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In Kilifi (Kenya), a pneumococcal conjugate vaccine (PCV10) was introduced in 2011 in infants (aged <1 year, 3 + 0 schedule) with a catch-up campaign in children aged 1–4 years. We aimed to measure the effect of PCV10 on population immunity. In this observational study, repeated cross-sectional serosurveys were conducted in independent random samples of 500 children younger than 15 years every 2 years between 2009 and 2017. During these surveys, blood samples were collected by venesection. Concentrations of anti-capsular IgGs against vaccine serotypes (VTs) 1, 4, 5, 6B, 7F, 9V, 14, 18C, 19F, and 23F, and against serotypes 6A and 19A, were assayed by ELISA. We plotted the geometric mean concentrations (GMCs) by birth year to visualise age-specific antibody profiles. In infants, IgG concentrations of 0·35 μg/mL or higher were considered protective. Of 3673 volunteers approached, 2152 submitted samples for analysis across the five surveys. Vaccine introduction resulted in an increase in the proportion of young children with protective IgG concentrations, compared with before vaccine introduction (from 0–33% of infants with VT-specific levels over the correlate of protection in 2009, to 60–94% of infants in 2011). However, among those vaccinated in infancy, GMCs of all ten VTs had waned rapidly by the age of 1, but rose again later in childhood. GMCs among children aged 10–14 years were consistently high over time (eg, the range of GMCs across survey rounds were between 0·45 μg/mL and 1·00 μg/mL for VT 23F and between 2·00 μg/mL and 3·11 μg/mL for VT 19F). PCV10 in a 3 + 0 schedule elicited protective IgG levels during infancy, when disease risk is high. The high antibody levels in children aged 10–14 years might indicate continued exposure to vaccine serotypes due to residual carriage or to memory responses to cross-reactive antigens. Despite rapid waning of IgG after vaccination, disease incidence among young children in this setting remains low, suggesting that lower thresholds of antibody, or other markers of immunity (eg, memory B cells), may be needed to assess population protection among children who have aged past infancy. Gavi, the Vaccine Alliance; Wellcome Trust. [ABSTRACT FROM AUTHOR]

Mpox (formerly known as monkeypox) is a zoonotic viral disease endemic in parts of Africa. In May, 2022, the world was alerted to circulation of monkeypox virus in many high-income countries outside of Africa. Continued spread resulted in a WHO declaration of a Public Health Emergency of International Concern. Although there has been much attention on the global outbreak, most of the focus has been on high-income countries outside of Africa, despite the fact that monkeypox virus has been causing disease in parts of Africa for at least 50 years. Furthermore, the long-term consequences of this event, especially the risk that mpox fills the niche vacated through smallpox eradication, have not been sufficiently considered. The heart of the problem is the historical neglect of mpox in Africa where the disease is endemic, and the actual and potential consequences if this neglect is left uncorrected. [ABSTRACT FROM AUTHOR]

We propose a novel, non-discriminatory classification of monkeypox virus. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomics surveillance. The current nomenclature for monkeypox virus is stigmatising and misleading. This Perspective article proposes a practical and neutral system of nomenclature that will allow efficient communication without the risk of further misconceptions, discrimination and stigmatisation. [ABSTRACT FROM AUTHOR]

World Health Organization (WHO) preferred product characteristics describe preferences for product attributes that would help optimize value and use to address global public health needs, with a particular focus on low- and middle-income countries. Having previously published preferred product characteristics for both maternal and paediatric respiratory syncytial virus (RSV) vaccines, WHO recently published preferred product characteristics for monoclonal antibodies to prevent severe RSV disease in infants. This article summarizes the key attributes from the preferred product characteristics and discusses key considerations for future access and use of preventive RSV monoclonal antibodies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Tungiasis is a highly neglected tropical skin disease caused by the sand flea, Tunga penetrans. The flea burrows into the skin inducing a strong inflammatory response, leading to pain and mobility restrictions with potential impacts on quality of life. Few countries implement control efforts and there are few data on the impact of the disease to support policy decisions. We conducted a survey to determine the impact of tungiasis among primary school children across nine counties of Kenya. A total of 10,600 pupils aged 8 to 14 years were randomly selected from 97 primary schools and examined for tungiasis. For 81 cases and 578 randomly selected controls, anthropometric measurements were made, and school attendance and exam scores were collected from school records. Of those with tungiasis, 73 were interviewed regarding their quality of life using a tungiasis-specific instrument. Mixed effect ordered logistic and linear models were used to assess associations between disease status and impact variables. Compared to uninfected pupils, those with tungiasis had lower weight-for-age z-scores (adjusted β -0.41, 95% CI: -0.75–0.06, p = 0.020), missed more days of school the previous term (adjusted Incidence Rate Ratio: 1.49, 95% CI: 1.01–2.21, p = 0.046) and were less likely to receive a high score in mathematics (aOR 0.18, 95% CI: 0.08–0.40, p<0.001) and other subjects. Pupils with severe disease (clinical score >10) were four times more likely to experience severe pain than those with mild disease (OR 3.96, 95% CI: 1.35–11.64, p = 0.012) and a higher impact on their quality of life than those with mild disease (aOR 3.57, 95% CI: 1.17–10.8, p = 0.025) when adjusted for covariates. This study has demonstrated tungiasis has a considerable impact on children's lives and academic achievement. This indicates the need for integrated disease management for school-aged children to protect their physical and cognitive development and their future prospects. Author summary: Tungiasis is one of the most neglected tropical diseases (NTDs). It is caused by a flea which burrows into the skin, usually of the feet. The neglect has resulted in large gaps in our knowledge of the disease, how to treat and prevent infection. This is partly due to a lack of appreciation for the impact the disease has on patients' lives by health officials, policymakers and the research community. In this study we aimed to determine the impact on school children in nine counties of Kenya. We found evidence that children experience considerable pain and itching which affects their ability to attend school and to concentrate on their classes. They had lower exam scores in mathematics, English and science than uninfected children. This study has provided evidence that tungiasis is a disease that has a considerable impact on children and urgently needs more attention from researchers, donors, and policy makers. Integrating tungiasis into comprehensive disease management for school-aged children will protect their physical and cognitive development and their future prospects. [ABSTRACT FROM AUTHOR]

Population-level health and mortality data are crucial for evidence-informed policy but scarce in Nigeria. To fill this gap, we undertook a comprehensive assessment of the burden of disease in Nigeria and compared outcomes to other west African countries. In this systematic analysis, using data and results of the Global Burden of Diseases, Injuries, and Risk Factors Study 2019, we analysed patterns of mortality, years of life lost (YLLs), years lived with disability (YLDs), life expectancy, healthy life expectancy (HALE), and health system coverage for Nigeria and 15 other west African countries by gender in 1998 and 2019. Estimates of all-age and age-standardised disability-adjusted life-years for 369 diseases and injuries and 87 risk factors are presented for Nigeria. Health expenditure per person and gross domestic product were extracted from the World Bank repository. Between 1998 and 2019, life expectancy and HALE increased in Nigeria by 18% to 64·3 years (95% uncertainty interval [UI] 62·2–66·6), mortality reduced for all age groups for both male and female individuals, and health expenditure per person increased from the 11th to third highest in west Africa by 2018 (US$18·6 in 2001 to $83·75 in 2018). Nonetheless, relative outcomes remained poor; Nigeria ranked sixth in west Africa for age-standardised mortality, seventh for HALE, tenth for YLLs, 12th for health system coverage, and 14th for YLDs in 2019. Malaria (5176·3 YLLs per 100 000 people, 95% UI 2464·0–9591·1) and neonatal disorders (4818·8 YLLs per 100 000, 3865·9–6064·2) were the leading causes of YLLs in Nigeria in 2019. Nigeria had the fourth-highest under-five mortality rate for male individuals (2491·8 deaths per 100 000, 95% UI 1986·1–3140·1) and female individuals (2117·7 deaths per 100 000, 1756·7–2569·1), but among the lowest mortality for men older than 55 years. There was evidence of a growing non-communicable disease burden facing older Nigerians. Health outcomes remain poor in Nigeria despite higher expenditure since 2001. Better outcomes in countries with equivalent or lower health expenditure suggest health system strengthening and targeted intervention to address unsafe water sources, poor sanitation, malnutrition, and exposure to air pollution could substantially improve population health. The Bill & Melinda Gates Foundation. [ABSTRACT FROM AUTHOR]

Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were detected spreading internationally beyond countries with known endemic reservoirs. When the first cases from 2022 were sequenced, they shared 42 nucleotide differences from the closest mpox virus (MPXV) previously sampled. Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function. Assuming APOBEC3 editing is characteristic of human MPXV infection, we developed a dual-process phylogenetic molecular clock that—inferring a rate of ~6 APOBEC3 mutations per year—estimates that MPXV has been circulating in humans since 2016. These observations of sustained MPXV transmission present a fundamental shift to the perceived paradigm of MPXV epidemiology as a zoonosis and highlight the need for revising public health messaging around MPXV as well as outbreak management and control. [ABSTRACT FROM AUTHOR]

Background: Tungiasis is a highly neglected tropical skin disease caused by the sand flea, Tunga penetrans, the female of which burrows into the skin, causing pain and itching. The disease occurs throughout South America and sub-Saharan Africa but there are few systematic data on national disease burdens. The tungiasis research community is keen to develop survey methods to fill this gap. Here we used a school-based, thorough examination method to determine the prevalence and risk factors for tungiasis in Kenya. Methods: We conducted the first nationally representative survey of tungiasis, including nine counties covering the major ecological zones of Kenya. A stratified multistage random sampling was used to select 22 primary schools from each of the nine counties and to select up to 114 pupils aged 8 to 14 years in each school. Pupils were examined thoroughly for tungiasis. Two surveys were conducted, the first between May and July 2021 and the second between October 2021 and April 2023 when pupils were also interviewed for risk factors. Mixed effect logistic regression models were used to test associations of independent variables with tungiasis using the school as a random effect. Results: The overall prevalence of tungiasis in the first survey was 1.35% [95% confidence interval (CI): 1.15–1.59%], and 0.89% in the second survey. The prevalence ranged from 0.08% (95% CI: 0.01–0.59%) in Taita Taveta county to 3.24% (95% CI: 2.35–4.44%) in Kajiado county. Tungiasis infection was associated with county of residence, male sex [adjusted odds ratio (aOR) = 2.01, 95% CI: 1.52–2.67], and lower age (aOR = 0.81, 95% CI: 0.75–0.88). For the first time we demonstrate an association with attending public schools rather than private schools (aOR = 5.62, 95% CI: 1.20–26.22) and lower socioeconomic status (aOR = 0.10, 95% CI: 0.03–0.33). Using a rapid screening method of the top of feet only, would have missed 62.9% of all cases, 78.9% of mild cases and 20.0% of severe cases. Conclusions: Tungiasis is widely but heterogeneously distributed across Kenya. School-based surveys offer an efficient strategy for mapping tungiasis distribution. [ABSTRACT FROM AUTHOR]

Background Vaccination against coronavirus disease 2019 (COVID-19) is a cost-effective mitigation strategy against the pandemic. As the COVID-19 vaccine becomes more available, low uptake is now a global threat and understanding the underpinnings in local contexts is a priority for intervention development. We aimed to evaluate behavioural determinants of COVID-19 vaccine acceptance that could inform engagement strategies to improve vaccine uptake in Makoko, an urban slum in Lagos, Nigeria. Methods A population-based case–control study utilized the barrier analysis (BA) approach to evaluate the beliefs and behaviours of 45 'doers' and 45 'non-doers'. The standardized BA tabulation sheet was used to assess differences in the proportions between the two groups to identify significant factors that could be addressed through a behaviour change strategy. Results Perceived social norms (family, friend, healthcare workers) that approve the vaccine and expected vaccine protection against diseases among doers were determinants of behaviour. Perceived poor accessibility, safety concerns, lack of trust, low vaccine efficacy and low susceptibility to the infection were the most important determinants of behaviour among non-doers. Conclusions Measures to improve COVID-19 vaccine acceptance in Makoko should include improvement in accessibility and exposing myths and misinformation through clear, concise and evidence-based community education delivered by trusted persons such as healthcare workers and religious leaders. [ABSTRACT FROM AUTHOR]

Introduction: Estimates suggest that one-third of snakebite cases in sub-Saharan Africa affect children. Despite children being at a greater risk of disability and death, there are limited published data. This study has determined the: population-incidence and mortality rate of hospital-attended paediatric snakebite; clinical syndromes of snakebite envenoming; and predictors of severe local tissue damage. Methods: All children presenting to Kilifi County Hospital, Kenya with snakebite were identified through the Kilifi Health and Demographic Surveillance System (KHDSS). Cases were prospectively registered, admitted for at least 24-hours, and managed on a paediatric high dependency unit (HDU). Households within the KHDSS study area have been included in 4-monthly surveillance and verbal autopsy, enabling calculation of population-incidence and mortality. Predictors of severe local tissue damage were identified using a multivariate logistic regression analysis. Results: Between 2003 and 2021, there were 19,606 admissions to the paediatric HDU, of which 584 were due to snakebite. Amongst young children (≤5-years age) the population-incidence of hospital-attended snakebite was 11.3/100,000 person-years; for children aged 6–12 years this was 29.1/100,000 person-years. Incidence remained consistent over the study period despite the population size increasing (98,967 person-years in 2006; and 153,453 person-years in 2021). Most cases had local envenoming alone, but there were five snakebite associated deaths. Low haemoglobin; raised white blood cell count; low serum sodium; high systolic blood pressure; and an upper limb bite-site were independently associated with the development of severe local tissue damage. Conclusion: There is a substantial burden of disease due to paediatric snakebite, and the annual number of cases has increased in-line with population growth. The mortality rate was low, which may reflect the species causing snakebite in this region. The identification of independent predictors of severe local tissue damage can help to inform future research to better understand the pathophysiology of this important complication. Author summary: The nature of disease caused by snakebite amongst children in rural Africa is poorly understood. All children presenting to Kilifi County Hospital, Kenya with snakebite between 2003 and 2021 were recruited into a study that was nested in an ongoing hospital and community surveillance study. 584 children presented following snakebite and the incidence was 29.1/100,000 person-years amongst children aged 6–12 years. The incidence remained consistent over the course of the study despite the population increasing by over 50%, highlighting that the burden of disease is increasing in-line with population growth. Many children initially sought traditional therapies, which was associated with delayed presentation to hospital. The mortality rate was low, and most children had local, rather than systemic, envenoming. Predictors of severe local envenoming at the time of admission included a high white blood cell count, low haemoglobin, and an upper limb bite site. The findings of this study highlight the need to strengthen strategies to prevent snakebite in children, to overcome barriers to attending hospital, and to develop therapeutics that better treat local envenoming. [ABSTRACT FROM AUTHOR]

Lassa fever (LF) remains endemic in Nigeria with the country reporting the highest incidence and mortality globally. Recent national data suggests increasing incidence and expanding geographic spread. Predictors of LF case positivity in Nigeria have been sparsely studied. We thus sought to determine the sociodemographic and clinical determinants of LF positivity amongst suspected cases presenting to health facilities from 2018 to 2021. A secondary analysis of the national LF surveillance data between January 2018 and December 2021. Socio-demographic and clinical data of 20,027 suspected LF cases were analysed using frequencies and Chi-square statistics with significant p-value set at p < 0.05. The outcome variable was LF case status (positive or negative). Predictors of LF case positivity were assessed using multiple logistic regression models with 95% confidence intervals (CI). Case positivity rate (CPR) for the four years was 15.8% with higher odds of positivity among age group 40–49 years (aOR = 1.40; 95% CI 1.21–1.62), males (aOR = 1.11; 95% CI 1.03–1.20), those with formal education (aOR = 1.33; 95% CI 1.13–1.56), artisans (aOR = 1.70; 95% CI 1.28–2.27), religious leaders (aOR = 1.62; 95% CI 1.04–2.52), farmers (aOR = 1.48; 95% CI 1.21–1.81), and symptomatic individuals (aOR = 2.36; 95% CI 2.09–2.68). Being a health worker (aOR = 0.69; 95% CI 0.53–0.91), a teacher (aOR = 0.69; 95% CI 0.53–0.89) and cases reporting in the 3rd quarter (aOR = 0.79; 95% CI 0.69–0.92) had lower odds. In a sex-disaggregated analysis, female farmers had higher odds of positivity (aOR = 2.43; 95% CI 1.76–3.38; p < 0.001) than male farmers (aOR = 1.52; 95% CI 1.19–1.96; p < 0.01). Fever (aOR = 2.39; 95% CI 2.00–2.84) and gastrointestinal (GI) symptoms (aOR = 2.15; 95% CI 1.94–2.37) had the highest odds among symptoms. Combination of fever and GI symptoms (aOR = 2.15; 95% CI 1.50–3.10), fever and neurological symptoms (aOR = 6.37; 95% CI 1.49–27.16), fever and musculo-skeletal symptoms (aOR = 2.95; 95% CI 1.37–6.33), fever and cardiopulmonary symptoms (aOR = 1.81; 95% CI 1.24–2.64), and cardiopulmonary and general symptoms (aOR = 1.50; 95% CI 1.19–1.89) were also predictive. Cumulative LF CPR appears high with clearly identified predictors. Targeted interventions with heightened index of suspicion for sociodemographic categories predictive of LF in suspected cases are recommended. Ethnographic and further epidemiological studies could aid better understanding of these associations. [ABSTRACT FROM AUTHOR]

Background: Lassa fever (LF), a haemorrhagic illness caused by the Lassa fever virus (LASV), is endemic in West Africa and causes 5000 fatalities every year. The true prevalence and incidence rates of LF are unknown as infections are often asymptomatic, clinical presentations are varied, and surveillance systems are not robust. The aim of the Enable Lassa research programme is to estimate the incidences of LASV infection and LF disease in five West African countries. The core protocol described here harmonises key study components, such as eligibility criteria, case definitions, outcome measures, and laboratory tests, which will maximise the comparability of data for between-country analyses. Method: We are conducting a prospective cohort study in Benin, Guinea, Liberia, Nigeria (three sites), and Sierra Leone from 2020 to 2023, with 24 months of follow-up. Each site will assess the incidence of LASV infection, LF disease, or both. When both incidences are assessed the LASV cohort (nmin = 1000 per site) will be drawn from the LF cohort (nmin = 5000 per site). During recruitment participants will complete questionnaires on household composition, socioeconomic status, demographic characteristics, and LF history, and blood samples will be collected to determine IgG LASV serostatus. LF disease cohort participants will be contacted biweekly to identify acute febrile cases, from whom blood samples will be drawn to test for active LASV infection using RT-PCR. Symptom and treatment data will be abstracted from medical records of LF cases. LF survivors will be followed up after four months to assess sequelae, specifically sensorineural hearing loss. LASV infection cohort participants will be asked for a blood sample every six months to assess LASV serostatus (IgG and IgM). Discussion: Data on LASV infection and LF disease incidence in West Africa from this research programme will determine the feasibility of future Phase IIb or III clinical trials for LF vaccine candidates. [ABSTRACT FROM AUTHOR]

Background: Lassa fever is a viral haemorrhagic fever endemic in Nigeria. Improved surveillance and testing capacity have revealed in an increased number of reported cases and apparent geographic spread of Lassa fever in Nigeria. We described the recent four-year trend of Lassa fever in Nigeria to improve understanding of its epidemiology and inform the design of appropriate interventions. Methods: We analysed the national surveillance data on Lassa fever maintained by the Nigeria Centre for Diseases Control (NCDC) and described trends, sociodemographic, geographic distribution, and clinical outcomes. We compared cases, positivity, and clinical outcomes in the period January 2018 to December 2021. Results: We found Lassa fever to be reported throughout the year with more than half the cases reported within the first quarter of the year, a recent increase in numbers and geographic spread of the virus, and male and adult (>18 years) preponderance. Case fatality rates were worse in males, the under-five and elderly, during off-peak periods, and among low reporting states. Conclusion: Lassa fever is endemic in Nigeria with a recent increase in numbers and geographical distribution. Sustaining improved surveillance, enhanced laboratory diagnosis and improved case management capacity during off-peak periods should remain a priority. Attention should be paid to the very young and elderly during outbreaks. Further research efforts should identify and address specific factors that determine poor clinical outcomes. [ABSTRACT FROM AUTHOR]

The clinical relevance of pulmonary non-tuberculous mycobacteria (PNTM) in The Gambia is unknown. The aim of this study was to estimate the prevalence of non-tuberculous mycobacteria (NTM) in colonisation, and the burden of clinically relevant pulmonary NTM (PNTM) disease in The Gambia. This was a cross-sectional study of the prevalence of NTM in participants aged ≥ 15 years, in a nationwide tuberculosis (TB) prevalence survey between December 2011 and January 2013. We enrolled 903 participants with suspected NTM and NTM cultures were confirmed by 16S rRNA gene sequencing analyses. We applied the American Thoracic Society/Infectious Disease Society of America (ATS/IDSA) diagnostic criteria to determine clinical relevance of NTM. A total of 575 participants had acid-fast bacilli (AFB) positive Mycobacterial Growth Indicator Tube (MGIT) cultures and 229 (39.8%) were NTM. M. avium complex was by far the most isolated NTM (71.0%), followed by M. fortuitum (9.5%) and M. nonchromogenicum (2.9%). Older participants (> 24 years old) were four times more likely to have NTM in their sputa. Only 20.5% (9/44) NTM cases met the ATS/IDSA criteria for NTM disease. This study provides important data on the prevalence of NTM in pulmonary samples of suspected TB cases with AFB positive cultures from a nationally representative population in The Gambia. Enhanced PNTM surveillance is recommended to better understand the contribution of NTM to pulmonary disease. [ABSTRACT FROM AUTHOR]

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 FROM AUTHOR]

The burden of severe Covid-19 has been relatively low in sib-Saharan Africa compared to Europe and the Americas. However, SARS-CoV-2 sero-prevalence data has demonstrated that there has been more widespread transmission than can be deduced from reported cases. This could be attributed to under reporting due to low testing capacity or high numbers of asymptomatic SARS-CoV-2 infection in communities. Recent data indicates that prior SARS-CoV-2 exposure is protective against reinfection and that vaccination of previously SARS-CoV-2 infected individuals induces robust cross-reactive antibody responses. Considering these data, calls for a need for a re-think of the COVID-19 vaccination strategy in sub-Saharan African settings with high SARSCoV-2 population exposure but limited available vaccine doses. A potential recommendation would be to prioritize rapid and widespread vaccination of the first dose, while waiting for more vaccines to become available. [ABSTRACT FROM AUTHOR]

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 urbanÐrural population structure are critical determinants of viral transmission in Kenya. [ABSTRACT FROM AUTHOR]

• Both assays discriminate SARS-CoV-2 seropositive and seronegative individuals. • Both assays correctly estimate seroprevalence in a wide range of seroprevalences. • WANTAI has slightly higher sensitivity than KWTRP. • KWTRP has slightly higher specificity than WANTAI. 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. [ABSTRACT FROM AUTHOR]