Malaria epidemic early warning and detection in African highlands

Malaria epidemics have long been known to recur in the African highlands. Efforts to develop systems of early warning and detection for epidemics are outlined here with special emphasis on the Highland Malaria Project (HIMAL). This project has been conducting research on the operational implementation of a district-based surveillance and epidemic-monitoring system using a network of sentinel sites in four pilot districts of Kenya and Uganda. The potential use of weather monitoring as well as disease surveillance for effective early warning is being investigated.     

Drug resistance to sulphadoxine-pyrimethamine in Plasmodium falciparum malaria in Mlimba, Tanzania

Background

In the past two decades the east African highlands have experienced several major malaria epidemics. Currently there is a renewed interest in exploring the possibility of anopheline larval control through environmental management or larvicide as an additional means of reducing malaria transmission in Africa. This study examined the landscape determinants of anopheline mosquito larval habitats and usefulness of remote sensing in identifying these habitats in western Kenya highlands.

Methods

Panchromatic aerial photos, Ikonos and Landsat Thematic Mapper 7 satellite images were acquired for a study area in Kakamega, western Kenya. Supervised classification of land-use and land-cover and visual identification of aquatic habitats were conducted. Ground survey of all aquatic habitats was conducted in the dry and rainy seasons in 2003. All habitats positive for anopheline larvae were identified. The retrieved data from the remote sensors were compared to the ground results on aquatic habitats and land-use. The probability of finding aquatic habitats and habitats with Anopheles larvae were modelled based on the digital elevation model and land-use types.

Results

The misclassification rate of land-cover types was 10.8% based on Ikonos imagery, 22.6% for panchromatic aerial photos and 39.2% for Landsat TM 7 imagery. The Ikonos image identified 40.6% of aquatic habitats, aerial photos identified 10.6%, and Landsate TM 7 image identified 0%. Computer models based on topographic features and land-cover information obtained from the Ikonos image yielded a misclassification rate of 20.3–22.7% for aquatic habitats, and 18.1–25.1% for anopheline-positive larval habitats.

Conclusion

One-metre spatial resolution Ikonos images combined with computer modelling based on topographic land-cover features are useful tools for identification of anopheline larval habitats, and they can be used to assist to malaria vector control in western Kenya highlands.     

Modeling the spatial distribution of anthrax in southern Kenya

BackgroundAnthrax is an important zoonotic disease in Kenya associated with high animal and public health burden and widespread socio-economic impacts. The disease occurs in sporadic outbreaks that involve livestock, wildlife, and humans, but knowledge on factors that affect the geographic distribution of these outbreaks is limited, challenging public health intervention planning.MethodsAnthrax surveillance data reported in southern Kenya from 2011 to 2017 were modeled using a boosted regression trees (BRT) framework. An ensemble of 100 BRT experiments was developed using a variable set of 18 environmental covariates and 69 unique anthrax locations. Model performance was evaluated using AUC (area under the curve) ROC (receiver operating characteristics) curves.ResultsCattle density, rainfall of wettest month, soil clay content, soil pH, soil organic carbon, length of longest dry season, vegetation index, temperature seasonality, in order, were identified as key variables for predicting environmental suitability for anthrax in the region. BRTs performed well with a mean AUC of 0.8. Areas highly suitable for anthrax were predicted predominantly in the southwestern region around the shared Kenya-Tanzania border and a belt through the regions and highlands in central Kenya. These suitable regions extend westwards to cover large areas in western highlands and the western regions around Lake Victoria and bordering Uganda. The entire eastern and lower-eastern regions towards the coastal region were predicted to have lower suitability for anthrax.ConclusionThese modeling efforts identified areas of anthrax suitability across southern Kenya, including high and medium agricultural potential regions and wildlife parks, important for tourism and foreign exchange. These predictions are useful for policy makers in designing targeted surveillance and/or control interventions in Kenya.We thank the staff of Directorate of Veterinary Services under the Ministry of Agriculture, Livestock and Fisheries, for collecting and providing the anthrax historical occurrence data.     

Parasitoids of medfly, Ceratitis capitata, and related tephritids in Kenyan coffee: a predominantly koinobiont assemblage

Arabica coffee was sampled from two sites in the central highlands of Kenya (Rurima, Ruiru) and one site on the western side of the Rift Valley (Koru). Three species of ceratitidine Tephritidae, Ceratitis capitata (Wiedemann), C. rosa Karsch and Trirhithrum coffeae Bezzi, were reared from sites in the central highlands, and an additional species, C. anonae Graham, was recovered from the western-most site. Ten species of parasitic Hymenoptera were reared from these tephritids. The parasitoid assemblage was dominated by koinobionts. Eight of the species are koinobiont endoparasitoids, but only one idiobiont larval ectoparasitoid was reared, and only one idiobiont pupal endoparasitoid. The effects of sampling bias on determination of parasitoid assemblage size associated with concealed hosts are discussed. The potential for use of these parasitoids in biological control is also discussed. Most of the parasitoid species recovered during this study are capable of developing on C. capitata, while several also attack C. rosa. Both flies are notorious pests of tropical and subtropical fruits.     

Occurrence and distribution of cassava begomoviruses in Kenya

A survey for cassava mosaic disease (CMD) was conducted in Kenya, to investigate the factors contributing to the generally increased incidence and severity of CMD in the cassava growing regions and to study the distribution of the disease's causal begomoviruses, African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) and their strains. Special emphasis was given to the occurrence of the destructive recombinant Uganda variant strain of EACMV (EACMV-UG2). Samples from 91 farmers' fields in the main cassava-growing areas of coastal and western Kenya were collected and subjected to ELISA and PCR for detection and typing of the begomoviruses present. CMD incidence was highest in western Kenya (80–100%) and lowest in the Coast province (25–50%). In Western and Nyanza provinces, 52% of the samples tested contained EACMV-UG2, 22% ACMV and 17% contained both ACMV and EACMV-UG2. EACMV was found in four cases at different sites. In cassava samples from the coast province, only EACMV with DNA-A sequences similar to EACMV strains present in Kenya and Tanzania was found. East African cassava mosaic Zanzibar virus (EACMZV) was present in several farms in the Kilifi district. In 15% of all cassava samples with CMD symptoms, flexuous, filamentous virus-like particles were also found, providing evidence for a more complex virus situation in cassava grown at the Kenyan coast. In western Kenya, where intense cassava cultivation takes place, CMD is rampant and EACMV-UG2 was found in mixed virus infections with ACMV driving the epidemics. In coastal areas, where farms are scattered and in isolation, EACMV is endemic, however, with a lower disease incidence and with a limited impact to cassava production.     

Ranking Malaria Risk Factors to Guide Malaria Control Efforts in African Highlands

Introduction

Malaria is re-emerging in most of the African highlands exposing the non immune population to deadly epidemics. A better understanding of the factors impacting transmission in the highlands is crucial to improve well targeted malaria control strategies.

Methods and Findings

A conceptual model of potential malaria risk factors in the highlands was built based on the available literature. Furthermore, the relative importance of these factors on malaria can be estimated through “classification and regression trees”, an unexploited statistical method in the malaria field. This CART method was used to analyse the malaria risk factors in the Burundi highlands. The results showed that Anopheles density was the best predictor for high malaria prevalence. Then lower rainfall, no vector control, higher minimum temperature and houses near breeding sites were associated by order of importance to higher Anopheles density.

Conclusions

In Burundi highlands monitoring Anopheles densities when rainfall is low may be able to predict epidemics. The conceptual model combined with the CART analysis is a decision support tool that could provide an important contribution toward the prevention and control of malaria by identifying major risk factors.     

Spatial distribution of bednet coverage under routine distribution through the public health sector in a rural district in Kenya

Insecticide-treated nets (ITNs) are one of the most important and cost-effective tools for malaria control. Maximizing individual and community benefit from ITNs requires high population-based coverage. Several mechanisms are used to distribute ITNs, including health facility-based targeted distribution to high-risk groups; community-based mass distribution; social marketing with or without private sector subsidies; and integrating ITN delivery with other public health interventions. The objective of this analysis is to describe bednet coverage in a district in western Kenya where the primary mechanism for distribution is to pregnant women and infants who attend antenatal and immunization clinics. We use data from a population-based census to examine the extent of, and factors correlated with, ownership of bednets. We use both multivariable logistic regression and spatial techniques to explore the relationship between household bednet ownership and sociodemographic and geographic variables. We show that only 21% of households own any bednets, far lower than the national average, and that ownership is not significantly higher amongst pregnant women attending antenatal clinic. We also show that coverage is spatially heterogeneous with less than 2% of the population residing in zones with adequate coverage to experience indirect effects of ITN protection.     

Climate variability and malaria epidemics in the highlands of East Africa

Malaria epidemics in the highlands of East Africa garner significant research attention, due, in part, to their proposed sensitivity to climate change. In a recent article, Zhou et al. claim that increases in climate variance, rather than simple increases in climate mean values, have had an important role in the resurgence of malaria epidemics in the East African highlands since the early 1980s. If proven, this would be an interesting result but we believe that the methods used do not test the hypothesis suggested.     

Habitat characteristics of Anopheles gambiae s.s. larvae in a Kenyan highland

Anopheline larval habitats associated with a swamp, were examined in a highland area (1910 m elevation) of western Kenya. A significant association was found between occurrence of Anopheles gambiae Giles s.s. (Diptera: Culicidae) larvae and two factors, habitat size and vegetation type. Over 80% of An. gambiae s.s. larvae were found in small isolated pools, characterized by short plants, occurring in both swamp margins and roadside ditches. However, Anopheles gambiae s.s. was not found in habitats marked by papyrus and floating plants. The larval habitat of An. gambiae s.s. was characterized by warmer daytime temperatures of water, which were significantly affected by habitat size and plant size. The density of indoor resting An. gambiae s.s. was 0.22 per house and negatively associated with distance from the swamp. These results indicate that the practice of swamp cultivation, in populated areas of the African highlands, increases availability and enhances habitat conditions for the malaria vector.     

Temperature and malaria trends in highland East Africa

There has been considerable debate on the existence of trends in climate in the highlands of East Africa and hypotheses about their potential effect on the trends in malaria in the region. We apply a new robust trend test to mean temperature time series data from three editions of the University of East Anglia's Climatic Research Unit database (CRU TS) for several relevant locations. We find significant trends in the data extracted from newer editions of the database but not in the older version for periods ending in 1996. The trends in the newer data are even more significant when post-1996 data are added to the samples. We also test for trends in the data from the Kericho meteorological station prepared by Omumbo et al. We find no significant trend in the 1979-1995 period but a highly significant trend in the full 1979-2009 sample. However, although the malaria cases observed at Kericho, Kenya rose during a period of resurgent epidemics (1994-2002) they have since returned to a low level. A large assembly of parasite rate surveys from the region, stratified by altitude, show that this decrease in malaria prevalence is not limited to Kericho.     

High-Resolution Spatial Distribution and Estimation of Access to Improved Sanitation in Kenya

BackgroundAccess to sanitation facilities is imperative in reducing the risk of multiple adverse health outcomes. A distinct disparity in sanitation exists among different wealth levels in many low-income countries, which may hinder the progress across each of the Millennium Development Goals.MethodsThe surveyed households in 397 clusters from 2008–2009 Kenya Demographic and Health Surveys were divided into five wealth quintiles based on their national asset scores. A series of spatial analysis methods including excess risk, local spatial autocorrelation, and spatial interpolation were applied to observe disparities in coverage of improved sanitation among different wealth categories. The total number of the population with improved sanitation was estimated by interpolating, time-adjusting, and multiplying the surveyed coverage rates by high-resolution population grids. A comparison was then made with the annual estimates from United Nations Population Division and World Health Organization /United Nations Children''s Fund Joint Monitoring Program for Water Supply and Sanitation.ResultsThe Empirical Bayesian Kriging interpolation produced minimal root mean squared error for all clusters and five quintiles while predicting the raw and spatial coverage rates of improved sanitation. The coverage in southern regions was generally higher than in the north and east, and the coverage in the south decreased from Nairobi in all directions, while Nyanza and North Eastern Province had relatively poor coverage. The general clustering trend of high and low sanitation improvement among surveyed clusters was confirmed after spatial smoothing.ConclusionsThere exists an apparent disparity in sanitation among different wealth categories across Kenya and spatially smoothed coverage rates resulted in a closer estimation of the available statistics than raw coverage rates. Future intervention activities need to be tailored for both different wealth categories and nationally where there are areas of greater needs when resources are limited.     

Physical,Chemical and Biological Characteristics in Habitats of High and Low Presence of Anopheline Larvae in Western Kenya Highlands

Background

Characteristics of aquatic habitats determine whether mosquitoes will oviposit, hatch, develop, pupate and successfully emerge into adults or not, thus influencing which mosquito species will occupy a habitat. This study determined whether physiochemical and biological characteristics differ between habitats with high and low presence of anopheline larvae.

Methods

Physical, chemical and biological characteristics were evaluated in selected habitats twice per month within three highland valleys in western Kenya. Aquatic macro-organisms were sampled using a sweep-net. Colorimetric methods were used to determine levels of iron, phosphate, nitrate, ammonium and nitrite in water samples. Generalized Estimating Equations (GEE) was used to compare parameters between the two categories of anopheline presence.

Results

Habitats with high anopheline presence had greater abundance of mosquito aquatic stages and tadpoles and two times more levels of nitrate in water, whereas habitats with low anopheline presence had wider biofilm cover and higher levels of iron in water.

Conclusion

Habitats of high and low presence of anopheline larvae, which differed in a number of physical, chemical and biological characteristics, were identified in valleys within western Kenya highlands. Differences in habitat characteristics are critical in determining the number of anopheline larvae that will fully develop and emerge into adults.     

The biogeographical assignment of a west Kenyan rain forest remnant: further evidence from analysis of its reptile fauna

Aim The Kakamega Forest, western Kenya, has been biogeographically assigned to both lowland and montane forest biomes, or has even been considered to be unique. Most frequently it has been linked with the Guineo‐Congolian rain forest block. The present paper aims to test six alternative hypotheses of the zoogeographical relationships between this forest remnant and other African forests using reptiles as a model group. Reptiles are relatively slow dispersers, compared with flying organisms (Aves and Odonata) on which former hypotheses have been based, and may thus result in a more conservative biogeographical analysis. Location Kakamega Forest, Kenya, Sub‐Saharan Africa. Methods The reptile diversity of Kakamega Forest was evaluated by field surveys and data from literature resources. Faunal comparisons of Kakamega Forest with 16 other African forests were conducted by the use of the ‘coefficient of biogeographic resemblance’ using the reptile communities as zoogeographic indicators. Parsimony Analysis of Endemism and Neighbour Joining Analysis of Endemism were used to generate relationship trees based on an occurrence matrix with paup *. Results The analysis clearly supports the hypothesis that the Kakamega Forest is the easternmost fragment of the Guineo‐Congolian rain forest belt, and thus more closely related to the forests of that Central–West African complex than to any forest further east, such as the Kenyan coastal forests. Many Kenyan reptile species occur exclusively in the Kakamega Forest and its associated forest fragments. Main conclusions The Kakamega Forest is the only remnant of the Guineo‐Congolian rain forest in the general area. We assume that the low degree of resemblance identified for the Guineo‐Congolian forest and the East African coastal forest reflect the long history of isolation of the two forest types from each other. Kenyan coastal forests may have been historically connected through forest ‘bridges’ of the southern highlands with the Congo forest belt, allowing reptile species to migrate between them. The probability of a second ‘bridge’ located in the region of southern Tanzanian inselbergs is discussed. Although not particularly rich in reptile species, the area should be considered of high national priority for conservation measures.     

Regime shifts and heterogeneous trends in malaria time series from Western Kenya Highlands

Large malaria epidemics in the East African highlands during the mid and late 1990s kindled a stream of research on the role that global warming might have on malaria transmission. Most of the inferences using temporal information have been derived from a malaria incidence time series from Kericho. Here, we report a detailed analysis of 5 monthly time series, between 15 and 41 years long, from West Kenya encompassing an altitudinal gradient along Lake Victoria basin. We found decreasing, but heterogeneous, malaria trends since the late 1980s at low altitudes (<1600 m), and the early 2000s at high altitudes (>1600 m). Regime shifts were present in 3 of the series and were synchronous in the 2 time series from high altitudes. At low altitude, regime shifts were associated with a shift from increasing to decreasing malaria transmission, as well as a decrease in variability. At higher altitudes, regime shifts reflected an increase in malaria transmission variability. The heterogeneity in malaria trends probably reflects the multitude of factors that can drive malaria transmission and highlights the need for both spatially and temporally fine-grained data to make sound inferences about the impacts of climate change and control/elimination interventions on malaria transmission.     

Genetic diversity and population structure of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L<Emphasis Type="Italic">.</Emphasis>) landraces from the East African highlands

The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region.     

New and noteworthy species of Indigofera (Leguminosae) from NE Africa

Six new species of Indigofera are described: I. eremophila Thulin from E Ethiopia, I. mooneyi Thulin from the highlands of SW Ethiopia, I. boranica Thulin from SE Ethiopia and NE Kenya, I. gyrata Thulin and I. ammophila Thulin from NE Kenya, and I. cana Thulin from north–central Ethiopia. I. cavallii Chiov., previously known only from the type from S Somalia, is reported also from NE Kenya.     

Important Bird Areas in Kenya

Bennun, L. & Njoroge, P. 2000. Important Bird Areas in Kenya. Ostrich 71 (1 & 2): 164–167.

The process of defining Important Bird Areas in Kenya has been underway since January 1995, with financial support from the Royal Society for the Protection of Birds. Literature review has proceeded in parallel with field surveys, which are still ongoing. Some 65 globally Important Bird Areas have so far been identified, and this total is likely to increase. Sites were intitially selected using the criteria of threatened species (37 sites) and congregatory species (15 sites). Additional sites were then identified for biome-restricted and restricted-range species, using information from the Bird Atlas of Kenya; these sites must form part of a regional set. Threatened species sites are concentrated in forests (on the coastal strip, in the central highlands and in western Kenya) and papyrus swamps. Congregatory-species sites are concentrated along the Rift Valley and the coast. The remaining sites are concentrated in semi-arid areas to the immediate north and east of the central plateau, and in highland forest on each side of the Rift Valley. No IBAs have yet been identified in the flat, arid north-eastern sector of the country. A large number of sites require additional protection and/or improved management. Particular priorities include several papyrus IBAs around Lake Victoria, among them Lake Kanyaboli and Yala and Sare Swamps, grassland pockets in Mungatsi and Nambale, Western Province; the Kakamega, South Nandi and North Nandi Forests; the increasingly fragmented coastal forests, including Arabuko-Sokoke Forest; and the Taita Hills. Information on the IBA process and its results is being distributed to decision-makers through a high-level IBA Advisory council, with encouraging intitial results.     

Tanapox: A New Disease Caused by a Pox Virus

Two epidemics of a new virus disease, tanapox, occurred in 1957 and 1962 among the Wapakomo tribe along the Tana River in Kenya. Several hundred people were affected by a short febrile illness with headache and prostration and the disease was characterized by a single pock-like lesion on the upper part of the body. A pox virus, unrelated to the vaccinia-variola group, has been incriminated as the causative agent. The virus has a limited host range and has been grown only in human and monkey tissue cultures, and so far the only animals that have proved susceptible in the laboratory have been monkeys. The characteristic lesions have been reproduced in a human volunteer. Histopathological and electron microscopic studies indicate that the virus belongs to the pox group, but serological tests show that it differs from other animal pox viruses, including yabapox virus of monkeys. A similar if not identical pox virus has caused epidemics in primate colonies in the U.S.A. It is suggested that tanapox is a zoonosis and that the disease is transmitted from monkeys to man in Kenya.     

Modeling the Cost Effectiveness of Malaria Control Interventions in the Highlands of Western Kenya

Introduction

Tools that allow for in silico optimization of available malaria control strategies can assist the decision-making process for prioritizing interventions. The OpenMalaria stochastic simulation modeling platform can be applied to simulate the impact of interventions singly and in combination as implemented in Rachuonyo South District, western Kenya, to support this goal.

Methods

Combinations of malaria interventions were simulated using a previously-published, validated model of malaria epidemiology and control in the study area. An economic model of the costs of case management and malaria control interventions in Kenya was applied to simulation results and cost-effectiveness of each intervention combination compared to the corresponding simulated outputs of a scenario without interventions. Uncertainty was evaluated by varying health system and intervention delivery parameters.

Results

The intervention strategy with the greatest simulated health impact employed long lasting insecticide treated net (LLIN) use by 80% of the population, 90% of households covered by indoor residual spraying (IRS) with deployment starting in April, and intermittent screen and treat (IST) of school children using Artemether lumefantrine (AL) with 80% coverage twice per term. However, the current malaria control strategy in the study area including LLIN use of 56% and IRS coverage of 70% was the most cost effective at reducing disability-adjusted life years (DALYs) over a five year period.

Conclusions

All the simulated intervention combinations can be considered cost effective in the context of available resources for health in Kenya. Increasing coverage of vector control interventions has a larger simulated impact compared to adding IST to the current implementation strategy, suggesting that transmission in the study area is not at a level to warrant replacing vector control to a school-based screen and treat program. These results have the potential to assist malaria control program managers in the study area in adding new or changing implementation of current interventions.     

Using patterns of distribution and diversity of Kenyan birds to select and prioritize areas for conservation

Patterns and environmental correlates of species distributions and richness are identified for Kenyan birds at a quarter degree-square scale. This information is used together with iterative complementarity analyses, which employ species richness, taxonomic dispersion and range-restrictedness, to identify priority areas for possible conservation attention. Bird species apparently not conserved by existing protected areas in Kenya are identified. Six avifaunal zones (and one transitional zone) are distinguished based on distributions of suites of bird species. Variation in biotope diversity (the number of forest and aquatic systems) accounts for 79% of the observed variation in Kenyan bird species richness. Although both rainfall and altitudinal range are significantly correlated with species richness, they only explain an additional 3% of the observed variation. The priority areas identified are situated mainly within highlands and coastal lowlands. Although few priority areas are identified in northern Kenya, this region also constitutes a priority, as it contains a suite of xeric species with habitats that are not represented elsewhere in Kenya. The papyrus yellow warbler, Chloropeta gracilirostris, William's bush lark, Mirafra williamsi, white-winged dove, Streptopelia reichenowi, and Jubaland weaver, Ploceus dichrocephalus, are identified as endemics or near-endemics that are probably not adequately conserved in Kenya at present.