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.

Acceptability of contact management and care of simple cases of COVID-19 at home: a cross-sectional study in Senegal.

BACKGROUND: COVID-19 is a major public health problem. In mid-2020, due to the health system challenges from increased COVID-19 cases, the Ministry of Health and Social Action in Senegal opted for contact management and care of simple cases at home. The objective of the study was to determine the acceptability of contact and simple case management of COVID-19 at home and its associated factors in Senegal. METHODS: This was a descriptive and analytical cross-sectional study. We collected data from 11 June to 10 July 2020. We used a marginal quota sampling strategy. A total of 813 individuals took part in the survey. We collected data using a telephone interview. RESULTS: The care of simple cases of COVID-19 at home was well accepted (78.5%). The use of home contact management was less accepted (51.4%). Knowledge of the modes of transmission of the virus and confidence in institutional information were associated with the acceptability of home care for simple cases. Regularly searching for information on COVID-19 and confidence in the government's control of the epidemic were associated with the acceptability of managing contacts at home. CONCLUSIONS: Authorities should take these factors into account for better communication to improve the acceptability and confidence in home-based care for COVID-19 and future epidemics.

Acceptability of government measures against COVID-19 pandemic in Senegal: A mixed methods study

While the first case of COVID-19 was declared on March 2 2020 in Senegal, the government banned the attendance of places of worship on 14 March, as a first measure. On March 23, it introduced a curfew, a ban on movement between regions, and the closure of markets. The objective of this study is to measure and understand the acceptability of these four governmental measures as well as the level of public trust in the state to fight the pandemic. We carried out a mixed-method research. The acceptability variables were defined using the theoretical framework of acceptability (TFA). At the quantitative level, we carried out a telephone survey (June/July 2020) at the national level (n = 813) with a sampling strategy by marginal quotas. We conducted a qualitative survey (August/September 2020) with a nested sample (n = 30). The results show a relatively high acceptability of the measures but a heterogeneity of responses. People considered curfews to be much more important (85.7% [83.2%;88.0%]) than the closure of places of worship (55.4%;[51.9%;58.7%]), which is least in line with the values and positive affective attitude. Several positive unintended effects of the curfew were stated (security and social/family cohesion). People over the age of 60 have more confidence in the government to fight the pandemic than people under the age of 25, although not significant (7.72 ± 3.12 vs. 7.07 ± 3.11, p = 0.1);and they are more in favour of the closure of places of worship. The more regions are affected by the pandemic, the less confidence respondents report in the government and the less they perceive the measures as effective. The results confirm the importance of government communication and trust in the state to strengthen the acceptability of pandemic measures. Important differences in acceptability show the need to adapt measures and their explanations, instead of unqualified universal action.

The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage.

Introduction: The Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated. Methods: Viral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs. Results: The age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country. Discussion: This study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.

Factors associated with COVID-19 vaccine hesitancy in Senegal: A mixed study.

This study was an explanatory, sequential, mixed-methods design conducted in Senegal. We collected quantitative data from December 24, 2020, to January 16, 2021, and qualitative data from February 19 to March 30, 2021. We conducted a telephone survey among a marginal quota sample of 607 people over 18 years old. We performed descriptive, bivariate, and multivariate analyses with R software for the quantitative phase; and performed manual content analyses for the qualitative phase. We surveyed 607 people for the quantitative phase and interviewed 30 people for the qualitative phase. Individuals who hesitated or refused to be vaccinated represented 12.9% and 32.8%, respectively. Vaccine hesitancy was related to gender, living in large cities, having a poor attitude toward the vaccine, thinking that the vaccine would not help protect them from the virus, being influenced by people important to them, and lacking information from health professionals. Vaccine refusal was related to living in large cities, having a poor attitude toward the vaccine, thinking that the vaccine would not help protect them from the virus, thinking that the vaccine could endanger their health, trusting opinions of people who were important to them, and lacking information from health professionals. The results of the study show that the factors associated with COVID-19 vaccine hesitancy and refusal are diverse and complex. Addressing these factors will help to ensure better vaccination coverage. Governments and health authorities should intensify their efforts to promote vaccine confidence and reduce misinformation.

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.

Framing the future of the COVID-19 response operations in 2022 in the WHO African region.

BACKGROUND: With the evolving epidemiological parameters of COVID-19 in Africa, the response actions and lessons learnt during the pandemic's past two years, SARS-COV 2 will certainly continue to circulate in African countries in 2022 and beyond. As countries in the African continent need to be more prepared and plan to 'live with the virus' for the upcoming two years and after and at the same time mitigate risks by protecting the future most vulnerable and those responsible for maintaining essential services, WHO AFRO is anticipating four interim scenarios of the evolution of the pandemic in 2022 and beyond in the region. OBJECTIVE: In preparation for the rollout of response actions given the predicted scenarios, WHO AFRO has identified ten strategic orientations and areas of focus for supporting member states and partners in responding to the COVID-19 pandemic in Africa in 2022 and beyond. METHODS: WHO analysed trends of the transmissions since the first case in the African continent and reviewed lessons learnt over the past months. RESULTS: Establishing a core and agile team solely dedicated to the COVID-19 response at the WHO AFRO, the emergency hubs, and WCOs will improve the effectiveness of the response and address identified challenges. The team will collaborate with the various clusters of the regional office, and other units and subunits in the WCOs supported with good epidemics intelligence. COVID-19 pandemic has afflicted global humanity at unprecedented levels. CONCLUSION: Two years later and while starting the third year of the COVID-19 response, we now need to change and adapt our strategies, tools and approaches in responding timely and effectively to the pandemic in Africa and save more lives.

Institut Pasteur Dakar Mobile Lab: Part of the Solution to Tackle COVID Pandemic in Senegal, a Model to Be Exploited

The COVID-19 pandemic required massive testing of potential patients in resource-constrained areas in Senegal. The first case of COVID-19 was reported on 2 March 2020 in Dakar city and on 10 March, the first cases were reported in Touba city, the second most populous city in Senegal. Following the scale of confirmed COVID-19 cases in Touba city, the Institut Pasteur de Dakar mobile laboratory truck (MLT) was deployed on March 13 to bring diagnostics to the point of need for better management of patient and outbreak control. The MLT deployed is a 6 ×6 truck equipped with an isolator for sample inactivation, a generator and batteries to ensure energy autonomy, and a molecular platform for pathogens detection. Nasal and oropharyngeal swabs were collected from suspected COVID-19 cases and sent to the MLT located at the Touba primary healthcare center. Samples were extracted and RNA amplified by real time qRT-PCR. A total of 11,693 samples were collected from 14 regions of Senegal and tested between March to August 2021. Within the samples tested, 10.6% (1240/1693) were positive for SARS-CoV-2. Furthermore, the MLT allowed the confirmation of the first cases of COVID-19 in 25 out of 79 health districts of Senegal. Thereby, the MLT deployment during the first 6 months of COVID-19 in Senegal allowed rapid processing of suspected case samples collected in Touba and other surrounding areas and, thus, significantly contributed to the outbreak response and early case management in Senegal.

First wave COVID-19 pandemic in Senegal: Epidemiological and clinical characteristics.

BACKGROUND: The novel coronavirus disease 2019 (COVID-19) pandemic has spread from China to the rest of the world. Africa seems less impacted with lower number of cases and deaths than other continents. Senegal recorded its first case on March 2, 2020. We present here data collected from March 2 to October 31, 2020 in Senegal. METHODS: Socio-demographic, epidemiological, clinical and virological information were collected on suspected cases. To determine factors associated with diagnosed infection, symptomatic disease and death, multivariable binary logistic regression and log binomial models were used. Epidemiological parameters such as the reproduction number and growth rate were estimated. RESULTS: 67,608 suspected cases were tested by the IPD laboratories (13,031 positive and 54,577 negative). All age categories were associated with SARS-CoV-2 infection, but also patients having diabetes or hypertension or other cardiovascular diseases. With diagnosed infection, patients over 65 years and those with hypertension and cardiovascular disease and diabetes were highly associated with death. Patients with co-morbidities were associated with symptomatic disease, but only the under 15 years were not associated with. Among infected, 27.67% were asymptomatic (40.9% when contacts were systematically tested; 12.11% when only symptomatic or high-risk contacts were tested). Less than 15 years-old were mostly asymptomatic (63.2%). Dakar accounted for 81.4% of confirmed cases. The estimated mean serial interval was 5.57 (± 5.14) days. The average reproduction number was estimated at 1.161 (95%CI: 1.159-1.162), the growth rate was 0.031 (95%CI: 0.028-0.034) per day. CONCLUSIONS: Our findings indicated that factors associated with symptomatic COVID-19 and death are advanced age (over 65 years-old) and comorbidities such as diabetes and hypertension and cardiovascular disease.

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

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

Assessment of COVID-19 pandemic responses in African countries: thematic synthesis of WHO intra-action review reports.

OBJECTIVES: We conducted a review of intra-action review (IAR) reports of the national response to the COVID-19 pandemic in Africa. We highlight best practices and challenges and offer perspectives for the future. DESIGN: A thematic analysis across 10 preparedness and response domains, namely, governance, leadership, and coordination; planning and monitoring; risk communication and community engagement; surveillance, rapid response, and case investigation; infection prevention and control; case management; screening and monitoring at points of entry; national laboratory system; logistics and supply chain management; and maintaining essential health services during the COVID-19 pandemic. SETTING: All countries in the WHO African Region were eligible for inclusion in the study. National IAR reports submitted by March 2021 were analysed. RESULTS: We retrieved IAR reports from 18 African countries. The COVID-19 pandemic response in African countries has relied on many existing response systems such as laboratory systems, surveillance systems for previous outbreaks of highly infectious diseases and a logistics management information system. These best practices were backed by strong political will. The key challenges included low public confidence in governments, inadequate adherence to infection prevention and control measures, shortages of personal protective equipment, inadequate laboratory capacity, inadequate contact tracing, poor supply chain and logistics management systems, and lack of training of key personnel at national and subnational levels. CONCLUSION: These findings suggest that African countries' response to the COVID-19 pandemic was prompt and may have contributed to the lower cases and deaths in the region compared with countries in other regions. The IARs demonstrate that many technical areas still require immediate improvement to guide decisions in subsequent waves or future outbreaks.

SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic.

SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds mutations of concern. Here, we report additional lineage A.27 data and sequences from five African countries and describe the molecular characteristics, and the genetic history of this lineage worldwide. Based on the new sequences investigated, the most recent ancestor (tMRCA) of lineage A.27 was estimated to be from April 2020 from Niger. It then spread to Europe and other parts of the world with a peak observed between February and April 2021. The detection rate of A.27 then decreased with only a few cases reported during summer 2021. The phylogenetic analysis revealed many sub-lineages. Among them, one was defined by the substitution Q677H in the spike (S) gene, one was defined by the substitution D358N in the nucleoprotein (N) gene and one was defined by the substitution A2143V in the ORF1b gene. This work highlights the importance of molecular characterization and the timely submission of sequences to correctly describe the circulation of particular strains in order to be proactive in monitoring the pandemic.

Acceptability of government measures against COVID-19 pandemic in Senegal: A mixed methods study.

While the first case of COVID-19 was declared on March 2 2020 in Senegal, the government banned the attendance of places of worship on 14 March, as a first measure. On March 23, it introduced a curfew, a ban on movement between regions, and the closure of markets. The objective of this study is to measure and understand the acceptability of these four governmental measures as well as the level of public trust in the state to fight the pandemic. We carried out a mixed-method research. The acceptability variables were defined using the theoretical framework of acceptability (TFA). At the quantitative level, we carried out a telephone survey (June/July 2020) at the national level (n = 813) with a sampling strategy by marginal quotas. We conducted a qualitative survey (August/September 2020) with a nested sample (n = 30). The results show a relatively high acceptability of the measures but a heterogeneity of responses. People considered curfews to be much more important (85.7% [83.2%; 88.0%]) than the closure of places of worship (55.4%; [51.9%; 58.7%]), which is least in line with the values and positive affective attitude. Several positive unintended effects of the curfew were stated (security and social/family cohesion). People over the age of 60 have more confidence in the government to fight the pandemic than people under the age of 25, although not significant (7.72 ± 3.12 vs. 7.07 ± 3.11, p = 0.1); and they are more in favour of the closure of places of worship. The more regions are affected by the pandemic, the less confidence respondents report in the government and the less they perceive the measures as effective. The results confirm the importance of government communication and trust in the state to strengthen the acceptability of pandemic measures. Important differences in acceptability show the need to adapt measures and their explanations, instead of unqualified universal action.

Factors associated with the acceptability of government measures to address COVID-19 in Senegal.

INTRODUCTION: Three months after the first appearance of the new coronavirus (COVID-19), Senegal recorded its first case on March 2, 2020. Faced with this pandemic, the State reacted quickly with public measures : instituting a curfew, placing a ban on travel between regions, and closing shops and places of worship. This research aims to study the acceptability of these non-pharmaceutical measures by the Senegalese population. METHOD: This study was a cross-sectional and analytical survey conducted in June and July 2020 among Senegalese over 18 years old. Sampling by the representative quota method was distributed proportionally to age, gender and region. We constructed the questionnaire using the theoretical framework of acceptability of health interventions. Through a telephone call center synchronised to an internet server, we collected data on personal characteristics, knowledge of the disease, trust in information sources, trust in government, concern about the pandemic, and the seven dimensions of acceptability. We performed descriptive analysis and structural equation with R software version 4.0.2. RESULTS: This study included a total of 813 individuals. The average age was 34.7 years ( ± 14.2 years). They were predominantly male (54.6 %), with no education (42.6 %). The increased level of knowledge of the disease was associated with confidence in national media information sources provided by the administrative and health authorities (ß=0.11, p<0.01). The increase in the level of trust in the government in response to COVID-19 was positively related to the acceptability of curfew (ß=0.16, p<0.001), travel ban between regions (ß=0.11, p<0.001), and closure of places of worship (ß=0.1, p<0.01) and markets (ß=0.09, p<0.01). CONCLUSION: In Senegal, the acceptability of the measures depended on knowledge of the disease, perception of the risk of the disease, and trust in the government. There is a need to strengthen awareness and risk communication of COVID-19.

SARS-CoV-2 Circulation, Guinea, March 2020-July 2021.

This overview of severe acute respiratory syndrome coronavirus 2 circulation over 1.5 years in Guinea demonstrates that virus clades and variants of interest and concern were progressively introduced, mostly by travellers through Conakry, before spreading through the country. Sequencing is key to following virus evolution and establishing efficient control strategies.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

[Risk perception of COVID-19 pandemic among health care providers: qualitative study conducted at the King Baudoin Hospital in Guédiawaye, the first hospital faced with managing a community-acquired COVID-19 case in Senegal]. / Analyse des risques perçus des prestataires de santé en milieu hospitalier dans le cadre de la pandémie à COVID-19: une étude qualitative dans le Centre Hospitalier Roi Baudoin de Guédiawaye, lors de la réception du 1er cas communautaire du Sénégal.

INTRODUCTION: health care systems in West Africa have been under strain since the beginning of the COVID-19 pandemic. The exposure of health personnel to infection during the COVID-19 pandemic has been reported in several studies. The purpose of this study was to analyze health workers' actual and perceived risk in the first hospital faced with managing a community-acquired COVID-19 case in Senegal. METHODS: we conducted an exploratory descriptive study of health care providers' perception about their own risk during the COVID-19 pandemic. Forty-seven health-care providers were interviewed in personal, extensive interviews in this hospital. RESULTS: the fear of disease was present among the health staff. This fear was caused by several exogenous and endogenous factors, including the lack of knowledge of the virus and COVID-19 disease, the feeling of vulnerability due to insufficient availability of personal protective equipment, healthcare professionals' position in relation to the priesthood from the medical profession and the real and perceived risk of putting their family and their entourage in potentially dangerous situations. CONCLUSION: this study highlights the need for psycho-affective management of health care workers during this pandemic by taking the gender dimension into account. The provision of personal adequate protective equipment and stress management measures could enable front-line workers to cope with this pandemic in complete serenity.