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International audience; Background: Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015.Methods: We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164.Findings: Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (

The World Health Organization aims at achieve global elimination and eradication of hepatitis C virus (HCV) by 2030. Illustrating the burden of the disease among people who inject drugs (PWIDs) in Kenya is essential in management of the infection. We undertook a cross-sectional study aimed at determining sero-prevalence and genotypes of HCV among PWIDs from two dropping centers in Nairobi Kenya. Random sampling technique was used to recruit participant; a self administered questionnaire was used to obtain information on clinical history and socio-demographic factors. Missing and nonresponsive information were obtained from the facility records. Up to 5mL of whole blood samples were collected from participants whose information had been obtained. Serological analysis was done to determine sero-prevalence; molecular analysis was done on sero positive samples. Positive samples on gel electrophoresis were used for sequencing. MEGA6 was used to draw the phylogenetic tree and analyze the sequences. A total of 212 PWID were successfully recruited for the study of whom 29(13.7%) tested positive for hepatitis C antibody. Majority of them were males 21(72.4%) and females were 8(27.6%). Age (P=0.001), marital status (P=0.008), duration of injecting drugs (P=0.001) and the frequency of injecting drugs (P=0.010) were found to be significantly associated with HCV infection. 27/29(93.1%) were PCR-positive and were used for genotypic identification. HCV strains detected were genotype 1, 14(51.8%); genotype 4, 4(14.8%); genotype 6, 4(14.8%); genotype 5, 2(7.4%); genotype 3 1(3.7%) and 2(7.4%) was of undefined genotype. Earlier studies by different study groups have shown genotype 1 and 4 to be predominantly found within the region, detection of genotype5, 6 and the undefined genotypes in the current study is an indication of cross infection from other regions. This may imply a negative effect in the effort to eradicate hepatitis C in the region using the genotype specific drugs.

Background Soil transmitted helminths (STHs) are among the world’s neglected tropical diseases. Morbidity due to STHs is greatest in school-age children who typically have the highest burden of infection. In 2001, WHO passed a resolution for the use of large-scale mass drug administration (MDA) to deworm vulnerable children through school based programs. Though effective, there is concern that MDA might not be sustainable over extended periods. Additionally the current MDA strategy does not consider child malnutrition, a very common malady in resource limited countries. We report a pilot evaluation of an innovation that bundles school feeding and deworming. Methods We designed a maize (corn) flour fortified with grounded dried papaya (Carica papaya) seeds and used it to prepare porridge as per the usual school meal recipe Children from three primary schools from Nandi County in Kenya were randomized into three arms: One school received 300 ml papaya fortified porridge daily (papaya group), the second school received similar serving of plain porridge without the pawpaw ingredient (control group) and the third school received plain porridge and the conventional MDA approach of one time 400 mg dosage of albendazole (albendazole arm). Prior to the randomization, an initial baseline stool microscopy analysis was done to determine presence and intensity of intestinal worms. Core indicators of nutrition-height, weight and hemoglobin counts were also assessed. The children were monitored daily for two months and final stool sample analysis and clinical monitoring done at the end of the study. Baseline and follow-up data were analyzed and compared through SAS version 9.1 statistical package. Results A total of 326 children participated in the trial. The overall prevalence of Ascaris lumbricoides was 29.4% (96), Trichuris Trichura 5.2% (17) and hookworm 1 (0.3%). Papaya seed fortified porridge reduced the Ascaris lumbricoides egg count by 63.9% after the two month period (mean 209.7epg to 75.7 p

Occult hepatitis B infection (OBI) is defined as the presence of hepatitis B virus (HBV) DNA in the liver or serum in the absence of detectable HBV surface antigen (HBsAg). OBI poses a risk for the development of cirrhosis and hepatocellular carcinoma. The prevalence of OBI in Kenya is unknown, thus a study was undertaken to determine the prevalence and molecular characterization of OBI in Kenyan populations at high risk of HBV infection. Sera from two Nairobi cohorts, 99 male sex workers, primarily having sex with men (MSM-SW), and 13 non-MSM men having HIV-positive partners, as well as 65 HBsAg-negative patients presenting with jaundice at Kenyan medical facilities, were tested for HBV serological markers, including HBV DNA by real-time PCR. Positive DNA samples were sequenced and MSM-SW patients were further tested for hepatitis C virus (HCV) infection. Of the 166 HBsAg-negative samples tested, 31 (18.7%; 95% confidence interval [CI] 13.5-25.3) were HBV DNA positive (i.e., occult), the majority (20/31; 64.5%) of which were HBV core protein antibody positive. HCV infection was not observed in the MSM-SW participants, although the prevalence of HBsAg positivity was 10.1% (10/99; 95% CI 5.6-17.6). HBV genotype A was predominant among study cases, including both HBsAg-positive and OBI participants, although the data suggests a non-African network transmission source among MSM-SW. The high prevalence of HBV infection among MSM-SW in Kenya suggests that screening programmes be instituted among high-risk cohorts to facilitate preventative measures, such as vaccination, and establish entry to treatment and linkage to care.

BACKGROUND: Sub-Saharan Africa has a large population of people with hepatitis C virus (HCV) infection, yet little is known about HCV among people who inject drugs this region. We assessed the prevalence of HCV mono-infection and HIV–HCV co-infection, and the estimated incidence, genotypes, and risk behaviours associated with HCV among people who inject drugs in Kenya. METHODS: People aged 18 years or older who were living in Nairobi, coastal Kenya, or western Kenya, had a history of injection drug use, and had used any illicit drugs in the past 12 months were recruited at needle and syringe programme sites using respondent-driven sampling. Participants were screened for the presence of an anti-HCV antibody. Those who were anti-HCV positive underwent confirmatory HCV RNA testing, and those with detectable HCV RNA were genotyped. Participants were interviewed regarding parenteral risk behaviours and exposure to services received at the needle and syringe programme sites. We examined correlates of HCV infection and HIV–HCV co-infection using bivariate and multivariate regression, and estimated HCV incidence. FINDINGS: Of 2188 enrolled participants, 291 (13%) were anti-HCV positive: 183 (22%) of 842 participants in coastal Kenya, 105 (13%) of 817 in Nairobi, and three (1%) of 529 in western Kenya. 284 anti-HCV-positive participants underwent successful HCV RNA testing, of whom 230 (81%) were viraemic. Estimated incidence rates of anti-HCV positivity per 100 person-years were 6·31 in coastal Kenya, 3·19 in Nairobi, and 0·22 in western Kenya. HCV incidence rate was greater in coastal Kenya compared with Nairobi (incidence rate ratio 1·97 [95% CI 1·35–2·93], p=0·0001) and the western region (28·17 [7·55–236·58], p

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.

Background: The Ebola virus disease outbreak of 2014 was the largest, longest and most devastating in the history of the disease. It demonstrated the social and economic impact an emerging infectious disease can have in a globalized world. Health systems in affected countries were stretched to the point of near collapse, while social relations and traditional practices were negatively impacted. Heads of African research institutions, African government representatives, leaders of global pharmaceutical companies, global infectious disease experts and close to 100 young African researchers from 25 countries; Assembled in Geneva on 19 and 20th October 2015, for the inaugural UNESCO-Merck Africa Summit sponsored by the United Nations Educational, Science and Culture Organization and Merck KGAGoal of Summit: The primary goal of the summit was to develop strategies to increase health research capacity in Africa, with special focus on Ebola and enhancing pandemic preparation for emerging infectious diseases. The summit was also provide a forum to showcase the research taking place in Africa, and provided platform for African researchers to network. Some of the key issues discussed included; strategies for enhancing policy frameworks to promote knowledge translation, strengthening of health systems, enhancing knowledge and data sharing, and increasing innovation in Africa.Conclusions: Summit attendees recognized that Africa still bore the heaviest burden of infectious disease, and increased commitment by African governments to fund health research, offered the best hope for developing health solutions and interventions to improve the health of Africans. Improved health in turn would enhance the productivity of Africans, further supporting the socio-economic transformation currently taking place on the continent.Research is a catalyst for Social, Economic and Sustainable development in Africa.

Papaya seeds, a high source of dietary nutrients and phytochemicals are wasted when Carica papaya fruit is processed and consumed. This study investigates bioactivity of papaya seeds (PS) from 3 different locations in Kenya for potential valorization as porridge. PS was treated with acetic acid and sodium bicarbonate to improve pallatability. HPLC analysis revealed that PS flour added compounds which were absent from cornmeal (p-hydroxybenzoic, 2,4-dihydroxybenzoic and vanillic acids) and increased over 25% the pre-existing ones. Acid and alkali treatments increased the phenolic compounds content and antioxidant capacities of the seed 1 porridges in ≈19% average. The differential scanning calorimetry and the rapid visco analysis showed a significant decrease in the enthalpy required (≈44%) to gelatinize cornmeal-PS blend and the tendency for retrogradation (from 2188 to 700 cP average). Therefore, our findings indicate that PS can contribute to improved phytochemical and functional properties of cornmeal porridges.

Objective We conducted a retrospective cohort study to evaluate the efficacy of the World Health Organization (WHO) “Universal Test and Treat” (UTT) policy, initiated in Kenya in September 2016. Under this policy, every human immunodeficiency virus (HIV)-infected person should be initiated on antiretroviral therapy (ART). We compared intra- and inter-group viral suppression and ART adherence rates for pre-UTT (initiated on ART in March–August 2016) and UTT groups (initiated in September 2016). The study was conducted in a community outreach Program in Nairobi with 3500 HIV-infected children enrolled. Results 122 children and adolescents were initiated on first-line ART pre-UTT, and 197 during the UTT period. The 6 month viral suppression rate was 79.7% pre-UTT versus 76.6% UTT (P

The advent of antiretroviral treatment (ART) has resulted in a dramatic reduction in AIDS-related morbidity and mortality. However, the emergence and spread of antiretroviral drug resistance (DR) threaten to negatively impact treatment regimens and compromise efforts to control the epidemic. It is recommended that surveillance of drug resistance occur in conjunction with scale-up efforts to ensure that appropriate first-line therapy is offered relative to the resistance that exists. However, standard resistance testing methods used in Sub-Saharan Africa rely on techniques that do not include low abundance DR variants (LADRVs) that have been documented to contribute to treatment failure. The use of next generation sequencing (NGS) has been shown to be more sensitive to LADRVS. We have carried out a preliminary investigation using NGS to determine the prevalence of LDRVS among a drug-naive population in North Rift Kenya. Antiretroviral-naive patients attending a care clinic in North Rift Kenya were requested to provide and with consent provided blood samples for DR analysis. DNA was extracted and amplified and nested PCR was conducted on the pol RT region using primers tagged with multiplex identifiers (MID). Resulting PCR amplicons were purified, quantified, and pyrosequenced using a GS FLX Titanium PicoTiterPlate (Roche). Valid pyrosequencing reads were aligned with HXB-2 and the frequency and distribution of nucleotide and amino acid changes were determined using an in-house Perl script. DR mutations were identified using the IAS-USA HIV DR mutation database. Sixty samples were successfully sequenced of which 26 were subtype A, 9 were subtype D, 2 were subtype C, and the remaining were recombinants. Forty-six (76.6%) had at least one drug resistance mutation, with 25 (41.6%) indicated as major and the remaining 21 (35%) indicated as minor. The most prevalent mutation was NRTI position K219Q/R (11/46, 24%) followed by NRTI M184V (5/46, 11%) and NNRTI K103N (4/46, 9%). Our use of NGS technology revealed a high prevalence of LADRVs among drug-naive populations in Kenya, a region with predominantly non-B subtypes. The impact of these mutations on the clinical outcome of ART can be ascertained only through long-term follow-up.

Background: The Government of Kenya started offering ART in the public sector since 2003. Despite the dramatic reduction in AIDS related morbidity and mortality, the emergence and spread of drug resistance (DR) threatens to negatively impact on treatment regimens and compromise efforts to control the epidemic. Therefore, there is a need for information on the situation of DR Mutations (DRMS) and their implications on treatment.

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 ( 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 RD 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.

Introduction : Antiretroviral therapy plays a major role in reducing the impact of Human Immunodeficiency Virus/Acquired Immune Disease Syndrome, especially in resource-limited settings. However, without proper infrastructure, it has resulted in emergence of drug resistance mutations in infected populations. To determine drug resistance mutations among patients attending a comprehensive care facility in Nairobi, 65 blood samples were successfully sequenced. Methods : Whole blood samples were also tested for CD4+T-cell count and plasma HIV-1 RNA Viral load. Drug-resistance testing targeting the HIV-1 RT gene was determined. Patients were on first line ART that consisted of two NRTIs, and one NNRTI. Results : Females were younger (mean 42) than males (mean 45) and lower median CD4+ counts (139 cells/μl) than males (152 cells/μl). The prevalence of drug resistance mutations (any major mutation) in this population was 23.1% (15/65). Major NRTI mutations were detected in 11 patient samples, which included M184V (n = 6), M41L (n=3), D67N (n=2), K219Q (n=3) and T215F (n=2). Major NNRTI mutations were detected in 14 patient samples. They included K103N (n = 10), G190A (n = 1), Y181C (n = 1) and Y188L (n = 1). Conclusion : Presence of major mutations in this study calls for proper laboratory infrastructure to monitor treatment as well as regular appraisals of available regimens.

Background: Human TP53 is the gatekeeper for generation of human cells and is highly conserved. Any alteration/mutation to TP53 adversely affects the regulatory function of the protein, potentially resulting in cancer. This study investigated mutations in codons 7 and 249 of TP53, among patients with hepatocellular carcinoma (HCC) and chronic hepatitis B virus (HBV) infection at the Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya. Methods: In total, 33 HBV-positive patients attending MTRH hospital between September 2013 and July 2017 were purposely selected from medical records for the study; those with HCC were confirmed from the cancer registry. The patients were aged between 25-67 years, with a male-to-female ratio of 1.1:1. Blood samples were collected from the patients. DNA was extracted, amplified and sequenced using TP53 forward and reverse primers. Gene mutation detection and analysis was done on exons 4 and 7 Results: Of the 33 patients, 75.8% were chronically infected with HBV and had HCC; the rest were HBsAg positive without HCC. Homozygous proline was prevalent (54.5%) at exon 4 codon 72, followed by heterozygous Arg/Pro (33.3%) and lastly homozygous Arg/Arg (12.1%,). Pro/Pro allele was frequent in HCC group while Arg/Arg allele was common in patients without HCC. There was no significant association between the HCC and codon polymorphisms (p=0.12). In exon 7, codon 249, 24.2% of patients had an Arg-Ser mutation of which, 75.0% had HCC and 25.0% did not. There was no significant association between HCC patients and codon 249 mutation (p=0.15). Conclusion: TP53 is a gene gate keeper, the mutations under study may dependently play a role in HCC development. This study did not find any association or clear mutational pattern between P53 mutations and HCC development. Therefore, TP53 mutation is a poor indicator for prognosis and a tumor’s biological behavior among HBV-positive subjects in Kenya.

A cross-sectional molecular epidemiological study of Giardia intestinalis infection was conducted among asymptomatic Kenyan children with (n = 123) and without (n = 111) HIV infection. G. intestinalis assemblage B infection was positively correlated with HIV infection [HIV (+), 18.7% vs. HIV (-), 11.7%; P = 0.013], whereas assemblage A infection was not [HIV (+), 4.1% vs. HIV (-), 6.3%; P = 0.510]. Thus, HIV infection is a risk factor for G. intestinalis assemblage B infection but not for assemblage A infection.

A cross-sectional molecular epidemiological study of Entamoeba species was conducted among asymptomatic Kenyan children with (n=123) and without (n=111) HIV infection. The prevalence of E. histolytica was low (0.4%). Entamoeba species infection was inversely related with HIV infection [HIV(+): 29.3% vs. HIV(-): 55.0%, P

HIV genetic recombination and high mutation rate increase diversity allowing it to escape from host immune response or antiretroviral drugs. This diversity has enabled specific viral subtypes to be predominant in specific regions. To determine HIV-1 subtypes among seropositive antenatal clinic attendees in Kenya's North Rift Valley, a cross-sectional study was carried out on 116 HIV-1-positive blood samples. Proviral DNA was extracted from peripheral blood mononuclear cells by DNAzol lysis and ethanol precipitation. Polymerase chain reactions using specific primers for HIV-1 gag and population sequencing on resulting amplicons were carried out. Phylogenetic analysis revealed that 81 (70%) were subtype A1, 13 (11%) subtype D, 8 (7%) subtype C, 3 (3%) subtype A2, 1 (1%) subtype G, and 10 showed possible recombinants: 5 (4%) subtype A1D, 4 (3%) subtype A1C, and 1 (1%) subtype A2C. These data support the need to establish circulating subtypes for better evaluation of effective HIV diagnostic and treatment options in Kenya.

Human immunodeficiency virus 1 (HIV-1) infection is characterized by genetic diversity such that specific viral subtypes are predominant in specific geographic areas. To determine circulating subtypes of HIV-1 in different parts of central Kenya, a cross-sectional study was carried out on HIV-1-positive blood samples collected from consenting individuals in eight hospitals of Kenya's central province. Proviral DNA was extracted from peripheral blood mononuclear cells. Polymerase chain reaction and direct sequencing using primers generated from a highly conserved region of HIV-1 env gp41 were carried out. Ninety-six samples were successfully amplified and sequenced. Analysis of the sequences showed that a majority of them belonged to subtype A1 (67/96, 69.8%), followed by subtypes D (18, 18.7%) and C (11/96, 11.5%). Consistent with findings in other parts of Kenya, HIV-1 subtype A1 was the most dominant virus in circulation. Continued surveillance of circulating subtypes of HIV-1 in Kenya is important in determining the evolution of the HIV/AIDS epidemic in Kenya.

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 1.5 log10 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. © 2011 Elsevier B.V. All rights reserved.

Monitoring the distribution of HIV-1 subtypes and recombinants among infected individuals has become a priority in HIV therapy. A laboratory analysis of samples collected from HIV-positive patients attending an STI clinic in Nairobi was done between March and May 2004. PCR was carried out on pol (intergrase) and env (C2V3) regions and resulting data on the 54 samples successfully analyzed revealed the following as circulating subtypes: 35/54(65%) were A1/A1, 5/54(9%) were A/C, 4/54 (7%) were A1/D, 1/54 (2%) was C/D, 1/54 (2%) was D/D, 1/54 (2%) was A1/A2, 1/54 (2%)was G/G, 1/54 (2%) was A2/D, 1/54 (2%) was C/C, and 4/54 (7%) were CRF02_ AG. The results show an increase in HIV-1 recombinants with the emergence of A1/A2 and an increase in CRF02_AG recombinants. Subtype diversity in the advent of ARV use will impact negatively on treatment outcomes. As such, increased viral evolution and recombination will call for continuous evaluation of available anti-HIV regimens for better management of those infected with HIV-1.

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 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 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.

To investigate the route of zoonotic transmission of HIV-1, we isolated three and seven HIV-1 strains from 449 Pygmy hunter gatherers and 169 neighboring Bantu, respectively, in southern Cameroon. Phylogenetic analysis based on pol-integrase and env-C2V3 sequences revealed that strains from Pygmies were 1 CRF02_AG/CRF02_AG, 1 subtype G/CRF02_AG (pol/env), and 1 CRF11_cpx/CRF11_cpx, and that those from Bantu were 2 CRF02_AG/CRF02_AG, 1 CRF02_AG/CRF01_AE/A, 1 CRF02_AG/subtype A, 1 G/A, 1 G/CRF02_AG, and 1 unclassified/H. CRF02_AG and CRF11_cpx have been identified in Cameroon. The results suggest that HIV-1 has been introduced into Pygmies through their neighboring Bantu rather than directly from nonhuman primates.

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.

In their meta-analysis V Bhargavi Rao and colleagues assessed the seroprevalence of hepatitis C virus (HCV) infection among sub-Saharan populations including HIV-positive adults. Their fi ndings delineate regional variation for estimated levels of infection and outline possible trends in HCV evolution in countries with previously described seroprevalence data. A limitation of this and other reviews covering this region is that they often have to rely on studies that use only screening assays for which the initial reactive anti-HCV results are rarely scrutinised by confi rmatory immunoblot tests. Crossreactivity due to higher infection rates for syphilis, HIV, malaria, and schistosomiasis, compounded by technical challenges related to the quality of screening kits, sample storage, and proper interpretation of weak positive test results all contribute to falsepositive outcomes in resource-scarce settings. There fore, data from studies reporting initial anti-HCV reactive samples without further confi rmatory testing by immunoblot or PCR assays should be regarded as ambiguous evidence of seroreactivity rather than true seroprevalence. A fi tting example of this is our experience with HCV prevalence in high-risk and low-risk cohorts in Kenya (table), in which none of the initially anti-HCV screen positive results were confi rmed by immunoblot and PCR testing. In particular, we noted initial high seroreactivity in two cohorts of female sex workers, each one consisting roughly of 100 participants, from whom two consecutive samples were collected about 5 years apart. Although the level of infection with hepatitis B virus was quite high, especially for the fi rst cohort (data not shown), this was not the case for HCV—of 62 participants who were initially anti-HCV screen positive, none were confi rmed anti-HCV by immunoblot and PCR. Most of these initial results were only weakly positive with signal-to-cutoff ratios of less than 3·0 and therefore, unsurprisingly, confi rmatory testing was not successful. We believe Rao and colleagues might have overestimated HCV seroprevalence in HIV-positive cohorts in Kenya, because only two of seven studies included in their meta-analysis claimed confi rmatory testing was used but no specifi c immunoblot results were provided for either of those studies. Drug injecting is a known risk factor for blood-borne viruses, hence the high HCV seroprevalence reported in the drug-user cohort is not surprising; however, sexual transmission remains the major method of HIV spread in Kenya and the surrounding region. Therefore the inclusion of this study in the metaanalysis might have also contributed to the high HIV and HCV co-infection estimate for Kenya.

Background CCR5 antagonists have clinically been approved for prevention or treatment of HIV/AIDS. Countries in Sub-Saharan Africa with the highest burden of HIV/AIDS are due to adopt these regimens. However, HIV-1 can also use CXCR4 as a co-receptor. There is hence an urgent need to map out cellular tropism of a country’s circulating HIV strains to guide the impending use of CCR5 antagonists. Objectives To determine HIV-1 coreceptor usage among patients attending a comprehensive care centre in Nairobi, Kenya. Methods Blood samples were obtained from HIV infected patients attending the comprehensive care centre, Kenyatta National Hospital in years 2008 and 2009. The samples were separated into plasma and peripheral blood mononuclear cells (PBMCs). Proviral DNA was extracted from PBMCs and Polymerase Chain reaction (PCR) done to amplify the HIV env fragment spanning the C2-V3 region. The resultant fragment was directly sequenced on an automated sequencer (ABI, 3100). Co-receptor prediction of the env sequences was done using Geno2pheno[co-receptor], and phylogenetic relationships determined using CLUSTALW and Neighbor Joining method. Results A total of 67 samples (46 treatment experienced and 21 treatment naive) were successfully amplified and sequenced. Forty nine (73%) sequences showed a prediction for R5 tropism while 18(27%) were X4 tropic. Phylogenetic analysis showed that 46(69%) were subtype A, 11(16%) subtype C, and 10(15%) subtype D. No statistical significant associations were observed between cell tropism and CD4+ status, patient gender, age, or treatment option. There was a tendency for more X4 tropic strains being in the treatment experienced group than the naive group: Of 46 treatment experiencing participants, 14(30%) harboured X4, compared with 4(19%) of 21 of the treatment-naïve participants, the association is however not statistically significant (p = 0.31). However, a strong association was observed between subtype D and CXCR4 co- receptor usage (p = 0.015) with 6(60%) of the 10 subtype D being X4 tropic and 4(40%) R5 tropic. Conclusion HIV-1 R5 tropic strains were the most prevalent in the study population and HIV infected patients in Kenya may benefit from CCR5 antagonists. However, there is need for caution where subtype D infection is suspected or where antiretroviral salvage therapy is indicated.

To identify novel biomarkers for HIV-1 resistance, including pathways that may be critical in anti-HIV-1 vaccine design, we carried out a gene expression analysis on blood samples obtained from HIV-1 highly exposed seronegatives (HESN) from a commercial sex worker cohort in Nairobi and compared their profiles to HIV-1 negative controls. Whole blood samples were collected from 43 HIV-1 resistant sex workers and a similar number of controls. Total RNA was extracted and hybridized to the Affymetrix HUG 133 Plus 2.0 micro arrays (Affymetrix, Santa Clara CA). Output data was analysed through ArrayAssist software (Agilent, San Jose CA). More than 2,274 probe sets were differentially expressed in the HESN as compared to the control group (fold change ≥1.3; p value ≤0.0001, FDR

Background Design of effective vaccines against the human immunodeficiency virus (HIV-1) continues to present formidable challenges. However, individuals who are exposed HIV-1 but do not get infected may reveal correlates of protection that may inform on effective vaccine design. A preliminary gene expression analysis of HIV resistant female sex workers (HIV-R) suggested a high expression CD26/DPPIV gene. Previous studies have indicated an anti-HIV effect of high CD26/DPPIV expressing cells in vitro. Similarly, high CD26/DPPIV protein levels in vivo have been shown to be a risk factor for type 2 diabetes. We carried out a study to confirm if the high CD26/DPPIV gene expression among the HIV-R were concordant with high blood protein levels and its correlation with clinical type 2 diabetes and other perturbations in the insulin signaling pathway. Results A quantitative CD26/DPPIV plasma analysis from 100 HIV-R, 100 HIV infected (HIV +) and 100 HIV negative controls (HIV Neg) showed a significantly elevated CD26/DPPIV concentration among the HIV-R group (mean 1315 ng/ml) than the HIV Neg (910 ng/ml) and HIV + (870 ng/ml, p < 0.001). Similarly a FACs analysis of cell associated DPPIV (CD26) revealed a higher CD26/DPPIV expression on CD4+ T-cells derived from HIV-R than from the HIV+ (90.30% vs 80.90 p = 0.002) and HIV Neg controls (90.30% vs 82.30 p < 0.001) respectively. A further comparison of the mean fluorescent intensity (MFI) of CD26/DPPIV expression showed a higher DPP4 MFI on HIV-R CD4+ T cells (median 118 vs 91 for HIV-Neg, p = 0.0003). An evaluation for hyperglycemia, did not confirm Type 2 diabetes but an impaired fasting glucose condition (5.775 mmol/L). A follow-up quantitative PCR analysis of the insulin signaling pathway genes showed a down expression of NFκB, a central mediator of the immune response and activator of HIV-1 transcription. Conclusion HIV resistant sex workers have a high expression of CD26/DPPIV in tandem with lowered immune activation markers. This may suggest a novel role for CD26/DPPIV in protection against HIV infection in vivo.

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.

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.

Background The HIV/AIDS epidemic in Kenya is a major public-health problem. Estimating the prevalence of HIV in pregnant women provides essential information for an effective implementation of HIV/AIDS control measures and monitoring of HIV spread within a country. The objective of this study was to determine the prevalence of HIV infection, risk factors for HIV/AIDS and immunologic (lymphocyte profile) characteristics among pregnant women attending antenatal clinics in three district hospitals in North-Rift, Kenya. Methods Blood samples were collected from pregnant women attending antenatal clinics in three district hospitals (Kitale, Kapsabet and Nandi Hills) after informed consent and pre-test counseling. The samples were tested for HIV antibodies as per the guidelines laid down by Ministry of Health, Kenya. A structured pretested questionnaire was used to obtain demographic data. Lymphocyte subset counts were quantified by standard flow cytometry. Results Of the 4638 pregnant women tested, 309 (6.7%) were HIV seropositive. The majority (85.1%) of the antenatal attendees did not know their HIV status prior to visiting the clinic for antenatal care. The highest proportion of HIV infected women was in the age group 21–25 years (35.5%). The 31–35 age group had the highest (8.5%) HIV prevalence, while women aged more than 35 years had the lowest (2.5%). Women in a polygamous relationship were significantly more likely to be HIV infected as compared to those in a monogamous relationship (p = 0.000). The highest HIV prevalence (6.3%) was recorded among antenatal attendees who had attended secondary schools followed by those with primary and tertiary level of education (6% and 5% respectively). However, there was no significant relationship between HIV seropositivity and the level of education (p = 0.653 and p = 0.469 for secondary and tertiary respectively). The mean CD4 count was 466 cells/mm3 (9–2000 cells/mm3). Those that had less than 200 cells/mm3 accounted for 14% and only nine were on antiretroviral therapy. Conclusion Seroprevalence of HIV was found to be consistent with the reports from the national HIV sentinel surveys. Enumeration of T-lymphocyte (CD4/8) should be carried out routinely in the antenatal clinics for proper timing of initiation of antiretroviral therapy among HIV infected pregnant women.

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.

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.

金沢大学大学院医学系研究科感染症制御学, Recently increased availability of antiretroviral 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_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. © 2007 Wiley-Liss, Inc.

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 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. © 2015 Saina et al.

Circulating strains of human immunodeficiency virus (HIV) exhibit an extraordinary degree of genetic diversity and have been classified on the basis of relationships into distinct lineages called groups, types, subtypes, and subsubtypes. Sexually transmitted infections (STIs) are known to be a risk factor for HIV infection. To establish HIV-1 subtype diversity among STI patients in Nairobi, 140 samples were collected and partial pol gene sequencing done. From the analysis it was established that subtype A1 was the major subtype (64%) followed by D (17%), C (9%), G (1%), and recombinants AD (4%), AC (3%), CRF02()AG (1%), and CRF16()A2D (1%). These results suggest that the HIV-1 epidemic may be evolving toward more virulent and complex subtypes through transmission of complex recombinants due to viral mixing. Any use of ARVs may therefore require initial testing for de novo resistance before commencement of treatment and/or management.

To monitor the presence of genotypic HIV-1 variants circulating in eastern Cameroon, blood samples from 57 HIV-1-infected individuals attending 3 local health centers in the bordering rural villages with Central African Republic (CAR) were collected and analyzed phylogenetically. Out of the 40 HIV-1 strains with positive polymerase chain reaction (PCR) profile for both gag and env-C2V3,12 (30.0%) had discordant subtype or CRF designation: 2 subtype B/A (gag/env), 1 B/CRF01, 2 B/CRF02, 1 CRF01/CRF01.A, 2 CRF11/CRF01, 1 CRF13/A, 1 CRF13/CRF01, 1 CRF13/CRF11, and 1 G/U (unclassified). Twenty-eight strains (70.0%) had concordant subtypes or CRF designation between gag and env: 27 subtype A and 1 F2. Out of the remaining 17HIV-1 strains negative for PCR with the env-C2V3 primers used, 10 (58.8%) had discordant subtype or CRF, and 7 (41.2%) had concordant one based on gag/pol/env-gp41 analysis. Altogether, a high proportion (22/57, 38.6%) of the isolates were found to be recombinant strains. In addition, an emergence of new forms of HIV-1 strains, such as subtype B/A (gag/env), B/CRF01 and B/CRF02, was identified. The epidemiologic pattern of HIV-1 in eastern Cameroon, relatively low and high prevalence of CRF02 and CRF11, respectively, was more closely related to those of CAR and Chad than that of other regions of Cameroon, where CRF02 is the most predominant HIV-1 strain. These findings strongly suggest that this part of Cameroon is a potential hotspot of HIV-1 recombination, with a likelihood of an active generation of new forms of HIV-1 variants, though epidemiologic significance of new HIV-1 forms is unknown.

The first diagnostic kits utilizing the enzyme-linked immunosorbent assay (ELISA) technique were developed in mid-eighties, and since then, this technique has become an increasingly important tool for screening multiple samples of blood or serum for presence of antibodies to various infectious pathogens, especially human immunodeficiency virus (HIV) in blood banks. However, most of the commercial diagnostic kits currently available in the market are too expensive, hence not easily affordable in most Diagnostic Laboratories. We designed an ELISA kit for diagnosis of HIV and compared it with some of the commercial kits. We used blood samples from the blood bank at the National Public Health Laboratory Services (NPHLS) in Nairobi and from patients referred to the Kenya Medical Research Institute (KEMRI) for HIV screening. Two commercial kits were used, Wellcozyme HIV Recombinant kit and Recombigen (env & gag) HIV-1 EIA kit. Out of 1350 samples tested by Recombigen (env & gag) HIV-1 EIA kit, 419 (31.0% ) were positive while 421 (31.2% ) samples were positive by Wellcozyme HIV Recombinant kit. Our ELISA kit detected a total of 431 positive samples out of 1350 (31.9% ), which was almost identical to the results from the other kits. Our kit was nearly identical in terms of sensitivity and specificity to the other two commercial kits used in this study. Thus our ELISA system, which is much cheaper than the commercial kits currently available in the market, offers a more affordable system for routine HIV tests.

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 (P0.001) and prenatal ZDV compliance (P0.003). 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.

Objective: To investigate the effects of short-course nucleoside reverse transcriptase inhibitor (Zidovudine, ZDW/AZT) on maternal immune responses and risk of infant infection with HIV-1 among rural-based mothers in western Kenya. Design: A prospective cohort study involving HIV-1 seropositive pregnant mothers and their infants. Subjects: One hundred and seven HIV-1 seropositive asymptomatic pregnant women and their infants. Methods: After informed consent, the women were enrolled at gestation age between 16-24 weeks. For cultural and economic reasons, all mothers were allowed to breast feed their infants. Short-course antepartum regime of AZT was administered to all mothers starting at 36 weeks gestation until start of labour. Maternal absolute CD4+ T cell subset assays were performed before 3rd trimester (about 36 weeks gestation) and after a 4-week therapy of AZT (at least one month post-nuptially). Infant HIV- 1 status was determined by HIV-1 DNA polymerase chain reaction (PCR) on samples sequentially taken at 1, 2, 3, 4, 6 and 9 months and confirmed by serology at 18 months of age. Interventions: Antepartum short-course orally administered AZT: 300mg twice-daily starting at 36 weeks gestation until start of labour, 300mg at labour onset and 300mg every three hours during labour until delivery. Main Outcome Measures: Maternal CD4+ T cell counts before and after AZT treatment. Determination of infant HIV-1 infection status. Results: Among 107 women sampled, only 59 received full dose of AZT and thus qualified for present analysis. Of these, 12 infected their children with HIV, while 47 did not. Comparison of CD4+ T cells before and after AZT treatment scored a significant rise in all mothers (P = 0.01). This increase in CD4+ T cells was not significant among mothers who infected their infants with HIV-1 (P = 0.474). However, a significant rise in CD4+ T cells following AZT therapy was observed only in mothers who did not transmit HIV-1 to their infants (P=0.014). Conclusion: These data suggest that a rise in the CD4+ T cell counts following short AZT regimen, now widely in use in resource-weak countries, may be evidence of the active suppression of the replication of HIV. However, further studies to examine the multi-factorial effect of CD4+ lymphocytes and pregnancy on MTCT of HIV need to be carried out to help fully explain the effect of AZT on immune response and whether the CD4+T cell count can be used as a true test of immunological normalisation during antiretroviral therapy.