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

La gestion du cancer du rectum en Belgique: une enquête auprès de notre pratique

In 1995, a Peer Review Commission Radiotherapy was installed at the initiative of the Belgian Ministry of Health as part of a larger pilot project on quality assurance. This commission was composed of 14 members, 8 radiation oncologists (appointed by the Belgian Association of Radiation Oncology) and 6 physicists (appointed by the Belgian Association of Hospital Physicists). Peer review is only one of the activities within the Quality control of the medical performance aiming to improve quality in diagnostic and therapeutic procedures. Other activities in Quality assurance are development of standards and guidelines, continuous education and measurements of the treatment process. In 1998, the Peer review Commission Radiotherapy has proposed to make a survey of rectal cancer management including diagnostic procedures and therapeutic approaches. More than 1300 questionnaires were sent to the chairman of the 25 Belgian radiotherapy departments, asking them to have it filled in by the radiation oncologist in charge of rectal cancer treatment in their department and to all the known surgeons from a list provided by the Ministry of Health. The paper reports and discuss the results of this survey.En 1995, un examen par les pairs de la Commission de radiothérapie a été installée à l'initiative du Ministère belge de la Santé dans le cadre d'un projet pilote plus vaste sur l'assurance de la qualité. Cette commission était composée de 14 membres, 8 radio-oncologues (nommé par l'Association belge de radio-oncologie ) et 6 physiciens (nommé par l'Association belge des Physiciens Hospital). Peer review is only one of the activities within the Quality control of the medical performance aiming to improve quality in diagnostic and therapeutic procedures. Examen par les pairs n'est que l'une des activités au sein du contrôle de la qualité de la performance médicale visant à améliorer la qualité des procédures diagnostiques et thérapeutiques. Other activities in Quality assurance are development of standards and guidelines, continuous education and measurements of the treatment process. Autres activités dans l'assurance de la qualité sont le développement de normes et directives, formation continue et les mesures des processus de traitement. In 1998, the Peer review Commission Radiotherapy has proposed to make a survey of rectal cancer management including diagnostic procedures and therapeutic approaches. En 1998, la Commission d'examen par les pairs radiothérapie a proposé de faire une enquête sur la gestion du cancer du rectum, y compris les procédures diagnostiques et des approches thérapeutiques. More than 1300 questionnaires were sent to the chairman of the 25 Belgian radiotherapy departments, asking them to have it filled in by the radiation oncologist in charge of rectal cancer treatment in their department and to all the known surgeons from a list provided by the Ministry of Health. Plus de 1300 questionnaires ont été envoyés au président des 25 départements belges de radiothérapie, leur demandant de faire remplir par le radio-oncologue en charge du traitement du cancer du rectum dans leur ministère et à tous les chirurgiens connus à partir d'une liste fournie par le ministère de santé. The paper reports and discuss the results of this survey. Les rapports de papier et de discuter des résultats de cette enquête