Implementing adaptive e-learning for newborn care in Tanzania: an observational study of provider engagement and knowledge gains

INTRODUCTION

To improve healthcare provider knowledge of Tanzanian newborn care guidelines, we developed adaptive Essential and Sick Newborn Care (aESNC), an adaptive e-learning environment. The objectives of this study were to (1) assess implementation success with use of in-person support and nudging strategy and (2) describe baseline provider knowledge and metacognition.

METHODS

6-month observational study at one zonal hospital and three health centres in Mwanza, Tanzania. To assess implementation success, we used the Reach, Efficacy, Adoption, Implementation and Maintenance framework and to describe baseline provider knowledge and metacognition we used Howell's conscious-competence model. Additionally, we explored provider characteristics associated with initial learning completion or persistent activity.

RESULTS

aESNC reached 85% (195/231) of providers: 75 medical, 53 nursing and 21 clinical officers; 110 (56%) were at the zonal hospital and 85 (44%) at health centres. Median clinical experience was 4 years (IQR 1-9) and 45 (23%) had previous in-service training for both newborn essential and sick newborn care. Efficacy was 42% (SD ±17%). Providers averaged 78% (SD ±31%) completion of initial learning and 7% (SD ±11%) of refresher assignments. 130 (67%) providers had ≥1 episode of inactivity >30 day, no episodes were due to lack of internet access. Baseline conscious-competence was 53% (IQR: 38%-63%), unconscious-incompetence 32% (IQR: 23%-42%), conscious-incompetence 7% (IQR: 2%-15%), and unconscious-competence 2% (IQR: 0%-3%). Higher baseline conscious-competence (OR 31.6 (95% CI 5.8 to 183.5)) and being a nursing officer (aOR: 5.6 (95% CI 1.8 to 18.1)), compared with medical officer, were associated with initial learning completion or persistent activity.

CONCLUSION

aESNC reach was high in a population of frontline providers across diverse levels of care in Tanzania. Use of in-person support and nudging increased reach, initial learning and refresher assignment completion, but refresher assignment completion remains low. Providers were often unaware of knowledge gaps, and lower baseline knowledge may decrease initial learning completion or activity. Further study to identify barriers to adaptive e-learning normalisation is needed.

Harmonizing Data Visualizations on Child Health and Well-Being to Strengthen Advocacy and Monitoring Efforts

Data visualization tools on child health have improved data accessibility but caused confusion over indicator data sources and which tools to use for specific purposes. We propose principles for generating future tools that can effectively trigger action and accountability for children everywhere.

Advocacy for Better Integration and Use of Child Health Indicators for Global Monitoring

Making better use of harmonized indicators to monitor child health and well-being at the global level will avoid duplicative monitoring and evaluation exercises, improve evidence-based programming, and preserve resources that can be used to improve the quality of national data collection platforms.

Prevalence and risk factors for long COVID and post-COVID-19 condition in Africa: a systematic review

BACKGROUND

An improved estimation of the clinical sequelae of SARS-CoV-2 infection is crucial in African countries, where the subject has received little attention despite more than 12 million reported cases and evidence that many more people were infected. We reviewed the evidence on prevalence, associated risk factors for long COVID, and systemic or sociocultural determinants of reporting long COVID.

METHODS

We conducted a systematic review, searching PubMed, the Living OVerview of Evidence platform, and grey literature sources for publications from Dec 1, 2019, to Nov 23, 2022. We included articles published in English, French, Spanish, or Portuguese that reported on any study type in Africa with participants of any age who had symptoms for 4 weeks or more after an acute SARS-CoV-2 infection. We excluded secondary research, comments, and correspondence. Screening and data extraction were performed by two reviewers. Summary estimates were extracted, including sociodemographic factors, medical history, prevalence of persistent symptoms, and symptoms and associated factors. Results were analysed descriptively. The study was registered on the Open Science Framework platform.

FINDINGS

Our search yielded 294 articles, of which 24 peer-reviewed manuscripts were included, reporting on 9712 patients from eight African countries. Only one study exclusively recruited children, and one other study included children as part of their study population. Studies indicated moderate to low risk of bias. Prevalence of long COVID varied widely, from 2% in Ghana to 86% in Egypt. Long COVID was positively associated with female sex, older age, non-Black ethnicity, low level of education, and the severity of acute infection and underlying comorbidity. HIV and tuberculosis were not identified as risk factors. Factors influencing reporting included absence of awareness, inadequate clinical data and diagnostics, and little access to health-care services.

INTERPRETATION

In Africa, research on long COVID is scarce, particularly among children, who represent the majority of the population. However, existing studies show a substantial prevalence across settings, emphasising the importance of vaccination and other prevention strategies to avert the effects of long COVID on individual wellbeing, the increased strain on health systems, and the potential negative effects on economically vulnerable populations. At a global level, including African countries, tools for research on long COVID need to be harmonised to maximise the usefulness of the data collected.

FUNDING

None.

Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study

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.

Symptom prevalence and secondary attack rate of SARS-CoV-2 in rural Kenyan households: A prospective cohort study

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 analyse 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, and 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, eight 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.

SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February-December 2022

BACKGROUND

We sought to estimate SARS-CoV-2 antibody seroprevalence within representative samples of the Kenyan population during the third year of the COVID-19 pandemic and the second year of COVID-19 vaccine use.

METHODS

We conducted cross-sectional serosurveys among randomly selected, age-stratified samples of Health and Demographic Surveillance System (HDSS) residents in Kilifi and Nairobi. Anti-spike (anti-S) immunoglobulin G (IgG) serostatus was measured using a validated in-house ELISA and antibody concentrations estimated with reference to the WHO International Standard for anti-SARS-CoV-2 immunoglobulin.

RESULTS

HDSS residents were sampled in February-June 2022 (Kilifi HDSS N = 852; Nairobi Urban HDSS N = 851) and in August-December 2022 (N = 850 for both sites). Population-weighted coverage for ≥1 doses of COVID-19 vaccine were 11.1% (9.1-13.2%) among Kilifi HDSS residents by November 2022 and 34.2% (30.7-37.6%) among Nairobi Urban HDSS residents by December 2022. Population-weighted anti-S IgG seroprevalence among Kilifi HDSS residents increased from 69.1% (65.8-72.3%) by May 2022 to 77.4% (74.4-80.2%) by November 2022. Within the Nairobi Urban HDSS, seroprevalence by June 2022 was 88.5% (86.1-90.6%), comparable with seroprevalence by December 2022 (92.2%; 90.2-93.9%). For both surveys, seroprevalence was significantly lower among Kilifi HDSS residents than among Nairobi Urban HDSS residents, as were antibody concentrations (p < 0.001).

CONCLUSION

More than 70% of Kilifi residents and 90% of Nairobi residents were seropositive for anti-S IgG by the end of 2022. There is a potential immunity gap in rural Kenya; implementation of interventions to improve COVID-19 vaccine uptake among sub-groups at increased risk of severe COVID-19 in rural settings is recommended.

Feasibility of an Adaptive E-Learning Environment to Improve Provider Proficiency in Essential and Sick Newborn Care in Mwanza, Tanzania

Introduction

To improve healthcare provider knowledge of Tanzanian newborn care guidelines, we developed adaptive Essential and Sick Newborn Care (aESNC), an adaptive e-learning environment (AEE). The objectives of this study were to 1) assess implementation success with use of in-person support and nudging strategy and 2) describe baseline provider knowledge and metacognition.

Methods

6-month observational study at 1 zonal hospital and 3 health centers in Mwanza, Tanzania. To assess implementation success, we used the RE-AIM framework and to describe baseline provider knowledge and metacognition we used Howell's conscious-competence model. Additionally, we explored provider characteristics associated with initial learning completion or persistent activity.

Results

aESNC reached 85% (195/231) of providers: 75 medical, 53 nursing, and 21 clinical officers; 110 (56%) were at the zonal hospital and 85 (44%) at health centers. Median clinical experience was 4 years [IQR 1,9] and 45 (23%) had previous in-service training for both newborn essential and sick newborn care. Efficacy was 42% (SD±17%). Providers averaged 78% (SD±31%) completion of initial learning and 7%(SD±11%) of refresher assignments. 130 (67%) providers had ≥1 episode of inactivity >30 day, no episodes were due to lack of internet access. Baseline conscious-competence was 53% [IQR:38-63%], unconscious-incompetence 32% [IQR:23-42%], conscious-incompetence 7% [IQR:2-15%], and unconscious-competence 2% [IQR:0-3%]. Higher baseline conscious-competence (OR 31.6 [95%CI:5.8, 183.5) and being a nursing officer (aOR: 5.6 [95%CI:1.8, 18.1]), compared to medical officer) were associated with initial learning completion or persistent activity.

Conclusion

aESNC reach was high in a population of frontline providers across diverse levels of care in Tanzania. Use of in-person support and nudging increased reach, initial learning, and refresher assignment completion, but refresher assignment completion remains low. Providers were often unaware of knowledge gaps, and lower baseline knowledge may decrease initial learning completion or activity. Further study to identify barriers to adaptive e-learning normalization is needed.

Clinical epidemiology of COVID-19 among hospitalized children in rural western Kenya

The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection.

Regular measurement is essential but insufficient to improve quality of healthcare

Ambrose Agweyu and colleagues argue that large scale improvements in quality of healthcare require strong change management as well as health information systems that can provide continuous and rapid feedback

Mortality in rural coastal Kenya measured using the Kilifi Health and Demographic Surveillance System: a 16-year descriptive analysis

Background: The Kilifi Health and Demographic Surveillance System (KHDSS) was established in 2000 to define the incidence and prevalence of local diseases and evaluate the impact of community-based interventions. KHDSS morbidity data have been reported comprehensively but mortality has not been described. This analysis describes mortality in the KHDSS over 16 years. Methods: We calculated mortality rates from 2003-2018 in four intervals of equal duration and assessed differences in mortality across these intervals by age and sex. We calculated the period survival function and median survival using the Kaplan-Meier method and mean life expectancies using abridged life tables. We estimated trend and seasonality by decomposing a time series of monthly mortality rates. We used choropleth maps and random-effects Poisson regression to investigate geographical heterogeneity. Results: Mortality declined by 36% overall between 2003-2018 and by 59% in children aged <5 years. Most of the decline occurred between 2003 and 2006. Among adults, the greatest decline (49%) was observed in those aged 15-54 years. Life expectancy at birth increased by 12 years. Females outlived males by 6 years. Seasonality was only evident in the 1-4 year age group in the first four years. Geographical variation in mortality was ±10% of the median value and did not change over time. Conclusions: Between 2003 and 2018, mortality among children and young adults has improved substantially. The steep decline in 2003-2006 followed by a much slower reduction thereafter suggests improvements in health and wellbeing have plateaued in the last 12 years. However, there is substantial inequality in mortality experience by geographical location.

Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro

OBJECTIVES

Many regions of Africa have experienced lower COVID-19 morbidity and mortality than Europe. Pre-existing humoral responses to endemic human coronaviruses (HCoV) may cross-protect against SARS-CoV-2. We investigated the neutralizing capacity of SARS-CoV-2 spike reactive and nonreactive immunoglobulin (Ig)G and IgA antibodies in prepandemic samples.

METHODS

To investigate the presence of pre-existing immunity, we performed enzyme-linked immunosorbent assay using spike antigens from reference SARS-CoV-2, HCoV HKU1, OC43, NL63, and 229E using prepandemic samples from Kilifi in coastal Kenya. In addition, we performed neutralization assays using pseudotyped reference SARS-CoV-2 to determine the functionality of the identified reactive antibodies.

RESULTS

We demonstrate the presence of HCoV serum IgG and mucosal IgA antibodies, which cross-react with the SARS-CoV-2 spike. We show pseudotyped reference SARS-CoV-2 neutralization by prepandemic serum, with a mean infective dose 50 of 1: 251, which is 10-fold less than that of the pooled convalescent sera from patients with COVID-19 but still within predicted protection levels. The prepandemic naso-oropharyngeal fluid neutralized pseudo-SARS-CoV-2 at a mean infective dose 50 of 1: 5.9 in the neutralization assay.

CONCLUSION

Our data provide evidence for pre-existing functional humoral responses to SARS-CoV-2 in Kilifi, coastal Kenya and adds to data showing pre-existing immunity for COVID-19 from other regions.

Development of pediatric acute care education (PACE): An adaptive electronic learning (e-learning) environment for healthcare providers in Tanzania

Globally, inadequate healthcare provider (HCP) proficiency with evidence-based guidelines contributes to millions of newborn, infant, and child deaths each year. HCP guideline proficiency would improve patient outcomes. Conventional (in person) HCP in-service education is limited in 4 ways: reach, scalability, adaptability, and the ability to contextualize. Adaptive e-learning environments (AEE), a subdomain of e-learning, incorporate artificial intelligence technology to create a unique cognitive model of each HCP to improve education effectiveness. AEEs that use existing internet access and personal mobile devices may overcome limits of conventional education. This paper provides an overview of the development of our AEE HCP in-service education, Pediatric Acute Care Education (PACE). PACE uses an innovative approach to address HCPs' proficiency in evidence-based guidelines for care of newborns, infants, and children. PACE is novel in 2 ways: 1) its patient-centric approach using clinical audit data or frontline provider input to determine content and 2) its ability to incorporate refresher learning over time to solidify knowledge gains. We describe PACE's integration into the Pediatric Association of Tanzania's (PAT) Clinical Learning Network (CLN), a multifaceted intervention to improve facility-based care along a single referral chain. Using principles of co-design, stakeholder meetings modified PACE's characteristics and optimized integration with CLN. We plan to use three-phase, mixed-methods, implementation process. Phase I will examine the feasibility of PACE and refine its components and protocol. Lessons gained from this initial phase will guide the design of Phase II proof of concept studies which will generate insights into the appropriate empirical framework for (Phase III) implementation at scale to examine effectiveness.

A pragmatic randomized controlled trial of standard care versus steroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals (SONIA)

Background: It is unclear if adjunctive steroid therapy reduces mortality in community-acquired pneumonia, as very few studies have had mortality as a primary outcome. This question has become even more relevant following demonstration of a mortality benefit of dexamethasone when used in patients with COVID-19 who had severe disease. This has led to increased prescription of steroids in adults with community acquired pneumonia in low-resource settings even when their COVID-19 diagnosis is uncertain due to low testing rates. This pragmatic parallel randomised-controlled open-label trial will determine if adjunctive low-dose steroids for treatment of adults admitted to hospital with community acquired pneumonia whose SARS-CoV-2 status is either unknown or negative reduces mortality. Methods: We will enroll and randomize 2180 patients admitted with a clinical diagnosis of community acquired pneumonia into two arms; in Stratum A-participants will receive standard care for the treatment of community acquired pneumonia. In Stratum B-participants will receive a 10-day course of low-dose oral corticosteroids in addition to standard care. All participants will be followed up to 30 days post randomization and their final status recorded (alive or dead). An immunology sub study will be conducted on a subset of the trial participants (50 per arm) to determine the correlation of pre-existing and treatment induced immune and metabolic changes with study outcomes. Discussion: Mortality among adults admitted to hospital with community acquired pneumonia in resource-limited settings is high. Steroids are readily available in these settings. If the addition of steroids to standard care for community acquired pneumonia is found to be beneficial, this easily scalable intervention would significantly reduce the currently high mortality associated with the illness.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.

SARS-CoV-2 seroprevalence in three Kenyan health and demographic surveillance sites, December 2020-May 2021

BACKGROUND

Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. We conducted population-based serosurveys at three Health and Demographic Surveillance Systems (HDSSs) to determine the cumulative incidence of infection with SARS-CoV-2.

METHODS

We selected random age-stratified population-based samples at HDSSs in Kisumu, Nairobi and Kilifi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. No participant had received a COVID-19 vaccine. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally-validated assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. We adjusted prevalence estimates using classical methods and Bayesian modelling to account for the sampling scheme and assay performance.

RESULTS

We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27 (10-78) years and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kisumu, Nairobi and Kilifi, seroprevalences (95% CI) at the beginning of the study were 36.0% (28.2-44.4%), 32.4% (23.1-42.4%), and 14.5% (9.1-21%), and respectively; at the end they were 42.0% (34.7-50.0%), 50.2% (39.7-61.1%), and 24.7% (17.5-32.6%), respectively. Seroprevalence was substantially lower among children (<16 years) than among adults at all three sites (p≤0.001).

CONCLUSION

By May 2021 in three broadly representative populations of unvaccinated individuals in Kenya, seroprevalence of anti-SARS-CoV-2 IgG was 25-50%. There was wide variation in cumulative incidence by location and age.

Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya

BACKGROUND

A few studies have assessed the epidemiological impact and the cost-effectiveness of COVID-19 vaccines in settings where most of the population had been exposed to SARS-CoV-2 infection.

METHODS

We conducted a cost-effectiveness analysis of COVID-19 vaccine in Kenya from a societal perspective over a 1.5-year time frame. An age-structured transmission model assumed at least 80% of the population to have prior natural immunity when an immune escape variant was introduced. We examine the effect of slow (18 months) or rapid (6 months) vaccine roll-out with vaccine coverage of 30%, 50% or 70% of the adult (>18 years) population prioritising roll-out in those over 50-years (80% uptake in all scenarios). Cost data were obtained from primary analyses. We assumed vaccine procurement at US$7 per dose and vaccine delivery costs of US$3.90-US$6.11 per dose. The cost-effectiveness threshold was US$919.11.

FINDINGS

Slow roll-out at 30% coverage largely targets those over 50 years and resulted in 54% fewer deaths (8132 (7914-8373)) than no vaccination and was cost saving (incremental cost-effectiveness ratio, ICER=US$-1343 (US$-1345 to US$-1341) per disability-adjusted life-year, DALY averted). Increasing coverage to 50% and 70%, further reduced deaths by 12% (810 (757-872) and 5% (282 (251-317) but was not cost-effective, using Kenya's cost-effectiveness threshold (US$919.11). Rapid roll-out with 30% coverage averted 63% more deaths and was more cost-saving (ICER=US$-1607 (US$-1609 to US$-1604) per DALY averted) compared with slow roll-out at the same coverage level, but 50% and 70% coverage scenarios were not cost-effective.

INTERPRETATION

With prior exposure partially protecting much of the Kenyan population, vaccination of young adults may no longer be cost-effective.

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

Background

Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.

Methods

Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis.

Results

During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.

Conclusions

Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.

Funding

This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.

Measuring and monitoring child health and wellbeing: recommendations for tracking progress with a core set of indicators in the Sustainable Development Goals era

Although great improvements in child survival were achieved in the past two decades, progress has been uneven within and across countries, and the COVID-19 pandemic threatens to reverse previous advances. Demographic and epidemiological transitions around the world have resulted in shifts in the causes and distribution of child death and diseases, and many children are living with short-term and long-term chronic illnesses and disabilities. These changes, plus global threats such as pandemics, transnational and national security issues, and climate change, mean that regular monitoring of child health and wellbeing is essential if we are to achieve the Sustainable Development Goals. This Health Policy describes the three-phased process undertaken by the Child Health Accountability Tracking technical advisory group (CHAT) to develop a core set of indicators on child health and wellbeing for global monitoring purposes, and presents CHAT's research recommendations to address data gaps. CHAT reached consensus on 20 core indicators specific to the health sector, which include 11 impact-level indicators and nine outcome-level indicators that cover the topics of: acute conditions and prevention; health promotion and child development; and chronic conditions, disabilities, injuries, and violence against children. An additional six indicators (three impact and three outcome) that capture information on child health issues such as malaria and HIV are recommended; however, these indicators are only relevant to high-burden regions. CHAT's four research priorities will require investments in health information systems and measurement activities. These investments will help to increase data on children aged 5-9 years; develop standard metadata and data collection processes to enable cross-country comparisons and progress assessments over time; reach a global consensus on essential interventions and associated indicators for monitoring emerging priority areas such as child development, chronic conditions, disabilities, and injuries; and implement strategies to increase the uptake of data on child health to improve evidence-based planning, programming, and advocacy efforts.

Unmet need for COVID-19 vaccination coverage in Kenya

COVID-19 has impacted the health and livelihoods of billions of people since it emerged in 2019. Vaccination for COVID-19 is a critical intervention that is being rolled out globally to end the pandemic. Understanding the spatial inequalities in vaccination coverage and access to vaccination centres is important for planning this intervention nationally. Here, COVID-19 vaccination data, representing the number of people given at least one dose of vaccine, a list of the approved vaccination sites, population data and ancillary GIS data were used to assess vaccination coverage, using Kenya as an example. Firstly, physical access was modelled using travel time to estimate the proportion of population within 1 hour of a vaccination site. Secondly, a Bayesian conditional autoregressive (CAR) model was used to estimate the COVID-19 vaccination coverage and the same framework used to forecast coverage rates for the first quarter of 2022. Nationally, the average travel time to a designated COVID-19 vaccination site (n = 622) was 75.5 min (Range: 62.9 - 94.5 min) and over 87% of the population >18 years reside within 1 hour to a vaccination site. The COVID-19 vaccination coverage in December 2021 was 16.70% (95% CI: 16.66 - 16.74) - 4.4 million people and was forecasted to be 30.75% (95% CI: 25.04 - 36.96) - 8.1 million people by the end of March 2022. Approximately 21 million adults were still unvaccinated in December 2021 and, in the absence of accelerated vaccine uptake, over 17.2 million adults may not be vaccinated by end March 2022 nationally. Our results highlight geographic inequalities at sub-national level and are important in targeting and improving vaccination coverage in hard-to-reach populations. Similar mapping efforts could help other countries identify and increase vaccination coverage for such populations.

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.

Seroprevalence of Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 Among Healthcare Workers in Kenya

BACKGROUND

Few studies have assessed the seroprevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among healthcare workers (HCWs) in Africa. We report findings from a survey among HCWs in 3 counties in Kenya.

METHODS

We recruited 684 HCWs from Kilifi (rural), Busia (rural), and Nairobi (urban) counties. The serosurvey was conducted between 30 July and 4 December 2020. We tested for immunoglobulin G antibodies to SARS-CoV-2 spike protein, using enzyme-linked immunosorbent assay. Assay sensitivity and specificity were 92.7 (95% CI, 87.9-96.1) and 99.0% (95% CI, 98.1-99.5), respectively. We adjusted prevalence estimates, using bayesian modeling to account for assay performance.

RESULTS

The crude overall seroprevalence was 19.7% (135 of 684). After adjustment for assay performance, seroprevalence was 20.8% (95% credible interval, 17.5%-24.4%). Seroprevalence varied significantly (P < .001) by site: 43.8% (95% credible interval, 35.8%-52.2%) in Nairobi, 12.6% (8.8%-17.1%) in Busia and 11.5% (7.2%-17.6%) in Kilifi. In a multivariable model controlling for age, sex, and site, professional cadre was not associated with differences in seroprevalence.

CONCLUSION

These initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.

Malaria hospitalisation in East Africa: age, phenotype and transmission intensity

BACKGROUND

Understanding the age patterns of disease is necessary to target interventions to maximise cost-effective impact. New malaria chemoprevention and vaccine initiatives target young children attending routine immunisation services. Here we explore the relationships between age and severity of malaria hospitalisation versus malaria transmission intensity.

METHODS

Clinical data from 21 surveillance hospitals in East Africa were reviewed. Malaria admissions aged 1 month to 14 years from discrete administrative areas since 2006 were identified. Each site-time period was matched to a model estimated community-based age-corrected parasite prevalence to provide predictions of prevalence in childhood (PfPR2-10). Admission with all-cause malaria, severe malaria anaemia (SMA), respiratory distress (RD) and cerebral malaria (CM) were analysed as means and predicted probabilities from Bayesian generalised mixed models.

RESULTS

52,684 malaria admissions aged 1 month to 14 years were described at 21 hospitals from 49 site-time locations where PfPR2-10 varied from < 1 to 48.7%. Twelve site-time periods were described as low transmission (PfPR2-10 < 5%), five low-moderate transmission (PfPR2-10 5-9%), 20 moderate transmission (PfPR2-10 10-29%) and 12 high transmission (PfPR2-10 ≥ 30%). The majority of malaria admissions were below 5 years of age (69-85%) and rare among children aged 10-14 years (0.7-5.4%) across all transmission settings. The mean age of all-cause malaria hospitalisation was 49.5 months (95% CI 45.1, 55.4) under low transmission compared with 34.1 months (95% CI 30.4, 38.3) at high transmission, with similar trends for each severe malaria phenotype. CM presented among older children at a mean of 48.7 months compared with 39.0 months and 33.7 months for SMA and RD, respectively. In moderate and high transmission settings, 34% and 42% of the children were aged between 2 and 23 months and so within the age range targeted by chemoprevention or vaccines.

CONCLUSIONS

Targeting chemoprevention or vaccination programmes to areas where community-based parasite prevalence is ≥10% is likely to match the age ranges covered by interventions (e.g. intermittent presumptive treatment in infancy to children aged 2-23 months and current vaccine age eligibility and duration of efficacy) and the age ranges of highest disease burden.

Comparative performance of WANTAI ELISA for total immunoglobulin to receptor binding protein and an ELISA for IgG to spike protein in detecting SARS-CoV-2 antibodies in Kenyan populations

Many SARS-CoV-2 antibody detection assays have been developed but their differential performance is not well described. In this study we compared an in-house (KWTRP) ELISA which has been used extensively to estimate seroprevalence in the Kenyan population with WANTAI, an ELISA which has been approved for widespread use by the WHO. Using a wide variety of sample sets including pre-pandemic samples (negative gold standard), SARS-CoV-2 PCR positive samples (positive gold standard) and COVID-19 test samples from different periods (unknowns), we compared performance characteristics of the two assays. The overall concordance between WANTAI and KWTRP was 0.97 (95% CI, 0.95-0.98). For WANTAI and KWTRP, sensitivity was 0.95 (95% CI 0.90-0.98) and 0.93 (95% CI 0.87-0.96), respectively. Specificity for WANTAI was 0.98 (95% CI, 0.96-0.99) and 0.99 (95% CI 0.96-1.00) while KWTRP specificity was 0.99 (95% CI, 0.98-1.00) and 1.00 using pre-pandemic blood donors and pre-pandemic malaria cross-sectional survey samples respectively. Both assays show excellent characteristics to detect SARS-CoV-2 antibodies.

Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals: Repeated cross-sectional surveys 2020-21

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.

Modelling the cost-effectiveness of essential and advanced critical care for COVID-19 patients in Kenya

BACKGROUND

Case management of symptomatic COVID-19 patients is a key health system intervention. The Kenyan government embarked to fill capacity gaps in essential and advanced critical care (ACC) needed for the management of severe and critical COVID-19. However, given scarce resources, gaps in both essential and ACC persist. This study assessed the cost-effectiveness of investments in essential and ACC to inform the prioritisation of investment decisions.

METHODS

We employed a decision tree model to assess the incremental cost-effectiveness of investment in essential care (EC) and investment in both essential and ACC (EC +ACC) compared with current healthcare provision capacity (status quo) for COVID-19 patients in Kenya. We used a health system perspective, and an inpatient care episode time horizon. Cost data were obtained from primary empirical analysis while outcomes data were obtained from epidemiological model estimates. We used univariate and probabilistic sensitivity analysis to assess the robustness of the results.

RESULTS

The status quo option is more costly and less effective compared with investment in EC and is thus dominated by the later. The incremental cost-effectiveness ratio of investment in essential and ACC (EC+ACC) was US$1378.21 per disability-adjusted life-year averted and hence not a cost-effective strategy when compared with Kenya's cost-effectiveness threshold (US$908).

CONCLUSION

When the criterion of cost-effectiveness is considered, and within the context of resource scarcity, Kenya will achieve better value for money if it prioritises investments in EC before investments in ACC. This information on cost-effectiveness will however need to be considered as part of a multicriteria decision-making framework that uses a range of criteria that reflect societal values of the Kenyan society.

Mortality in rural coastal Kenya measured using the Kilifi Health and Demographic Surveillance System: a 16-year descriptive analysis

Background: The Kilifi Health and Demographic Surveillance System (KHDSS) was established in 2000 to define the incidence and prevalence of local diseases and evaluate the impact of community-based interventions. KHDSS morbidity data have been reported comprehensively but mortality has not been described. This analysis describes mortality in the KHDSS over 16 years. Methods: We calculated mortality rates from 2003–2018 in four intervals of equal duration and assessed differences in mortality across these intervals by age and sex. We calculated the period survival function and median survival using the Kaplan–Meier method and mean life expectancies using abridged life tables. We estimated trend and seasonality by decomposing a time series of monthly mortality rates. We used choropleth maps and random-effects Poisson regression to investigate geographical heterogeneity. Results: Mortality declined by 36% overall between 2003–2018 and by 59% in children aged <5 years. Most of the decline occurred between 2003 and 2006. Among adults, the greatest decline (49%) was observed in those aged 15–54 years. Life expectancy at birth increased by 12 years. Females outlived males by 6 years. Seasonality was only evident in the 1–4 year age group in the first four years. Geographical variation in mortality was ±10% of the median value and did not change over time. Conclusions: Between 2003 and 2018, mortality among children and young adults has improved substantially. The steep decline in 2003–2006 followed by a much slower reduction thereafter suggests improvements in health and wellbeing have plateaued in the last 12 years. However, there is substantial inequality in mortality experience by geographical location.

COVID-19 transmission dynamics underlying epidemic waves in Kenya

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or infection spreads to susceptible subpopulations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model, we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of higher-transmissibility variants. Reopening schools led to a minor increase in transmission between the second and third waves. Socioeconomic and urban–rural population structure are critical determinants of viral transmission in Kenya.

Quantifying previous SARS-CoV-2 infection through mixture modelling of antibody levels

As countries decide on vaccination strategies and how to ease movement restrictions, estimating the proportion of the population previously infected with SARS-CoV-2 is important for predicting the future burden of COVID-19. This proportion is usually estimated from serosurvey data in two steps: first the proportion above a threshold antibody level is calculated, then the crude estimate is adjusted using external estimates of sensitivity and specificity. A drawback of this approach is that the PCR-confirmed cases used to estimate the sensitivity of the threshold may not be representative of cases in the wider population-e.g., they may be more recently infected and more severely symptomatic. Mixture modelling offers an alternative approach that does not require external data from PCR-confirmed cases. Here we illustrate the bias in the standard threshold-based approach by comparing both approaches using data from several Kenyan serosurveys. We show that the mixture model analysis produces estimates of previous infection that are often substantially higher than the standard threshold analysis.

Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Immunoglobulin G Antibody Seroprevalence Among Truck Drivers and Assistants in Kenya

In October 2020, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among healthcare workers and blood donors. Truck drivers and their assistants transport essential supplies during the coronavirus disease 2019 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 over a wide geographical area.

Prevalence of SARS-CoV-2 Antibodies From a National Serosurveillance of Kenyan Blood Donors, January-March 2021

This study examines the prevalence of SARS-CoV-2 antibodies among blood donors aged 16 to 64 years in Kenya from January to March 2021.

Pulse oximetry adoption and oxygen orders at paediatric admission over 7 years in Kenya: a multihospital retrospective cohort study

OBJECTIVES

To characterise adoption and explore specific clinical and patient factors that might influence pulse oximetry and oxygen use in low-income and middle-income countries (LMICs) over time; to highlight useful considerations for entities working on programmes to improve access to pulse oximetry and oxygen.

DESIGN

A multihospital retrospective cohort study.

SETTINGS

All admissions (n=132 737) to paediatric wards of 18 purposely selected public hospitals in Kenya that joined a Clinical Information Network (CIN) between March 2014 and December 2020.

OUTCOMES

Pulse oximetry use and oxygen prescription on admission; we performed growth-curve modelling to investigate the association of patient factors with study outcomes over time while adjusting for hospital factors.

RESULTS

Overall, pulse oximetry was used in 48.8% (64 722/132 737) of all admission cases. Use rose on average with each month of participation in the CIN (OR: 1.11, 95% CI 1.05 to 1.18) but patterns of adoption were highly variable across hospitals suggesting important factors at hospital level influence use of pulse oximetry. Of those with pulse oximetry measurement, 7% (4510/64 722) had hypoxaemia (SpO2 <90%). Across the same period, 8.6% (11 428/132 737) had oxygen prescribed but in 87%, pulse oximetry was either not done or the hypoxaemia threshold (SpO2 <90%) was not met. Lower chest-wall indrawing and other respiratory symptoms were associated with pulse oximetry use at admission and were also associated with oxygen prescription in the absence of pulse oximetry or hypoxaemia.

CONCLUSION

The adoption of pulse oximetry recommended in international guidelines for assessing children with severe illness has been slow and erratic, reflecting system and organisational weaknesses. Most oxygen orders at admission seem driven by clinical and situational factors other than the presence of hypoxaemia. Programmes aiming to implement pulse oximetry and oxygen systems will likely need a long-term vision to promote adoption, guideline development and adherence and continuously examine impact.

Malaria infection and severe disease risks in Africa

The relationship between community prevalence of Plasmodium falciparum and the burden of severe, life-threatening disease remains poorly defined. To examine the three most common severe malaria phenotypes from catchment populations across East Africa, we assembled a dataset of 6506 hospital admissions for malaria in children aged 3 months to 9 years from 2006 to 2020. Admissions were paired with data from community parasite infection surveys. A Bayesian procedure was used to calibrate uncertainties in exposure (parasite prevalence) and outcomes (severe malaria phenotypes). Each 25% increase in prevalence conferred a doubling of severe malaria admission rates. Severe malaria remains a burden predominantly among young children (3 to 59 months) across a wide range of community prevalence typical of East Africa. This study offers a quantitative framework for linking malaria parasite prevalence and severe disease outcomes in children.

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

Revitalizing child health: lessons from the past

Essential health, education and other service disruptions arising from the COVID-19 pandemic risk reversing some of the hard-won gains in improving child survival over the past 40 years. Although children have milder symptoms of COVID-19 disease than adults, pandemic control measures in many countries have disrupted health, education and other services for children, often leaving them without access to birth and postnatal care, vaccinations and early childhood preventive and treatment services. These disruptions mean that the SARS-CoV-2 virus, along with climate change and shifting epidemiological and demographic patterns, are challenging the survival gains that we have seen over the past 40 years. We revisit the initiatives and actions of the past that catalyzed survival improvements in an effort to learn how to maintain these gains even in the face of today's global challenges.

Temporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya

Observed SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality.

Prevalence and fluid management of dehydration in children without diarrhoea admitted to Kenyan hospitals: a multisite observational study

OBJECTIVES

To examine the prevalence of dehydration without diarrhoea among admitted children aged 1-59 months and to describe fluid management practices in such cases.

DESIGN

A multisite observational study that used routine in-patient data collected prospectively between October 2013 and December 2018.

SETTINGS

Study conducted in 13 county referral hospitals in Kenya.

PARTICIPANTS

Children aged 1-59 months with admission or discharge diagnosis of dehydration but had no diarrhoea as a symptom or diagnosis. Children aged <28 days and those with severe acute malnutrition were excluded.

RESULTS

The prevalence of dehydration in children without diarrhoea was 3.0% (2019/68 204) and comprised 15.9% (2019/12 702) of all dehydration cases. Only 55.8% (1127/2019) of affected children received either oral or intravenous fluid therapy. Where fluid treatment was given, the volumes, type of fluid, duration of fluid therapy and route of administration were similar to those used in the treatment of dehydration secondary to diarrhoea. Pneumonia (1021/2019, 50.6%) and malaria (715/2019, 35.4%) were the two most common comorbid diagnoses. Overall case fatality in the study population was 12.9% (260/2019).

CONCLUSION

Sixteen per cent of children hospitalised with dehydration do not have diarrhoea but other common illnesses. Two-fifths do not receive fluid therapy; a regimen similar to that used in diarrhoeal cases is used in cases where fluid is administered. Efforts to promote compliance with guidance in routine clinical settings should recognise special circumstances where guidelines do not apply, and further studies on appropriate management for dehydration in the absence of diarrhoea are required.

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.

Neonatal mortality in Kenyan hospitals: a multisite, retrospective, cohort study

BACKGROUND

Most of the deaths among neonates in low-income and middle-income countries (LMICs) can be prevented through universal access to basic high-quality health services including essential facility-based inpatient care. However, poor routine data undermines data-informed efforts to monitor and promote improvements in the quality of newborn care across hospitals.

METHODS

Continuously collected routine patients' data from structured paper record forms for all admissions to newborn units (NBUs) from 16 purposively selected Kenyan public hospitals that are part of a clinical information network were analysed together with data from all paediatric admissions ages 0-13 years from 14 of these hospitals. Data are used to show the proportion of all admissions and deaths in the neonatal age group and examine morbidity and mortality patterns, stratified by birth weight, and their variation across hospitals.

FINDINGS

During the 354 hospital months study period, 90 222 patients were admitted to the 14 hospitals contributing NBU and general paediatric ward data. 46% of all the admissions were neonates (aged 0-28 days), but they accounted for 66% of the deaths in the age group 0-13 years. 41 657 inborn neonates were admitted in the NBUs across the 16 hospitals during the study period. 4266/41 657 died giving a crude mortality rate of 10.2% (95% CI 9.97% to 10.55%), with 60% of these deaths occurring on the first-day of admission. Intrapartum-related complications was the single most common diagnosis among the neonates with birth weight of 2000 g or more who died. A threefold variation in mortality across hospitals was observed for birth weight categories 1000-1499 g and 1500-1999 g.

INTERPRETATION

The high proportion of neonatal deaths in hospitals may reflect changing patterns of childhood mortality. Majority of newborns died of preventable causes (>95%). Despite availability of high-impact low-cost interventions, hospitals have high and very variable mortality proportions after stratification by birth weight.

Employing learning health system principles to advance research on severe neonatal and paediatric illness in Kenya

We have worked to develop a Clinical Information Network (CIN) in Kenya as an early form of learning health systems (LHS) focused on paediatric and neonatal care that now spans 22 hospitals. CIN's aim was to examine important outcomes of hospitalisation at scale, identify and ultimately solve practical problems of service delivery, drive improvements in quality and test interventions. By including multiple routine settings in research, we aimed to promote generalisability of findings and demonstrate potential efficiencies derived from LHS. We illustrate the nature and range of research CIN has supported over the past 7 years as a form of LHS. Clinically, this has largely focused on common, serious paediatric illnesses such as pneumonia, malaria and diarrhoea with dehydration with recent extensions to neonatal illnesses. CIN also enables examination of the quality of care, for example that provided to children with severe malnutrition and the challenges encountered in routine settings in adopting simple technologies (pulse oximetry) and more advanced diagnostics (eg, Xpert MTB/RIF). Although regular feedback to hospitals has been associated with some improvements in quality data continue to highlight system challenges that undermine provision of basic, quality care (eg, poor access to blood glucose testing and routine microbiology). These challenges include those associated with increased mortality risk (eg, delays in blood transfusion). Using the same data the CIN platform has enabled conduct of randomised trials and supports malaria vaccine and most recently COVID-19 surveillance. Employing LHS principles has meant engaging front-line workers, clinical managers and national stakeholders throughout. Our experience suggests LHS can be developed in low and middle-income countries that efficiently enable contextually appropriate research and contribute to strengthening of health services and research systems.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa.

Prognostic models for predicting in-hospital paediatric mortality in resource-limited countries: a systematic review

OBJECTIVES

To identify and appraise the methodological rigour of multivariable prognostic models predicting in-hospital paediatric mortality in low-income and middle-income countries (LMICs).

DESIGN

Systematic review of peer-reviewed journals.

DATA SOURCES

MEDLINE, CINAHL, Google Scholar and Web of Science electronic databases since inception to August 2019.

ELIGIBILITY CRITERIA

We included model development studies predicting in-hospital paediatric mortality in LMIC.

DATA EXTRACTION AND SYNTHESIS

This systematic review followed the Checklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies framework. The risk of bias assessment was conducted using Prediction model Risk of Bias Assessment Tool (PROBAST). No quantitative summary was conducted due to substantial heterogeneity that was observed after assessing the studies included.

RESULTS

Our search strategy identified a total of 4054 unique articles. Among these, 3545 articles were excluded after review of titles and abstracts as they covered non-relevant topics. Full texts of 509 articles were screened for eligibility, of which 15 studies reporting 21 models met the eligibility criteria. Based on the PROBAST tool, risk of bias was assessed in four domains; participant, predictors, outcome and analyses. The domain of statistical analyses was the main area of concern where none of the included models was judged to be of low risk of bias.

CONCLUSION

This review identified 21 models predicting in-hospital paediatric mortality in LMIC. However, most reports characterising these models are of poor quality when judged against recent reporting standards due to a high risk of bias. Future studies should adhere to standardised methodological criteria and progress from identifying new risk scores to validating or adapting existing scores.

PROSPERO REGISTRATION NUMBER

CRD42018088599.

The Clinical Profile of Severe Pediatric Malaria in an Area Targeted for Routine RTS,S/AS01 Malaria Vaccination in Western Kenya

BACKGROUND

The malaria prevalence has declined in western Kenya, resulting in the risk of neurological phenotypes in older children. This study investigates the clinical profile of pediatric malaria admissions ahead of the introduction of the RTS,S/AS01 vaccine.

METHODS

Malaria admissions in children aged 1 month to 15 years were identified from routine, standardized, inpatient clinical surveillance data collected between 2015 and 2018 from 4 hospitals in western Kenya. Malaria phenotypes were defined based on available data.

RESULTS

There were 5766 malaria admissions documented. The median age was 36 months (interquartile range, 18-60): 15% were aged between 1-11 months of age, 33% were aged 1-23 months of age, and 70% were aged 1 month to 5 years. At admission, 2340 (40.6%) children had severe malaria: 421/2208 (19.1%) had impaired consciousness, 665/2240 (29.7%) had an inability to drink or breastfeed, 317/2340 (13.6%) had experienced 2 or more convulsions, 1057/2340 (45.2%) had severe anemia, and 441/2239 (19.7%) had severe respiratory distress. Overall, 211 (3.7%) children admitted with malaria died; 163/211 (77% deaths, case fatality rate 7.0%) and 48/211 (23% deaths, case fatality rate 1.4%) met the criteria for severe malaria and nonsevere malaria at admission, respectively. The median age for fatal cases was 33 months (interquartile range, 12-72) and the case fatality rate was highest in those unconscious (44.4%).

CONCLUSIONS

Severe malaria in western Kenya is still predominantly seen among the younger pediatric age group and current interventions targeted for those <5 years are appropriate. However, there are increasing numbers of children older than 5 years admitted with malaria, and ongoing hospital surveillance would identify when interventions should target older children.

Examining which clinicians provide admission hospital care in a high mortality setting and their adherence to guidelines: an observational study in 13 hospitals

BACKGROUND

We explored who actually provides most admission care in hospitals offering supervised experiential training to graduating clinicians in a high mortality setting where practices deviate from guideline recommendations.

METHODS

We used a large observational data set from 13 Kenyan county hospitals from November 2015 through November 2018 where patients were linked to admitting clinicians. We explored guideline adherence after creating a cumulative correctness of Paediatric Admission Quality of Care (cPAQC) score on a 5-point scale (0-4) in which points represent correct, sequential progress in providing care perfectly adherent to guidelines comprising admission assessment, diagnosis and treatment. At the point where guideline adherence declined the most we dichotomised the cPAQC score and used multilevel logistic regression models to explore whether clinician and patient-level factors influence adherence.

RESULTS

There were 1489 clinicians who could be linked to 53 003 patients over a period of 3 years. Patients were rarely admitted by fully qualified clinicians and predominantly by preregistration medical officer interns (MOI, 46%) and diploma level clinical officer interns (COI, 41%) with a median of 28 MOI (range 11-68) and 52 COI (range 5-160) offering care per study hospital. The cPAQC scores suggest that perfect guideline adherence is found in ≤12% of children with malaria, pneumonia or diarrhoea with dehydration. MOIs were more adherent to guidelines than COI (adjusted OR 1.19 (95% CI 1.07 to 1.34)) but multimorbidity was significantly associated with lower guideline adherence.

CONCLUSION

Over 85% of admissions to hospitals in high mortality settings that offer experiential training in Kenya are conducted by preregistration clinicians. Clinical assessment is good but classifying severity of illness in accordance with guideline recommendations is a challenge. Adherence by MOI with 6 years' training is better than COI with 3 years' training, performance does not seem to improve during their 3 months of paediatric rotations.