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

Desymetrisation de cyclohexa-1,4-diènes (nouvelle voie d'accès stéréocontrôlée à des systèmes cycliques ou acycliques fonctionnalisés)

BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF

Extraction of Uranium(VI) and Plutonium(IV) with Tetra-Alkylcarbamides

International audienc

Improving the pre-screening of eligible patients in order to increase enrollment in cancer clinical trials.

The trials evaluated in this study were previously registered with clinicaltrials.gov (registration number: NCT00104741 webcite on 3 March 2005; NCT00104715 webcite on 3 March 2005; NCT00423475 webcite on 16 January 2007; and NCT00667069 webcite on 24 April 2008).International audienceBackground. The performance of randomized controlled trials (RCTs) is often hindered by recruitment difficulties. This study aims to explore the pre-screening phase of four prostate cancer RCTs to identify the impact of a systematic pre-selection of eligible patients for RCT recruitment.Methods. The pre-screening of four RCTs opened at the Comprehensive Cancer Center in Rennes was analyzed retrospectively (French Genitourinary Tumor Group (GETUG) 14, 15, 16, and 17). Data were extracted from electronic multidisciplinary cancer (MDC) reports and manually completed by physicians and medical secretaries. These data were the main source of information for clinicians to discuss treatment alternatives during MDC sessions. The pre-screening decisions made by the clinicians during these MDC meetings were compared with those made after a systematic review of the MDC reports by a clinical research assistant (CRA). Any inconsistencies in decisions between the CRA and the MDC physicians were corrected by the principal investigator (PI).Results. The pre-screening rate was 9.1% during the MDC meetings, while it was estimated to be 12.9% after the final review by the PI, and 29% after the systematic review by the CRA. The study showed that 77% and 67% of the MDC reports did not mention clinical and pathological Tumor, lymph node and metastasis classification of malignant tumors (TNM) staging, respectively, and that 35 of the CRA’s 47 proposals rejected by the PI concerned implicit information (not specified in the MDC reports). Only one patient was proposed by the PI, and none by the CRA.Conclusions. These results confirm that pre-screening could be improved by a systematic review of the medical reports. They also highlight the fact that missing data in electronic MDC reports leads to over-enrollment of non-eligible patients, but not to over-exclusion of eligible patients. Thus, our study confirms the potential gain in using semi-automated pre-selection of MDC reports, in order to avoid missing out on patients eligible for RCTs