A social acceptability scale: validation in the context of government measures to curb the COVID-19 pandemic in Senegal.

INTRODUCTION: In March 2020, the government of Senegal introduced a curfew, a ban on travel between regions, the closure of markets, and a ban on attending places of worship to contain the spread of the COVID-19 pandemic. As part of research into the response to COVID-19, we developed a scale to measure the social acceptability of these measures. METHODS: We used Sekhon's theoretical framework of acceptability (TFA) to formulate the content of the scale items. We assessed the homogeneity of the scale using Cronbach's Alpha and average interitem correlations. We measured the dimensional properties of the scale using rating scale models. We tested the sensitivity of the scale to sociodemographic characteristics using mixed linear regressions and rating scale models. RESULTS: The final scale consisted of seven items corresponding to the constructs of acceptability. Analysis performed on data from 813 individuals showed that the scale has satisfactory statistical properties (Cronbach's α>0.8, Loevinger's coefficient>0.3, intraclass correlation>0.4). CONCLUSION: This scale was one of the first to test the TFA. The small number of items was advantageous for use under challenging data collection contexts. Measuring the acceptability of public health interventions with this tool can help in their design and implementation.

Creating culturally-informed protocols for a stunting intervention using a situated values-based approach (WeValue InSitu): a double case study in Indonesia and Senegal.

International development work involves external partners bringing expertise, resources, and management for local interventions in LMICs, but there is often a gap in understandings of relevant local shared values. There is a widespread need to better design interventions which accommodate relevant elements of local culture, as emphasised by recent discussions in global health research regarding neo-colonialism. One recent innovation is the concept of producing 'cultural protocols' to precede and guide community engagement or intervention design, but without suggestions for generating them. This study explores and demonstrates the potential of an approach taken from another field, named WeValue InSitu, to generate local culturally-informed protocols. WeValue InSitu engages stakeholder groups in meaning-making processes which 'crystallize' their envelope of local shared values, making them communicable to outsiders.Our research context is understanding and reducing child stunting, including developing interventions, carried out at the Senegal and Indonesia sites of the UKRI GCRF Action Against Stunting Hub. Each national research team involves eight health disciplines from micro-nutrition to epigenetics, and extensive collection of samples and questionnaires. Local culturally-informed protocols would be generally valuable to pre-inform engagement and intervention designs. Here we explore generating them by immediately following the group WeValue InSitu crystallization process with specialised focus group discussions exploring: what local life practices potentially have significant influence on the environments affecting child stunting, and which cultural elements do they highlight as relevant. The discussions will be framed by the shared values, and reveal linkages to them. In this study, stakeholder groups like fathers, mothers, teachers, market traders, administrators, farmers and health workers were recruited, totalling 83 participants across 20 groups. Themes found relevant for a culturally-informed protocol for locally-acceptable food interventions included: specific gender roles; social hierarchies; health service access challenges; traditional beliefs around malnutrition; and attitudes to accepting outside help. The concept of a grounded culturally-informed protocol, and the use of WeValue InSitu to generate it, has thus been demonstrated here. Future work to scope out the advantages and limitations compared to deductive culture studies, and to using other formative research methods would now be useful.

Factors associated with diabetes knowledge, attitudes and practices among people aged 18 and over in the commune of Niakhene in Senegal.

More than 422 million people worldwide have diabetes in 2016, and 1.6 million deaths are attributed to diabetes each year. Knowledge of preventive measures would enable the adjustment of preventive policies. Hence this study on knowledge and practices in rural Senegal. This was a cross-sectional, descriptive and analytical survey of subjects aged at least 18 and living in the commune of Niakhene, carried out in October 2020. A systematic random sample, stratified by sex and age group, was used. The questionnaire was based on the STEPS 2015 tool and a review of the literature. In addition to personal characteristics, the questionnaire was used to measure knowledge of symptoms, complications, risk factors, attitude to the disease and screening practices. Descriptive and analytical analyses were performed using R 4.0.2 software. A total of 300 subjects were surveyed. The average age was 35.3 years (+/-16.9), and 52.3% were women. Knowledge (62.7%) was associated with higher education (ORaj2.46{1.16-3.44}), awareness by healthcare staff (ORaj2.88{1.60-5.34}), and a family history of diabetes (ORaj3.09{1.06-11.3}). The positive attitude (53%) was associated with male sex (ORaj1.98{2.07-7.52}), awareness via audio-visual information sources (ORaj3.87{2.07-7.52}), community awareness (ORaj 3.87{2.07-7.52}), existence of a family history of hypertension and knowledge of diabetes (ORaj3.34{2.5-7.69}). Screening was carried out in 34.3% of patients. The associated risk factors were male sex (ORaj 1.95{1.12-3.34}), higher education (ORaj2.49{1.12-559}) and positive attitudes to diabetes (ORaj1.83{1.04-3.26}). One of the most effective interventions against this disease is the adoption of preventive measures which involve early detection and strengthening communication for more effective prevention.

Cross-sectional study on intention to be vaccinated against Coronavirus Disease 2019 (COVID-19) in Benin and Senegal: A structural equation modeling (SEM).

Vaccination is considered one of the solutions to the Coronavirus Disease 2019 (COVID-19) pandemic. However, a small proportion of the population were fully vaccinated in Benin (20.9%) and Senegal (7.6%) by December 2022. This study explores the determinants of intent to vaccinate. This was a cross-sectional, descriptive, and analytical study of 865 Beninese and 813 Senegalese aged 18 years and older. Marginal quota sampling by age, gender and region was adopted. Data collection, using a survey instrument based on the Random Digit Dialing method, was conducted from December 24, 2020, to January 16, 2021, in Senegal and from March 29 to May 14, 2021, in Benin. The questionnaire used the Theory of Planned Behavior and the Health Belief Model. The influence of factors was assessed using a structural equation model based on a diagonally weighted least squares estimator to account for ordered categorical data (Likert scales). In Benin and Senegal, the intention to vaccinate against COVID-19 is influenced by distinct factors. In Benin, social influence (ß = 0.42, p = 0.003) and perception of vaccine safety (ß = -0.53, p<0.001) play pivotal roles, suggesting those socially influenced have a higher vaccination intention. In Senegal, vaccination intentions are primarily driven by positive attitudes towards the vaccine (ß = 0.65, p = 0.013) and social influence (ß = 0.25, p = 0.048). This underscores the importance of individual beliefs, personal perceptions, and supportive social contexts in decision-making. Notably, positive vaccination attitudes and perceptions in both countries are strongly tied to increased social influence. While nuances exist between Benin and Senegal regarding factors influencing COVID-19 vaccination intentions, both nations underscore the pivotal roles of social influence and individual vaccination perceptions. Emphasizing trust in vaccine safety and promoting positive attitudes through effective communication are crucial for enhancing vaccination uptake in these West African countries.

Reemergence of Sylvatic Dengue Virus Serotype 2 in Kedougou, Senegal, 2020.

In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance and updated molecular diagnostic tools are needed to effectively prevent dengue virus infections in Senegal.

Sociocultural environmental factors and childhood stunting: qualitative studies - a protocol for the Shared Values theme of the UKRI GCRF Action Against Stunting Hub.

INTRODUCTION: Stunting is a significant and growing global problem that is resisting scientific attempts to understand it in terms of direct nutrition-related determinants. In recent years, research included more complex, indirect and multifactorial determinants and expanded to include multisectoral and lifestyle-related approaches. The United Kingdom Research Initiative Global Challenges Research Fund's (UKRI GCRF) Action Against Stunting Hub starts on the premise that dominant factors of stunting may vary between contexts and life phases of the child. Thus, the construction of a typology of clustered factors will be more useful to design effective programmes to alleviate it.The Shared Values theme seeks to build a bottom-up holistic picture of interlinked cultural contextual factors that might contribute to child stunting locally, by first eliciting shared values of the groups closest to the problem and then enquiring about details of their relevant daily activities and practices, to reveal links between the two. We define shared values as what groups consider 'valuable, worthwhile and meaningful' to them. METHODS AND ANALYSIS: We will recruit 12-25 local stakeholder groups in each site (in India, Indonesia and Senegal) involved in children's food and early learning environments, such as mothers, fathers, grandmothers, teachers, market vendors and health workers. The WeValue InSitu process will be used to assist them to collectively elicit, negotiate and self-articulate their own shared values through exploration of shared tacit knowledge. Focus group discussions held immediately subsequently will ask about daily activities relevant to the children's environment. These contain many examples of cultural contextual factors potentially influencing stunting locally, and intrinsically linked to shared values articulated in the previous session.

Detection of a cluster of Omicron's BA.4 sublineage in Northern Senegal and identification of the first XAS recombinant variant in Senegal.

In Senegal, since its first detection in early March 2020, genomic surveillance of SARS-CoV-2 isolates has led to the identification of the emergence of the Omicron BA.4 and BA.5 sublineages from early June 2022. To investigate the origin of a cluster of cases in Northern Senegal on July 2022, isolates were analysed using Next-generation sequencing and phylogeny. Our data provided evidence of the origin of the cluster of BA.4 cases from a XAS recombinant, that is to date, the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is a crucial need.

Nothing in Excess: Physical Activity, Health, and Life World in Senegalese Fulani Male Pastoralists, a Mixed Method Approach.

OBJECTIVES: The goal of this study was to evaluate the application of the short form of the International Physical Activity Questionnaire Survey (IPAQ-SF) in the rural Senegalese Fulani pastoralist population by combining quantitative and qualitative methods. DESIGN AND PARTICIPANTS: For the quantitative method, 101 men completed the IPAQ-SF questionnaire measuring moderate, vigorous, and walking physical activity. Self-rated health, BMI, and sociodemographic variables were also collected. With regard to the qualitative methods, a total of 22 participants were recruited and interviewed. Four themes were addressed, including (i) physical activity (PA) and its definition, description, related experiences, and representations of social actors; (ii) PA and health; (iii) PA and sport; and (iv) the body and Fulani world of life (i.e., Pulaagu/Ndimaagu). RESULTS: Sahelian herders have a high level of self-reported PA and a low amount of daily sitting time. The measure of PA as proposed by the IPAQ-SF is not adapted to the Senegalese Ferlo pastoralists, mainly because this scale gives too much importance to leisure-time PA, perceived as unproductive energy expenditure, which is factually and symbolically antinomic to the Fulani lifeworld. Thus, neither intense nor moderate PA is related to self-rated health. However, sedentary lifestyles are linked to self-rated health and, therefore, to mortality and morbidity in Fulani pastoralists. Finally, walking, which is the dominant PA during transhumance and herd surveillance, is related to BMI. It therefore represents a protective factor against the occurrence of overweight and associated chronic non-communicable diseases. CONCLUSION: The mixed method approach developed in this study has shown that the IPAQ-SF is not a valid measure of PA in the population of Fulani male herders from the Ferlo region, given that unproductive energy expenditure is incompatible with the Fulani way of life, which condemns excess and immoderation.

Implementing Joint External Evaluations of the International Health Regulations (2005) capacities in all countries in the WHO African region: process challenges, lessons learnt and perspectives for the future.

Following the West Africa Ebola virus disease outbreak (2013-2016), the Joint External Evaluation (JEE) is one of the three voluntary components recommended by the WHO for evaluating the International Health Regulations (2005) capacities in countries. Here, we share experience implementing JEEs in all 47 countries in the WHO African region. In February 2016, the United Republic of Tanzania (Mainland) was the first country globally to conduct a JEE. By April 2022, JEEs had been conducted in all 47 countries plus in the island of Zanzibar. A total of 360 subject matter experts (SMEs) from 88 organisations were deployed 607 times. Despite availability of guidelines, the process had to be contextualised while avoiding jeopardising the quality and integrity of the findings. Key challenges were: inadequate understanding of the process by in-country counterparts; competing country priorities; limited time for validating subnational capacities; insufficient availability of SMEs for biosafety and biosecurity, antimicrobial resistance, points of entry, chemical events and radio-nuclear emergencies; and inadequate financing to fill gaps identified. Key points learnt were: importance of country leadership and ownership; conducting orientation workshops before the self-assessment; availability of an external JEE expert to support the self-assessment; the skills, attitudes and leadership competencies of the team lead; identifying national experts as SMEs for future JEEs to promote capacity building and experience sharing; the centrality of involving One Health stakeholders from the beginning to the end of the process; and the need for dedicated staff for planning, coordination, implementation and timely report writing. Moving forward, it is essential to draw from this learning to plan future JEEs. Finally, predictable financing is needed immediately to fill gaps identified.

High-dimensional supervised classification in a context of non-independence of observations to identify the determining SNPs in a phenotype.

This work addresses the problem of supervised classification for highly correlated high-dimensional data describing non-independent observations to identify SNPs related to a phenotype. We use a general penalized linear mixed model with a single random effect that performs simultaneous SNP selection and population structure adjustment in high-dimensional prediction models. Specifically, the model simultaneously selects variables and estimates their effects, taking into account correlations between individuals. Single nucleotide polymorphisms (SNPs) are a type of genetic variation and each SNP represents a difference in a single DNA building block, namely a nucleotide. Previous research has shown that SNPs can be used to identify the correct source population of an individual and can act in isolation or simultaneously to impact a phenotype. In this regard, the study of the contribution of genetics in infectious disease phenotypes is of great importance. In this study, we used uncorrelated variables from the construction of blocks of correlated variables done in a previous work to describe the most related observations of the dataset. The model was trained with 90% of the observations and tested with the remaining 10%. The best model obtained with the generalized information criterion (GIC) identified the SNP named rs2493311 located on the first chromosome of the gene called PRDM16 ((PR/SET domain 16)) as the most decisive factor in malaria attacks.

Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal.

During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease.

Novel Amplicon-Based Sequencing Approach to West Nile Virus.

West Nile virus is a re-emerging arbovirus whose impact on public health is increasingly important as more and more epidemics and epizootics occur, particularly in America and Europe, with evidence of active circulation in Africa. Because birds constitute the main reservoirs, migratory movements allow the diffusion of various lineages in the world. It is therefore crucial to properly control the dispersion of these lineages, especially because some have a greater health impact on public health than others. This work describes the development and validation of a novel whole-genome amplicon-based sequencing approach to West Nile virus. This study was carried out on different strains from lineage 1 and 2 from Senegal and Italy. The presented protocol/approach showed good coverage using samples derived from several vertebrate hosts and may be valuable for West Nile genomic surveillance.

Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains.

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.

Local contextual factors of child stunting found via shared values of stakeholder groups: an exploratory case study in Kaffrine, Senegal.

OBJECTIVE: This work aims to demonstrate an original approach to identify links between locally situated shared values and contextual factors of stunting. Stunting results from multi-factorial and multi-sectoral determinants, but interventions typically neglect locally situated lived experiences, which contributes to problematic designs that are not meaningful for those concerned and/or relatively ineffective. DESIGN: This case study investigates relevant contextual factors in two steps: by first facilitating local stakeholder groups (n 11) to crystallise their shared-values-in-action using a specialised method from sustainability studies (WeValue_InSitu (WVIS)). Secondly, participants (n 44) have focus group discussions (FGD) about everyday practices around child feeding/food systems, education and/or family life. Because the first step strongly grounds participants in local shared values, the FGD can reveal deep links between contextual factors and potential influences on stunting. SETTING: Kaffrine, Senegal, an 'Action Against Stunting Hub' site. December 2020. PARTICIPANTS: Eleven stakeholder groups of mothers, fathers, grandmothers, pre-school teachers, community health workers, farmers, market traders and public administrators. RESULTS: Local contextual factors of stunting were identified, including traditional beliefs concerning eating and growing practices; fathers as decision-makers; health worker trust; financial non-autonomy for women; insufficient water for preferred crops; merchants' non-access to quality produce; religious teachings and social structures affecting children's food environment. CONCLUSIONS: Local contextual factors were identified. Pre-knowledge of these could significantly improve effectiveness of intervention designs locally, with possible applicability at other sites. The WVIS approach proved efficient and useful for making tangible contextual factors and their potential links to stunting, via a lens of local shared values, showing general promise for intervention research.

Performance assessment and validation of a plaque reduction neutralization test (PRNT) in support to yellow fever diagnostic and vaccine clinical trials.

Yellow fever (YF) virus is a mosquito-borne virus belonging to the Flaviviridae family that circulates in tropical and subtropical areas of Africa and South America. Despite the availability of an effective vaccine, YF remains a threat to travelers, residents of endemic areas, and unvaccinated populations. YF vaccination and natural infection both induce the production of neutralizing antibodies. Serological diagnostic methods detecting YF virus-specific antibodies demonstrate high levels of cross-reactivities with other flaviviruses. To date, the plaque reduction neutralization test (PRNT) is the most specific serological test for the differentiation of flavivirus infections and is considered the reference method for detecting YF neutralizing antibodies and assessing the protective immune response following vaccination. In this study, we developed and validated a YF PRNT. We optimized different parameters including cell concentration and virus-serum neutralization time period and then assessed the intra- and inter-assay precisions, dilutability, specificity, and lower limit of quantification (LLOQ) using international standard YF serum, sera from vaccinees and human specimens collected through YF surveillance. The YF PRNT has shown good robustness and 100% of intra-assay precision, 95.6% of inter-assay precision, 100% of specificity, 100% of LLOQ, and 95.3% of dilutability. The test is, therefore, suitable for use in the YF diagnostic as well as evaluation of the YF vaccine neutralizing antibody response and risk assessment studies.

How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.

The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.

Investing in preparedness for rapid detection and control of epidemics: analysis of health system reforms and their effect on 2021 Ebola virus disease epidemic response in Guinea.

The 2014-2016 West Africa Ebola Virus Disease (EVD) Epidemic devastated Guinea's health system and constituted a public health emergency of international concern. Following the crisis, Guinea invested in the establishment of basic health system reforms and crucial legal instruments for strengthening national health security in line with the WHO's recommendations for ensuring better preparedness for (and, therefore, a response to) health emergencies. The investments included the scaling up of Integrated Disease Surveillance and Response; Joint External Evaluation of International Health Regulation capacities; National Action Plan for Health Security; Simulation Exercises; One Health platforms; creation of decentralised structures such as regional and prefectural Emergency Operation Centres; Risk assessment and hazard identification; Expanding human resources capacity; Early Warning Alert System and community preparedness. These investments were tested in the subsequent 2021 EVD outbreak and other epidemics. In this case, there was a timely declaration and response to the 2021 EVD epidemic, a lower-case burden and mortality rate, a shorter duration of the epidemic and a significant reduction in the cost of the response. Similarly, there was timely detection, response and containment of other epidemics including Lassa fever and Marburg virus disease. Findings suggest the utility of the preparedness activities for the early detection and efficient containment of outbreaks, which, therefore, underlines the need for all countries at risk of infectious disease epidemics to invest in similar reforms. Doing so promises to be not only cost-effective but also lifesaving.