Investigation of rodent reservoirs of emerging pathogens in Côte d'Ivoire, West Africa

Background: One of the main health problems in West Africa remains upsurge of emerging pathogens. Ebola virus disease outbreak occurred in 2014 in Liberia, Guinea and Sierra Leone, Monkeypox virus in Nigeria in 2017 and most recently Lassa virus in Nigeria, Togo and Benin in 2018.  These pathogens have animal reservoirs as vectors for transmission. Proper investigation of the pathogens in their rodent vectors could help  reduce and manage their emergence and spread. Methodology: This study was conducted with an approval from the Côte d’Ivoire Bioethics Community. Small mammal trappings were carried out in  9 sites within three zones namely, peri-urban, peri-rural and protected areas. Liver, lung and kidney tissues from trapped small mammals were  sampled in accordance with the recommended conditions of biosafety and bioethics. The organs were transported in liquid nitrogen to the  laboratory. Molecular tests were used to detect pathogens. Orthopoxviruses and Monkeypox virus were detected in the organs by PCR using  consensus primers targeting the virus surface membrane haemagglutinin (HA) genes, while Leptospira species were detected by PCR using primers  targeting the rrs and lfb1 genes. Results: Out of 4930 night-traps, 256 (5.19%) small mammals were trapped including Crocidura, Rattus, Lophuromys, Praomys, Mus and Mastomys.  Leptospira species were detected in 6 genera from 7 study sites and the infected small mammals accounted for 13.3%. Leptospira sp was detected  mainly in the rodent vector genera Rattus (32.3%), Lophuromys (29.0%), and Praomys (16.1%). Three species of Leptospira were detected and  Leptospira interrogans was the most common frequent species (74.2%). Monkeypox virus was not detected from studied small mammals. Conclusion: The initial data from our investigation indicates the presence of Leptospira sp in rodent vectors, Rattus, Lophuromys and Praomys,  which are the potential small mammalian reservoirs of this pathogen in Cote d’Ivoire

Molecular diagnostics by PCR of poxviruses (Orthopoxvirus (OPV) and Molluscum contagiosum virus (MCV)) in Cote d'Ivoire West Africa

The Orthopoxvirus (OPV) and the Molluscum contagiosum virus (MCV) are Poxviruses involved in viruses skin lesions in humans. OPV infects many vertebrates and MCV mainly infects humans. A diagnostic confusion is often observed between the clinical lesions due to the different Poxviruses firstly and secondly with other viruses like the virus of the chickenpox. In Côte d'Ivoire, the diagnosis of MCV remains essentially clinical and that of OPV is non-existent despite the risk of circulation of the virus. This study aims to implementthe molecular detection of the OPV and the MVC in Côte d'Ivoire. Material and method: Cowpoxvirus DNA and 21 DNA extracts from suspicious cutaneous lesions of the MCV were analyzed by conventional PCR. The consensus primers (EACP1, EACP2) designed from the surface hemagglutin gene were used for the detection of the OPVs and the primers (MCV1, MCV2) targeting the K fragment of the MCV were used for the MCV’s detection . A growing dilution series of the Cowpoxvirus DNA and the MCV allowed the study of the method’s sensitivity used. The DNAs of S.aureus, M. ulcerans, VZV, HSV, the Measles virus and Varicella virus were used for the specificity tests. Results: The detection of the OPV from the Cowpoxvirus viral strain was positive with a positivity threshold at 10-1 dilution. That of the MCV DNA from the suspected MCV's lesion was positive with a positivity threshold of up to 10 -6 dilution. No non-specific amplification was observed with the DNAs of the other pathogens responsible for lesions Cutaneous. The clinical diagnosis of the MCV was confirmed by PCR in 18 out of the 21 patients, ie 85.71%. On the 3 patients with a negative MCV PCR, 2 were positive for the OPV PCR , reflecting the risk of confusion between clinical lesions due to Poxviruses.Keyvords: Molecular diagnostic, Poxviruses, West Afric

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

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Experience de SPES dans la prise en charge des enfants places en institution en Afrique

Introduction: nombreuses familles sont en difficulté partout dans le monde, surtout dans les pays en développement. La difficulté s’exprime sous différents aspects, et les principales causes sont la pauvreté, les épidémies et les conflits armés. De ces difficultés résulte l’existence d’enfants orphelins en souffrance nécessitant toute sorte de soutien.Patient et méthode: une étude prospective transversale réalisée en mai 2010 a porté sur l’institution « Soutien Pour l’Enfance en Souffrance » (SPES) à Lomé au Togo. A l’aide d’une consultation de documents et d’interview du personnel et des enfants, nous avons évalué la qualité de prise en charge des enfants dans cette institution et déterminé les contraintes du personnel dans l’exercice de sa fonction.Résultats: 99 enfants étaient en placement au centre d’accueil SPES de Lomé au moment de notre étude ; dont 13% des enfants étaient orphelins des deux parents, 23% orphelins de père seul et 39% orphelins de mère seule. Tous les enfants en âge scolaire étaient scolarisés. Les enfants et le personnel étaient tous à jour pour les principaux vaccins habituels. Les pathologies courantes les plus observées chez les enfants étaient les infections cutanées (36%), le paludisme (24%) et les affections respiratoires aiguës (17%). Trois décès avaient été malheureusement enregistrés peu de temps après l’admission dans le centre. Les difficultés du personnel d’appui résidaient surtout dans l’éducation des plus grands enfants et l’insuffisance de l’effectif du personnel. Cette insuffisance d’effectif s’est traduite par une charge de travail trop importante pour le staff.Conclusion: SPES est une institution qui donnait à l’enfance en souffrance le confort psychosocial dont elle a besoin. Les conditions de travail pouvaient y être améliorées à travers une prise en charge spécifique des grands enfants et une augmentation de l’effectif du personnel.Mots clés: enfance en souffrance, placement, SPES, problématique, TogoEnglish Title: SPES experience in support for institutional placement children in AfricaEnglish AbstractBackground: many families are in difficulty worldwide, especially in developing countries. The difficulty is expressed in various ways; and its main causes are poverty, epidemics and armed conflicts. From this difficulty result sufferance orphaned children requiring any kind of support.Patient and method: a prospective transversal study was conducted in May 2010  focused on the institution named “Support for Childhood in Sufferance” (SPES) based in Lome, Togo. Through documents review and interview of the children and the staff, we have assessed quality of care for the children; and have identified constraints of the staff in exercising its function.Results: 99 children were in the centre during our study; and 13% of them were fatherless and motherless, 23% were fatherless only and 39% were motherless only. All school-age children were enrolled for school. The children and the staff were both up to date for major conventional vaccines. The most common pathologies were skin infections (36%), malaria (24%) and acute respiratory diseases (17%). Three deaths were unfortunately registered shortly after admission to the centre. Difficulties of the staff were mostly in education of the older children and insufficient number of the staff. This reduced staff number has produced an excessive workload for them.Conclusion: SPES was an institution that gives to the childhood in sufferance the comfort he needs. Working conditions can be improved there through specific care for the older children and staff number increasing.Keywords: childhood in sufferance, placement, SPES, issue, Tog

Severe chronic allergic (and related) diseases: A uniform approach - A MeDALL - GA2 LEN - ARIA position paper

Concepts of disease severity, activity, control and responsiveness to treatment are linked but different. Severity refers to the loss of function of the organs induced by the disease process or to the occurrence of severe acute exacerbations. Severity may vary over time and needs regular follow-up. Control is the degree to which therapy goals are currently met. These concepts have evolved over time for asthma in guidelines, task forces or consensus meetings. The aim of this paper is to generalize the approach of the uniform definition of severe asthma presented to WHO for chronic allergic and associated diseases (rhinitis, chronic rhinosinusitis, chronic urticaria and atopic dermatitis) in order to have a uniform definition of severity, control and risk, usable in most situations. It is based on the appropriate diagnosis, availability and accessibility of treatments, treatment responsiveness and associated factors such as comorbidities and risk factors. This uniform definition will allow a better definition of the phenotypes of severe allergic (and related) diseases for clinical practice, research (including epidemiology), public health purposes, education and the discovery of novel therapies. Copyright © 2012 S. Karger AG, Basel

MACVIA-ARIA Sentinel NetworK for allergic rhinitis (MASK-rhinitis): The new generation guideline implementation

Several unmet needs have been identified in allergic rhinitis: identification of the time of onset of the pollen season, optimal control of rhinitis and comorbidities, patient stratification, multidisciplinary team for integrated care pathways, innovation in clinical trials and, above all, patient empowerment. MASK-rhinitis (MACVIA-ARIA Sentinel NetworK for allergic rhinitis) is a simple system centred around the patient which was devised to fill many of these gaps using Information and Communications Technology (ICT) tools and a clinical decision support system (CDSS) based on the most widely used guideline in allergic rhinitis and its asthma comorbidity (ARIA 2015 revision). It is one of the implementation systems of Action Plan B3 of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA). Three tools are used for the electronic monitoring of allergic diseases: a cell phone-based daily visual analogue scale (VAS) assessment of disease control, CARAT (Control of Allergic Rhinitis and Asthma Test) and e-Allergy screening (premedical system of early diagnosis of allergy and asthma based on online tools). These tools are combined with a clinical decision support system (CDSS) and are available in many languages. An e-CRF and an e-learning tool complete MASK. MASK is flexible and other tools can be added. It appears to be an advanced, global and integrated ICT answer for many unmet needs in allergic diseases which will improve policies and standards. © 2015 John Wiley and Sons A/S. Published by John Wiley and Sons Ltd

MACVIA-ARIA Sentinel NetworK for allergic rhinitis (MASK-rhinitis)

Several unmet needs have been identified in allergic rhinitis: identification of the time of onset of the pollen season, optimal control of rhinitis and comorbidities, patient stratification, multidisciplinary team for integrated care pathways, innovation in clinical trials and, above all, patient empowerment. MASK-rhinitis (MACVIA-ARIA Sentinel NetworK for allergic rhinitis) is a simple system centred around the patient which was devised to fill many of these gaps using Information and Communications Technology (ICT) tools and a clinical decision support system (CDSS) based on the most widely used guideline in allergic rhinitis and its asthma comorbidity (ARIA 2015 revision). It is one of the implementation systems of Action Plan B3 of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA). Three tools are used for the electronic monitoring of allergic diseases: a cell phone-based daily visual analogue scale (VAS) assessment of disease control, CARAT (Control of Allergic Rhinitis and Asthma Test) and e-Allergy screening (premedical system of early diagnosis of allergy and asthma based on online tools). These tools are combined with a clinical decision support system (CDSS) and are available in many languages. An e-CRF and an e-learning tool complete MASK. MASK is flexible and other tools can be added. It appears to be an advanced, global and integrated ICT answer for many unmet needs in allergic diseases which will improve policies and standards