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Background: The Omicron variant B.1.1.529 has led to a new dynamic in the COVID-19 pan-demic, with an increase in cases worldwide. Its rapid propagation favors the emergence of novel sub-lineages, including BA.4 and BA.5. The latter has shown increased transmissibility compared to other Omicron sub-lineages. In Senegal, the emergence of the Omicron variant in December 2021 characterized the triggering of a short and dense epidemiological wave that peaked at the end of February. This wave was followed by a period with a significant drop in the number of COVID-19 cases, but an upsurge in SARS-CoV-2 infection has been noted since mid-June. Objective(s): The purpose of this brief report is to give an update regarding the genomic situation of SARS-CoV-2 in Dakar during this phase of recrudescence of cases. Method(s): We performed amplicon-based SARS-CoV-2 sequencing on nasopharyngeal swab samples from declared COVID-19 patients and outbound travelers that tested positive. Result(s): Ongoing genomic surveillance activities showed that more than half of recent COVID-19 cases were due to the BA.4 and BA.5 sub-lineages that share two critical mutations associated with increased transmissibility and immune response escape. The circulation of recombinants between Omicron sub-lineages was also noted. Conclusion(s): Despite the lack of proven severity of BA.4 and BA.5 sub-lineages, their increased transmis-sibility causes a rapid spread of the virus, hence a surge in the number of cases. This rapid spread consti-tutes a greater risk of exposure for vulnerable patients. To tackle this issue, any increase in the number of cases must be monitored to support public health stakeholders. Therefore, genomic surveillance is an ever-essential element in managing this pandemic.Copyright © 2022 Bentham Science Publishers.
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SARS-CoV-2 appeared in December 2019 in Wuhan, China. The Guinean Government has taken important measures since the notification of the first case on March 12, 2020, in particular the follow-up of the recovered. The objective of this study was to describe the health and socio-economic problems faced by those who recovered from COVID-19 in Guinea. This was a descriptive cross-sectional study by simple random sampling in the five communes of Conakry and the regions of Kindia, Labe, and Kankan. Up to 330 COVID-19 survivors responded to the survey, 99% of whom were from the urban area. The male gender represented 70.3%, and the 19-38 age group was the most represented (61.82%). Pupils, students/ teachers, health personnel, and academics respectively represented 10.91%, 17.58%, and 62.73%. In this study, 70% were married against 28.18% single, and 8.79% moved after leaving the CTEPI. There is a statically significant link between stigma and job loss with a p-value of 0.002. Stigma was strongly associated with community residence, change in income, and post Covid-19 stress (P <0.05). The cured people who live in the communes of Ratoma, Matam, and Matoto are more in the process of being stigmatized than the others, with respectively 27.6%, 23.4%, and 19.1% (p = 0.001). These results show the need to support COVID-19 survivors from health, psychological and socio-economic perspectives. Copyright © 2022, Institute of Medico-legal Publication. All rights reserved.
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Most evolutionary-oriented deep generative models do not explicitly consider the underlying evolutionary dynamics of biological sequences as it is performed within the Bayesian phylogenetic inference framework. In this study, we propose a method for a deep variational Bayesian generative model (EvoVGM) that jointly approximates the true posterior of local evolutionary parameters and generates sequence alignments. Moreover, it is instantiated and tuned for continuous-Time Markov chain substitution models such as JC69, K80 and GTR. We train the model via a low-variance stochastic estimator and a gradient ascent algorithm. Here, we analyze the consistency and effectiveness of EvoVGM on synthetic sequence alignments simulated with several evolutionary scenarios and different sizes. Finally, we highlight the robustness of a fine-Tuned EvoVGM model using a sequence alignment of gene S of coronaviruses. © 2022 Owner/Author.
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Introduction: Health measures taken during the pandemic, such as lockdowns, deeply modified the clinical research practices by restricting access to hospitals. Site personnel was also limited due to overload. At the same time, the demand for the results of the COVID-19 trials was urgent. Thus, the objective of this article is to share Inserm's experience in ensuring quality control in clinical trials in this challenging context. Material and methods: DisCoVeRy is a phase III adaptive, randomized study that aimed, in its first phase, at evaluating the safety and efficacy of four therapeutic strategies in hospitalized COVID-19 adult patients needing additional oxygen [1]. Between March 22, 2020, and January 20, 2021, 1,176 patients were included in France. In order to guarantee the best quality of data, the sponsor had to adapt to the current sanitary measures and to their impact on clinical research activity. There were notably adapted Monitoring Plan objectives (source data verification of 100% of critical data of all participants), involvement of the research departments (DRI) of the participating hospitals, a network of CRAs, and Inserm personnel. Results: Overall, 91 clinical research assistants (CRA) were involved in France and performed 834 monitoring visits from April 24, 2020, to October 15, 2021. The monitoring of 100% of critical data for all patients included in the analysis was achieved, and despite of the pandemic context, a conform consent was recovered for more than 99% of patients. Results of the study were published in May and September 2021 [2,3]. Discussion/Conclusion: Our main monitoring objective was met thanks to the mobilization of considerable personnel resources, within a very tight time frame and despite external hurdles. However, the implementation of such an organization emphasizes the importance of having easy indicators which can be accessed in due course to help steering the study and planning database usage and results publication.
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The SARS-CoV-2 genetic variants emergence doesn't spare the West African continent which has to face vaccination implementation delay. Beside classical qRT-PCR diagnostic testing, strengthening of sequencing capacity is the cornerstone for tracking and fighting the emergence of SARS-CoV-2 variants in real time. From March 12th, 2020 to July 16th, 2021, a panel of 136 full length genomes of SARS-CoV-2 mutants/variants present in human nasopharyngeal swab samples conserved in the Biobank of the Institut Pasteur De Guinée were sequenced using Illumina methodology. The Guinean sequences, originating from the general population, expatriates, and travelers, were distributed into 7 clades. During March- August 2020, the sequences were exclusively distributed into 2 clades, 20A and 20B, most originating from Europe. The 20D and 20C clades were furtively observed in October 2020 and February 2021 respectively. The SARS-CoV-2 variant of concern (VOC) 20I/B.1.1.7/Alpha was first identified in January 2021, increased in incidence up to March 2021, and then decreased from April to June 2021, corresponding to the dynamic described in Africa. The variant of interest (VOI) 21D/B.1.525/Eta originating from Nigeria circulated in February-May 2021. The 21A/B.1.617.2/Delta VOC was detected from May 2021 in Guinea, became dominant in July and persisted behind the present sampling over August and September 2021. A similar dynamic was globally observed in Africa resulting in a clear increase of lethality in the population. In contrast, other variants previously found in Africa, such as the 20H/B.1.351/Beta VOC and variants from the sublineage A (A.23.1 lineage from East Africa and the A.27 lineage), were not detected in this study. This overview of SARS-CoV-2 over 1.5 years in Guinea demonstrates that virus clades, VOC and VOI were progressively introduced, mostly by travelers through the Conakry Airport, before spreading through the country. The tracking of viral evolution by sequencing is a continuous task. Since November 2021, a new wave is related to the emergence of the VOC Omicron. Making countries autonomous in sequencing is a challenge in Africa, not only to fight Covid-19, but also to face the numerous other emerging zoonoses which circulate across the continent.
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Introduction: In response to the COVID-19 pandemic, the WHO launched a strategic preparedness and response plan, outlining public health measures to support countries worldwide. Objectives: Our study aimed to assess the level of preparedness of health care workers (HCWs) towards COVID-19 and strenghten HCWs knowledge and perception of the SARS-COV-2 pandemic and its related Infection prevention and control (IPC) measures in Faranah, Guinea. Methods: We conducted a cross-sectional pre- and post-intervention study between april 2020 and march 2021. This consisted of a baseline assessment, in-person training, an immediate post-training follow-up and a three months follow-up. Participants were HCWs from the Faranah Regional Hospital (HRF) and two health care centres (HCC). The assessment was carried-out using a questionnaire developed based on WHO recommendations. Data was analysed using STATA Version 17. Results: There was no significant difference in the overall mean knowledge score during baseline (32.67 ± 5.81) and second follow-up (33.96 ± 4.04 p < 0.467). Subgroup analysis found significant improvement in knowledge for the HCC, but not for the hospital, comparing baseline (29.35 ± 6.89) and second follow-up (34.38 ± 3.89, p < 0.007). Overall, there was significant improvement in knowledge among Auxiliary Nurses in the HCC (baseline 28.21 ± 6.68, follow-up 33.87 ± 4.26 p < 0.010), while no significant improvement was observed in other profession groups in both HRF and HCC. Assessment of perception towards Covid-19 pandemic revealed that 48.6% of participants responded feeling helpless regarding the pandemic at baseline, while only 12.9% responded this way after second follow-up. Conclusion: The study highlighted optimal level of preparedness towards COVID-19 and its IPC measures among HCWs in both HRF and HCC as reflected by the good knowledge score noted in both baseline and follow-ups. Knowledge was further strengthened in the HCC-relatively low resourced facilities as compared to HRF, as shown by improvement in knowledge after training. Furthermore, IPC training was a key component in improving certain perceptions HCW's had towards COVID-19.
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Introduction: The Multimodal WHO Hand Hygiene (HH) Strategy is a widely used and well recognized approach. However, the evidence on the sustainability in low-resource settings is still scarce. The WHO strategy was implemented at the Regional Hospital of Faranah (HRF), but context specific challenges developed. Objectives: We aimed to promote HH culture by addressing these challenges and implementing appropriate solutions. Methods: Over a period of 3 years, the project team used quantitative and qualitative methods to assess HH improvement. Local staff was trained and instructed to track the development, identify barriers and find solutions to build a sustained HH culture. Results: Four main barriers were identified and addressed by targeted measures. 1) The lack of staff for local production was overcome by implementing a train the trainer approach. The initially trained pharmacist trained four other team members. To further strengthen the production team, a national solution of training and sending staff is proposed by the HRF. 2) Difficulties in obtaining production ingredients in high quality were addressed by purchasing large quantities and the establishment of a storage room in the hospital pharmacy. 3) To prepare for sustainable local production, the return, recycling and exchange of empty bottles was planned by opening a register of distribution. 4) To stop the decrease in knowledge and compliance over time, a HH championship every 6 months was initiated. All hospital departments were invited to participate and staff assessed via the WHO knowledge questionnaires and HH observations. Furthermore, refresher trainings and demonstrations of HH were given in daily staff meetings. Conclusion: To build HH culture is feasible in low-resource hospitals such as the HRF. However, context specific challenges require locally designed solutions such as the introduction of recycling systems for ABHR bottles, organizing HH championships, or promoting daily staff trainings to maintain the improvement on HH practises and creating a HH culture. This development of a HH culture and its sustainable local production helped the HRF to respond to the current COVID-19 pandemic.
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Déclaration de liens d’intérêts: Les auteurs déclarent ne pas avoir de liens d’intérêts.
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This research aims to understand the level and determinants of people's willingness to participate in a vaccine trial for COVID-19 in Senegal. We conducted a telephone survey among a marginal quota sample of 607 people over 18 years of age. Only 44.3% of the participants wanted to participate in a vaccine trial for COVID-19, with females intending to participate more than males (AOR = 1.82, 95% CI [1.22-2.72]). Participants who intended to be vaccinated against COVID-19 (AOR = 6.48, 95% CI [4.12-10.4]) and who thought that being infected with the coronavirus would have a significant impact on their health (AOR = 2.34, 95% CI [1.57, 3.51]) were more likely to agree to take part in the COVID-19 vaccine trial. Confidence in the vaccine, health personnel, and the government in the fight against the pandemic are key factors in participants' willingness to participate in a vaccine trial in Senegal.
Subject(s)
COVID-19 , Vaccines , Adolescent , Adult , COVID-19 Vaccines , Female , Humans , Male , SARS-CoV-2 , Senegal/epidemiology , TrustSubject(s)
COVID-19/epidemiology , Lung Diseases/etiology , Postoperative Complications/etiology , Surgical Procedures, Operative/adverse effects , Adult , Comorbidity , Female , France/epidemiology , Humans , Lung Diseases/mortality , Male , Middle Aged , Postoperative Complications/mortality , Retrospective Studies , SARS-CoV-2 , Survival Rate/trendsABSTRACT
The main objective of this study was to focus on the microbiological aspects of acute respiratory infections (ARI) in children in Senegalese hospitals. The hospital frequency of acute respiratory infections in children was 3.7%. The average age was 23.7 months with extremes between 1 month and 144 months. Peaks of consultations were found in August, March and April with 22%, 15.6%, and 12.8% respectively. Fever, respiratory distress and pulmonary condensation syndrome were the main signs found on examination in our patients. Bacteriology was positive in 82.6% of the samples and the most frequently found bacteria were: Streptococcus pneumoniae in 38.5%, Haemophilus influenza b in 32.1% and Moraxella catarrhalis in 25.7%. Virological tests were positive in 80.7%. The viruses most frequently found in the samples were Rhinovirus in 33% of the samples, Human respiratory syncytial virus in 24.8% and coronavirus in 15.6%. On mycological examination, only 4 samples out of 109 were positive, i.e. 3.7%. The only fungi found was Pneumocystis with its two serotypes Pneumocystis jirovecii and Pneumocystis pneumonia in equal proportions. Among the diagnoses retained, pneumonia was predominant and found in 61 of the cases, with a prevalence of 59.9%, followed by acute bronchiolitis with a prevalence of 16.51%. The average length of hospitalization was 10 days. Lethality was 1.8% or 2 cases. Acute respiratory infections in children still remain a public health problem in developing countries, with children under 5 years of age being the most affected, hence the need to strengthen programs to combat ARI.