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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

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

Are we Over Treating Ductal Carcinoma in Situ? – Single Center Experience

Background and Aim: Breast cancer is the most common cancer among females worldwide. Ductal carcinoma in situ (DCIS) is a heterogeneous group of neoplastic lesions confined to the breast ducts with the absence of the basement membrane infiltrations. It is usually diagnosed accidently as micro calcifications on mammograms. Materials and Methods: This is a retrospective cohort study which includes all patients who were managed surgically as cases of DCIS at Royal hospital between 2006 and 2019. Clinicopathological data were collected for all patient. The samples were divided into three groups according to their pathological analysis: Positive margin, close margin (0.1 mm to 1.9 mm), and negative margin group (&gt; 2 mm). The recurrence rate for each group was assessed. A p-value &lt;0.05 was considered statistical significant. Results: 72 patients with pure DCIS were included in the present analysis, the mean age was 47.9 years. Ten (13.0%) patients had a positive margin, 29 (37.7%) patients had a close margin, and 33 (42.9%) patients had a negative margin. There was recurrence in 3 patients) 30%) in positive margin group and 7 patients (70%) had no recurrence. On the other hand, 5 patients (17.2%) in close margin group and 1 patient (3%) in clear margin group had recurrence. The recurrence rate was higher in the non-re-excision group compare to the re-excision group. In univariate analysis, there was a significant difference in IBTR by comparing positive versus close and negative margins of excision (p = 0.040). Conclusion: The optimal margin for DCIS tumors remain controversial, nonetheless, our study highlighted the importance and the effect of following the current recommendations of a minimal 2 mm margin width in the breast conserving surgery of DCIS. Also, we have concluded that radiotherapy and hormonal therapy cannot replace obtaining a clear margin of &gt; 2 mm after breast conserving surgery in DCIS.</jats:p

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Ileosigmoid knot: A case report of the lethal twist

Ileosigmoid knot (ISK) is a rare and rapidly fatal surgical emergency characterized by the twisting of the ileum around the sigmoid colon, leading to acute bowel obstruction, ischemia, and gangrene. Due to its nonspecific clinical presentation, ISK is often misdiagnosed causing a delay of definitive treatment. The condition is most frequently reported in regions with high-fiber diets and anatomical predispositions, but remains a globally uncommon entity. Radiological imaging, particularly CT scans, plays a crucial role in preoperative diagnosis, with the whirl sign including sigmoid and ileum being a key diagnostic clue. However, most cases are only confirmed intraoperatively, and outcomes depend on the extent of bowel necrosis and the timeliness of surgical intervention. Mortality rates remain high, particularly in cases complicated by sepsis and multiorgan failure. We present the case of a 49-year-old male who developed acute abdominal pain, with CT imaging and laparotomy confirming an ileosigmoid knot, ultimately resulting in a fatal outcome

Picking Up the PiecesHarmonising and Collating Seabed Substrate Data for European Maritime Areas

The poor access to data on the marine environment is a handicap to government decision-making, a barrier to scientific understanding and an obstacle to economic growth. In this light, the European Commission initiated the European Marine Observation and Data Network (EMODnet) in 2009 to assemble and disseminate hitherto dispersed marine data. In the ten years since then, EMODnet has become a key producer of publicly available, harmonised datasets covering broad areas. This paper describes the methodologies applied in EMODnet Geology project to produce fully populated GIS layers of seabed substrate distribution for the European marine areas. We describe steps involved in translating national seabed substrate data, conforming to various standards, into a uniform EMODnet substrate classification scheme (i.e., the Folk sediment classification). Rock and boulders form an additional substrate class. Seabed substrate data products at scales of 1:250,000 and 1:1 million, compiled using descriptions and analyses of seabed samples as well as interpreted acoustic images, cover about 20% and 65% of the European maritime areas, respectively. A simple confidence assessment, based on sample and acoustic coverage, is helpful in identifying data gaps. The harmonised seabed substrate maps are particularly useful in supraregional, transnational and pan-European marine spatial planning