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

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

High-Resolution Simulations of the 2010 Pakistan Flood Event: Sensitivity to Parameterizations and Initialization Time

Estimating the risk of flood-generating precipitation events in high-mountain regions with complex orography is a difficult but crucial task. Quantitative precipitation forecasts (QPFs) at fine resolution are an essential ingredient to address this issue. Along these lines, the ability of the Weather Research and Forecasting (WRF) Model, operated at 3.5-km grid spacing, to reproduce the extreme meteorological event that led to the 2010 Pakistan flood and produced heavy monsoonal rain in the Indus basin is explored. The model results are compared with Tropical Rainfall Measuring Mission (TRMM) rainfall estimates, the available ground measurements, and radar observations from the CloudSat mission. In particular, the sensitivity of the WRF simulations to the use of different convective closures (explicit and Kain-Fritsch) and microphysical parameterizations (WRF single-moment 6-class microphysics scheme and Thompson) is analyzed. The impact of using different initial conditions, associated with a different initialization day, is also examined. The use of the new-generation Distributed Simulation and Stimulation System NASA Earth Observing System Simulators Suite radar simulator allows a more accurate and extensive representation of the mesoscale processes and of the interaction with the complex orography. The results reported here indicate that the quality of the large-scale initial conditions is a prominent factor affecting the possibility of retrieving a realistic representation of this event when using a nonhydrostatic regional model

Toward improving ice water content and snow-rate retrievals from radars. Part II: results from three wavelength radar–collocated in situ measurements and CloudSat–GPM–TRMM radar data

Two methods for deriving relationships between the equivalent radar reflectivity factor Ze and the snowfall rate S at three radar wavelengths are described. The first method uses collocations of in situ aircraft (microphysical observations) and overflying aircraft (radar observations) from two field programs to develop Ze–S relationships. In the second method, measurements of Ze at the top of the melting layer (ML), from radars on the Tropical Rainfall Measuring Mission (TRMM), Global Precipitation Measurement (GPM), and CloudSat satellites, are related to the retrieved rainfall rate R at the base of the ML, assuming that the mass flux through the ML is constant. Retrievals of R are likely to be more reliable than S because far fewer assumptions are involved in the retrieval and because supporting ground-based validation data are available. The Ze–S relationships developed here for the collocations and the mass-flux technique are compared with those derived from level 2 retrievals from the standard satellite products and with a number of relationships developed and reported by others. It is shown that there are substantial differences among them. The relationships developed here promise improvements in snowfall-rate retrievals from satellite-based radar measurements.This research is supported by the National Science Foundation, CloudSat NASA Grant NNX16AP28G and PMM NNX13AH73G (AH, PI), by the Jet Propulsion Laboratory (JPL), sponsored by the National Aeronautics and Space Administration, Deb Vane, contract monitor. GL is supported by NASA NNX16AP27G. Portions of this work by NBW were performed at the University of Wisconsin–Madison for JPL. Operations of the Citation were supported by NASA grants GCPEX—NNX11AP12G, and OLYMPEX—NNX15AL39G. CL was supported by PMM NNX16AD76G. The work performed by S. Tanelli and O. Sy was carried out at the Jet Propulsion Laboratory, California Institute of Technology under a contract with the National Aeronautics and Space Administration. Support from the ACE mission concept Science Working Group, Precipitation Measurement Missions program and NASA Weather Focus Area are gratefully acknowledged

Insecticide resistance in Anopheles arabiensis populations from Dakar and its suburbs: role of target site and metabolic resistance mechanisms

Abstract Background Urban malaria is an increasing concern in most of the sub-Saharan Africa countries. In Dakar, the capital city of Senegal, the malaria epidemiology has been complicated by recurrent flooding since 2005. The main vector control measure for malaria prevention in Dakar is the community use of long-lasting insecticide-treated nets. However, the increase of insecticide resistance reported in this area needs to be better understood for suitable resistance management. This study reports the situation of insecticide resistance and underlying mechanisms in Anopheles arabiensis populations from Dakar and its suburbs. Results All the populations tested showed resistance to almost all insecticides except organophosphates families, which remain the only lethal molecules. Piperonil butoxide (PBO) and ethacrinic acid (EA) the two synergists used, have respectively and significantly restored the susceptibility to DDT and permethrin of Anopheles population. Molecular identification of specimens revealed the presence of An. arabiensis only. Kdr genotyping showed the presence of the L1014F mutation (kdr-West) as well as L1014S (kdr-East). This L1014S mutation was found at very high frequencies (89.53%) in almost all districts surveyed, and in association with the L1014F (10.24%). Conclusion Results showed the contribution of both target-site and metabolic mechanisms in conferring pyrethroid resistance to An. arabiensis from the flooded areas of Dakar suburbs. These data, although preliminary, stress the need for close monitoring of the urban An. arabiensis populations for a suitable insecticide resistance management system to preserve core insecticide-based vector control tools in this flooded area

De la culture orale à la production écrite : littératures africaines

On parle assez souvent de Littérature africaine sans que ce terme ait reçu une définition précise. Que faut–il entendre par littérature(s) africaine(s) ? Ne faut-il voir dans cette notion que les productions écrites des auteurs africains et africanistes ? Ou faut-il prendre en compte la littérature orale, et si oui comment la définir ? La littérature africaine n’est-elle pas plutôt la somme des productions à la fois orales et écrites, envisagées comme formes d’expression d’une culture orale qui a subi l’influence des autres cultures?Cet ancrage double de la littérature africaine moderne incite le chercheur à effectuer un mouvement de va et vient constant entre ce qu’on peut qualifier de sources d’inspiration et les productions littéraires écrites. C’est à ce niveau qu’intervient la notion d’entre-deux ou d’hétéroglossie qui présuppose la prise en compte de la dimension esthétique de l’interlangue.Le champ de réflexion ainsi défini n’implique pas seulement le texte littéraire, il englobe aussi la pluralité des discours dans leur confrontation. Réunissant quatorze contributions, Semen 18 vous propose une étude approfondie de toutes les questions se rapportant au mode l’expression d’une culture et de ses représentations. En abordant la problématique des littératures africaines, cette étude, menée par de grands spécialistes en ce domaine, apporte des réponses qui permettent de saisir à la fois la dimension sociale, idéologique et poétique des discours littéraires africains

De la culture orale à la production écrite : littératures africaines

On parle assez souvent de Littérature africaine sans que ce terme ait reçu une définition précise. Que faut–il entendre par littérature(s) africaine(s) ? Ne faut-il voir dans cette notion que les productions écrites des auteurs africains et africanistes ? Ou faut-il prendre en compte la littérature orale, et si oui comment la définir ? La littérature africaine n’est-elle pas plutôt la somme des productions à la fois orales et écrites, envisagées comme formes d’expression d’une culture orale qui a subi l’influence des autres cultures?Cet ancrage double de la littérature africaine moderne incite le chercheur à effectuer un mouvement de va et vient constant entre ce qu’on peut qualifier de sources d’inspiration et les productions littéraires écrites. C’est à ce niveau qu’intervient la notion d’entre-deux ou d’hétéroglossie qui présuppose la prise en compte de la dimension esthétique de l’interlangue.Le champ de réflexion ainsi défini n’implique pas seulement le texte littéraire, il englobe aussi la pluralité des discours dans leur confrontation. Réunissant quatorze contributions, Semen 18 vous propose une étude approfondie de toutes les questions se rapportant au mode l’expression d’une culture et de ses représentations. En abordant la problématique des littératures africaines, cette étude, menée par de grands spécialistes en ce domaine, apporte des réponses qui permettent de saisir à la fois la dimension sociale, idéologique et poétique des discours littéraires africains

Diagnostic options for pulmonary fungal diseases in Africa

BACKGROUND: Fungal lung diseases are global in distribution and require specific tests for diagnosis. We report a survey of diagnostic service provision in Africa.METHODS: A written questionnaire was followed by a video conference call with each respondent(s) and external validation. To disseminate the questionnaire, a snowball sample was used.RESULTS: Data were successfully collected from 50 of 51 African countries with populations &gt;1 million. The questionnaire was completed by respondents affiliated with 72 health facilities. Of these 72 respondents, 33 (45.8%) reported data for the whole country while others reported data for a specific region/province within their country. In the public sector, chest X-ray and computed tomography are performed often in 49 countries (98%) and occasionally in 37 countries (74%), and less often in the private sector. Bronchoscopy and spirometry were done often in 28 countries (56%) and occasionally in 18 countries (36%) in the tertiary health facilities of public sector. The most conducted laboratory diagnostic assay was fungal culture (often or occasionally) in 29 countries (58%). In collaboration with the Africa Centre for Disease Control and Prevention, regional webinars and individual country profiles provided further data validation.CONCLUSION: This survey has found a huge disparity of diagnostic test capability across the African continent. Some good examples of good diagnostic provision and very high-quality care were seen, but this was unusual. The unavailability of essential testing such as spirometry was noted, which has a high impact in the diagnosis of lung diseases. It is important for countries to implement tests based on the World Health Organization Essential Diagnostics List.</p