Development of a trash classification system to map potential Aedes aegypti breeding grounds using unmanned aerial vehicle imaging.

Aedes aegypti mosquitos are the primary vector for dengue, chikungunya, and Zika viruses and tend to breed in small containers of water, with a propensity to breed in small piles of trash and abandoned tires. This study piloted the use of aerial imaging to map and classify potential Ae. aegypti breeding sites with a specific focus on trash, including discarded tires. Aerial images of coastal and inland sites in Kenya were obtained using an unmanned aerial vehicle. Aerial images were reviewed for identification of trash and suspected trash mimics, followed by extensive community walk-throughs to identify trash types and mimics by description and ground photography. An expert panel reviewed aerial images and ground photos to develop a classification scheme and evaluate the advantages and disadvantages of aerial imaging versus walk-through trash mapping. A trash classification scheme was created based on trash density, surface area, potential for frequent disturbance, and overall likelihood of being a productive Ae. aegypti breeding site. Aerial imaging offers a novel strategy to characterize, map, and quantify trash at risk of promoting Ae. aegypti proliferation, generating opportunities for further research on trash associations with disease and trash interventions.

Low Rate of Asymptomatic Dengue Infection Detected in Coastal Kenya Using Pooled Polymerase Chain Reaction Testing.

Asymptomatic dengue virus (DENV) infections have important public health implications but are challenging to identify. We performed a cross-sectional study of reverse transcription quantitative polymerase chain reaction on pooled sera of asymptomatic individuals from the south coast of Kenya at two time periods to identify cases of asymptomatic viremia. Among 2,460 samples tested in pools of 9 or 10, we found only one positive case (0.04% incidence). Although pooling of samples has the potential to be a cost-effective and time-efficient method for asymptomatic DENV detection, mass cross-sectional pooled testing may not provide accurate data on rates of asymptomatic infection, likely owing to a decrease in the sensitivity with pooling of samples, a short period of viremia, or testing in the absence of an outbreak.

Non-household environments make a major contribution to dengue transmission: Implications for vector control.

Aedes-borne pathogens have been increasing in incidence in recent decades despite vector control activities implemented in endemic settings. Vector control for Aedes-transmitted arboviruses typically focuses on households because vectors breed in household containers and bite indoors. Yet, our recent work shows a high abundance of Aedes spp. vectors in public spaces. To investigate the impact of non-household environments on dengue transmission and control, we used field data on the number of water containers and abundance of Aedes mosquitoes in Household (HH) and Non-Household (NH) environments in two Kenyan cities, Kisumu and Ukunda, from 2019-2022. Incorporating information on human activity space, we developed an agent-based model to simulate city-wide conditions considering HH and five types of NH environments in which people move and interact with other humans and vectors during peak biting times. We additionally evaluated the outcome of vector control activities implemented in different environments in preventive (before an epidemic) and reactive (after an epidemic commences) scenarios. We estimated that over half of infections take place in NH environments, where the main spaces for transmission are workplaces, markets, and recreational locations. Accordingly, results highlight the important role of vector control activities at NH locations to reduce dengue. A greater reduction of cases is expected as control activities are implemented earlier, at higher levels of coverage, with greater effectiveness when targeting only NH as opposed to when targeting only HH. Further, local ecological factors such as the differential abundance of water containers within cities are also influential factors to consider for control. This work provides insight into the importance of vector control in both household and non-household environments in endemic settings. It highlights a specific approach to inform evidence-based decision making to target limited vector control resources for optimal control.

Detection of acute dengue virus infection, with and without concurrent malaria infection, in a cohort of febrile children in Kenya, 2014-2019, by clinicians or machine learning algorithms.

Poor access to diagnostic testing in resource limited settings restricts surveillance for emerging infections, such as dengue virus (DENV), to clinician suspicion, based on history and exam observations alone. We investigated the ability of machine learning to detect DENV based solely on data available at the clinic visit. We extracted symptom and physical exam data from 6,208 pediatric febrile illness visits to Kenyan public health clinics from 2014-2019 and created a dataset with 113 clinical features. Malaria testing was available at the clinic site. DENV testing was performed afterwards. We randomly sampled 70% of the dataset to develop DENV and malaria prediction models using boosted logistic regression, decision trees and random forests, support vector machines, naïve Bayes, and neural networks with 10-fold cross validation, tuned to maximize accuracy. 30% of the dataset was reserved to validate the models. 485 subjects (7.8%) had DENV, and 3,145 subjects (50.7%) had malaria. 220 (3.5%) subjects had co-infection with both DENV and malaria. In the validation dataset, clinician accuracy for diagnosis of malaria was high (82% accuracy, 85% sensitivity, 80% specificity). Accuracy of the models for predicting malaria diagnosis ranged from 53-69% (35-94% sensitivity, 11-80% specificity). In contrast, clinicians detected only 21 of 145 cases of DENV (80% accuracy, 14% sensitivity, 85% specificity). Of the six models, only logistic regression identified any DENV case (8 cases, 91% accuracy, 5.5% sensitivity, 98% specificity). Without diagnostic testing, interpretation of clinical findings by humans or machines cannot detect DENV at 8% prevalence. Access to point-of-care diagnostic tests must be prioritized to address global inequities in emerging infections surveillance.

The Importance of Including Non-Household Environments in Dengue Vector Control Activities.

Most vector control activities in urban areas are focused on household environments; however, information relating to infection risks in spaces other than households is poor, and the relative risk that these spaces represent has not yet been fully understood. We used data-driven simulations to investigate the importance of household and non-household environments for dengue entomological risk in two Kenyan cities where dengue circulation has been reported. Fieldwork was performed using four strategies that targeted different stages of mosquitoes: ovitraps, larval collections, Prokopack aspiration, and BG-sentinel traps. Data were analyzed separately between household and non-household environments to assess mosquito presence, the number of vectors collected, and the risk factors for vector presence. With these data, we simulated vector and human populations to estimate the parameter m and mosquito-to-human density in both household and non-household environments. Among the analyzed variables, the main difference was found in mosquito abundance, which was consistently higher in non-household environments in Kisumu but was similar in Ukunda. Risk factor analysis suggests that small, clean water-related containers serve as mosquito breeding places in households as opposed to the trash- and rainfall-related containers found in non-household structures. We found that the density of vectors (m) was higher in non-household than household environments in Kisumu and was also similar or slightly lower between both environments in Ukunda. These results suggest that because vectors are abundant, there is a potential risk of transmission in non-household environments; hence, vector control activities should take these spaces into account.

Oviposition Preferences of Aedes aegypti in Msambweni, Kwale County, Kenya.

Aedes aegypti is the primary vector of dengue fever virus (DENV) worldwide. Infusions made from organic materials have been shown to act as oviposition attractants for Ae. aegypti; however, studies on locally suitable infusion materials are lacking. The current study assessed the suitability of 4 locally available materials as oviposition infusions for use in surveillance and control of Ae. aegypti in Kwale County, Kenya. Oviposition infusion preferences were assessed in laboratory, semifield, and field conditions, using 4 infusions made from banana, grass, neem, and coconut. In addition, ovitrapping in wall, grass, bush, and banana microhabitats was done in 10 houses each in urban and rural coastal households to determine suitable oviposition microhabitats. Overall, the highest oviposition responses were observed for banana infusion, followed by neem and grass infusions, which were comparable. Coconut infusion resulted in the lowest oviposition response. Although female Ae. aegypti did not show preference for any microhabitat, the oviposition activity across all the microhabitats was highly enhanced by use of the organic infusions. Banana, neem, and grass infusions could be used to attract gravid mosquitoes to oviposition sites laced with insecticide to kill eggs. Additionally, banana plantings could be important targets for integrated vector control programs.

Spatiotemporal overlapping of dengue, chikungunya, and malaria infections in children in Kenya.

Malaria, chikungunya virus (CHIKV), and dengue virus (DENV) are endemic causes of fever among children in Kenya. The risks of infection are multifactorial and may be influenced by built and social environments. The high resolution overlapping of these diseases and factors affecting their spatial heterogeneity has not been investigated in Kenya. From 2014-2018, we prospectively followed a cohort of children from four communities in both coastal and western Kenya. Overall, 9.8% were CHIKV seropositive, 5.5% were DENV seropositive, and 39.1% were malaria positive (3521 children tested). The spatial analysis identified hot-spots for all three diseases in each site and in multiple years. The results of the model showed that the risk of exposure was linked to demographics with common factors for the three diseases including the presence of litter, crowded households, and higher wealth in these communities. These insights are of high importance to improve surveillance and targeted control of mosquito-borne diseases in Kenya.

Pupal productivity of larval habitats of Aedes aegypti in Msambweni, Kwale County, Kenya.

Aedes aegypti is an important vector of several arboviruses including dengue and chikungunya viruses. Accurate identification of larval habitats of Ae. aegypti is considered an essential step in targeted control. This study determined Ae. aegypti productivity in selected larval habitats in Msambweni, Kwale County, Kenya. Three sequential larval habitat surveys were conducted. The first survey was habitat census (baseline) through which 83 representative larval habitats were identified and selected. The second and third surveys involved estimating daily productivity of the 83 selected larval habitats for 30 consecutive days during a wet and a dry season, respectively. Of 664 larval habitats examined at baseline, 144 larval habitats (21.7%) were found to be infested with Ae. aegypti larvae. At baseline, majority (71%) of the pupae were collected from two (2/6) larval habitat types, tires and pots. Multivariate analysis identified habitat type and the habitat being movable as the predictors for pupal abundance. During the 30-day daily pupal production surveys, only a few of the habitats harbored pupae persistently. Pupae were found in 28% and 12% of the larval habitats during the wet and dry seasons, respectively. In the wet season, drums, tires, and pots were identified as the key habitat types accounting for 85% of all pupae sampled. Three habitats (all drums) accounted for 80% of all the pupae collected in the dry season. Predictors for pupal productivity in the wet season were habitat type, place (whether the habitat is located at the back or front of the house), habitat purpose (use of the water in the habitat), and source of water. Although the multivariate model for habitat type did not converge, habitat type and habitat size were the only significant predictors during the dry season. Drums, pots, and tires were sources of more than 85% of Ae. aegypti pupae, reinforcing the "key container concept." Targeting these three types of habitats makes epidemiological sense, especially during the dry season.

Exploring potential risk pathways with high risk groups for urban Rift Valley fever virus introduction, transmission, and persistence in two urban centers of Kenya.

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.

Leveraging livestock movements to urban slaughterhouses for wide-spread Rift Valley fever virus surveillance in Western 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.

Resistance of Anopheles gambiae sensu lato to Pirimiphos-methyl Insecticide in Kakamega County, Highlands of Western Kenya.

Background: Insecticide treated bed nets and Indoor residual spraying remains the principal interventional malaria control strategies. To achieve malaria disease eradication, vector control programmes that monitor insecticide resistance profiles are necessary. Objective: The study evaluated pirimiphos-methyl susceptibility of Anopheles gambiae sensu lato in Kakamega County, western Kenya. Methods: Adult Anopheles gambiae sensu lato mosquitoes were assayed using World Health Organization tube bioassay against 0.25% pirimiphos-methyl. Susceptible and non-susceptible populations were characterized to species-level using Polymerase Chain Reaction. Susceptible and resistant mosquitoes were further subjected to G119S Acetylcholisterase (ace 1R) mutation detection. Results: Anopheles arabiensis was the predominant species in all study population Mumias east (62%), Malava (68%), Ikolomani (77%) and Lurambi (82%). Results showed phenotypic susceptibility to pirimiphos-methyl. Mortality was low in Mumias east (80.6%) and high in Lurambi (89.0%). G119S mutations ranged from 3.0% to 8.9% in Anopheles arabiensis whereas G119S mutations were relatively low ranging from 0.0% to 3.1% in Anopheles gambiae s.s populations. Study populations tested were consistent with Hardy-Weinberg equilibrium (P>0.05). Conclusion: We observed pirimiphos-methyl resistance in Anopheles arabiensis and Anopheles gambiae s.s. study populations. Results showed G119S mutation in resistance population. Resistance monitoring and management are urgently required.

Night Time Extension of Aedes aegypti Human Blood Seeking Activity.

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.

Majority of pediatric dengue virus infections in Kenya do not meet 2009 WHO criteria for dengue diagnosis.

From 1975-2009, the WHO guidelines classified symptomatic dengue virus infections as dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. In 2009 the case definition was changed to a clinical classification after concern the original criteria was challenging to apply in resource-limited settings and not inclusive of a substantial proportion of severe dengue cases. Our goal was to examine how well the current WHO definition identified new dengue cases at our febrile surveillance sites in Kenya. Between 2014 and 2019 as part of a child cohort study of febrile illness in our four clinical study sites (Ukunda, Kisumu, Msambweni, Chulaimbo) we identified 369 dengue PCR positive symptomatic cases and characterized whether they met the 2009 revised WHO diagnostic criteria for dengue with and without warning signs and severe dengue. We found 62% of our PCR-confirmed dengue cases did not meet criteria per the guidelines. Our findings also correlate with our experience that dengue disease in children in Kenya is less severe as reported in other parts of the world. Although the 2009 clinical classification has recently been criticized for being overly inclusive and non-specific, our findings suggest the 2009 WHO dengue case definition may miss more than 50% of symptomatic infections in Kenya and may require further modification to include the African experience.

Urban risk factors for human Rift Valley fever virus exposure in Kenya.

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.

Impact of recent climate extremes on mosquito-borne disease transmission in Kenya.

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.

No Evidence of O'nyong-nyong Viremia among Children with Febrile Illness in Kenya (2015-2018).

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.

Climate predicts geographic and temporal variation in mosquito-borne disease dynamics on two continents.

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.

High Frequency of Antibiotic Prescription in Children With Undifferentiated Febrile Illness in Kenya.

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.

Risk factors for Aedes aegypti household pupal persistence in longitudinal entomological household surveys in urban and rural 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.

High Dengue Burden and Circulation of 4 Virus Serotypes among Children with Undifferentiated Fever, Kenya, 2014-2017.

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.