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

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

Bovine trypanosomosis and gastrointestinal helminthosis in settlement villages of Bedele district, South-western Ethiopia

This cross-sectional study was carried out from October 2011 to March 2012 to assess the concurrent infections of bovine trypanosomosis with gastrointestinal (GI) helminthes in Peasant Associations of Bedele district settlement areas located in Illubabor Zone, Southwestern part of Ethiopia. A total of 500 randomly selected cattle were examined using Buffy Coat Technique and coprological examinations. Faecal examination was done by sedimentation and flotation techniques following the standard procedures to identify eggs of parasitic helminthes. Those faecal samples that were positive for flotation technique were subjected to eggs per gram (EPG) count using Mc Master egg counting technique and the degree of infestation was categorized as light, moderate and severe. Out of total cattle examined, 21(4.2%) were positive for Trypanosoma congolense and 321(64.2%) were found to harbor one or more gastrointestinal helminthes infection. Helminthes identified were Fasciola species (51.4%), paramphistomum species (18.7%), the protozoan Eimeria species (6.2%), Trichuris species (6.85%), Trichostrongyles (11 %) and mixed infections (6%). The overall mean PCV value recorded was 26.7±3.9 and it was 26.8±3.9 in trypanosome negative animals and 22.9±3.3 in trypanosome positive animals. The overall mean EPG recorded was 172±99.6. Among 21 cattle found positive for T. congolense, 18 (85.7%) were concurrently infected with (GI) helminthes particularly Fasciolosis (38.1%) and statistically there was significant association (P < 0.05) between trypanososmosis and GI helminthes infection. Age and sex of sampled cattle were not found to influence GI helminthes prevalence (p>0.05). Infection with T. congolense and Fasciola species is the most prevalent form of co-infection in cattle within study areas. In conclusion, any attempts to control or prevent trypanosomosis or GI helminthes infection through different management approaches, need to address the possibility of concurrent infections especially in trypanosomosis endemic areas to save the losses in advance.Key words: Bedele, Cattle, Concurrent, Ethiopia, GI helminthes, Trypanosomosi

Study of Alkane Thiols as a Blocking Mechanism for Specific Adsorption for Application of Charge Selective Membrane Transport

Electrodialysis (ED) is an electrochemical process used for separation of ions across perm-selective membranes. ED uses a DC bias to selectively transport ions across membranes for applications ranging from desalination of water to demineralization of fruit juice. The energy cost of ED is due to accumulation of hydroxide and hydronium ions from the electrochemical process of water; additionally there is the cost of using platinum electrodes. This paper addresses the idea of using polycarbonate track etched membrane (PCTE) coated with gold between the membranes to reduce the energy cost and to explore a wider selection of electrode materials. This paper aims to show how thiol monolayers on gold can be used as ideal polarizable electrodes (electrode behaves like a capacitor with only charging current and no faradaic current) for application of potential to the membrane surface double layer. We report the characterization of such monolayers on gold-coated microscope slides. The goal is to control the diffuse layer potential at each membrane-solution interface while at the same time prevent adsorption on the electrode surface and minimize Faradaic activity due to electrolyte and redox species in solution. This lays the groundwork for the application of thiol-modified polycarbonate track-etched membranes for ion-selective transport. The paper proposes the use of electrochemical impedance spectroscopy (EIS) to measure characteristics of gold (Au)-coated membranes and their inherent limitations. In this work, the fabrication of a membrane permeate flow cell is described with the aim of subsequently studying the transport of ions through conductive polycarbonate track etched membrane (PCTE) by interrogating the system using EIS and CV measurements. In particular, we would like to ascertain the voltage range that can be applied to the Au-coated membrane without getting a considerable faradaic activity; the difference between platinum and Au electrode; the effects of different electrolyte concentrations and various applied DC potentials.</jats:p

Surface Characterization Studies of Thiols as a Blocking Mechanism for Specific Adsorption for Application of Charge Selective Membrane Transport

This paper proposes the use of electrochemical impedance spectroscopy (EIS) to measure characteristics of gold (Au)-coated membranes and their inherent limitations. In this work, the fabrication of a membrane permeate flow cell is described with the aim of subsequently studying the transport of ions through conductive polycarbonate track etched membrane (PCTE) by interrogating the system using EIS and CV measurements. In particular, we would like to ascertain the voltage range that can be applied to the Au-coated membrane without getting a considerable faradaic activity; the difference between platinum and Au electrode; the effects of different electrolyte concentrations and various applied DC potentials. We extend our previous work done [1] by studying the differences of using a hrydroxyl and methyl terminated self assembled monolayer (SAM). We also extend the quality of the monolayer with respect to the amount of time in which the monolayer is grown. Finally, finding the voltage in which a ‘defect free’ monolayer transforms from insulative to ‘leaky’ behavior extends a detailed analysis of the critical voltage of an alkane thiol.</jats:p