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

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at √s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into diferent pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at √s = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, tt¯, and tb) or third-generation leptons (τν and τ τ ) are included in this kind of combination for the frst time. A simplifed model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confdence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Measurement of vector boson production cross sections and their ratios using pp collisions at √s = 13.6 TeV with the ATLAS detector

Abstract available from publisher's website

Immunomodulatory effect of propofol versus sevoflurane in patients undergoing thoracic surgery using one lung ventilation technique

Introduction: One lung ventilation (OLV) has become a standard procedure for many interventions in thoracic surgery with a need for deflation of the lung to facilitate the surgical procedure. Mechanical ventilation can induce a proinflammatory reaction in the non-deflated ventilated lung. However only limited data exist on inflammatory alterations in the temporarily deflated, non-ventilated lung in patients undergoing thoracic surgery. Aim of the work: The aim of this work is to compare between the effects of propofol and sevoflurane as regards: the systemic inflammatory response, the pulmonary inflammatory response, C-reactive protein, leucocyte count, and recovery status, in patients undergoing thoracic surgery using OLV technique. Patients and methods: This study include 40 adult patients, who were randomly classified into two groups: group (I) 20 patients received total intravenous anesthesia with propofol. Group (II) 20 patients received inhalational anesthesia with sevoflurane. Every patient was subjected to a careful pre-anaesthetic assessment, anaesthesia, bronchoalveolar lavage (BAL) analysis for human inflammatory mediators (IL-6 and TNF-α), serum analysis for systemic inflammatory mediators (IL-6 and TNF-α) (Both were measured before OLV and 15 min after OLV ended and resumption of two lung ventilation (TLV) at the end of surgery, and C-reactive protein and leukocyte count in blood (before OLV, 15 min after OLV ended and resumption of (TLV) at the end of surgery and on the 2nd postoperative day). Results: According to IL-6 and TNF-α, there was no statistically significant difference between the two groups before OLV, however they were significantly increased in both groups in serum and BAL after OLV in relation to before OLV with significant increase in group I relative to group II. A significant correlation was present between increased level of IL-6 and TNF-α in BAL and their levels in serum after OLV in the group II but this correlation was not present in the group I. Also no significant correlation between duration of OLV and inflammatory mediators (IL-6 and TNF-α) in serum and BAL in both groups. As regarding to CRP, there was no statistically significant difference between the two groups before OLV. After OLV and on the 2nd postoperative day the level of CRP increased significantly in both groups with significant increase in group I relative group II. According to WBC count there was no statistically significant difference between the two groups as regards the level of WBC before OLV. After OLV the level of WBC increased significantly in group I only. On the 2nd postoperative day the level of WBC increased significantly in both groups with significant increase in group I relative to group II. Also no significant correlation between duration of OLV with the increased levels of CRP and WBC count in both groups. Conclusion: Propofol increased pulmonary and systemic cytokine release more than sevoflurane during OLV. Propofol has increased CRP level and WBC count more than sevoflurane during OLV

Exploring the cost-effectiveness of high versus low perioperative fraction of inspired oxygen in the prevention of surgical site infections among abdominal surgery patients in three low- and middle-income countries

Background: This study assessed the potential cost-effectiveness of high (80–100%) vs low (21–35%) fraction of inspired oxygen (FiO2) at preventing surgical site infections (SSIs) after abdominal surgery in Nigeria, India, and South Africa. Methods: Decision-analytic models were constructed using best available evidence sourced from unbundled data of an ongoing pilot trial assessing the effectiveness of high FiO2, published literature, and a cost survey in Nigeria, India, and South Africa. Effectiveness was measured as percentage of SSIs at 30 days after surgery, a healthcare perspective was adopted, and costs were reported in US dollars ($). Results: High FiO2 may be cost-effective (cheaper and effective). In Nigeria, the average cost for high FiO2 was$216 compared with $222 for low FiO2 leading to a −$6 (95% confidence interval [CI]: −$13 to −$1) difference in costs. In India, the average cost for high FiO2 was $184 compared with$195 for low FiO2 leading to a −$11 (95$15 to −$6) difference in costs. In South Africa, the average cost for high FiO2 was$1164 compared with $1257 for low FiO2 leading to a −$93 (95% CI: −$132 to −$65) difference in costs. The high FiO2 arm had few SSIs, 7.33% compared with 8.38% for low FiO2, leading to a −1.05 (95% CI: −1.14 to −0.90) percentage point reduction in SSIs. Conclusion: High FiO2 could be cost-effective at preventing SSIs in the three countries but further data from large clinical trials are required to confirm this