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

Solid Mechanics-Inspired Sensor-based Motion Planner

Abstract- In this paper a motion planner capable of laying a trajectory for a robot operating in a complex, stationary, unknown environment based on the sensory data it acquires online from its finite range sensors is suggested. The planner utilizes concepts from the area of mechanics of solids to generate the navigation field. A new setting for the bi-harmonic potential field approach to planning [1] is suggested. The new setting makes it possible to gradually feed the parts of the environment, as they are discovered on-line by the sensors of the robot, to the bi-harmonic potential-based planner. Theoretical development of the method as well as simulation results are provided. I

Microfiltration of saline crude oil emulsions: Effects of dispersant and salinity

Dispersants reduce oil-water interfacial tension making the separation of oil-water emulsions challenging. In this study, crude oil stabilized by the dispersant, Corexit EC9500A, was emulsified in synthetic sea water using a range of Corexit/crude oil concentration ratios (up to 10% by volume). With an interfacial tension of only 8.0 mJ/m2 at 0.5 mL(Corexit)/L, approximately 50% of the crude was dispersed into droplets <10 µm. Near complete rejection of oil in crossflow separation tests was accompanied by a precipitous flux decline attributable in part to dispersant- and salinity-induced decrease in membrane's oleophobicity (4.2 mJ/m2 decrease in surface energy). Screening of electrostatic interactions prompted oil coalescence that occurred at the membrane surface but not in the bulk of the emulsion. Real-time in situ visualization by Direct Observation Through Membrane gave direct evidence of surface coalescence pointing to both its detrimental effects (spread of contiguous films) and possible advantages (removal of large droplets by crossflow shear).This material is based upon work supported in part by the National Science Foundation Partnerships for International Research and Education Program under Grant IIA-1243433. SK was supported by a scholarship from the Turkish Petroleum Corporation. CAH also acknowledges MSU Environmental Science and Policy program for the support via the doctoral recruiting fellowship. ISK’s research stay at MSU was funded by Kyiv Mohyla Foundation of America

Membrane fouling by emulsified oil: a review

Separation of liquid–liquid emulsions is a challenging problem that has gained importance with the development of unconventional oil resources. Large volumes of water contaminated by emulsified oil need to be treated for safe disposal or efficient reuse. Among technologies capable of removing oil dispersed into smaller size droplets (<15 µm), membrane processes occupy a unique niche where the required separation performance and throughput can be achieved at a relatively modest cost. As with most membrane-based processes, separation of emulsified oil entails membrane fouling that requires regular maintenance and imposes additional operational costs. Emulsions present unique challenges as their fouling behavior is affected by droplets’ deformability, coalescence both in the bulk and on the membrane surface, membrane wetting by droplets and films, pore blockage and intrusion by oil. The purpose of this paper is to overview the literature on the separation of oil–water emulsions by pressure-driven membrane processes with an emphasis on how properties of emulsions and membranes affect separation performance. A particular focus is on membrane fouling by oil including physicochemical bases, detection, diagnosis, and visualization. The review spans studies with both industrial oily wastewater and synthetic model emulsions of various types of oil. The discussion of membrane materials is limited to surface modifications that render more fouling-resistant membranes.Economic Development Board (EDB)Ministry of Education (MOE)Nanyang Technological UniversityThis material is based upon work supported in part by the U.S. National Science Foundation Partnerships for International Research and Education program under Grant IIA-1243433 and the U.S. National Science Foundation Graduate Research Fellowship for Emily N. Tummons under Grant No. DGE-0802267. We also acknowledge funding from NTU iFood Research Grant (M4081465.120) and Singapore Ministry of Education Academic Research Fund Tier 2 (MOE2014-T2-2-074). The Singapore Membrane Technology Centre acknowledges support from Singapore’s Economic Development Board

Oil droplet behavior on model nanofiltration membrane surfaces under conditions of hydrodynamic shear and salinity

Oil droplet stability and electrical charge, and membrane's affinity for oil govern droplet attachment to a membrane surface. Moderate droplet-surface affinity encourages surface coalescence and removal of droplets to help maintain the membrane relatively oil-free.Ministry of Education (MOE)Nanyang Technological UniversityThis material is based upon work supported in part by the U.S. National Science Foundation Partnerships for International Research and Education program under Grant IIA-1243433 and the U.S. National Science Foundation Graduate Research Fellowship for Emily N. Tummons under Grant No. DGE-0802267. We also acknowledge funding from an NTU iFood Research Grant (M4081465.120) and the Singapore Ministry of Education Academic Research Fund Tier 2 (MOE2014-T2-2-074). The Singapore Membrane Technology Centre acknowledges support from Singapore’s Economic Development Board