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Salivary protein polymorphism in Kenya: evidence for a new AMY1 allele.

Salivary protein polymorphism was studied in 200 schoolboys, mainly Kisii and Luo from Kenya, East Africa. The frequencies of PR, PA, DB, PB and AMY1 genes were as follows: PR*1: 0.66, PA*(+): 0.18, DB*(+): 0.55, PB*2: 0.12, AMY1*A2: 0.008, AMY1*E: 0.03. These frequencies were compared with other population data, in particular from West African and US Negroes. The most interesting finding with respect to the gene frequencies is the low PB*2 frequency and the absence of AMY1*3 in Kenya. Furthermore, a new phenotype in the AMY1 system was described which suggests the presence of an allele with an estimated frequency of 0.02.

Adolescent↗

Dental fluorosis in an area of Kenya with 2 ppm fluoride in the drinking water.

We examined 102 children born and reared in an area of rural Kenya with 2 ppm fluoride in the drinking water for dental fluorosis, using the index developed by Thylstrup and Fejerskov (1978). The prevalence of dental fluorosis was 100%, 92% of all teeth exhibited a TFI score of 4 or higher, and 50% of the children had pitting or more severe enamel damage in at least half the teeth present. The fluorotic changes showed a high degree of bilateral symmetry. The intra-oral distribution of the changes corresponded to the pattern of fluoride-induced enamel changes reported by other investigators in high-fluoride areas. The high prevalence and severity of dental fluorosis in a 2-ppm-fluoride area is in accordance with recent observations on dental fluorosis being very prevalent in Kenya, even in low-fluoride areas (less than 1 ppm F). We are presently investigating the possible variables which may explain this unexpected susceptibility of large populations in Eastern Africa to fluorosis from exposure to low levels of fluoride.

Adolescent↗

Conformity and change: community effects on female genital cutting in Kenya.

In this article, I analyze women's decisions to have their daughters circumcised based on data from 7,873 women in Kenya collected in the 1998 Kenya Demographic and Health Survey. I use multilevel models to assess the degree to which women s decisions are correlated with the decisions of other women in their community, in addition to studying the effects of socioeconomic characteristics measured at both the individual and community levels. I find some support for modernization theories, which argue that economic development leads to gradual erosion of the practice of female circumcision. However, more community-level variation is explained by the convention hypothesis, which proposes that the prevalence of female circumcision will decline rapidly once parents see that a critical mass of other parents have stopped circumcising their daughters. I also find substantial variation among different ethnic groups in the pace and onset of the decline of female genital cutting.

Adolescent↗

The demographic transition in Kenya: a portent for Africa?

It is contended that issues of population growth will continue to be an important frontier of international health. Kenya's case is examined and its achievements in arresting its population growth are analyzed. The case is made that Kenya's experience is transferable to other countries in Africa.

Adult↗

Rabies among African wild dogs (Lycaon pictus) in the Masai Mara, Kenya.

A pack of African wild dogs (Lycaon pictus) ranging to the north of the Masai Mara National Reserve in southwestern Kenya was monitored from 1988 to 1989. During a 6-week period (August 1-September 13, 1989), 21 of 23 members of this pack died. Seven carcasses were retrieved, of which 4 were suitable for necropsy and histopathologic examination. Gross findings varied among individuals and included multiple bite wounds, synovitis, lymphadenopathy, submandibular, cervical, and vocal cord edema, blood in bronchi, bronchioles, stomach, and intestine, and interioventral lung lobe consolidation. Histologic examination of 2 available brain samples revealed nonsuppurative encephalitis with eosinophilic intracytoplasmic inclusions (Negri bodies). An additional brain sample tested positive for rabies via a fluorescent antibody test. Other histologic features included severe suppurative bronchopneumonia, myocarditis, and lymphoid depletion of the lymph nodes, tonsils, and spleen. A 304-base pair (bp) nucleotide sequence from the N gene and a 310-bp sequence from the G gene from rabies isolates of 4 wild dogs indicated that infection was with a rabies variant common among domestic dogs in Kenya and Tanzania.

Animals↗

Stability of salt double-fortified with ferrous fumarate and potassium iodate or iodide under storage and distribution conditions in Kenya.

The stability of table salt double-fortified with iron as ferrous fumarate, and with iodine as potassium iodide or potassium iodate, has been investigated under actual field conditions of storage and distribution in the coastal and highland regions of Kenya. Seven 200-g sample packets of double-fortified salt in sealed polyethylene bags and a similar packet containing a datalogger for monitoring temperature and humidity were packaged with 21 sample bags of salt from another study into a bundle, which then entered the distribution network from a salt manufacturer's facility to the consumer. Iodine retention values of up to 90% or more were obtained during the three-month study. Double-fortified salt was prepared using ferrous fumarate microencapsulated with a combination of binders and coloring agents and coated with soy stearine, in combination with either iodated salt or salt iodized with potassium iodide microencapsulated with dextrin and coated with soy stearine. Most of the ferrous iron was retained, with less than 17% being oxidized to the ferric state. The polyethylene film overwrap of salt packs in the bundles provided significant protection from ambient humidity. Salt double-fortified with iodine and microencapsulated iron ferrous fumarate premix was generally quite stable, because both iodine and ferrous iron were protected during distribution and retail in typical tropical conditions in Kenya's highlands and humid lowlands.

Anemia, Iron-Deficiency↗

Field assessments in western Kenya link malaria vectors to environmentally disturbed habitats during the dry season.

BACKGROUND: Numerous malaria epidemics have occurred in western Kenya, with increasing frequency over the past 20 years. A variety of hypotheses on the etiology of these epidemics have been put forth, with different implications for surveillance and control. We investigated the ecological and socioeconomic factors promoting highland malaria vectors in the dry season after the 2002 epidemic. METHODS: Investigations were conducted in Kisii District during the dry season. Aquatic habitats in were surveyed for presence of malaria vectors. Brick-making pits were further investigated for co-associations of larval densities with emergent vegetation, habitat age, and predator diversity. Indoor spray catches were completed in houses near aquatic habitats. Participatory rural appraisals (PRAs) were conducted with 147 community members. RESULTS: The most abundant habitat type containing Anopheles larvae was brick-making pits. Vegetation and habitat age were positively associated with predator diversity, and negatively associated with mosquito density. Indoor spray catches found that houses close to brick-making sites had malaria vectors, whereas those next to swamps did not. PRAs revealed that brick-making has grown rapidly in highland swamps due to a variety of socioeconomic pressures in the region. CONCLUSION: Brick-making, an important economic activity, also generates dry season habitats for malaria vectors in western Kenya. Specifically, functional brick making pits contain less that 50% as many predator taxa and greater than 50% more mosquito larvae when compared with nearby abandoned brick making pits. Further evaluations of these disturbed, man-made habitats in the wet season may provide information important for malaria surveillance and control.

Animals↗

Immunization coverage and risk factors for failure to immunize within the Expanded Programme on Immunization in Kenya after introduction of new Haemophilus influenzae type b and hepatitis b virus antigens.

BACKGROUND: Kenya introduced a pentavalent vaccine including the DTP, Haemophilus influenzae type b and hepatitis b virus antigens in Nov 2001 and strengthened immunization services. We estimated immunization coverage before and after introduction, timeliness of vaccination and risk factors for failure to immunize in Kilifi district, Kenya. METHODS: In Nov 2002 we performed WHO cluster-sample surveys of >200 children scheduled for vaccination before or after introduction of pentavalent vaccine. In Mar 2004 we conducted a simple random sample (SRS) survey of 204 children aged 9-23 months. Coverage was estimated by inverse Kaplan-Meier survival analysis of vaccine-card and mothers' recall data and corroborated by reviewing administrative records from national and provincial vaccine stores. The contribution to timely immunization of distance from clinic, seasonal rainfall, mother's age, and family size was estimated by a proportional hazards model. RESULTS: Immunization coverage for three DTP and pentavalent doses was 100% before and 91% after pentavalent vaccine introduction, respectively. By SRS survey, coverage was 88% for three pentavalent doses. The median age at first, second and third vaccine dose was 8, 13 and 18 weeks. Vials dispatched to Kilifi District during 2001-2003 would provide three immunizations for 92% of the birth cohort. Immunization rate ratios were reduced with every kilometre of distance from home to vaccine clinic (HR 0.95, CI 0.91-1.00), rainy seasons (HR 0.73, 95% CI 0.61-0.89) and family size, increasing progressively up to 4 children (HR 0.55, 95% CI 0.41-0.73). CONCLUSION: Vaccine coverage was high before and after introduction of pentavalent vaccine, but most doses were given late. Coverage is limited by seasonal factors and family size.

Child Health Services↗

The relationship between the Plasmodium falciparum parasite ratio in childhood and climate estimates of malaria transmission in Kenya.

BACKGROUND: Plasmodium falciparum morbid and fatal risks are considerably higher in areas supporting parasite prevalence > or =25%, when compared with low transmission areas supporting parasite prevalence below 25%. Recent descriptions of the health impacts of malaria in Africa are based upon categorical descriptions of a climate-driven fuzzy model of suitability (FCS) for stable transmission developed by the Mapping Malaria Risk in Africa collaboration (MARA). METHODS: An electronic and national search was undertaken to identify community-based parasite prevalence surveys in Kenya. Data from these surveys were matched using ArcView 3.2 to extract spatially congruent estimates of the FCS values generated by the MARA model. Levels of agreement between three classes used during recent continental burden estimations of parasite prevalence (0%, >0-<25% and > or =25%) and three classes of FCS (0, >0-<0.75 and > or =0.75) were tested using the kappa (k) statistic and examined as continuous variables to define better levels of agreement. RESULTS: Two hundred and seventeen independent parasite prevalence surveys undertaken since 1980 were identified during the search. Overall agreement between the three classes of parasite prevalence and FCS was weak although significant (k = 0.367, p < 0.0001). The overall correlation between the FCS and the parasite ratio when considered as continuous variables was also positive (0.364, p < 0.001). The margins of error were in the stable, endemic (parasite ratio > or =25%) class with 42% of surveys represented by an FCS <0.75. Reducing the FCS value criterion to > or =0.6 improved the classification of stable, endemic parasite ratio surveys. Zero values of FCS were not adequate discriminators of zero parasite prevalence. CONCLUSION: Using the MARA model to categorically distinguish populations at differing intensities of malaria transmission in Kenya may under-represent those who are exposed to stable, endemic transmission and over-represent those at no risk. The MARA approach to defining FCS values of suitability for stable transmission represents our only contemporary continental level map of malaria in Africa but there is a need to redefine Africa's population at risk in accordance with both climatic and non-climatic determinants of P. falciparum transmission intensity to provide a more informed approach to estimating the morbid and fatal consequences of infection across the continent.

Adolescent↗

Plant use of the Maasai of Sekenani Valley, Maasai Mara, Kenya.

Traditional plant use is of tremendous importance in many societies, including most rural African communities. This knowledge is however, rapidly dwindling due to changes towards a more Western lifestyle, and the influence of modern tourism.In case of the Sekenani Maasai, the recent change from a nomadic to a more sedentary lifestyle has not, thus far lead to a dramatic loss of traditional plant knowledge, when compared to other Maasai communities. However, in Sekenani, plants are used much less frequently for manufacturing tools, and for veterinary purposes, than in more remote areas. While the knowledge is still present, overgrazing and over-exploitation of plant resources have already led to a decline of the plant material available.This paper examines the plant use of the Maasai in the Sekenani Valley, North of the Masaai Mara National Reserve. The Maasai pastoralists of Kenya and Tanzania use a large part of the plants in their environment for many uses in daily life. The plant use and knowledge of the Sekenani Maasai is of particular interest, as their clan, the "Il-Purko", was moved from Central Kenya to this region by the British Colonial Administration in 1904.The results of this study indicate that despite their relocation 100 years ago, the local population has an extensive knowledge of the plants in their surroundings, and they ascribe uses to a large percentage of the plants found. One-hundred-fifty-five plant species were collected, identified and their Maa names and traditional uses recorded. Although fifty-one species were reported as of "no use", only eighteen of these had no Maasai name. Thirty-three were recognized by a distinctive Maa name. Thirty-nine species had a medicinal use, and 30 species served as fodder for livestock. Six species could not be identified. Of these plants five were addressed by the Maasai with distinct names. This exemplifies the Sekenani Maasai's in-depth knowledge of the plant resources.Traditionally, the Maasai attribute most illnesses to the effect of pollutants that block or inhibit digestion. These pollutants can include "polluted" food, contact with sick people and witchcraft. In most cases the treatment of illness involves herbal purgatives to cleanse the patient. There are also frequent indications of plant use for common problems like wounds, parasites, body aches and burns.

Animal Feed↗

Ethnobotany of the Samburu of Mt. Nyiru, South Turkana, Kenya.

Traditional plant use is of extremely high importance in many societies, and prevalent in African communities. This knowledge is however dwindling rapidly due to changes towards a more Western lifestyle. The influence of modern tourism cannot be neglected in this context. This paper examines the plant use of the Samburu of the Mt. Nyiru area in Northern Kenya. The Samburu pastoralists of Kenya are still amongst the most traditional communities of the country and have retained most of their knowledge about the use of a large part of the plants in their environment for a wide variety of purposes. The results indicate that the local population has a very high knowledge of the plants in their surroundings, and attributes a purpose to a large percentage of the plants found. 448 plant species were collected, identified and their Samburu names and traditional uses recorded. 199 species were reported as of "no use". The high proportion of 249 plant species however had some traditional use: The highest number (180 species) was used as fodder, followed by 80 species that had medicinal use. Firewood (59 species), construction (42 species), tools (31 species), food (29 species) and ceremonial use (19 species) ranked far behind. Traditionally the Samburu attribute most illnesses to the effect of pollutants that block or inhibit digestion. This can include "polluted" food, contagion through sick people as well as witchcraft. In most cases the treatment of illness involves herbal purgatives to cleanse the patient. There are however frequent indications of plant use for common problems like wounds, parasites, body aches and burns. The change from a nomadic to a more sedentary lifestyle, often observed in other areas of the country, has affected the Samburu of remote Mt. Nyiru to a much lesser extent and did so far not lead to a major loss of traditional plant knowledge. However, overgrazing and over-exploitation of plant resources have already led to a decline of the plant material available.

Animal Feed↗

Genomic and clinical epidemiology of SARS-CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave.

BACKGROUND: Between November 2023 and March 2024, coastal Kenya experienced another wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections detected through our continued genomic surveillance. Herein, we report the clinical and genomic epidemiology of SARS-CoV-2 infections from 179 individuals (a total of 185 positive samples) residing in the Kilifi Health and Demographic Surveillance System (KHDSS) area (~&#x2009;900 km2). METHODS: We analyzed genetic, clinical, and epidemiological data from SARS-CoV-2 positive cases across pediatric inpatient, health facility outpatient, and homestead community surveillance platforms. Phylogenetic analyses were performed using maximum-likelihood and Bayesian frameworks. Temporal trends were summarized, comparisons conducted using Kruskal-Wallis and Wilcoxon tests, and associations examined using univariate and multivariable logistic regression models. RESULTS: Sixteen SARS-CoV-2 lineages within 3 subvariants [XBB.2.3-like (58.4%), JN.1-like (40.5%), and XBB.1-like (1.1%)] were identified. The symptomatic infection rate was estimated at 16.0% (95% CI, 11.1-23.9%) based on community testing regardless of symptom status and did not differ across the subvariants (p&#x2009;=&#x2009;0.13). The most common infection symptoms in community cases were cough (49.2%), fever (27.0%), sore throat (7.3%), headache (6.9%), and difficulty in breathing (5.5%). One case succumbed to the infection. Genomic analysis of the virus from serial positive samples confirmed repeat infections among 5 participants under follow-up (median interval 21&#xa0;days, range 16-95&#xa0;days); in 4 participants, the same virus lineage was responsible in both episodes, whereas 1 participant had a different lineage in the second compared with the first episode. Phylogenetic analysis including&#x2009;>&#x2009;18,000 contemporaneous global sequences provided evidence for at least 38 independent virus introduction events into the study area (KHDSS) during the wave, the majority likely originating in North America and Europe. CONCLUSIONS: Our study highlights that coastal Kenya, like most other localities, continues to face new SARS-CoV-2 infection waves characterized by circulation of new variants, multiple lineage importations, and reinfections. Locally, the virus may circulate unrecognized, as most infections are asymptomatic in part due to high population immunity after several waves of infection. Our findings highlight the need for sustained SARS-CoV-2 surveillance to inform appropriate public health responses, such as scheduled vaccination for populations at risk of severe infection.

COVID-19↗

Rabbit encephalitozoonosis in Kenya.

Encephalitozoon cuniculi infection was diagnosed in a laboratory rabbit breeding colony at Muguga, Kenya. This is the first report of the disease in rabbits in Kenya. Post-mortem examination showed gross renal lesions and the presence of the parasite in histological sections of the cerebrum and cerebellum. On Gram stain, spores were observed in the kidney sections.

Animals↗

Mortality and burden of disease in a cohort of HIV-seropositive adults in Nairobi, Kenya.

The purposes of this study were to measure incidence and determine risk factors associated with opportunistic infections (OIs) and mortality among an HIV-infected cohort in Nairobi, Kenya. Three hundred and eighty-one seropositive ambulatory adults in Nairobi, Kenya were followed from 1997 to 2000 with participants visiting the clinic every two months and when acutely ill. Acute bronchitis was the most frequent diagnosis, followed by sexually transmitted infections, candida vaginitis (among women), fever, diarrhoea, pneumonia, HIV-associated skin rash, oral candidiasis and urinary tract infection. Associations between the frequency of these diagnoses including survival and sociodemographic factors and initial CD4 count were assessed. A CD4 count <200 cells/mL at recruitment was strongly associated with decreased survival (adjusted odds ratio=3.0, 95% confidence interval 1.7-5.1). These findings may help to target high-risk populations and guide OI prevention and treatment strategies including decisions regarding initiation of antiretroviral therapy in sub-Saharan Africa.

AIDS-Related Opportunistic Infections↗

Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024.

BACKGROUND: Human metapneumovirus (hMPV) is a major contributor of acute respiratory infections (ARI) in childhood and vulnerable adults. It comprises two antigenically distinct lineages (A and B), with multiple sub-lineages. Genomic analyses of hMPV strains enable monitoring of viral evolution and transmission to inform future interventions but remain underutilized in Africa. METHODS: We generated 52 near-complete hMPV genomes from respiratory samples collected in Kilifi, Coastal Kenya, using a tiled-amplicon approach and Oxford Nanopore Technologies sequencing. These samples had been identified as hMPV positive by quantitative PCR during (a) a multi-facility outpatient ARI surveillance in nine health facilities in Kilifi between 2016 and 2017, and 2021 to 2023 and (b) a community-based respiratory infection cohort surveillance study between 2023-2024 that sampled enrolled participants irrespective of symptom status. RESULTS: Of the 192 positive samples analyzed from the two studies, children under 5 years accounted for most hMPV cases (134/186, 72%). 52 samples were sequenced (>70% genome coverage), and hMPV-A (27/52, 53.8%) and hMPV-B (25/52, 46.2%) lineages were identified. The recovered sequences mapped into sub-lineages A2c (27/52, 53.8%), B1 (12/52, 21.2%), and B2b (13/52, 25%). A shift in the predominant sub-lineage was observed from B2b (2016) to B1 (2021), and finally to A2c-wild type (2023). In February 2021, for the first time, we detected a single A2c strain with a 111-nucleotide duplication in the G gene among Kenyan samples. CONCLUSION: Our study expands the global nucleotide sequence database for hMPV by adding new whole-genome sequences from Kenya collected over the last decade. It highlights the ongoing replacement of locally predominant hMPV lineages and the importation and local transmission of globally circulating strains. These findings underscore the importance of sustained hMPV genomic surveillance to detect emerging variants and monitor lineage circulation patterns that may impact viral transmission, molecular detection, and future control measures.

A2c-111nt-dup↗

Characterization of West Nile virus Koutango lineage from phlebotomine sandflies in Kenya.

The West Nile virus (WNV), primarily transmitted by mosquitoes, is one of the most widespread flaviviruses globally, with past outbreaks occurring in the USA and Europe. Recent studies in parts of Africa, including Kenya, have identified the West Nile virus Koutango lineage (WN-KOUTV) among phlebotomine sandfly populations, however, our understanding of this virus remains limited. This study aimed to characterize WN-KOUTV from phlebotomine sandflies. Sandflies were sampled between 12th -16th March 2021 and 16th -20th March 2023 from six villages each in Baringo and Isiolo Counties, using CDC light traps. Female sandflies were taxonomically identified and pooled based on genus and site of collection. Virus isolation was performed in Vero cells. Viral genomes were determined using next-generation sequencing. Phylogenetic and molecular clock analyses were done to decipher the virus's evolutionary relationships. Comparative analyses of amino acid sequences were performed to determine variations. Protein modeling in Pymol was conducted to elucidate variations in key protein regions. Evolutionary pressure analysis investigated the selection pressures on the virus. In vitro experiments were done to investigate the virus growth kinetics in mammalian Vero E6 and mosquito C6/36 cells. We report the isolation of WN-KOUTV from Salabani in Baringo and Aremet in Isiolo, Kenya. The isolated WN-KOUTVs clustered with previously identified WN-KOUTV strains. Comparative analysis revealed a unique amino acid at NS5 653. The WN-KOUTV lineage as a whole is under purifying selective pressure, with diversifying pressure acting at site NS3 267. The current WN-KOUTV replicated in Vero E6 and C6/36 cells comparable to West Nile virus Lineage 1a, isolated from mosquitoes. Subsequent isolations of WN-KOUTV in phlebotomine sandflies suggest potential vectors, however, vector competence studies would confirm this. Replication in mammalian and insect cell lines suggests there may exist a vector/host relationship. We speculate the close genetic relationship of WN-KOUTV strains from East and West Africa may potentially be enabled by bird migratory routes between the two regions. If proven, this could point to a potential future pandemic pathway for this virus.

Animals↗

Climate-disease connections: Rift Valley Fever in Kenya.

All known Rift Valley fever(RVF) outbreaks in Kenya from 1950 to 1998 followed periods of abnormally high rainfall. On an interannual scale, periods of above normal rainfall in East Africa are associated with the warm phase of the El Niño/Southern Oscillation (ENSO) phenomenon. Anomalous rainfall floods mosquito-breeding habitats called dambos, which contain transovarially infected mosquito eggs. The eggs hatch Aedes mosquitoes that transmit the RVF virus preferentially to livestock and to humans as well. Analysis of historical data on RVF outbreaks and indicators of ENSO (including Pacific and Indian Ocean sea surface temperatures and the Southern Oscillation Index) indicates that more than three quarters of the RVF outbreaks have occurred during warm ENSO event periods. Mapping of ecological conditions using satellite normalized difference vegetation index (NDVI) data show that areas where outbreaks have occurred during the satellite recording period (1981-1998) show anomalous positive departures in vegetation greenness, an indicator of above-normal precipitation. This is particularly observed in arid areas of East Africa, which are predominantly impacted by this disease. These results indicate a close association between interannual climate variability and RVF outbreaks in Kenya.

Aedes↗

Population dynamics of malaria vectors in western Kenya highlands.

Studies were carried out at three sites in the highlands of western Kenya (Iguhu and Mbale in Kakamega and Vihiga districts, respectively, and Marani in Kisii district) and at one site in the western Kenya lowlands (Kombewa in Kisumu district) to determine the spatial-temporal dynamics of malaria vectors and intensity of malaria transmission from June 2003 to June 2004. At the highland sites, Anopheles gambiae Giles predominated, constituting >80% of the vector species, whereas An. funestus Giles made up <20%. In contrast, at the lowland site, An. funestus made up 68% of the vector species. The mean annual indoor resting densities of An. gambiae at Iguhu were 5.0 female mosquitoes per house per night, 14.2- and 26.3-fold greater than those at Mbale and Marani. During the main transmission season, the indoor resting densities of An. gambiae increased 4.1-, 10.1-, and 5.0-fold over the dry season period in Iguhu, Mbale, and Marani, respectively. The estimated annual entomological inoculation rate (EIR) at Iguhu was 16.6 infectious bites per person per year (ib/p/yr), 1.1 at Mbale, and 0.4 at Marani. This suggests high spatial variation in vector abundance and malaria transmission intensity. At the lowland site, Kombewa, the total annual EIR was 31.1 ib/p/yr and the indoor resting densities during the transmission season increased 7.1-fold in An. funestus and 18.5-fold in An. gambiae sensu lato over the dry season. The low level of transmission in the highlands suggests that it may be disrupted by vector control methods such as residual spraying.

Animals↗