A scoping review of ethics review processes during public health emergencies in Africa.

BACKGROUND: The COVID-19 pandemic forced governments, multilateral public health organisations and research institutions to undertake research quickly to inform their responses to the pandemic. Most COVID-19-related studies required swift approval, creating ethical and practical challenges for regulatory authorities and researchers. In this paper, we examine the landscape of ethics review processes in Africa during public health emergencies (PHEs). METHODS: We searched four electronic databases (Web of Science, PUBMED, MEDLINE Complete, and CINAHL) to identify articles describing ethics review processes during public health emergencies and/or pandemics. We selected and reviewed those articles that were focused on Africa. We charted the data from the retrieved articles including the authors and year of publication, title, country and disease(s) reference, broad areas of (ethical) consideration, paper type, and approach. RESULTS: Of an initial 4536 records retrieved, we screened the titles and abstracts of 1491 articles, and identified 72 articles for full review. Nine articles were selected for inclusion. Of these nine articles, five referenced West African countries including Liberia, Guinea and Sierra Leone, and experiences linked to the Ebola virus disease. Two articles focused on South Africa and Kenya, while the other two articles discussed more general experiences and pitfalls of ethics review during PHEs in Africa more broadly. We found no articles published on ethics review processes in Africa before the 2014 Ebola outbreak, and only a few before the COVID-19 outbreak. Although guidelines on protocol review and approval processes for PHEs were more frequently discussed after the 2014 Ebola outbreak, these did not focus on Africa specifically. CONCLUSIONS: There is a gap in the literature about ethics review processes and preparedness within Africa during PHEs. This paper underscores the importance of these processes to inform practices that facilitate timely, context-relevant research that adequately recognises and reinforces human dignity within the quest to advance scientific knowledge about diseases. This is important to improve fast responses to PHEs, reduce mortality and morbidity, and enhance the quality of care before, during, and after pandemics.

How to improve research capacity strengthening efforts: learning from the monitoring and evaluation of four research consortia in Africa.

Recent efforts to shift the control and leadership of health research on African issues to Africa have led to increased investments for scientific research capacity strengthening (RCS) on the continent and a greater demand for accountability, value for money and demonstration of return on investment. There is limited literature on monitoring and evaluation (M&E) of RCS systems and there is a clear need to further explore whether the M&E frameworks and approaches that are currently used are fit for purpose. The M&E approaches taken by four African RCS consortia funded under the Developing Excellence in Leadership, Training and Science in Africa (DELTAS) I initiative were assessed using several methods, including a framework comparison of the M&E approaches, semi-structured interviews and facilitated discussion sessions. The findings revealed a wide range in the number of indicators used in the M&E plans of individual consortium, which were uniformly quantitative and at the output and outcome levels. Consortia revealed that additional information could have been captured to better evaluate the success of activities and measure the ripple effects of their efforts. While it is beneficial for RCS consortia to develop and implement their own M&E plans, this could be strengthened by routine engagement with funders/programme managers to further align efforts. It is also important for M&E plans to consider qualitative data capture for assessment of RCS efforts. Efforts could be further enhanced by supporting platforms for cross-consortia sharing, particularly when trying to assess more complex effects. Consortia should make sure that processes for developmental evaluation, and capturing and using the associated learning, are in place. Sharing the learning associated with M&E of RCS efforts is vital to improve future efforts. Investing and improving this aspect of RCS will help ensure tracking of progress and impact of future efforts, and ensure accountability and the return on investment. The findings are also likely applicable well beyond health research.

Determinants of utilization of malaria preventive measures during pregnancy among women aged 15 to 49 years in Kenya: an analysis of the Malaria Indicator Survey 2020.

BACKGROUND: Malaria is a significant cause of morbidity and mortality. Malaria infection in pregnancy can have severe consequences for the fetus and the mother. To fight against malaria infection in pregnancy, Kenya integrated the issuance of an insecticide-treated net (ITN) and intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTpSP) with antenatal care (ANC) for pregnant women. However, the uptake of the ITN and IPTpSP is still low. Individual, social, or structural factors may influence the low uptake. It is, therefore, important to identify the determinants associated with the uptake of ITN and IPTpSP during pregnancy in Kenya. METHODS: Data were from the 2020 Kenya Malaria Indicator Survey (MIS). A total of 1779 women between the ages of 15 to 49 years who had a history of either being pregnant or having given birth within 5 years before the MIS survey were included. Survey-adjusted multinomial logistic regression was used in the analysis. RESULTS: During pregnancy, ITN use was more than half (54.9%). The use of at least one dose of IPTpSP was 43.5%, three or more doses of IPTpSP was 27.2%, and only 28.2% of the participants used both ITN and IPTpSP during pregnancy. The significant determinants of combined use of ITN and IPTpSP during pregnancy were maternal age (RR 3.57, CI 1.80-7.08; p=<0.001), maternal education (RRR 2.84, CI 1.33-6.06; p=0.007), wealth index (RR 2.14, CI 1.19-3.84; p=0.011) and living in the different malaria epidemiological zones: lake endemic (RRR 10.57 CI 5.65-19.76; p=<0.001), coastal endemic area (RRR 4.86 CI 1.86-12.67; p=0.001), seasonal (RRR 0.21 CI 0.10-0.39; p=<0.001) and low risk (RRR 0.07, CI 0.03-0.17; p=<0.001). CONCLUSION: The uptake of malaria preventive measures is still below 80% for both ITN and IPTpSP during pregnancy in Kenya. The significant results on determinants of the use of ITN and IPTpSP could be considered in implementing malaria prevention programmes during pregnancy. For example, sensitizing the community on the importance of antenatal care visits will provide a platform to teach the importance of malaria prevention in pregnancy. Moreover, the pregnant mothers receive an ITN and IPTpSP during the ANC visit.

Malaria attributable fractions with changing transmission intensity: Bayesian latent class vs logistic models.

BACKGROUND: Asymptomatic carriage of malaria parasites is common in high transmission intensity areas and confounds clinical case definitions for research studies. This is important for investigations that aim to identify immune correlates of protection from clinical malaria. The proportion of fevers attributable to malaria parasites is widely used to define different thresholds of parasite density associated with febrile episodes. The varying intensity of malaria transmission was investigated to check whether it had a significant impact on the parasite density thresholds. The same dataset was used to explore an alternative statistical approach, using the probability of developing fevers as a choice over threshold cut-offs. The former has been reported to increase predictive power. METHODS: Data from children monitored longitudinally between 2005 and 2017 from Junju and Chonyi in Kilifi, Kenya were used. Performance comparison of Bayesian-latent class and logistic power models in estimating malaria attributable fractions and probabilities of having fever given a parasite density with changing malaria transmission intensity was done using Junju cohort. Zero-inflated beta regressions were used to assess the impact of using probabilities to evaluate anti-merozoite antibodies as correlates of protection, compared with multilevel binary regression using data from Chonyi and Junju. RESULTS: Malaria transmission intensity declined from over 49% to 5% between 2006 and 2017, respectively. During this period, malaria attributable fraction varied between 27-59% using logistic regression compared to 10-36% with the Bayesian latent class approach. Both models estimated similar patterns of fevers attributable to malaria with changing transmission intensities. The Bayesian latent class model performed well in estimating the probabilities of having fever, while the latter was efficient in determining the parasite density threshold. However, compared to the logistic power model, the Bayesian algorithm yielded lower estimates for both attributable fractions and probabilities of fever. In modelling the association of merozoite antibodies and clinical malaria, both approaches resulted in comparable estimates, but the utilization of probabilities had a better statistical fit. CONCLUSIONS: Malaria attributable fractions, varied with an overall decline in the malaria transmission intensity in this setting but did not significantly impact the outcomes of analyses aimed at identifying immune correlates of protection. These data confirm the statistical advantage of using probabilities over binary data.

Neurological impairment and disability in children in rural Kenya.

AIM: To investigate geographical change over time in the burden of neurological impairments in school-aged children in a demographic surveillance area. METHOD: We investigated changes in neurological impairment prevalence in five domains (epilepsy and cognitive, hearing, vision, and motor impairments) using similar two-phase surveys conducted in 2001 (n=10 218) and 2015 (n=11 223) and determined changes in location-level prevalence, geographical clustering, and significant risk factors for children aged 6 to 9 years (mean 7y 6mo, SD 1y) of whom 50.4% were males. Admission trends for preterm birth, low birthweight (LBW), and encephalopathy were determined using admission data to a local hospital. RESULTS: Overall prevalence for any neurological impairment decreased from 61 per 1000 (95% confidence interval [CI] 48.0-74.0) in 2001 to 44.7 per 1000 (95% CI 40.9-48.6) in 2015 (p<0.001). There was little evidence of geographical variation in the prevalence of neurological impairments in either survey. The association between neurological impairments and some risk factors changed significantly with year of survey; for example, the increased association of adverse perinatal events with hearing impairments (exponentiated coefficient for the interaction=5.94, p=0.03). Annual admission rates with preterm birth (rate ratio 1.08, range 1.07-1.09), LBW (rate ratio 1.08, range 1.06-1.10), and encephalopathy (rate ratio 1.08, range 1.06-1.09) significantly increased between 2005 and 2016 (p<0.001). INTERPRETATION: There was a significant decline in the prevalence of neurological impairments and differential changes in the associations of some risk factors with neurological impairments over the study period. Limited geographical variation suggests that similar interventions are appropriate across the defined area.

Antibody-Dependent Respiratory Burst against Plasmodium falciparum Merozoites in Individuals Living in an Area with Declining Malaria Transmission.

Malaria transmission intensity affects the development of naturally acquired immunity to malaria. An absolute correlate measure of protection against malaria is lacking. However, antibody-mediated functions against Plasmodium falciparum correlate with protection against malaria. In children, antibody-mediated functions against P. falciparum decline with reduced exposure. It is unclear whether adults maintain antibody-mediated functions as malaria transmission declines. This study assessed antibody-dependent respiratory burst (ADRB) in individuals from an area with declining malaria transmission. In an age-matched analysis, we compare ADRB activity during high versus low malaria transmission periods. Age significantly predicted higher ADRB activity in the high (p < 0.001) and low (p < 0.001) malaria transmission periods. ADRB activity was higher during the high compared to the low malaria transmission period in older children and adults. Only older adults during the high malaria transmission period had their median ADRB activity above the ADRB cut-off. Ongoing P. falciparum infection influenced ADRB activity during the low (p = 0.01) but not the high (p = 0.29) malaria transmission period. These findings propose that naturally acquired immunity to P. falciparum is affected in children and adults as malaria transmission declines, implying that vaccines will be necessary to induce and maintain protection against malaria.

The burden of neurological impairments and disability in older children measured in disability-adjusted life-years in rural Kenya.

Neurological impairment (NI) and disability are common in sub-Saharan Africa (SSA), but the overall burden in terms of morbidity and mortality in older children remains unknown. We estimated the burden of NI in disability-adjusted life years (DALYs), years of life lost to premature mortality (YLLs), and years lived with disability (YLDs) for older children in a defined rural setting in Kenya. We used empirical and literature estimates to model the overall burden for children aged 5-14 years in five domains: epilepsy (lifetime and active) and moderate/severe cognitive, hearing, motor, and visual impairments. We obtained internally consistent estimates of prevalence, mortality, and transitional hazards using DisMod II software. Disability weights and life expectancy estimates were based on the global burden of disease (GBD) studies. We used the most plausible parameters to calculate YLLs, YLDs, and DALYs and their bootstrapped 95% uncertainty intervals (95%UI) for the defined area. NI in the five domains resulted in a total of 4587 (95%UI 4459-4715) absolute DALYs or 53 (95%UI 39-67) DALYs per 1000 children aged 5-14 years, of which 83% were YLLs and 17% YLDs. Girls had significantly more YLLs and DALYs than boys (p-values <0.001, respectively). Besides being the leading cause of fatal and non-fatal outcomes, epilepsy accounted for the greatest proportion of the total burden for a single domain (20 DALYs per 1000, 95%UI 11-26, or 38.5% of the total DALYs). Visual impairment accounted for the least proportion of the total burden (6 per 1000, 95%UI 1-17, or 12.1%). Children with NI and disability bear a significantly high burden of fatal and non-fatal outcomes. The burden is highest among girls and those with childhood-onset epilepsy. We recommend active identification, treatment, and rehabilitative support for the affected children to prevent premature mortality and improve their quality of life.

Pandemic preparedness and responsiveness of research review committees: lessons from review of COVID-19 protocols at KEMRI Wellcome Trust Research Programme in Kenya.

Background: The scale of the COVID-19 pandemic and novelty of SARS-CoV-2 presented unprecedented challenges in the review of COVID-19 protocols. We investigated how research at the Kenya Medical Research Institute - Wellcome Trust Research Programme (KWTRP) was reviewed, including by institutional and national level committees. Methods: A document review and in-depth interviews with researchers, regulators and research reviewers were conducted. Documents reviewed included research logs of all protocols submitted between April-1-2020 and March-31-2021, feedback letters from review committees for 10 new COVID-19 protocols (n=42), and minutes from 35 COVID-19 research review meetings. Fifteen in-depth interviews were conducted with respondents purposively selected because of their experience of developing or reviewing COVID-19 protocols at the institution level (n=9 researchers, engagement officers and regulators) or their experience in reviewing proposals at a national-level (n=6 committee members). Data were managed and analyzed using MS Excel and NVivo12. Results: Between April-1-2020 and March-31-2021, 30 COVID-19-related submissions by KWTRP researchers were approved. Changes to the review system included strengthening the online system for protocol submission and review, recruiting more reviewers, and trialing a joint review process. The turnaround time from submission to national approval/rejection over this period was faster than pre-pandemic, but slower than the national committee's target. COVID-19-specific ethics questions centred on: virtual informed consent and data collection; COVID-19 prevention, screening and testing procedures; and the challenges of study design and community engagement during the pandemic. Conclusions: The unprecedented challenges of the pandemic and added bureaucratic requirements created a more complex review process and delayed final approval of research protocols. The feasibility of conducting joint review of research during public health emergencies in Kenya needs further investigation. Consideration of the unique COVID-19 ethics issues raised in this paper might aid expedience in current and future reviews.

Breadth of Antibodies to Plasmodium falciparum Variant Surface Antigens Is Associated With Immunity in a Controlled Human Malaria Infection Study.

Background: Plasmodium falciparum variant surface antigens (VSAs) contribute to malaria pathogenesis by mediating cytoadhesion of infected red blood cells to the microvasculature endothelium. In this study, we investigated the association between anti-VSA antibodies and clinical outcome in a controlled human malaria infection (CHMI) study. Method: We used flow cytometry and ELISA to measure levels of IgG antibodies to VSAs of five heterologous and one homologous P. falciparum parasite isolates, and to two PfEMP1 DBLß domains in blood samples collected a day before the challenge and 14 days after infection. We also measured the ability of an individual's plasma to inhibit the interaction between PfEMP1 and ICAM1 using competition ELISA. We then assessed the association between the antibody levels, function, and CHMI defined clinical outcome during a 21-day follow-up period post infection using Cox proportional hazards regression. Results: Antibody levels to the individual isolate VSAs, or to two ICAM1-binding DBLß domains of PfEMP1, were not associated with a significantly reduced risk of developing parasitemia or of meeting treatment criteria after the challenge after adjusting for exposure. However, anti-VSA antibody breadth (i.e., cumulative response to all the isolates) was a significant predictor of reduced risk of requiring treatment [HR 0.23 (0.10-0.50) p= 0.0002]. Conclusion: The breadth of IgG antibodies to VSAs, but not to individual isolate VSAs, is associated with protection in CHMI.

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.

Effect of HIV infection on the acute antibody response to malaria antigens in children: an observational study.

BACKGROUND: In sub-Saharan Africa, the distributions of malaria and HIV widely overlap. Among pregnant and non-pregnant adults, HIV affects susceptibility to malaria, its clinical course and impairs antibody responses to malaria antigens. However, the relationship between the two diseases in childhood, when most deaths from malaria occur, is less clear. It was previously reported that HIV is associated with admission to hospital in rural Kenya with severe malaria among children, except in infancy. HIV-infected children with severe malaria were older, had higher parasite density and increased mortality, raising a hypothesis that HIV interferes with naturally acquired immunity to malaria, hence with little effect at younger ages (a shorter history of exposure). To test this hypothesis, levels of anti-merozoite and schizont extract antibodies were compared between HIV-infected and uninfected children who participated in the original study. METHODS: IgG responses to malaria antigens that are potential targets for immunity to malaria (AMA1, MSP2, MSP3 and schizont extract) were compared between 115 HIV-infected and 115 age-matched, HIV-uninfected children who presented with severe malaria. The children were classified as high and low responders for each antigen and assigned antibody-response breadth scores according to the number of antigens to which they were responsive. A predictive logistic regression model was used to test if HIV was an effect modifier on the age-related acquisition of antibody responses, with age as a continuous variable. RESULTS: Point estimates of the responses to all antigens were lower amongst HIV-infected children, but this was only statistically significant for AMA1 (P = 0.028). HIV-infected children were less likely to be high responders to AMA1 [OR 0.44 (95%CI, 0.2-0.90) P = 0.024]. HIV was associated with a reduced breadth of responses to individual merozoite antigens (P = 0.02). HIV strongly modified the acquisition of antibodies against schizont extract with increasing age (P < 0.0001), but did not modify the rate of age-related acquisition of responses to individual merozoite antigens. CONCLUSIONS: In children with severe malaria, HIV infection is associated with a lower magnitude and narrower breadth of IgG responses to merozoite antigens and stunting of age-related acquisition of the IgG antibody response to schizont extract.

Barriers to access and utilization of healthcare by children with neurological impairments and disability in low-and middle-income countries: a systematic review.

Background: Neurological impairments (NI) and disability are common among older children in low-and middle-income countries (LMICs). We conducted a systematic review to examine the barriers limiting access and utilization of biomedical and rehabilitative care by children and adolescents with NI in LMICs. Methods: We searched PubMed, Latin America and Caribbean Health Sciences Literature, Global Index Medicus, and Google Scholar for studies published between 01/01/1990 and 14/11/2019 to identify relevant studies. We included all studies reporting on barriers limiting access and utilization of preventive, curative, and rehabilitative care for children aged 0-19 years with NI in five domains: epilepsy, and cognitive, auditory, visual, and motor function impairment. Data from primary studies were synthesized using both qualitative and quantitative approaches. Results: Our literature searches identified 3,258 reports of which 20 were included in the final analysis. Fifteen studies (75.0%) originated from diverse settings in sub-Saharan Africa (SSA). Factors limiting access and utilization of healthcare services in >50% of the studies were: financial constraints (N=17, 85.0%), geographical and physical inaccessibility (N=14, 70.0%), inadequate healthcare resources (N=14, 70.0%), prohibitive culture and beliefs (N=12, 60.0%), and inadequate education/awareness (N=11, 55.0%). Factors reported in <50% of the studies included competing domestic roles (N=4, 20%) and a lack of confidentiality for personal information (N=2, 10.0%). Very few reports were identified from outside Africa preventing a statistical analysis by continent and economic level. Conclusions: Financial constraints, geographic and physical inaccessibility, and inadequate healthcare resources were the most common barriers limiting access and utilization of healthcare services by children with NI in LMICs. PROSPERO registration: CRD42020165296 (28/04/2020).

Premature Mortality, Risk Factors, and Causes of Death Following Childhood-Onset Neurological Impairments: A Systematic Review.

Background: Neurological impairment (NI) and disability are associated with reduced life expectancy, but the risk and magnitude of premature mortality in children vary considerably across study settings. We conducted a systematic review to estimate the magnitude of premature mortality following childhood-onset NI worldwide and to summarize known risk factors and causes of death. Methods: We searched various databases for published studies from their inception up to 31st October 2020. We included all cohort studies that assessed the overall risk of mortality in individuals with childhood-onset epilepsy, intellectual disability (ID), and deficits in hearing, vision and motor functions. Comparative measures of mortality such as the standardized mortality ratio (SMR), risk factors and causes were synthesized quantitatively under each domain of impairment. This review is registered on the PROSPERO database (registration number CRD42019119239). Results: The search identified 2,159 studies, of which 24 studies were included in the final synthesis. Twenty-two (91.7%) studies originated from high-income countries (HICs). The median SMR was higher for epilepsy compared with ID (7.1 [range 3.1-22.4] vs. 2.9 [range 2.0-11.6]). In epilepsy, mortality was highest among younger age groups, comorbid neurological disorders, generalized seizures (at univariable levels), untreatable epilepsy, soon after diagnosis and among cases with structural/metabolic types, but there were no differences by sex. Most deaths (87.5%) were caused by non-epilepsy-related causes. For ID, mortality was highest in younger age groups and girls had a higher risk compared to the general population. Important risk factors for premature mortality were severe-to-profound severity, congenital disorders e.g., Down Syndrome, comorbid neurological disorders and adverse pregnancy and perinatal events. Respiratory infections and comorbid neurological disorders were the leading causes of death in ID. Mortality is infrequently examined in impairments of vision, hearing and motor functions. Summary: The risk of premature mortality is elevated in individuals with childhood-onset NI, particularly in epilepsy and lower in ID, with a need for more studies for vision, hearing, and motor impairments. Survival in NI could be improved through interventions targeting modifiable risk factors and underlying causes.

protGear: A protein microarray data pre-processing suite.

Protein microarrays are versatile tools for high throughput study of the human proteome, but systematic and non-systematic sources of bias constrain optimal interpretation and the ultimate utility of the data. Published guidelines to limit technical variability whilst maintaining important biological variation favour DNA-based microarrays that often differ fundamentally in their experimental design. Rigorous tools to guide background correction, the quantification of within-sample variation, normalisation, and batch correction specifically for protein microarrays are limited, require extensive investigation and are not centrally accessible. Here, we develop a generic one-stop-shop pre-processing suite for protein microarrays that is compatible with data from the major protein microarray scanners. Our graphical and tabular interfaces facilitate a detailed inspection of data and are coupled with supporting guidelines that enable users to select the most appropriate algorithms to systematically address bias arising in customized experiments. The localization and distribution of background signal intensities determine the optimal correction strategy. A novel function overcomes the limitations in the interpretation of the coefficient of variation when signal intensities are at the lower end of the detection threshold. We demonstrate essential considerations in the experimental design and their impact on a range of algorithms for normalization and minimization of batch effects. Our user-friendly interactive web-based platform eliminates the need for prowess in programming. The open-source R interface includes illustrative examples, generates an auditable record, enables reproducibility, and can incorporate additional custom scripts through its online repository. This versatility will enhance its broad uptake in the infectious disease and vaccine development community.

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.

Developing excellence in biostatistics leadership, training and science in Africa: How the Sub-Saharan Africa Consortium for Advanced Biostatistics (SSACAB) training unites expertise to deliver excellence.

The increase in health research in sub-Saharan Africa (SSA) has generated large amounts of data and led to a high demand for biostatisticians to analyse these data locally and quickly.  Donor-funded initiatives exist to address the dearth in statistical capacity, but few initiatives have been led by African institutions. The Sub-Saharan African Consortium for Advanced Biostatistics (SSACAB) aims to improve biostatistical capacity in Africa according to the needs identified by African institutions, through (collaborative) masters and doctoral training in biostatistics. We describe the SSACAB Consortium, which comprises 11 universities and four research institutions- supported by four European universities. SSACAB builds on existing resources to strengthen biostatistics for health research with a focus on supporting biostatisticians to become research leaders; building a critical mass of biostatisticians, and networking institutions and biostatisticians across SSA.  In 2015 only four institutions had established Masters programmes in biostatistics and SSACAB supported the remaining institutions to develop Masters programmes. In 2019 the University of the Witwatersrand became the first African institution to gain Royal Statistical Society accreditation for a Biostatistics MSc programme. A total of 150 fellows have been awarded scholarships to date of which 123 are Masters fellowships (41 female) of which with 58 have already graduated. Graduates have been employed in African academic (19) and research (15) institutions and 10 have enrolled for PhD studies. A total of 27 (10 female) PhD fellowships have been awarded; 4 of them are due to graduate by 2020. To date, SSACAB Masters and PhD students have published 17 and 31 peer-reviewed articles, respectively. SSACAB has also facilitated well-attended conferences, face-to-face and online short courses. Pooling the limited biostatistics resources in SSA, and combining with co-funding from external partners is an effective strategy for the development and teaching of advanced biostatistics methods, supervision and mentoring of PhD candidates.

HIV infection, malnutrition, and invasive bacterial infection among children with severe malaria.

BACKGROUND: Human immunodeficiency virus (HIV) infection, malnutrition, and invasive bacterial infection (IBI) are reported among children with severe malaria. However, it is unclear whether their cooccurrence with falciparum parasitization and severe disease happens by chance or by association among children in areas where malaria is endemic. METHODS: We examined 3068 consecutive children admitted to a Kenyan district hospital with clinical features of severe malaria and 592 control subjects from the community. We performed multivariable regression analysis, with each case weighted for its probability of being due to falciparum malaria, using estimates of the fraction of severe disease attributable to malaria at different parasite densities derived from cross-sectional parasitological surveys of healthy children from the same community. RESULTS: HIV infection was present in 133 (12%) of 1071 consecutive parasitemic admitted children (95% confidence interval [CI], 11%-15%). Parasite densities were higher in HIV-infected children. The odds ratio for admission associated with HIV infection for admission with true severe falciparum malaria was 9.6 (95% CI, 4.9-19); however, this effect was restricted to children aged 1 year. Malnutrition was present in 507 (25%) of 2048 consecutive parasitemic admitted children (95% CI, 23%-27%). The odd ratio associated with malnutrition for admission with true severe falciparum malaria was 4.0 (95% CI, 2.9-5.5). IBI was detected in 127 (6%) of 2048 consecutive parasitemic admitted children (95% CI, 5.2%-7.3%). All 3 comorbidities were associated with increased case fatality. CONCLUSIONS: HIV, malnutrition and IBI are biologically associated with severe disease due to falciparum malaria rather than being simply alternative diagnoses in co-incidentally parasitized children in an endemic area.

What you see is not what you get: implications of the brevity of antibody responses to malaria antigens and transmission heterogeneity in longitudinal studies of malaria immunity.

BACKGROUND: A major handicap in developing a malaria vaccine is the difficulty in pinpointing the immune responses that protect against malaria. The protective efficacy of natural or vaccine-induced immune responses against malaria is normally assessed by relating the level of the responses in an individual at the beginning of a follow-up period and the individual's experience of malaria infection or disease during the follow-up. This approach has identified a number of important responses against malaria, but their protective efficacies vary considerably between studies. HYPOTHESIS: It is likely that apart from differences in study methodologies, differences in exposure among study subjects within each study and brevity of antibody responses to malaria antigen are important sources of the variation in protective efficacy of anti-malaria immune responses mentioned above. Since malaria immunity is not complete, anyone in an area of stable malaria transmission who does not become asymptomatically or symptomatically infected during follow-up subsequent to treatment is most likely unexposed rather than immune. TESTING THE HYPOTHESIS: It is proposed that individuals involved in a longitudinal study of malaria immunity should be treated for malaria prior to the start of the study and only those who present with at least an asymptomatic infection during the follow-up should be included in the analysis. In addition, it is proposed that more closely repeated serological survey should be carried out during follow-up in order to get a better picture of an individual's serological status. IMPLICATIONS OF THE HYPOTHESIS: Failure to distinguish between individuals who do not get a clinical episode during follow-up because they were unexposed and those who are genuinely immune undermines our ability to assign a protective role to immune responses against malaria. The brevity of antibodies responses makes it difficult to assign the true serological status of an individual at any given time, i.e. those positive at a survey may be negative by the time they encounter the next infection.

Enhancing fieldworkers' performance management support in health research: an exploratory study on the views of field managers and fieldworkers from major research centres in Africa.

INTRODUCTION: Fieldworkers are part of the system that promotes scientific and ethical standards in research, through data collection, consenting and supporting research, due to their insider cultural knowledge and fluency in local languages. The credibility and integrity of health research, therefore, rely on how fieldworkers adhere to institutional and research procedures and guidelines. OBJECTIVES: This study mapped out existing practices in training, support and performance management of fieldworkers in Africa, described fieldworkers' and their managers' experiences, and lessons learnt. A consultative process, involving field managers from 15 international health research institutions, was used to identify appropriate ways of addressing the challenges fieldworkers face. METHODS: In phase 1, we conducted 32 telephone interviews with 20 field managers and 12 senior fieldworkers from 18 major research centres in Africa, Medical Research Council-UK and the INDEPTH Network Secretariat. In phase 2, we held a 2.5-day workshop involving 25 delegates, including 18 field managers from the institutions that were involved in phase 1 and 7 additional stakeholders from the KEMRI Wellcome Trust Research Programme (KWTRP). An earlier report from phase 1 was published in BMC MedicalEthics in 2015. Data transcribed from the interviews and workshop proceedings were analysed thematically using NVivo V.10 software. RESULTS: Most institutions employed fieldworkers, usually with 12 years of formal education and residing within the geographical areas of research, to support studies. Although their roles were common, there were marked differences in the type of training, professional development schemes and fieldworkers support. Fieldworkers faced various challenges, with the potential to affect their ethical and scientific practices. DISCUSSION: Fieldworkers undertake vital tasks that promote data quality and ethical practice in research. There is a need for research institutions to develop a structured support system, provide fieldworkers with interpersonal skills training, and provide space for discussion, reflection and experience sharing to help fieldworkers tackle the practical and ethical challenges they face.

Premature mortality in children aged 6-9 years with neurological impairments in rural Kenya: a cohort study.

BACKGROUND: Neurological impairments might significantly contribute to reduced life expectancy in low-income and middle-income countries (LMICs). There are no empirical studies of premature mortality in children with neurological impairments in Africa. This study estimated the risk of premature mortality in children with neurological impairments and identified risk factors and causes of death. METHODS: We did a cohort study based on a two-stage epidemiological survey in the Kilifi Health and Demographic Surveillance System (Kilifi, Kenya). Study participants were children aged 6-9 years. In the first stage, five trained field workers administered a low-cost screening tool to a random sample of households. In the second stage, we assessed for neurological impairments in five domains (epilepsy, cognitive impairments, vision impairments, hearing impairments, and motor impairments) using comprehensive clinical evaluation and extensive neuropsychological assessments. From the two-stage survey we identified a cohort of children with neurological impairment and a cohort of matched controls. We also enrolled an age-matched sample from the general population. The primary outcome was all-cause mortality. Mortality rates, standardised mortality ratio (SMR), and hazard ratios (HR) for risk factors were estimated and causes of death identified. FINDINGS: We enrolled 306 children with neurological impairment, 9912 survey controls, and 22 873 age-matched participants from the general population, and followed up the cohorts between June 1, 2001, and Aug 31, 2018. Median follow-up was 14·5 years (IQR 8·6-17·2). 11 (3·9%) of 284 children with neurological impairment, 92 (1·0%) of 9009 controls, and 272 (1·2%) of 22 873 participants in the general population sample died during the follow-up. Overall mortality rates were 309·8 per 100 000 person-years of observation (95% CI 126·7-492·9) in children with neurological impairment, 80·8 per 100 000 person-years of observation (64·3-97·3) in controls, and 98·8 per 100 000 person-years of observation (87·1-110·6) in the general population sample (mortality rate ratio 3·83, 95% CI 2·05-7·16, p<0·001, compared with controls; 3·13, 1·71-5·72, p<0·001, compared with the general population). Mortality risk in children with neurological impairment was not dependent on the severity of impairment (p=0·291) nor on a specific neurological impairment domain (p=0·205). The overall risk of death adjusted for age and sex was higher in children with neurological impairment compared with controls (HR 4·24, 95% CI 2·26-7·94, p=0·002). An SMR of 3·15 (95% CI 1·66-5·49) was obtained after using the general population sample as the reference for indirect standardisation. In multivariable risk factor analysis, developmental delay (adjusted HR 18·92, 95% CI 2·23-160·44, p=0·007) and severe malnutrition (20·92, 3·14-139·11, p=0·002) increased the risk of mortality in children with neurological impairment. Infections such as HIV/AIDS and accidents were common among all decedents. INTERPRETATION: The risk of premature mortality was higher in children diagnosed with neurological impairments compared with the general population and was increased by developmental delay and severe malnutrition. Child development and nutritional status should be assessed in all children in LMICs and tailored interventions started to improve outcomes. FUNDING: Wellcome Trust, DELTAS Africa Initiative.