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In June 2022, a pool of five mosquitoes that were morphologically classified asAnopheles gambiaeand caught in Kisumu (Kenya) were tested for blood-meal analysis. Of the 19.6% (11/56) amplicon sequence variants assigned to mosquito species using basic local alignment search tool (BLAST), one had 15 hits matchingAnopheles stephensi.

Background Accurate identification of larval habitats of Ae. aegypti is considered an essential step in targeted control; of this important vector of several arboviruses including dengue and chikungunya viruses. This study determined Ae. aegyptiproductivity in selected larval habitats in Msambweni, Kwale County, Kenya. Methods A total of 664 potential larval habitats were identified and classified based on their use and material into seven habitat types including: buckets, drums, jerrycans, pots, small domestic containers (SDC), tires and others during the habitat census survey. All Ae. aegypti immatures in 83 representative larval habitats were counted daily for 30 consecutive days during a wet and a dry season. All pupae were removed and allowed to emerge in the laboratory. Results Of 664 larval habitats examined at baseline, 144 larval habitats (21.7%) were found to be infested with Aedes aegypti larvae. 71% of the pupae were collected from tires and pots combined, which together accounted for 17% of the habitats. In contrast, buckets and SDC represented 55% of the total habitats, but only had an infestation rate of 11.8%, with just 13.5% of the pupae found in them. Multivariate analysis showed that only habitat type and the habitat to being movable were associated with pupal abundance. During the 30-day daily pupal production studies, only a few of the habitats harbored pupae persistently. In the wet season, pupae were collected from 28% (23/83) of the larval habitats. In the dry season, only 12% (10/83) of the habitats were ever found with pupae during the 30-day sampling period, with three habitats (all drums) accounting for 80% (293/365) of all the pupae collected. The results of the multivariate modelsfor the risk factors for pupal productivity showed that habitat type, placing of larval habitats in the backyard, larval habitats without purpose and rain water were significant predictors of larval habitat productivity during the wet season.Although the multivariate model for habitat type did converge, habitat type and large size larval habitats were the only significant predictors during the dry season. Conclusion Drums, pots and tires were sources of more than 85% of Ae. aegypti pupae, reinforcing the ‘key containers concept’. Targeting these three types of habitats makes epidemiological sense, especially during the dry season.

This study examined whether Aedes aegypti extends its human blood seeking activity into night hours. Human landing catches (HLC) were conducted hourly from early morning (04:30) to late evening (21:30) in urban and rural sites in Kisumu County in western Kenya, and in Kwale County at the coast. Out of 842 female Ae. aegypti mosquitoes, 71 (8.5%) were collected at night (nocturnal), 151 (17.9%) at twilight (crepuscular), and 620 (73.6%) during the day (diurnal). Three-fold and significantly more Ae. aegypti female mosquitoes were collected during the twilight (crepuscular) hours than night (nocturnal) hours. Significantly more Ae. aegypti female mosquitoes were collected during daytime (diurnal) than night time (nocturnal). In general, the number of mosquitoes collected reduced as darkness increased. Extended time into the night to seek for blood meals enhances chances for Ae. aegypti to contact humans and transmit arboviruses diseases.

Little is known about the extent and serotypes of dengue viruses circulating in Africa. We evaluated the presence of dengue viremia during 4 years of surveillance (2014–2017) among children with febrile illness in Kenya. Acutely ill febrile children were recruited from 4 clinical sites in western and coastal Kenya, and 1,022 participant samples were tested by using a highly sensitive real-time reverse transcription PCR. A complete case analysis with genomic sequencing and phylogenetic analyses was conducted to characterize the presence of dengue viremia among participants during 2014–2017. Dengue viremia was detected in 41.9% (361/862) of outpatient children who had undifferentiated febrile illness in Kenya. Of children with confirmed dengue viremia, 51.5% (150/291) had malaria parasitemia. All 4 dengue virus serotypes were detected, and phylogenetic analyses showed several viruses from novel lineages. Our results suggests high levels of dengue virus infection among children with undifferentiated febrile illness in Kenya.

Rift Valley fever virus (RVFV) is an economically devastating, zoonotic arbovirus endemic across Africa with potential to cause severe disease in livestock and humans. Viral spread is primarily driven by movement of domestic ruminants and there is a high potential for transboundary spread. Despite influx of livestock to urban areas in response to the high demand for meat and animal products, RVFV has not been detected in any urban center. The objectives of this study were to determine the feasibility of assessing risk of RVFV introduction to urban Kisumu, Kenya, by testing slaughtered livestock for RVFV exposure and mapping livestock origins. Blood was collected from cattle, sheep, and goats directly after slaughter and tested for anti-RVFV IgG antibodies. Slaughterhouse businessmen responded to a questionnaire on their individual animals' origin, marketplace, and transport means. Thereafter, we mapped livestock flow from origin to slaughterhouse using participatory methods in focus group discussions with stakeholders. Qualitative data on route choice and deviations were spatially integrated into the map. A total of 304 blood samples were collected from slaughtered livestock in October and November 2021. Most (99%) of animals were purchased from 28 different markets across eight counties in Western Kenya. The overall RVFV seroprevalence was 9% (19% cattle, 3% in sheep, and 7% in goats). Migori County bordering Tanzania had the highest county-level seroprevalence (34%) and 80% of all seropositive cattle were purchased at the Suba Kuria market in Migori County. Road quality and animal health influenced stakeholders' decisions for choice of transport means. Overall, this proof-of-concept study offers a sampling framework for RVFV that can be locally implemented and rapidly deployed in response to regional risk. This system can be used in conjunction with participatory maps to improve active livestock surveillance and monitoring of RVFV in Western Kenya, and these methods could be extrapolated to other urban centers or livestock diseases.

Rift Valley fever virus (RVFV) is a zoonotic arbovirus that has profound impact on domestic ruminants and can also be transmitted to humans via infected animal secretions. Urban areas in endemic regions across Africa have susceptible animal and human hosts, dense vector distributions, and source livestock (often from high risk locations to meet the demand for animal protein). Yet, there has never been a documented urban outbreak of RVF. To understand the likely risk of RVFV introduction to urban communities from their perspective and guide future initiatives, we conducted focus group discussions with slaughterhouse workers, slaughterhouse animal product traders, and livestock owners in Kisumu City and Ukunda Town in Kenya. For added perspective and data triangulation, in-depth interviews were conducted one-on-one with meat inspector veterinarians from selected slaughterhouses. A theoretical framework relevant to introduction, transmission, and potential persistence of RVF in urban areas is presented here. Urban livestock were primarily mentioned as business opportunities, but also had personal sentiment. In addition to slaughtering risks, perceived risk factors included consumption of fresh milk. High risk groups’ knowledge and experience with RVFV and other zoonotic diseases impacted their consideration of personal risk, with consensus towards lower risk in the urban setting compared to rural areas as determination of health risk was said to primarily rely on hygiene practices rather than the slaughtering process. Groups relied heavily on veterinarians to confirm animal health and meat safety, yet veterinarians reported difficulty in accessing RVFV diagnostics. We also identified vulnerable public health regulations including corruption in meat certification outside of the slaughterhouse system, and blood collected during slaughter being used for food and medicine, which could provide a means for direct RVFV community transmission. These factors, when compounded by diverse urban vector breeding habitats and dense human and animal populations, could create suitable conditions for RVFV to arrive an urban center via a viremic imported animal, transmit to locally owned animals and humans, and potentially adapt to secondary vectors and persist in the urban setting. This explorative qualitative study proposes risk pathways and provides initial insight towards determining how urban areas could adapt control measures and plan future initiatives to better understand urban RVF potential.

O’nyong-nyong virus (ONNV) is a little-known arbovirus causing intermittent, yet explosive, outbreaks in Africa. It is closely related to chikungunya virus, an emerging infectious disease. O’nyong-nyong virus causes a self-limited illness characterized by bilateral polyarthritis, rash, low-grade fever, and lymphadenopathy. In 1959, an extensive outbreak of ONNV occurred in East Africa, and decades later, another large outbreak was documented in Uganda in 1996. Limited evidence for interepidemic transmission is available, although serologic studies indicate a high prevalence of exposure. 1,045 febrile child participants in western and coastal Kenya were tested for the presence of ONNV using a multiplexed real-time reverse transcriptase–PCR assay. More than half of the participants had malaria parasitemia, and there was no evidence of active ONNV viremia in these participants. Further work is required to better understand the interepidemic circulation of ONNV and to reconcile evidence of high serologic exposure to ONNV among individuals in East Africa.

The Rift Valley fever virus (RVFV) is a zoonotic arbovirus that can also transmit directly to humans from livestock. Previous studies have shown consumption of sick animal products are risk factors for RVFV infection, but it is difficult to disentangle those risk factors from other livestock rearing activities. Urban areas have an increased demand for animal source foods, different vector distributions, and various arboviruses are understood to establish localized urban transmission cycles. Thus far, RVFV is an unevaluated public health risk in urban areas within endemic regions. We tested participants in our ongoing urban cohort study on dengue (DENV) and chikungunya (CHIKV) virus for RVFV exposure and found 1.6% (57/3,560) of individuals in two urban areas of Kenya had anti-RVFV IgG antibodies. 88% (50/57) of RVFV exposed participants also had antibodies to DENV, CHIKV, or both. Although livestock ownership was very low in urban study sites, RVFV exposure was overall significantly associated with seeing goats around the homestead (OR = 2.34 (CI 95%: 1.18–4.69, p = 0.02) and in Kisumu, RVFV exposure was associated with consumption of raw milk (OR = 6.28 (CI 95%: 0.94–25.21, p = 0.02). In addition, lack of piped water and use of small jugs (15–20 liters) for water was associated with a higher risk of RVFV exposure (OR = 5.36 (CI 95%: 1.23–16.44, p = 0.01) and this may contribute to interepidemic vector-borne maintenance of RVFV. We also investigated perception towards human vaccination for RVFV and identified high acceptance (91% (97/105) at our study sites. This study provides baseline evidence to guide future studies investigating the urban potential of RVFV and highlights the unexplored role of animal products in continued spread of RVFV.

Climate change and variability influence temperature and rainfall, which impact vector abundance and the dynamics of vector-borne disease transmission. Climate change is projected to increase the frequency and intensity of extreme climate events. Mosquito-borne diseases, such as dengue fever, are primarily transmitted by Aedes aegypti mosquitoes. Freshwater availability and temperature affect dengue vector populations via a variety of biological processes and thus influence the ability of mosquitoes to effectively transmit disease. However, the effect of droughts, floods, heat waves, and cold waves is not well understood. Using vector, climate, and dengue disease data collected between 2013 and 2019 in Kenya, this retrospective cohort study aims to elucidate the impact of extreme rainfall and temperature on mosquito abundance and the risk of arboviral infections. To define extreme periods of rainfall and land surface temperature (LST), we calculated monthly anomalies as deviations from long-term means (1983–2019 for rainfall, 2000–2019 for LST) across four study locations in Kenya. We classified extreme climate events as the upper and lower 10% of these calculated LST or rainfall deviations. Monthly Ae. aegypti abundance was recorded in Kenya using four trapping methods. Blood samples were also collected from children with febrile illness presenting to four field sites and tested for dengue virus using an IgG enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). We found that mosquito eggs and adults were significantly more abundant one month following an abnormally wet month. The relationship between mosquito abundance and dengue risk follows a non-linear association. Our findings suggest that early warnings and targeted interventions during periods of abnormal rainfall and temperature, especially flooding, can potentially contribute to reductions in risk of viral transmission., Author summary Dengue is a rapidly spreading mosquito-borne disease transmitted primarily by Aedes aegypti mosquitoes. As climate change leads to extremes in rainfall and temperature, the abundance and populations of these vectors will be affected, thus influencing transmission of dengue. Using satellite-derived climate data for Kenya, we classified months that experienced highly abnormal rainfall and temperature as extreme climate events (floods, droughts, heat waves, or cold waves). We compared the average monthly Ae. aegypti abundance and confirmed dengue counts following extreme climate months using lag periods of one month and two months, respectively. This study utilized several statistical models to account for differences among study sites and time. Floods resulted in significantly increased egg and adult abundance. Our results contributed to a better understanding of the effect of climate variability and change on dengue. As suggested by our observed increase in vector counts yet a relatively unchanged dengue infection risk, human behavior can help reduce viral transmission. Targeted interventions should be focused on both reducing vector populations and limiting human-vector contact, especially during these climate anomalies.

Climate drives population dynamics through multiple mechanisms, which can lead to seemingly context-dependent effects of climate on natural populations. For climate-sensitive diseases, such as dengue, chikungunya, and Zika, climate appears to have opposing effects in different contexts. Here we show that a model, parameterized with laboratory measured climate-driven mosquito physiology, captures three key epidemic characteristics across ecologically and culturally distinct settings in Ecuador and Kenya: the number, timing, and duration of outbreaks. The model generates a range of disease dynamics consistent with observed Aedes aegypti abundances and laboratory-confirmed arboviral incidence with variable accuracy (28–85% for vectors, 44–88% for incidence). The model predicted vector dynamics better in sites with a smaller proportion of young children in the population, lower mean temperature, and homes with piped water and made of cement. Models with limited calibration that robustly capture climate-virus relationships can help guide intervention efforts and climate change disease projections., The effects of climate on vector-borne disease systems are highly context-dependent. Here, the authors incorporate laboratory-measured physiological traits of the mosquito Aedes aegypti into climate-driven mechanistic models to predict number, timing, and duration of outbreaks in Ecuador and Kenya.

Background Aedes aegypti is an efficient vector of several arboviruses of public health importance, including Zika and dengue. Currently vector management is the only available avenue for disease control. Development of efficient vector control strategies requires a thorough understanding of vector ecology. In this study, we identified households that are consistently productive for Ae. aegypti pupae and determined the ecological and socio-demographic factors associated with the persistence and abundance of pupae in households in rural and urban Kenya. Methods We collected socio-demographic, environmental and entomological data monthly from July 2014 to June 2018 from 80 households across four sites in Kenya. Pupae count data were collected via entomological surveillance of households and paired with socio-demographic and environmental data. We calculated pupal persistence within a household as the number of months of pupal presence within a year. We used spatially explicit generalized additive mixed models (GAMMs) to identify the risk factors for pupal abundance, and a logistic regression to identify the risk factors for pupal persistence in households. Results The median number of months of pupal presence observed in households was 4 and ranged from 0 to 35 months. We identified pupal persistence in 85 house-years. The strongest risk factors for high pupal abundance were the presence of bushes or tall grass in the peri-domicile area (OR: 1.60, 95% CI: 1.13–2.28), open eaves (OR: 2.57, 95% CI: 1.33–4.95) and high habitat counts (OR: 1.42, 95% CI: 1.21–1.66). The main risk factors for pupal persistence were the presence of bushes or tall grass in the peri-domicile (OR: 4.20, 95% CI: 1.42–12.46) and high number of breeding sites (OR: 2.17, 95% CI: 1.03–4.58). Conclusions We observed Ae. aegypti pupal persistence at the household level in urban and rural and in coastal and inland Kenya. High counts of potential breeding containers, vegetation in the peri-domicile area and the presence of eaves were strongly associated with increased risk of pupal persistence and abundance. Targeting households that exhibit pupal persistence alongside the risk factors for pupal abundance in vector control interventions may result in more efficient use of limited resources.

Arboviruses are among the most important emerging pathogens due to their increasing public health impact. In Kenya, continued population growth and associated urbanization are conducive to vector spread in both urban and rural environments, yet mechanisms of viral amplification in vector populations is often overlooked when assessing risks for outbreaks. Thus, the characterization of local arbovirus circulation in mosquito populations is imperative to better inform risk assessments and vector control practices. Aedes species mosquitoes were captured at varying stages of their life cycle during different seasons between January 2014 and May 2016 at four distinct sites in Kenya, and tested for chikungunya (CHIKV), dengue (DENV) and Zika (ZIKV) viruses by RT-PCR. CHIKV was detected in 45 (5.9%) and DENV in 3 (0.4%) mosquito pools. No ZIKV was detected. Significant regional variation in prevalence was observed, with greater frequency of CHIKV on the coast. DENV was detected exclusively on the coast. Both viruses were detected in immature mosquitoes of both sexes, providing evidence of transovarial transmission of these arboviruses in local mosquitoes. This phenomenon may be driving underlying viral maintenance that may largely contribute to periodic re-emergence among humans in Kenya., Author summary Transovarial transmission, or vertical transmission, is the spread of a pathogen from parent to offspring. It has been observed that some mosquito-borne viruses can be transmitted from female mosquitoes to their offspring during follicle development or during oviposition. The occurrence of transovarial transmission is evident in the presence of virally infected male mosquitoes, which typically do not take bloodmeals, and the presence of virus in immature mosquitoes of any sex. Transovarial transmission aids in the amplification of mosquito-borne viruses in the environment by increasing the number of infected mosquitoes in a given region, thus expanding the possibility of viral transmission to humans. The combination of transovarial transmission and the preservation of viable eggs during dry seasons may trigger sudden amplification of the virus after rainy periods, resulting in an outbreak. This study provides some of the first evidence of transovarial transmission of chikungunya and dengue viruses in Aedes aegypti mosquitoes in Africa during interepidemic periods, which has important implications for local virus persistence and epidemic patterns.

BackgroundAedes aegypti is the major mosquito vector of many burdensome human diseases. While behavioral research has focused primarily on understanding the importance of olfactory stimuli in its host-seeking abilities, Ae. aegypti’s vision has also been shown to contribute significantly to locating a human host. In this semi-field study conducted in Kisian, Kisumu County, Kenya, we explored the role of visual properties in Aedes host-seeking by testing four different visual characteristics presented in host decoy traps (HDT). This surveillance trap presents a combination of visual, thermal, and odor stimuli to attract bloodmeal-seeking mosquitoes. This was also the first test of HDT for sampling Aedes mosquitoes, having previously been shown to be effective for capture of other vector genera such as Anopheles, Mansonia, and Culex in field settings.ResultsOur results show that the HDT is an effective means of capturing Ae. aegypti mosquitoes, with a per trial capture rate of up to 69% across four visually distinct HDTs deployed simultaneously in a semi-field arena. Of these four, a solid black HDT (HDT B) captured more mosquitoes than HDTs with: black-white stripes (HDT S), black-white checkerboard patches (HDT P), and a solid white color (HDT W). Across 16 replicates wherein 200 mosquitoes were released per trial, HDT B caught more mosquitoes than HDTs S, P, and W by a factor of 1.9, 1.7, and 1.5 respectively. In all cases, mosquito capture was not evenly distributed on the HDT surface, with captures on the HDT’s outer half, away from the odor delivery, exceeding captures on the inner half facing towards the odor delivery by a factor of 4.8, 3.7, 3.7, and 5.1 on HDTs B, S, P, and W respectively.Conclusions: Our results establish that in semi-field conditions, the HDT is effective for the capture of Ae. aegypti mosquitoes and provides a flexible platform to test experimental parameters pertinent to the host-seeking behavior of mosquito vector species. We show that Ae. aegypti makes use of dark, but not light, high contrast visual information while responding to both the olfactory and thermal stimuli associated with hosts. The results further show that the solid black surface of the original HDT design is more effective than the other surfaces (white or black/white patterns) for the capture of Ae. aegypti.

Background In low-resource, malaria-endemic settings, accurate diagnosis of febrile illness in children is challenging. The World Health Organization (WHO) currently recommends laboratory-confirmed diagnosis of malaria prior to starting treatment in stable children. Factors guiding management of children with undifferentiated febrile illness outside of malaria are not well understood. Methods This study examined clinical presentation and management of a cohort of febrile Kenyan children at 5 hospital/clinic sites from January 2014 to December 2017. Chi-squared and multivariate regression analyses were used to compare frequencies and correlate demographic, environmental, and clinical factors with patient diagnosis and prescription of antibiotics. Results Of 5735 total participants, 68% were prescribed antibiotic treatment (n = 3902), despite only 28% given a diagnosis of bacterial illness (n = 1589). Factors associated with prescription of antibiotic therapy included: negative malaria testing, reporting head, ears, eyes, nose and throat (HEENT) symptoms (ie, cough, runny nose), HEENT findings on exam (ie, nasal discharge, red throat), and having a flush toilet in the home (likely a surrogate for higher socioeconomic status). Conclusion In a cohort of acutely ill Kenyan children, prescription of antimalarial therapy and malaria test results were well correlated, whereas antibiotic treatment was prescribed empirically to most of those who tested malaria negative. Clinical management of febrile children in these settings is difficult, given the lack of diagnostic testing. Providers may benefit from improved clinical education and implementation of enhanced guidelines in this era of malaria testing, as their management strategies must rely primarily on critical thinking and decision-making skills.

Background Clinicians in low resource settings in malaria endemic regions face many challenges in diagnosing and treating febrile illnesses in children. Given the change in WHO guidelines in 2010 that recommend malaria testing prior to treatment, clinicians are now required to expand the differential when malaria testing is negative. Prior studies have indicated that resource availability, need for additional training in differentiating non-malarial illnesses, and lack of understanding within the community of when to seek care play a role in effective diagnosis and treatment. The objective of this study was to examine the various factors that influence clinician behavior in diagnosing and managing children presenting with fever to health centres in Kenya. Methods A total of 20 clinicians (2 paediatricians, 1 medical officer, 2 nurses, and 15 clinical officers) were interviewed, working at 5 different government-sponsored public clinic sites in two areas of Kenya where malaria is prevalent. Clinicians were interviewed one-on-one using a structured interview technique. Interviews were then analysed qualitatively for themes. Results The following five themes were identified: (1) Strong familiarity with diagnosis of malaria and testing for malaria; (2) Clinician concerns about community understanding of febrile illness, use of traditional medicine, delay in seeking care, and compliance; (3) Reliance on clinical guidelines, history, and physical examination to diagnose febrile illness and recognize danger signs; (4) Clinician discomfort with diagnosis of primary viral illness leading to increased use of empiric antibiotics; and (5) Lack of resources including diagnostic testing, necessary medications, and training modalities contributes to the difficulty clinicians face in assessing and treating febrile illness in children. These themes persisted across all sites, despite variation in levels of medical care. Within these themes, clinicians consistently expressed a need for reliable basic testing, especially haemograms and bacterial cultures. Clinicians discussed the use of counseling and education to improve community understanding of febrile illness in order to decrease preventable deaths in children. Conclusion Results of this study suggest that since malarial testing has become more widespread, clinicians working in resource-poor environments still face difficulty when evaluating a child with fever, especially when malaria testing is negative. Improving access to additional diagnostics, continuing medical education, and ongoing evaluation and revision of clinical guidelines may lead to more consistent management of febrile illness by providers, and may potentially decrease prescription of unnecessary antibiotics. Additional interventions at the community level may also have an important role in managing febrile illness, however, more studies are needed to identify targets for intervention at both the clinic and community levels. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2021-7) contains supplementary material, which is available to authorized users.

O’nyong-nyong virus (ONNV), an alphavirus closely related to chikungunya virus (CHIKV), has been the documented cause of two large outbreaks in east Africa; however, little is known about the contribution of ONNV to cases of acute febrile illness during interepidemic periods. An ONNV real-time reverse transcription polymerase chain reaction (rRT-PCR) was developed and evaluated using clinical and mosquito pool samples. The ONNV rRT-PCR linear range extended from 8.0 to 2.0 log10 copies/μL, and the lower limit of 95% detection was 22.4 copies/μL. No cases of ONNV infection were identified in serum from 385 Kenyan children who presented with an acute febrile illness. Additionally, ONNV was not detected in 120 mosquito pools collected in coastal and western Kenya. The ONNV rRT-PCR demonstrated good analytical sensitivity when performed in monoplex or as a component of an ONNV–CHIKV duplex assay. This assay should provide a useful diagnostic for the detection of ONNV in surveillance studies.

Background Aedes aegypti, the principal vector for dengue and other emerging arboviruses, breeds preferentially in various man-made and natural container habitats. In the absence of vaccine, epidemiological surveillance and vector control remain the best practices for preventing dengue outbreaks. Effective vector control depends on a good understanding of larval and adult vector ecology of which little is known in Kenya. In the current study, we sought to characterize breeding habitats and establish container productivity profiles of Ae. aegypti in rural and urban sites in western and coastal Kenya. Methods Twenty sentinel houses in each of four study sites (in western and coastal Kenya) were assessed for immature mosquito infestation once a month for a period of 24 months (June 2014 to May 2016). All water-holding containers in and around the households were inspected for Ae. aegypti larvae and pupae. Results Collections were made from a total of 22,144 container visits: Chulaimbo (7575) and Kisumu (8003) in the west, and from Msambweni (3199) and Ukunda (3367) on the coast. Of these, only 4–5.6% were positive for Ae. aegypti immatures. In all four sites, significantly more positive containers were located outdoors than indoors. A total of 17,537 Ae. aegypti immatures were sampled from 10 container types. The most important habitat types were buckets, drums, tires, and pots, which produced over 75% of all the pupae. Key outdoor containers in the coast were buckets, drums and tires, which accounted for 82% of the pupae, while pots and tires were the only key containers in the western region producing 70% of the pupae. Drums, buckets and pots were the key indoor containers, producing nearly all of the pupae in the coastal sites. No pupae were collected indoors in the western region. The coastal region produced significantly more Ae. aegypti immatures than the western region both inside and outside the sentinel houses. Conclusions These results indicate that productive Ae. aegypti larval habitats are abundant outdoors and that only a few containers produce a majority of the pupae. Although the numbers were lower, productive habitats were detected within households. Targeting source reduction efforts towards these productive containers both inside and outside homes is likely to be a cost-effective way to reduce arboviral transmission in these regions.

Background Ambient temperature is an important determinant of malaria transmission and suitability, affecting the life-cycle of the Plasmodium parasite and Anopheles vector. Early models predicted a thermal malaria transmission optimum of 31 °C, later revised to 25 °C using experimental data from mosquito and parasite biology. However, the link between ambient temperature and human malaria incidence remains poorly resolved. Methods To evaluate the relationship between ambient temperature and malaria risk, 5833 febrile children (

We detected a cluster of dengue virus infections in children in Kenya during July 2014–June 2015. Most cases were serotype 1, but we detected all 4 serotypes, including co-infections with 2 serotypes. Our findings implicate dengue as a cause of febrile illness in this population and highlight a need for robust arbovirus surveillance.

The literature on sero-epidemiological studies of flaviviral infections in the African continent is quite scarce. Much of the viral epidemiology studies have been focussing on diseases such as HIV/AIDS because of their sheer magnitude and impact on the lives of people in the various affected countries. Increasingly disease outbreaks caused by arboviruses such as the recent cases of chikungunya virus, dengue virus and yellow fever virus have prompted renewed interest in studying these viruses. International agencies from the US, several EU nations and China are starting to build collaborations to build capacity in many African countries together with established institutions to conduct these studies. The Tofo Advanced Study Week (TASW) was established to bring the best scientists from the world to the tiny seaside town of Praia do Tofo to rub shoulders with African virologists and discuss cutting-edge science and listen to the work of researchers in the field. In 2015 the 1st TASW focussed on Ebola virus. The collections of abstracts from participants at the 2nd TASW which focused on Dengue and Zika virus as well as presentations on other arboviruses are collated in this chapter.

Background In sub-Saharan Africa, malaria is frequently overdiagnosed as the cause of an undifferentiated febrile illness, whereas arboviral illnesses are presumed to be underdiagnosed. Methods Sera from 385 febrile Kenyan children, who presented to 1 of 4 clinical sites, were tested using microscopy and real-time molecular assays for dengue virus (DENV), chikungunya virus (CHIKV), malaria, and Leptospira. Results Malaria was the primary clinical diagnosis for 254 patients, and an arboviral infection (DENV or CHIKV) was the primary diagnosis for 93 patients. In total, 158 patients (41.0%) had malaria and 32 patients (8.3%) had CHIKV infections. Compared with real-time polymerase chain reaction, microscopy demonstrated a percent positive agreement of 49.7%. The percentage of malaria cases detected by microscopy varied significantly between clinical sites. Arboviral infections were the clinical diagnosis for patients on the Indian Ocean coast (91 of 238, 38.2%) significantly more often than patients in the Lake Victoria region (2 of 145, 1.4%; P < .001). However, detection of CHIKV infections was significantly higher in the Lake Victoria region (19 of 145 [13.1%] vs 13 of 239 [5.4%]; P = .012). Conclusions The clinical diagnosis of patients with an acute febrile illness, even when aided by microscopy, remains inaccurate in malaria-endemic areas, contributing to inappropriate management decisions.

Background: Blood-meal sources of malaria vectors affect their capacity to transmit the disease. Most efficient malaria vectors prefer human hosts. However, with increasing personal protection measures it becomes more difficult for them to find human hosts. Here recent malaria vector blood-meal sources in western Kenya highlands were investigated.Methods: Adult mosquitoes resting indoors, outdoors and exiting through windows were collected in three study areas within the western Kenya highlands from June 2011 to June 2013. A census of people, livestock and of insecticide-treated nets was done per house. Mosquito blood-meal sources were determined as human, goat, bovine or chicken using enzyme-linked-immunosorbent assays.Results: Most (86.3 %) households possessed at least one bed net, 57.2 % had domesticated animals and 83.6 % had people sharing houses with livestock at night. Most (94.9 %) unfed malaria vectors were caught exiting through windows. Overall, 53.1 % of Anopheles gambiae sensu stricto obtained blood-meals from humans, 26.5 % from goats and 18.4 % from bovines. Single blood-meal sources by An. gambiae s.s. from humans were 26.5 %, 8.2 % from bovines and 2.0 % from goats. Mixed blood-meal sources by An. gambiae s.s. identified included: 24.5 % human/goat, 10.2 % human/bovine, 8.2 % human/bovine/goat and also 8.2 % bovine/goat. One An. arabiensis mosquito obtained blood-meal only from humans.Conclusion: An unusually high frequency of animal and mixed human-animal blood meals in the major malaria vector An. gambiae s.s. was revealed in the western Kenya highlands where bed net coverage is above the WHO target. The shift in blood-meal sources from humans to livestock is most likely the vectors’ response to increased bed net coverage and the close location of livestock frequently in the same house as people at night. Livestock-targeted interventions should be considered under these circumstances to address residual malaria transmission.

OBJECTIVE: To assess the contributions of both microbial larvicides and insecticide-treated nets (ITNs) in terms of reducing malaria incidence in an integrated vector management programme in an area moderately endemic for malaria in the western Kenyan highlands. METHODS: A pre-post, control group design was used. Larval and adult vector populations were surveyed weekly in six separate valley communities. The incidence of Plasmodium infections in children 6 months to 13 years of age was measured during the long and short rainy seasons each year. Baseline data were collected for 17 months, after which Bacillus-based larvicides were applied weekly to aquatic habitats in three of the valleys for another 19 months. At around the same time the larviciding was initiated, ITNs were introduced gradually into all study communities by the National Malaria Control Programme. The effect of larviciding, ITNs and other determinants of malaria risk was assessed by means of generalized estimating equations. FINDINGS: The risk of acquiring new parasite infections in children was substantially and independently reduced by ITN use (odds ratio, OR: 0.69; 95% confidence interval, CI: 0.48-0.99) and larvicide application (OR: 0.44; 95% CI: 0.23-0.82), after adjusting for confounders. CONCLUSION: Vector control with microbial larvicides enhanced the malaria control achieved with ITNs alone. Anti-larval measures are a promising complement to ITN distribution in the economically important highland areas and similar transmission settings in Africa.

A dynamical model of Anopheles gambiae larval and adult populations is constructed that matches temperature-dependent maturation times and mortality measured experimentally as well as larval instar and adult mosquito emergence data from field studies in the Kenya Highlands. Spectral classification of high-resolution satellite imagery is used to estimate household density. Indoor resting densities collected over a period of one year combined with predictions of the dynamical model give estimates of both aquatic habitat and total adult mosquito densities. Temperature and precipitation patterns are derived from monthly records. Precipitation patterns are compared with average and extreme habitat estimates to estimate available aquatic habitat in an annual cycle. These estimates are coupled with the original model to produce estimates of adult and larval populations dependent on changing aquatic carrying capacity for larvae and changing maturation and mortality dependent on temperature. This paper offers a general method for estimating the total area of aquatic habitat in a given region, based on larval counts, emergence rates, indoor resting density data, and number of households.Altering the average daily temperature and the average daily rainfall simulates the effect of climate change on annual cycles of prevalence of An. gambiae adults. We show that small increases in average annual temperature have a large impact on adult mosquito density, whether measured at model equilibrium values for a single square meter of habitat or tracked over the course of a year of varying habitat availability and temperature.

Distribution of chemokine receptors CCR5 and CXCR4, which are also coreceptors for human immunodeficiency virus type 1 invasion of cells, was measured on the surfaces of CD4 + T cells and monocytes in peripheral blood samples from a group of Kenyan car washers. Patients with active schistosomiasis displayed higher cell surface densities of these receptors than did cured schistosomiasis patients.

This paper describes a geographic sampling strategy for ecologic studies and describes the relationship between human activities and anopheline larval ecology in urban areas. Kisumu and Malindi, Kenya were mapped using global positioning systems, and a geographic information system was used to overlay a measured grid, which served as a sampling frame. Grid cells were stratified and randomly selected according to levels of planning and drainage. A cross-sectional survey was conducted in April and May 2001 to collect entomologic and human ecologic data. Multivariate regression analysis was used to test the relationship between the abundance of potential larval habitats, and house density, socioeconomic status, and planning and drainage. In Kisumu, 98 aquatic habitats were identified, 65% of which were human made and 39% were positive for anopheline larvae. In Malindi, 91 aquatic habitats were identified, of which, 93% were human made and 65% were harboring anopheline larvae. The regression model explains 82% of the variance associated with the abundance of potential larval habitats in Kisumu. In Malindi, 59% of the variance was explained. As the number of households increased, the number of larval habitats increased correspondingly to a point. Beyond a critical threshold, the density of households appeared to suppress the development of aquatic habitats. The proportion of high-income households and the planning and drainage variables tested insignificant in both locations. The integration of social and biologic sciences will allow local mosquito and malaria control groups an opportunity to assess the risk of encountering potentially infectious mosquitoes in a given area, and concentrate resources accordingly.

BackgroundCharacteristics 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.MethodsPhysical, 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.ResultsHabitats 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.ConclusionHabitats 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.

Background Mosquito Larval Source Management (LSM) could be a valuable additional tool for integrated malaria vector control especially in areas with focal transmission like the highlands of western Kenya if it were not for the need to target all potential habitats at frequent intervals. The ability to determine the productivity of malaria vectors from identified habitats might be used to target LSM only at productive ones. Methods Each aquatic habitat within three highland sites in western Kenya was classified as natural swamp, cultivated swamp, river fringe, puddle, open drain or burrow pit. Three habitats of each type were selected in each site in order to study the weekly productivity of adult malaria vectors from February to May 2009 using a sweep-net and their habitat characteristics recorded. Results All surveyed habitat types produced adult malaria vectors. Mean adult productivity of Anopheles gambiae sensu lato in puddles (1.8/m2) was 11–900 times higher than in the other habitat types. However, puddles were the most unstable habitats having water at 43% of all sampling occasions and accounted for 5% of all habitats mapped in the study areas whereas open drains accounted for 72%. Densities of anopheline late instars larvae significantly increased with the presence of a biofilm but decreased with increasing surface area or when water was flowing. Taking stability and frequency of the habitat into account, puddles were still the most productive habitat types for malaria vectors but closely followed by open drains. Conclusion Even though productivity of An. gambiae s.l. was greatest in small and unstable habitats, estimation of their overall productivity in an area needs to consider the more stable habitats over time and their surface extension. Therefore, targeting only the highly productive habitats is unlikely to provide sufficient reduction in malaria vector densities.

Background Recent resurgence of malaria in the highlands of Western Kenya has called for a more comprehensive understanding of the previously neglected complex highland vector ecology. Besides other drivers of malaria epidemiology, topography is likely to have a major effect on spatial vector and parasite distribution. The aim of this study was to determine the effects of topography on malaria spatial vector distribution and parasite prevalence. Methodology Indoor resting adult malaria vectors and blood parasites were collected in three villages along a 4 km transect originating from the valley bottom and ending at the hilltop for 13 months. Members of the Anopheles gambiae complex were identified by PCR. Blood parasites were collected from children 6–13 years old and densities categorized by site of home location and age of the children. Results Ninety eight percent (98%) of An. gambiae s.s. and (99%) Anopheles funestus were collected in houses located at the edge of the valley bottom, whereas 1% of An. gambiae s.s. were collected at mid hill and at the hilltop respectively. No An. funestus were collected at the hilltop. Malaria prevalence was 68% at the valley bottom, 40.2% at mid hill and 26.7% at the hilltop. Children aged six years and living at the edge of the valley bottom had an annual geometric mean number of 66.1 trophozoites for every 200 white blood cells, while those living at mid-hill had a mean of 84.8, and those living at hilltop had 199.5 trophozoites. Conclusion Malaria transmission in this area is mainly confined to the valley bottom. Effective vector control could be targeted at the foci. However, the few vectors observed at mid-hill maintained a relatively high prevalence rate. The higher variability in blood parasite densities and their low correlation with age in children living at the hilltop suggests a lower stability of transmission than at the mid-hill and valley bottom.