the HIV(+) than in the HIV(−) children (63.2% vs. 78.8%, P = 0.024), whereas the prevalence of G. intestinalis infection was not (27.6% vs. 32.9%, P = 0.445). "Not boiling drinking water" (adjusted odds ratio [aOR]: 3.8, P = 0.044) and "helping in nursery care" (aOR: 2.8, P = 0.009) were related to G. intestinalis assemblage B infection, and "CD4/CD8 ratio ≥1" was related to Entamoeba spp. infection (aOR: 3.3, P = 0.005). In stratified regression analyses, HIV infection was negatively associated with G. intestinalis assemblage B infection in females (aOR: 0.3, P = 0.022), but positively associated in males (aOR 3.8, P = 0.04). These results suggest that G. intestinalis assemblage B infection is related to hygienic conditions, while Entamoeba spp. infection is an indicator of better immunological status, and that the role of HIV infection in Giardia infection may differ between Kenyan boys and girls. [Display omitted] [ABSTRACT FROM AUTHOR]

Abstract: Background: Worldwide access to antiretroviral therapy (ART) in low- and middle-income countries has significantly increased. Although this presents better treatment options for HIV-infected individuals, the challenge of monitoring ART in these settings still remains. Objective: To investigate efficient and cost-effective criteria for assessing ART failure among HIV-1-infected children on first-line ART in resource-limited settings. Study design: Retrospective analysis of 75 HIV-1 vertically infected Kenyan children with a follow-up period of 24 months after initiating ART. Plasma viral load, peripheral CD4+T-cell counts and HIV-1 drug-resistance mutations were monitored biannually. Results: Plasma viral load (VL) was suppressed to undetectable level or more than 1.5log10 from baseline levels in 53 (70.7%) children within 24 months. VL in the remaining 22 (29.3%) children was not suppressed significantly. Of the 22 children, 21 were infected with HIV-1 strains that developed drug-resistance mutations; 9 within 12 months and 12 between 12 and 24 months. Among the 53 who were successfully treated, VL was suppressed in 33 within 12 months and in 20 between 12 and 24 months. There was no significant difference in VL at baseline and the change of CD4+T-cell counts after initiating ART between those treated successfully and the failure groups. Conclusion: After initiating ART, children may require longer times to achieve complete viral suppression. Plasma viral load testing 24 months after initiating ART could be used to differentiate ART failures among HIV-1 vertically infected children in resource-limited settings. Additionally, drug resistance testing, if affordable, would be helpful in identifying those failing therapy and in choosing second-line regimens. [Copyright &y& Elsevier]

In molecular epidemiological studies of Giardia intestinalis , an pathogenic intestinal flagellate, due to the presence of allelic sequence heterogeneity (ASH) on the tetraploid genome, the image of haplotype diversity in the field remains uncertain. Here we employed the nine assemblage B positive stool samples, which had previously reported from Kenyan children, for the clonal sequence analysis of multiple gene loci (glutamate dehydrogenase (GDH), triosephosphate isomerase (TPI), and beta-giardin (BG)). The diversified unique assemblage B haplotypes as GDH (n = 67), TPI (n = 84), and BG (n = 62), and the assemblage A haplotypes as GDH (n = 7), TPI (n = 14), and BG (n = 15), which were hidden in the previous direct-sequence results, were detected. Among the assemblage B haplotypes, Bayesian phylogeny revealed multiple statistically significant clusters (9, 7, and 7 clusters for GDH , TPI , and BG , respectively). A part of the clusters (2 for GDH and 1 for BG), which included >4 haplotypes from an individual sample, indicated the presence of co-transmission with multiple strains sharing a recent ancestor. Locus-dependent discrepancies, such as different compositions of derived samples in clusters and different genotyping results for the assemblages, were also observed and considered to be the traces of both intra- and inter-assemblage genetic recombination respectively. Our clonal sequence analysis for giardial population, which applied firstly in Kenya, could reveal the higher rates of ASH far beyond the levels reported in other areas and address the complex population structure. The clonal analysis is indispensable for the molecular field study of G. intestinalis. Unlabelled Image • A clonal sequence revealed the high frequency of allelic sequence heterogeneity among Giardia intestinalis in Kenya. • From the nine samples, the assemblage B haplotypes as GDH (n = 67), TPI (n = 84), and BG (n = 62) were detected. • Statistically significant clusters (9, 7, and 7 clusters for GDH , TPI , and BG , respectively) were confirmed. • Intra-assemblage genetic recombination was observed as different cluster compositions. • Inter-assemblage genetic recombination was observed as discrepancy of genotyping results. [ABSTRACT FROM AUTHOR]

Hepatitis C virus is a great public-health concern worldwide. Phylogenetic analysis of the HCV genome has identified six different genotypes that have generally been divided into several subtypes. There is very little information on HCV seroprevalence and genotypes in Kenya. To determine the genotypes of HCV circulating in Kenya, blood donor samples were serologically tested and confirmed by polymerase chain reaction (PCR). Positive samples were cloned and sequenced, and phylogenetic analysis conducted to determine the HCV genotypes. One hundred Murex-seropositive samples were re-tested using a passive hemagglutination test, and 16 of these were identified as seropositive. Further testing of all of the samples by PCR identified only 10 of the 16 samples as positive. Thus, only 10 % (10/100) of the samples were viremic. Six were from females (60 %), and four were from males (40 %). The mean age of the positive donors was considerably low, at 25 +/- 9 years. Genotypic testing indicated the presence of genotype 1a (10 %) and genotype 2b (90 %). This study reports on HCV genotypes in a blood donor population in Kenya where little had been done to provide information on HCV genotypes.

Objectives: Disease progression varies among HIV-1-infected individuals. The present study aimed to explore possible viral and host factors affecting disease progression in HIV-1-infected children., Methods: Since 2000, 102 HIV-1 vertically-infected children have been followed-up in Kenya. Here we studied 29 children (15 male/14 female) who started antiretroviral treatment at <5 years of age (rapid progressors; RP), and 32 (17 male/15 female) who started at >10 years of age (slow progressors; SP). Sequence variations in the HIV-1 gag and nef genes and the HLA class I-related epitopes were compared between the two groups., Results: Based on nef sequences, HIV-1 subtypes A1/D were detected in 62.5%/12.5% of RP and 66.7%/20% of SP, with no significant difference in subtype distribution between groups (p = 0.8). In the ten Nef functional domains, only the PxxP3 region showed significantly greater variation in RP (33.3%) than SP (7.7%, p = 0.048). Gag sequences did not significantly differ between groups. The reportedly protective HLA-A alleles, A*74:01, A*32:01 and A*26, were more commonly observed in SP (50.0%) than RP (11.1%, p = 0.010), whereas the reportedly disease-susceptible HLA-B*45:01 was more common in RP (33.3%) than SP (7.4%, p = 0.045). Compared to RP, SP showed a significantly higher median number of predicted HLA-B-related 12-mer epitopes in Nef (3 vs. 2, p = 0.037), HLA-B-related 11-mer epitopes in Gag (2 vs. 1, p = 0.029), and HLA-A-related 9-mer epitopes in Gag (4 vs. 1, p = 0.051). SP also had fewer HLA-C-related epitopes in Nef (median 4 vs. 5, p = 0.046) and HLA-C-related 11-mer epitopes in Gag (median 1 vs. 1.5, p = 0.044) than RP., Conclusions: Compared to rapid progressors, slow progressors had more protective HLA-A alleles and more HLA-B-related epitopes in both the Nef and Gag proteins. These results suggest that the host factor HLA plays a stronger role in disease progression than the Nef and Gag sequence variations in HIV-1-infected Kenyan children.

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.

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.

The aim of this study was to investigate an association between certain human papillomavirus (HPV) types and human immunodeficiency virus (HIV) infections. Sexually active females (n = 487; 19-61 years old) were enrolled in the study. Subjects underwent Pap testing and evaluations of HIV and HPV infection status on uterine cervical cell samples. HPV genotyping was performed using a Kurabo GeneSQUARE DNA microarray test. Overall, 23 HPV genotypes were detected, and the most prevalent HPV genotype was HPV-52, followed by HPV-39, -54, -45, -56, -53, -31, -42, -16, -68, and -51. HPV-30, -53, -54, -61, and -66, which are associated with abnormal cytology, are categorized as intermediate-risk in this study. Detection of both high- and intermediate-risk HPV types was significantly associated with cervical abnormality and HIV infection. Multivariate analysis revealed that some high-risk HPV types (HPV-31, -45, -51, -56, and -59) and most intermediate-risk HPV types were associated with HIV infection, while the high-risk types (HPV-16, -18, -33, -35, -39, -52, -58, and -68) were not. The oncogenic effect of the most malignant HPV types (e.g., HPV-16 and -18) appear to be lower, while that of intermediate-risk types are greater, in areas with a high prevalence of HIV infection., (Copyright © 2011 Wiley-Liss, Inc.)

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.

A switch of coreceptor usage from CCR5 to CXCR4 occurs in about half of HIV-1-infected individuals in the natural course of infection. To investigate whether antiretroviral therapy (ART) enhances the coreceptor switch of HIV-1, we genotypically analyzed the env-V3 amino acid sequences from 81 HIV-1-infected children in Kenya whose plasma samples were obtained between 2000 and 2007. Of 41 children on ART, 35 had HIV-1 using CCR5 as a coreceptor at baseline. In 7 (20%) of them HIV-1 switched the coreceptor usage during the follow-up period. The mean duration of ART to the time of coreceptor switch was 2.6 years (range: 0.5-5.2). Of the remaining 40 children without ART, 32 had HIV-1 using CCR5 as a coreceptor at baseline and in 3 (9.4%) HIV-1 switched the coreceptor usage. The mean age of the children with HIV-1 coreceptor switch with and without ART was 7.3 and 9.7 years, respectively. The difference in the rate and age of coreceptor switch between treated and untreated children was not significant (p = 0.38 and 0.31, respectively). Of the HIV-1-infected children, 10 started ART by the age of 5 years (rapid progressors) and 23 did not need ART by the age of 10 years (slow progressors). The rate of coreceptor switch was strongly higher in rapid progressors (40%) than slow progressors (8.7%) (p = 0.053). These results suggest that switching of coreceptor usage from CCR5 to CXCR4 among HIV-1-infected children is not influenced by ART, but by factors responsible for rapid disease progression.

The genetic diversity of HIV-1 subtypes circulating in three districts of northern Kenya, i.e., Turkana, Mandera, and Moyale, was studied. DNA sequences encoding a portion of the env-C2-V3 region of the virus were amplified by PCR and sequenced directly. One hundred and fifty-nine samples were successfully sequenced in the env-C2-V3 region and analyzed. From the analysis, 57% were subtype A1, 27% were subtype C, 9% were subtype D, and the remaining 7% were unclassified. This study showed that HIV-1 subtype A1 was the dominant subtype in circulation in this region, though there was a significant percentage of HIV-1 subtype C in circulation there.

The use of single dose nevirapine to prevent mother-to-child transmission of HIV has been reported to induce drug-resistant mutations and reduce options for antiretroviral treatment for HIV-infected mothers and their children. To explore the status of nevirapine-resistant HIV genotypes in rural hospitals in the North Rift Valley Province of Kenya, samples collected 3 months after single dose nevirapine from 36 mothers and their children were analyzed. Resistance mutations were genotypically evaluated through proviral DNA amplification, cloning, and sequencing. Ten mothers (27.8%) had antiretroviral-associated resistance mutations of whom four (11.1%) had specific nevirapine (NNRTI) resistance-associated mutations. Three mothers (8.3%) transmitted the infection to their infants. This presence of nevirapine mutations in rural antenatal clinic attendees confirms the importance of integrating antiretroviral resistance monitoring as a key component in programs geared to prevention of HIV mother-to-child transmission.

Human papillomavirus (HPV) infection and cervical abnormalities, and their association with human immunodeficiency virus (HIV) infection were studied in 488 women who visited a health center in Nairobi. PCR-based HPV and cervical cytology tests were carried out on all participants, and peripheral CD4+ T cells and plasma HIV RNA were quantitated in HIV positive women. HIV were positive in 32% (155/488) of the women; 77% of these were untreated, and the others had been treated with anti-retroviral drugs within 6 months. Cervical HPV infection was detected in 17% of HIV negative and 49% of HIV positive women. Low-grade squamous intraepithelial lesions were observed in 6.9% of HIV negative and 21% of HIV positive women, while high-grade squamous intraepithelial lesions and cancer were seen in 0.6% and 5.8%, respectively. Multivariate analysis revealed that HIV and HPV infections were associated with each other. Cervical lesions were significantly associated with high-risk HPVs and with HIV infection, depending on HPV infection. HPV infection increased in accordance with lower CD4+ T cell counts and higher HIV RNA levels, and high-grade lesions were strongly associated with high-risk HPV infection and low CD4+ T cell counts. Immunosuppression as a result of HIV infection appears to be important for malignant progression in the cervix. Nationwide prevention of HIV infection and cervical cancer screening are necessary for the health of women in this area. High-risk HPV infection and low CD4+ T cell counts are the risk factors for cervical cancer.

Recently increased availability of anti-retroviral therapy (ART) has mitigated HIV-1/AIDS prognoses especially in resource poor settings. The emergence of ART resistance-associated mutations from non-suppressive ART has been implicated as a major cause of ART failure. Reverse transcriptase inhibitor (RTI)-resistance mutations among 12 non-subtype B HIV-1-infected children with treatment failure were evaluated by genotypically analyzing HIV-1 strains isolated from plasma obtained between 2001 and 2004. A region of pol-RT gene was amplified and at least five clones per sample were analyzed. Phylogenetic analysis revealed HIV-1 subtype A1 (n = 7), subtype C (n = 1), subtype D (n = 3), and CRF02&#95;AG (n = 1). Before treatment, 4 of 12 (33.3%) children had primary RTI-resistance mutations, K103N (n = 3, ages 5-7 years) and Y181C (n = 1, age 1 year). In one child, K103N was found as a minor population (1/5 clones) before treatment and became major (7/7 clones) 8 months after RTI treatment. In 7 of 12 children, M184V appeared with one thymidine-analogue-associated mutation (TAM) as the first mutation, while the remaining 5 children had only TAMs appearing either individually (n = 2), or as TAMs 1 (M41L, L210W, and T215Y) and 2 (D67N, K70R, and K219Q/E/R) appearing together (n = 3). These results suggest that "vertically transmitted" primary RTI-resistance mutations, K103N and Y181C, can persist over the years even in the absence of drug pressure and impact RTI treatment negatively, and that appearing patterns of RTI-resistance mutations among non-subtype B HIV-1-infected children could possibly be different from those reported in subtype B-infected children.

The genetic subtypes of HIV-1 circulating in northern Kenya have not been characterized. Here we report the partial sequencing and analysis of samples collected in the years 2003 and 2004 from 72 HIV-1-positive patients in northern Kenya, which borders Ethiopia, Somalia, and Sudan. From the analysis of partial env sequences, it was determined that 50% were subtype A, 39% subtype C, and 11% subtype D. This shows that in the northern border region of Kenya subtypes A and C are the dominant HIV-1 subtypes in circulation. Ethiopia is dominated mainly by HIV-1 subtype C, which incidentally is the dominant subtype in the town of Moyale, which borders Ethiopia. These results show that cross-border movements play an important role in the circulation of subtypes in Northern Kenya.

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.

To determine the feasibility of using short-course zidovudine (ZDV) to prevent mother-to-child transmission of human immunodeficiency virus (HIV) in a breastfeeding population in a rural area in Kenya, pregnant mothers attending clinics in seven health centers in western Kenya between 1996 and 1998 were requested to volunteer for participation in this study. The HIV-infected mothers were given a daily dose of 400 mg of ZDV starting at 36 weeks of gestation and another 300 mg every three hours intrapartum. After delivery, mothers and their children were followed-up and clinically monitored every 3-4 months for two years, and child and mother mortality rates were analyzed. Of the 825 mothers who consented, 216 (26.2%) were infected with HIV. Of those infected, 51 (23.6%) took the full prescribed dose, 69 (31.9%) took only the prenatal dose, and the remaining 96 (44.4%) did not take any dose. Failure to take ZDV was attributed mainly to delivery occurring earlier than expected, while non-compliance to the intrapartum dose was due to mothers giving birth at home and fear of traditional birth attendants. By the end of the second year, 75 HIV-exposed children (34.7%) and 33 HIV-infected mothers (15.3%) had died. The HIV-free survival of children at 24 months was significantly associated with mother survival (P < 0.001) and prenatal ZDV compliance (P < 0.003). Our findings suggest that implementation of programs for prevention of mother-to-child transmission of HIV in rural areas of Africa need to consider the various socioeconomic and cultural barriers that may prevent successful uptake of antiretroviral prophylaxes. Similarly, the rapid disease progression in mothers may eliminate the increase in child survival due to ZDV prophylaxis.

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.