6 research outputs found

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

    Get PDF
    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

    Safety of anticoagulation with uninterrupted warfarin vs. interrupted dabigatran in patients requiring an implantable cardiac device

    Get PDF
    BACKGROUND: The optimal strategy of peri-procedural anticoagulation in patients undergoing permanent cardiac device implantation is controversial. Our objective was to compare the major bleeding and thromboembolic complications in patients managed with uninterrupted warfarin (UW) vs. interrupted dabigatran (ID) during permanent pacemaker (PPM) or implantable cardioverter defibrillators (ICD) implantation. METHODS: A retrospective cohort study of all eligible patients from July 2011 through January 2012 was performed. UW was defined as patients who had maintained a therapeutic international normalized ratio (INR) on the day of the procedure. ID was defined as stopping dabigatran \u3e /=12 hours prior to the procedure and then resuming after implantation. Major bleeding events included hemothorax, hemopericardium, intracranial hemorrhage, gastrointestinal bleed, epistaxis, or pocket hematoma requiring surgical intervention. Thromboembolic complications included stroke, transient ischemic attack, deep venous thrombosis, pulmonary embolism, or arterial embolism. RESULTS: Of the 133 patients (73.4+/-11.0 years; 91 males) in the study, 86 received UW and 47 received ID. One (1.2%) patient in the UW group sustained hemopericardium perioperatively and died. In comparison, the ID patients had no complications. As compared to the ID group, the UW group had a higher median CHADS2 score (2 vs. 3, P=0.04) and incidence of Grade 1 pocket hematoma (0% vs. 7%, P=0.09). Neither group developed any thromboembolic complications. CONCLUSIONS: Major bleeding rates were similar among UW and ID groups. Perioperative ID appears to be a safe anticoagulation strategy for patients undergoing PPM or ICD implantation
    corecore