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

Desalination of Red Sea water using both electrodialysis and reverse osmosis as complementary methods

Desalination process separates nearly salt free water from sea or brackish water. So, desalination process is becoming a solution for water scarcity all over the world. Two membrane methods of water desalination namely electrodialysis (ED) and reverse osmosis (RO) are used in this study as complementary methods. The results show that both ED and RO can be used as integrated system. This system is economic and cost effective compared with each individual method provided using the ED system before the RO. In this study, it was approved that seawater can be used as it is an electrolyte. TDS of Red Sea water was decreased from 42070 ppm to 2177 ppm achieving 94.8% removal efficiency using ED for half of its optimum time. Total removal efficiency of 99.4% can be obtained using the combined system of ED and RO

Determination of cadmium and lead in perch fish samples by differential pulse anodic stripping voltammetry and furnace atomic absorption spectrometry

Lead and cadmium contents in the edible parts (muscle, fillet) of 17 commercially used fish species from South Egypt River Nile (Aswan) were determined by means of DPSAV (differential pulse stripping anodic voltammetry). In the sample preparation step, all fish samples were lyophilised, milled in a ball mill and finally decomposed by using mixed acid (HNO3 + HClO4). The accuracy of the concentrations determined in this study was checked by the measurements of the certified reference material CRM No. 422, cod muscle from the Commission of the European Communities, Community Bureau of Reference. All Pb2+ and Cd2+ concentrations observed from species of Egypt River Nile showed that fish from this area are a good source of these essential elements and the developed method is accepted as a good analytical routine method for these samples

Impact of the International Nosocomial Infection Control Consortium (INICC)’s multidimensional approach on rates of ventilator-associated pneumonia in intensive care units in 22 hospitals of 14 cities of the Kingdom of Saudi Arabia

To analyze the impact of the International Nosocomial Infection Control Consortium (INICC) Multidimensional Approach (IMA) and use of INICC Surveillance Online System (ISOS) on ventilator-associated pneumonia (VAP) rates in Saudi Arabia from September 2013 to February 2017. A multicenter, prospective, before–after surveillance study on 14,961 patients in 37 intensive care units (ICUs) of 22 hospitals. During baseline, we performed outcome surveillance of VAP applying the definitions of the CDC/NHSN. During intervention, we implemented the IMA and the ISOS, which included: (1) a bundle of infection prevention practice interventions, (2) education, (3) outcome surveillance, (4) process surveillance, (5) feedback on VAP rates and consequences and (6) performance feedback of process surveillance. Bivariate and multivariate regression analyses were performed using generalized linear mixed models to estimate the effect of intervention. The baseline rate of 7.84 VAPs per 1000 mechanical-ventilator (MV)-days―with 20,927 MV-days and 164 VAPs―, was reduced to 4.74 VAPs per 1000 MV-days―with 118,929 MV-days and 771 VAPs―, accounting for a 39% rate reduction (IDR 0.61; 95% CI 0.5–0.7; P 0.001). Implementing the IMA was associated with significant reductions in VAP rates in ICUs of Saudi Arabia

Measurement of the CP-violating phase phi(s) in the B-s(0) -> J/psi phi(1020) -> mu(+)mu-K+K- channel in proton-proton collisions at root s=13 TeV

The CP-violating weak phase ?s and the decay width difference ??s between the light and heavy B0s mass eigenstates are measured with the CMS detector at the LHC in a sample of 48 500 reconstructed B0s? J/I) d (1020) ?11+11? K+K? events. The measurement is based on a data sample corresponding to an integrated luminosity of 96.4 fb?1, collected in proton-proton collisions at ?s = 13 TeV in 2017?2018. To extract the values of ?s and ??s, a time-dependent and flavor-tagged angular analysis of the 11+11?K+K? final state is performed. The analysis employs a dedicated tagging trigger and a novel opposite-side muon flavor tagger based on machine learning techniques. The measurement yields ?s = ?11 ?50 (stat) ? 10 (syst) mrad and ??s = 0.114 ? 0.014 (stat)? 0.007 (syst) ps?1, in agreement with the standard model predictions. When combined with the previous CMS measurement at ?s = 8 TeV, the following values are obtained: ?s = ?21 ? 44 (stat) ? 10 (syst) mrad, ??s = 0.1032 ? 0.0095 (stat) ? 0.0048 (syst) ps?1, a significant improvement over the 8 TeV result. ? 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY licens

Measurements of the W boson rapidity, helicity, double-differential cross sections, and charge asymmetry in pp collisions at s =13 TeV

© 2020 CERN. The differential cross section and charge asymmetry for inclusive W boson production at s=13 TeV is measured for the two transverse polarization states as a function of the W boson absolute rapidity. The measurement uses events in which a W boson decays to a neutrino and either a muon or an electron. The data sample of proton-proton collisions recorded with the CMS detector at the LHC in 2016 corresponds to an integrated luminosity of 35.9 fb-1. The differential cross section and its value normalized to the total inclusive W boson production cross section are measured over the rapidity range |yW|<2.5. In addition to the total fiducial cross section, the W boson double-differential cross section, d2σ/dpTd|η|, and the charge asymmetry are measured as functions of the charged lepton transverse momentum and pseudorapidity. The precision of these measurements is used to constrain the parton distribution functions of the proton using the next-to-leading order NNPDF3.0 set