This dataset contains clinical data from 18,000 children with severe malaria admitted to Kilifi County Hospital, Kenya, during a 27-year period of reducing transmission. Data collection was done through continuous surveillance of hospital admissions is ongoing in KCH since May 1989 as a partnership between the Research Programme and Kilifi County Department of Health. The dataset also includes demographic characteristics and malaria control activities such as distributions of insecticide-treated bed nets. A more detailed description of the data collection methodology is included in the related publication.
Abstract Introduction The high proportion of SARS-CoV-2 infections that have remained undetected presents a challenge to tracking the progress of the pandemic and estimating the extent of population immunity. Methods We used residual blood samples from women attending antenatal care services at three hospitals in Kenya between August 2020 and October 2021and a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. We fitted a two-component mixture model as an alternative to the threshold analysis to estimate of the proportion of individuals with past SARS-CoV-2 infection. Results We estimated seroprevalence in 2,981 women; 706 in Nairobi, 567 in Busia and 1,708 in Kilifi. By October 2021, 13% of participants were vaccinated (at least one dose) in Nairobi, 2% in Busia. Adjusted seroprevalence rose in all sites; from 50% (95%CI 42-58) in August 2020, to 85% (95%CI 78-92) in October 2021 in Nairobi; from 31% (95%CI 25-37) in May 2021 to 71% (95%CI 64-77) in October 2021 in Busia; and from 1% (95% CI 0-3) in September 2020 to 63% (95% CI 56-69) in October 2021 in Kilifi. Mixture modelling, suggests adjusted cross-sectional prevalence estimates are underestimates; seroprevalence in October 2021 could be 74% in Busia and 72% in Kilifi. Conclusions There has been substantial, unobserved transmission of SARS-CoV-2 in Nairobi, Busia and Kilifi Counties. Due to the length of time since the beginning of the pandemic, repeated cross-sectional surveys are now difficult to interpret without the use of models to account for antibody waning.
Abstract The mortality impact of COVID-19 in Africa remains controversial because most countries lack vital registration. We analysed excess mortality in Kilifi Health and Demographic Surveillance System, Kenya, using 9 years of baseline data. SARS-CoV-2 seroprevalence studies suggest most adults here were infected before May 2022. During 5 waves of COVID-19 (April 2020-May 2022) an overall excess mortality of 4.8% (95% PI 1.2%, 9.4%) concealed a significant excess (11.6%, 95% PI 5.9%, 18.9%) among older adults ( ≥ 65 years) and a deficit among children aged 1–14 years (−7.7%, 95% PI −20.9%, 6.9%). The excess mortality rate for January 2020-December 2021, age-standardised to the Kenyan population, was 27.4/100,000 person-years (95% CI 23.2-31.6). In Coastal Kenya, excess mortality during the pandemic was substantially lower than in most high-income countries but the significant excess mortality in older adults emphasizes the value of achieving high vaccine coverage in this risk group.
Abstract Background Up-to-date SARS-CoV-2 antibody seroprevalence estimates are important for informing public health planning, including priorities for Coronavirus disease 2019 (COVID-19) vaccination programs. We sought to estimate infection- and vaccination-induced SARS-CoV-2 antibody seroprevalence within representative samples of the Kenyan population approximately two years into the COVID-19 pandemic and approximately one year after rollout of the national COVID-19 vaccination program. Methods We conducted cross-sectional serosurveys within random, age-stratified samples of Kilifi Health and Demographic Surveillance System (HDSS) and Nairobi Urban HDSS residents. Anti-spike (anti-S) immunoglobulin G (IgG) and anti-nucleoprotein (anti-N) IgG were measured using validated in-house ELISAs. Target-specific Bayesian population-weighted seroprevalence was calculated overall, by sex and by age, with adjustment for test performance as appropriate. Anti-S IgG concentrations were estimated with reference to the WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin and their reverse cumulative distributions plotted. Results Between February and June 2022, 852 and 851 individuals within the Kilifi HDSS and the Nairobi Urban HDSS, respectively, were sampled. Only 11.0% (95% confidence interval [CI] 9.0-13.3) of all Kilifi HDSS participants and 33.4% (95%CI 30.2-36.6) of all Nairobi Urban HDSS participants had received any doses of COVID-19 vaccine. Population-weighted anti-S IgG seroprevalence was 69.1% (95% credible interval [CrI] 65.8-72.3) within the Kilifi HDSS and 88.5% (95%CrI 86.1-90.6) within the Nairobi Urban HDSS. Among COVID-unvaccinated residents of the Kilifi HDSS and Nairobi Urban HDSS, it was 66.7% (95%CrI 63.3-70.0) and 85.3% (95%CrI 82.1-88.2), respectively. Population-weighted, test-adjusted anti-N IgG seroprevalence within the Kilifi HDSS was 53.5% (95%CrI 46.5-61.1) and 65.5% (95%CrI 56.0-75.6) within the Nairobi Urban HDSS. The prevalence of anti-N antibodies was similar in vaccinated and unvaccinated subgroups in both HDSS populations. Anti-S IgG concentrations were significantly lower among Kilifi HDSS residents than among Nairobi Urban HDSS residents (p< 0.001). Conclusions Approximately, 7 in 10 Kilifi residents and 9 in 10 Nairobi residents were seropositive for anti-S IgG by May 2022 and June 2022, respectively. Given COVID-19 vaccination coverage, anti-S IgG seropositivity among COVID-unvaccinated individuals, and anti-N IgG seroprevalence, population-level anti-S IgG seroprevalence was predominantly derived from infection. Interventions to improve COVID-19 vaccination uptake should be targeted to individuals in rural Kenya who are at high risk of severe COVID-19.
This is a replication data package for the manuscript titled: "Incidence and Mortality of childhood Non-Traumatic Coma of Unknown Cause in Kilifi County between 2002 to 2018." This is a secondary analysis of data from children aged 2 months to 13 years admitted at Kilifi County hospital from January 2002 to December 2013. The study aimed to investigate the incidence and mortality among children presenting with acute non-traumatic coma of unknown cause in Kilifi County between 2002 and 2018.
ObjectivesThe prevalence of all epilepsies (both convulsive and non-convulsive seizures) in Low- and Middle-Income Countries (LMIC), particularly sub-Saharan Africa is unknown. Under estimation of non-convulsive epilepsies in data from these countries may lead to inadequate and sub-optimal allocation of resources to control and prevent epilepsy. We determined the prevalence of all types of epilepsies and compared the mortality between convulsive seizures and non-convulsive seizures in a resource limited rural area in Kenya.MethodsTrained clinicians identified cases of epilepsy in a randomly selected sample of 4,441 residents in the Kilifi Health and Demographic Surveillance System site using a cross-sectional survey design. Seizure types were classified by epileptologists using the current guidelines of the International League Against Epilepsy (ILAE). We estimated prevalence for epilepsy with convulsive seizures and non-convulsive seizures and for epilepsy with non-convulsive seizures only and compared premature mortality between these groups of seizures.ResultsOf the 4441 people visited, 141 had lifetime epilepsy and 96 active epilepsy, which is a crude prevalence of 31.7/1,000 persons (95% CI: 26.6-36.9) and 21.6/1,000 (95% CI: 17.3-25.9), respectively. Both convulsive and non-convulsive seizures occurred in 7% people with epilepsy (PWE), only convulsive seizures in 52% and only non-convulsive seizures in 35% PWE; there was insufficient information to classify epilepsy in the remainder 6%. The age- and sex-adjusted prevalence of lifetime people was 23.5/1,000 (95% CI: 11.0-36.0), with the adjusted prevalence of epilepsy with non-convulsive seizures only estimated at 8.2/1,000 (95%CI:3.9-12.6). The mortality rate in PWE was 6.3/1,000 (95%CI: 3.4-11.8), compared to 2.8/1,000 (2.3-3.3) in those without epilepsy; hazard ratio (HR) =2.31 (1.22-4.39; p=0.011). The annual mortality rate was 11.2/1,000 (95%CI: 5.3-23.4) in PWE with convulsive and non-convulsive seizures and none died in PWE with non-convulsive seizures alone.ConclusionsOur study shows that epilepsy with non-convulsive seizures is common and adds to the prevalence of previously reported estimates of active convulsive epilepsy. Both epilepsy with convulsive seizures and that with non-convulsive seizures should be identified for optimising treatment and for planning resource allocation.
Background We estimated the secondary attack rate of SARS-CoV-2 among household contacts of PCR-confirmed cases of COVID-19 in rural Kenya and analysed risk factors for transmission. Methods We enrolled incident PCR-confirmed cases and their household members. At baseline, a questionnaire, a blood sample, and naso-oropharyngeal swabs were collected. Household members were followed 4, 7, 10, 14, 21 and 28 days after the date of the first PCR-positive in the household; naso-oropharyngeal swabs were collected at each visit and used to define secondary cases. Blood samples were collected every 1-2 weeks. Symptoms were collected in a daily symptom diary. We used binomial regression to estimate secondary attack rates and survival analysis to analyze risk factors for transmission. Results A total of 119 households with at least one positive household member were enrolled between October 2020 and September 2022, comprising 503 household members; 226 remained in follow up at day-14 (45%). A total of 43 secondary cases arose within 14 days of identification of the primary case, 81 household members remained negative. The 7-day secondary attack rate was 4% (95%CI 1-10%), the 14-day secondary attack rate was 28% (95%CI 17-40%). Of 38 secondary cases with data, 8 reported symptoms (21%, 95%CI 8-34%). Antibody to SARS-CoV-2 spike protein at enrolment was not associated with risk of becoming a secondary case. Conclusion Households in our setting experienced a lower 7-day attack rate than a recent meta-analysis indicated as the global average (23-43% depending on variant), and infection is mostly asymptomatic in our setting.
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