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Seroprevalence of Chikungunya, West Nile Virus and Dengue Virus in Febrile Patients visiting selected health facilities in Trans Nzoia County
No full textIntroduction: Arboviruses of the families Flaviviridae, Togaviridae and Bunyaviridae are suspected to be an important cause of morbidity in Western Kenya. However, literature on the exact burden of disease is scanty. Methods: We collected 1578 serum samples collected from febrile adults with no evidence of malaria or typhoid exposure visiting Andersen Medical Clinic, Endebess Sub District Hospital and Kitale District Hospital. We used indirect ELISAs to screen for exposure to Dengue, Chikungunya and West Nile Viruses, and Plaque Reduction Neutralisation Tests to confirm the status of those samples that were ELISA positive. Results: Data on gender was available for 899 samples. Of those, 63.3% were female while 36.7% were male. The median age was 28 years, while the mean temperature was 39.1°C. Common symptoms included rash (29.7%), headache (74.1%) jaundice (15.0%) and eye infection (20.9%). Bleeding diatheses were uncommon (0.8%). Of the samples we tested, 8.1% (127/1578) were CHIKV PRNT positive, 0.4% (6/1379) Dengue PRNT positive and 0.9% (12/1370) WNV Positive. Conclusion: Exposure to Chikungunya virus is common in Trans Nzoia and may be an important cause of febrile illness
Challenges and opportunities: A framework for analysis of metagenomic sequencing data
No full textBackground: Next-generation sequencing (NGS) allows the analysis of viral sequence variants from select natural environments, presenting a novel opportunity for understanding the genetic diversity present in these ecosystems, virus evolution and allows outbreaks to be followed in great detail. Objective: To gain a better understanding of the potential factors influencing the spread of viruses (in space and time) in small farm ecosystems, we are currently investigating how these viral species are evolving across their entire geographical distribution using a combination of Genomics and Bioinformatics approaches. Methodology: We have developed a bioinformatics pipeline for automating the analyses of viral metagenomes. Furthermore, we are currently developing an information (GISbased) system for collecting, analyzing and reporting of all viral data related to small farm ecosystems to supplement the computational pipeline. Application of these methodologies to viruses will make it possible to explore viral diversity through automatically constructed time-measured phylogenies and perform comparison against thier viromes. Results: This bioinformatics pipeline is designed to provide answers to questions such as when and where did an epidemic begin, how viral populations are genetically structured in space and what are the key determinants of viral spread between geographical regions? The answers to these questions provide insights into the potential factors underlying both the spatio-temporal dynamics and evolution of members of viral families and will help to inform governmental policy aimed at restricting the movements of diseased plant and animal materials and virus-carrying insects within and across national borders by identifying both key transmission routes and the locations in Africa where viruses with increased disease-causing potential commonly arise
Phylogenetic analysis of the envelope HIV-1 type 1 isolates among Kenyan cohort
No full textBackground: As the AIDS pandemic progresses, an increasingly broad range of genetic diversity continues to be reported within the main (M) group of HIV-1 viruses with viral subtype predominating in specific geographical areas. Objective: Determine the genetic diversity and trends of HIV-1 subtypes among Kenyan individuals. Methodology: One hundred and seventy six subjects (176) were recruited from five study sites in Nairobi and its environs. The viral DNA was extracted using Qiagen® MiniViral DNA isolation kit and target env–C2-V3 gene amplified by nested PCR. The amplified products were analysed by gel electrophoresis and visualized under UV light. The successfully amplified products were then labeled with a sequence dye in sequence PCR reaction using the Big Dye® sequence terminator kit (Applied Biosystem®) and the products purified by use of Qiagen purification kit before directly sequenced using an automated ABI 310 sequencer ( Applied Biosystem, Foster City CA). In RT gene (288bp) of viruses sequenced. Results: Analysis of the sequences showed that a majority of them belonged to subtype A1: 73.9% (130/176), followed by C: 10.8% (19/176), D: 9.7% (17/176), G, AIC and A2 1.1% (2/176) each and 2.3% (4/176) were unique recombinants forms. As from previous studies conducted in other parts of Kenya, HIV-1 subtype A1 still remains the most predominant subtype while subtype C continues to show an increasing prevalence. Conclusion: Continued surveillance of circulating subtypes of HIV-1 in Kenya is important in determining the evolution of the HIV/AIDS epidemic in Kenya
Phenotypic and Genotypic Diversity of Bunyamwera Virus
No full textIntroduction: Bunyamwera virus belongs to the genus Orthobunyavirus of the family Bunyaviridae, segmented RNA viruses whose members have the potential for genetic reassortment and/or drift. Although arbovirus mutant spectra have been observed in nature, the diversity within the spectra is not well described, and the phenotypic roles of minority RNAs are unknown. Moreover, traditional sequencing methods generally detect the master sequences as consensus sequences. Understanding the mutation distribution in a heterogeneous arbovirus population is thus important, given that any variant can be favoured by selection and ultimately affects fitness. Objective: To evaluate phenotypic and genotypic diversity of Bunyamwera virus isolates obtained from diverse geographic space, time and vector species in Kenya Methods: Seven Bunyamwera viral strains isolated from previous GEIS surveillance exercises in Ijara, Garissa and Magadi from diverse mosquito species and sites at different times were cultured in Vero cells to prepare viral stocks for experimentation. Plaque assay was used to identify and purify clonal population of the virus based on plaque sizes. Bunyamwera-specific primers were used to amplify the S, M and L segments of the virus phenotypes. Results: The wild type of 6/7 viruses was composed of two major phenotypes; small plaque (SP) (0.468–0.656 mm) and large plaque (LP) (0.875–1.210 mm). One isolate consisted of a homogeneous SP size (0.305–0.372 mm). The plaque sizes were significantly different. Five isolates had plaque variants with similar S genotype as the wild type (Wt) using degenerate S primer. However, using Bunyamwera S segment-specific primers, only two samples constituted variants similar to the Wt. Three SP and two LP variants of four isolates failed to amplify with M segment-specific primer indicating possible co-circulation with another virus. Conclusions: There is need to improve arboviral surveillance methods to include detection of circulating minority variants. There is need for complete genome sequencing of the plaque variants and comparison to the consensus sequence of the parental wild type to identify mutations that could be responsible for the observed phenotypic differences
Automated real time detection of Arboviruses in culture
No full textBackground: Major methods of isolating and identifying arboviruses viruses from human and vector populations are tissue culture – based. Viral growth in culture is monitored by the detection of cytopathic effects (CPE) by microscopy. Some viruses do not cause visible CPE or have delayed CPE and can easily be missed because the assay is subjective and tedious. Host cell anomalies can mask or mimic true CPE. Cell culture assays are also limited by the difficulty in identifying novel or multiple infections, the high cost of culture reagents, and the ability to perform adequate quality controls. Objective: The automated XCELLigence system (Roche) uses plates lined with electrodes to continuously measure changes in electric impedance in cultured cells. This system was tested to validate its utility in addressing the challenges associated with cell-culture based assays. Methodology: Viruses were inoculated into VERO (green monkey kidney) cells in 96-well or 24-well plates and incubated at 37°C in a humidified CO2 incubator. Cells were monitored for CPE using the XCELLigence system in real-time or daily by microscopy. For the neutralization test viruses were serially diluted and combined with -positive serum, incubated for 30 minutes, inoculated onto VERO cells and monitored after using plaque assays after 3 days or the xCELLigence system. Results: On xCELLigence®, CPE was detected earlier than by microscopic with a signature proliferation profile that could be distinguished from cellular anomalies and other virus profiles and required only ~5 minutes of staff time daily to monitor. The automated methods for virus detection and neutralization gave more consistent and reliable results compared to the conventional assay, had internal quality control capabilities, and minimized reagent use significantly. Conclusions: Automated monitoring of virus cultures improves reproducibility and early virus detection, reduces staff time and error, provides quality control for cell lines and allows for virus quantification
Influenza in the East African Region
No full textPrior to 2006, little was known on influenza surveillance in the East African region. With the detection of avian influenza A (H5N1) in Africa, several countries in Africa started initiating influenza sentinel surveillance systems. We evaluated both published and unpublished literature to determine seasonal patterns and estimate burden of influenza in the East African region. Annually influenza has been observed to be associated with 9-25% of ILI outpatient visits and 5-10% of SARI hospitalizations in East Africa. Influenza circulates all year round peaking in the months of March to November. Most of the cases reported are children below five years of age. Despite the region having mostly a young population, and poor health seeking behavior, rates from this region are comparable to those seen in temperate countries. Seasonal vaccination using southern hemisphere vaccine in March may be more effective. Targeting selected populations of young children and pregnant women for influenza vaccination may be effective in controlling morbidity and mortality associated with influenza. Modification to the surveillance tools should be made to identify risk factors that may be present in the elderly population currently missed by the current surveillance system
The Arbovirus menace in Kenya; are we doing enough to stem it?
No full textIntroduction: Arthropod-borne viruses (arboviruses) cause many diseases worldwide and constitute a major group of the world’s emerging infectious disease problem. They are transmitted biologically among vertebrate hosts by hematophagous arthropod vectors such as mosquitoes and other biting flies, and ticks. Ecology: Most arboviruses circulate in Kenya among wild animals, and many cause disease following spillover transmission to humans and agricultural/commercial domestic animals that serve as incidental or dead-end hosts e.g RVF, YF, CCHF and WN. Another risk of arboviral emergence stems from tropical urbanization and the colonization and expanding habitat by the highly anthropophilic Aedes aegypti mosquito which has led to the emergence of endemic cycles of urban DEN and CHIK viruses. Arbovirus distribution, like other vector-borne diseases vary in space and time, related to the ecology of the vector species, particularly at their immature stage, virus evolution, in some cases the ecology of the reservoir host and their transmission is likely to change with land use, socioeconomic and climate changes. The increasing frequency of other hemorrhagic fever outbreaks including ebola and marburg in East Africa in the absence of sufficient data on the virus ecology presents additional challenge that we are yet to learn to cope with. Kenyan’s historical perspective: Between the 1950s and early1980s devastating arbovirus outbreaks including RVF, YF, ONN, CHIK, DEN stimulated a lot of research and surveillance in E. Africa leading to accumulation of extensive data, knowledge and African arbovirus repositories which exist to this day in the developed North. This was followed by a lull when attention and focus in funding and interest in virology shifted to HIV/AIDS at the start of the pandemic in early 1980s. The first outbreak of YF in Kenya 1993-95 and the devastating outbreak of RVF that swept across the East African region in 1997/98 brought about the realization that Arboviruses had re-emerged in the region all over again and this has re-energized arbovirus research and surveillance activities in the region. The recent outbreaks have provided opportunities for research and training for indigenous researchers and students. New knowledge has been added to what exists in terms of disease ecology, prevention, control, diagnosis and management. There are still gaps that are yet to be filled and the involvement of East African researchers and public health officers will be crucial in ensuring a real state of preparedness as we face the challenge of arbovirus outbreaks in to the future
A spatially-explicit simulation model of Rift Valley fever transmission
No full textBackground: Rift Valley fever (RVF) is an acute mosquito-borne viral zoonosis that causes periodic epizootics in sub-Saharan Africa. It mainly affects sheep, goats, cattle and camels. The epidemiology of the disease is poorly understood. This is partly because its transmission involves multiple vectors and hosts. Objective: The aim of this study was to develop a simulation model to evaluate processes involved in the occurrence and transmission of the RVF virus (RVFv). Methodology: The model involves two hosts (cattle and sheep) and two vectors (Aedes spp. and Culex spp.). Host dynamics are simulated using an individual-based model while vectors dynamics are simulated using compartmental model. Hosts’ characteristics and how they utilize their environment are programmed using static and dynamic rules. These are implemented in C++ programming language. The landscape on which the simulated processes take place is subdivided into spatial lattices of 500 x 500 m using a grid. Results: Simulations are carried out for the period 1990 – 2010. Initial model outputs captures the main outbreaks observed in 1997/98 and 2006/7. It also shows some inter-epidemic virus activity during the wet seasons. The model predicts that the incidence of the virus is higher in sheep than in cattle. Inter-epidemic virus transmission events do not, expectedly, get amplified to epidemic levels. Conclusions: The inter-epidemic virus activity is attributed to the emergence of Aedes mosquitoes which does not lead to epidemics. This is mainly because the vector population does not rise due to absence of flooding. The results could be used to assess processes that support RVF persistence and effectiveness of RVF interventions
Seroprevalence of Hepatitis B among HIV Infected Persons Receiving Care in a HIV Clinic in Kisumu Kenya
No full textBackground: Hepatitis B infection among HIV infected persons is of clinical importance because it’s a leading cause of morbidity and mortality. Hepatitis B leads to liver cirrhosis and liver cancer. In Kenya Hepatitis B testing is not presently part of routine care for HIV infected patients despite that HIV increases the progression of HBV related liver disease due to immunosuppression. Objective: To determine the seroprevalence of Hepatitis B virus infection and Alanine aminotransferase; ALT levels among HIV infected persons in a HIV care clinic. Methodology: Cross-sectional descriptive study conducted at Family Aids Care and Education Services (FACES) Kisumu, Kenya. A sample size of 136 HIV infected persons above the age of 18 years were recruited. A questionnaire collecting information on the socio demographic characteristic and exposure factors to Hepatitis B infection was administered, 4mls of blood was collected for the detection of HBsAg (Hepatitis B surface Antigens) by Enzyme Immunoassay with the Murex HBsAg kit. The ALT test was done using COBAS INTEGRAL® 400 plus, Roche. Statistical analysis was done using SPSS v.16. Results: The seroprevalence of Hepatitis B infection among HIV infected persons was 13%. Patients with elevated liver enzyme ALT among HIV/HBV co infected persons was 11.76%. A possible association between elevated ALT and Hepatitis B was found (Fishers exact test p=0.044). Exposure factors such as lack of vaccination and having more than one sexual partner were considered to be significantly associated with the Infection ( P<0.005) Conclusion: There is need for increased screening and awareness of HBV infection for individuals who are HIV positive as the prevalence of the Hepatitis B infection is comparatively high as compared to the prevalence of HBsAg in the general population. The government through the ministry of medical services should look into the policy of making vaccination against Hepatitis B accessible
Antiretroviral therapy monitoring among HIV-1 vertically infected children: implications of long term treatment on disease progression
No full textBackground: Antiretroviral therapy (ART) has mitigated the impact of HIV-1/AIDS among infected individuals in resource-poor settings. However, ART failure due to treatment interruption, bad adherence and emergence of drug resistance mutations has been a negative consequence. According to revised world health organization treatment guidelines in 2010, once a patient is found to be failing ART, change of regimen should be considered. Objective: To determine response to ART and evaluate the outcome among HIV-1 vertically-infected Kenyan children, Methodology: This was a longitudinal study involving 103 children. CD4+T-cell counts and plasma HIV-1 RNA load (VL) were determined biannually using the FACS caliber machine (Becton Dickinson) and Amplicor version 1.5, respectively, according to the manufacturers’ instructions. Further, drug-resistance mutations in the HIV pol gene were determined using an in-house protocol and results analyzed by comparing the mutations with the latest International AIDS Society (2011) mutation list and the Stanford University HIV database. Results: After an average of 4.2±2.0 years, 43 (41.7%) children failed first-line ART (VL＞5000 copies/ml) and changed to second-line regimen. A further follow up of those on second-line treatment showed one child (2.3%) with ART failure after 3.7±1.1 years. The remaining 60 children were on first-line ART for an average of 6.5±2.4 years. Of these, four had detectable viral load with emergence of drug resistance mutations. Conclusion: Even though the children failed first-line ART, second-line regimen was effective enough (97.7% treatment success in 3.7 years). With proper monitoring, ART among children in these settings is feasible and comparable to adults. However, salvage therapy options remain a challenge