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

Pressure control cam displacement in the Codman-Hakim programmable valve after a 3T MRI: Case report and review of the literature

Pressure control cam dislocation is a rare finding in patients with a programmable shunt valve that should be considered when evaluating patients with signs and symptoms of shunt malfunction. The objective of this paper is to review the mechanism, clinical presentation, and radiographic findings associated with pressure control cam (PCC) dislocation, in addition to presenting a novel case to add to the scarce literature on this topic. A systematic review of the literature were performed using PubMed, Embase, and Cochrane from database inception. PCC dislocation is exceedingly rare and can present with no symptoms, positional headache, neck pain, nausea, or vomiting. Skull x-ray findings demonstrate a clear black “X” at the distal end of the valve, due to the PCC disarticulation from atop the base plate of the plastic valve housing. Intraoperatively, a “Y”-shaped crack atop the plastic valve housing may be present and the PCC may be fully separated from the shunt or found at the distal end of the plastic valve housing. Prior reports of dislocation of the PCC have occurred 7-9 years after implantation, with inciting events including direct trauma, programmable valve adjustment, and utilization 3-Tesla magnetic resonance image scan

Seroprevalence of Toxoplasma gondii in commensal rodents sampled across Senegal, West Africa

International audienceRisks related to Toxoplasma gondii infection in humans remain poorly known in Senegal. Although rodent surveys could help to assess the circulation of T. gondii, they have seldom been set up in sub-Saharan Africa. The aim of this study was to examine Toxoplasma seroprevalence in rodents from villages and towns across Senegal. Rodents were sampled in 40 localities using a standardised trapping protocol. Detection of T. gondii antibodies was performed on 1205 rodents, using a modified agglutination test (MAT) technique. Seroprevalence data were analysed depending on geography, the local rodent community, and individual characteristics of the rodent hosts. We found 44 seropositive rodents from four different species (Mastomys erythroleucus, Mastomys natalensis, Mus musculus domesticus, Rattus rattus). Toxoplasma seroprevalence was low, averaging 4% in the localities. Higher Toxoplasma seroprevalence (up to 24%) was found in northern Senegal, a region known to be the heart of pastoral herding in the country.Séroprévalence de Toxoplasma gondii chez les rongeurs commensaux au Sénégal, Afrique de l’Ouest. Les risques liés à l’infection par Toxoplasma gondii chez l’homme restent mal connus au Sénégal. Bien que les rongeurs soient considérés comme des marqueurs pertinents de la circulation de T. gondii, peu d’études ont ciblé ces hôtes en Afrique sub-saharienne. Le but de cette étude était d’étudier la séroprévalence de Toxoplasma chez les rongeurs des villes et des villages du Sénégal. Les rongeurs ont été échantillonnés dans 40 localités avec un protocole de piégeage standardisé. La détection des anticorps contre T. gondii a été faite sur 1205 rongeurs avec un test d’agglutination modifié. Les données de séroprévalence ont été analysées en fonction de la géographie, de la communauté locale de rongeurs et de caractéristiques individuelles du rongeur. Nous avons trouvé 44 individus séropositifs, de quatre espèces différentes (Mastomys erythroleucus, Mastomys natalensis, Mus musculus domesticus, Rattus rattus). La séroprévalence moyenne est faible, de l’ordre de 4 % au sein des localités. Les plus fortes séroprévalences (jusqu’à 24 %) ont été observées dans le Nord du Sénégal, une région connue pour être le coeur de l’élevage pastoral dans le pays

Adaptation of the Wound Healing Questionnaire universal-reporter outcome measure for use in global surgery trials (TALON-1 study): mixed-methods study and Rasch analysis

BackgroundThe Bluebelle Wound Healing Questionnaire (WHQ) is a universal-reporter outcome measure developed in the UK for remote detection of surgical-site infection after abdominal surgery. This study aimed to explore cross-cultural equivalence, acceptability, and content validity of the WHQ for use across low- and middle-income countries, and to make recommendations for its adaptation.MethodsThis was a mixed-methods study within a trial (SWAT) embedded in an international randomized trial, conducted according to best practice guidelines, and co-produced with community and patient partners (TALON-1). Structured interviews and focus groups were used to gather data regarding cross-cultural, cross-contextual equivalence of the individual items and scale, and conduct a translatability assessment. Translation was completed into five languages in accordance with Mapi recommendations. Next, data from a prospective cohort (SWAT) were interpreted using Rasch analysis to explore scaling and measurement properties of the WHQ. Finally, qualitative and quantitative data were triangulated using a modified, exploratory, instrumental design model.ResultsIn the qualitative phase, 10 structured interviews and six focus groups took place with a total of 47 investigators across six countries. Themes related to comprehension, response mapping, retrieval, and judgement were identified with rich cross-cultural insights. In the quantitative phase, an exploratory Rasch model was fitted to data from 537 patients (369 excluding extremes). Owing to the number of extreme (floor) values, the overall level of power was low. The single WHQ scale satisfied tests of unidimensionality, indicating validity of the ordinal total WHQ score. There was significant overall model misfit of five items (5, 9, 14, 15, 16) and local dependency in 11 item pairs. The person separation index was estimated as 0.48 suggesting weak discrimination between classes, whereas Cronbach's α was high at 0.86. Triangulation of qualitative data with the Rasch analysis supported recommendations for cross-cultural adaptation of the WHQ items 1 (redness), 3 (clear fluid), 7 (deep wound opening), 10 (pain), 11 (fever), 15 (antibiotics), 16 (debridement), 18 (drainage), and 19 (reoperation). Changes to three item response categories (1, not at all; 2, a little; 3, a lot) were adopted for symptom items 1 to 10, and two categories (0, no; 1, yes) for item 11 (fever).ConclusionThis study made recommendations for cross-cultural adaptation of the WHQ for use in global surgical research and practice, using co-produced mixed-methods data from three continents. Translations are now available for implementation into remote wound assessment pathways