Insights into the genetic evolution of duck hepatitis a virus in Egypt

Duck hepatitis virus (DHV) is one of the commercially important diseases of ducklings worldwide. It is an acute and highly infectious disease of ducklings caused by three different sero-types (1–3) of duck hepatitis A virus (DHAV), and serotype 1 is the most common in poultry. To date, little is known about the prevalence and genetic characterisation of DHAV-1 in Egypt. In the current study, isolation and complete genomic analyses of DHAVs circulating in commercial duck farms in different Egyptian governorates were conducted. A total of eighteen samples were collected from six Egyptian governorates of 3–11 days old ducklings (Pekin and Mullard) with a his-tory of nervous signs and high mortality rates. Five out of eighteen (5/18) samples were screened positive for the DHAV-1 based on the VP1 gene. These samples were individually used for virus isolation in embryonated duck embryos (EDE), followed by complete genome sequencing. Phylo-genomic analyses showed that DHAV serotype I; genotype I were diversified into four different groups (1, 2, 3 and 4). Most of the recent circulating Egyptian DHAV strains are clustered within group 4, while isolates characterised within this study were clustered within group 1. Recombination analyses revealed that the emergence of a new recombinant virus—DHAV-1 strain Egypt-10/2019—through recombination. Likewise, the selective pressure analyses showed the existence, inside or near areas of the viral attachment or related functions, of positive scores highlighting the importance of natural selection and viral evolution mechanism at different protein domains. The findings of this study provide updated information on the epidemiological and genetic features of DHAV-1 strains and underscore the importance of DHAV surveillance as well as re-evaluation for currently used vaccines

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18–49, 50–69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population

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

Functionalized magnetic bentonite-iron oxide nanocomposite and its application to decrease scale formation in tubing of oil/gas production

This study reports the development of 3-aminopropyltriethoxysilane (APTES) functionalized magnetic bentonite (AMB) nanocomposite by microwave assisted route to adsorb and decrease Ba(II) and Sr(II) ions, which are responsible for scale formation in the tubing of gas and oil production. Phases, function groups, morphology and magnetic properties was investigated for the prepared samples as well as porosity and surface area. Adsorption results obtained at different temperatures shows that the adsorption process of the prepared AMB is exothermic and follows Langmuir adsorption isotherm model. Kinetics of the adsorption processes at AMB surface was investigated. The process was found to follow the pseudo-second order kinetic model. pH of the system has a great influence on the adsorption of both ions. At pH 9, maximum adsorption was achieved, 124.8 mg/g and 120.0 mg/g for strontium and barium ions, respectively. While it was 107.7 mg/g and 86.7 mg/g for strontium and barium, respectively, at pH 7 similar to produced water pH. AMB showed good removal efficiency that reached 41% and 76.2% for Ba(II) and Sr(II), respectively. Based on the experimental results, AMB is a good natural low-cost material that can be used to decrease scale formation in tubing of oil/gas production

Detection of Mechanically Recovered Poultry Meat (MRPM) in Traditional Egyptian Luncheon (Emulsion Type Sausage)

Detection of MRPM in emulsion type products is a challenge facing meat industry. Where, most of meat products processors in Egypt illegally replace beef meat partially or totally with MRPM in meat products to reduce products cost. Commercial and experimentally produced emulsion type sausage (traditional Egyptian luncheon) formulated with 0, 10, 30, 50, 70, 90% MRPM instead of the meat mass and cooked to different core temperature (70, 80 and 90°C) were examined for technological properties, ash, bones, cartilage and calcium (Ca) content, in addition to histological sections stained with H&E and Trichrome blue. Results indicated that all market samples showed unacceptable texture and binding scores with high ash, collagen, cartilage, bone and Ca content. Histological section showed the presence of skin and cartilage. Addition of 10% MRPM to luncheon formulation could not be detected at different cooking temperatures. While the use of 30% or more MRPM to luncheon formulation, significantly changed technological properties and chemical composition of the product. Thermal treatments of luncheon sausages changed their chemical composition as well as induced structural changes in bone and cartilage content