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

Shale Oil: Its Present Role in the World Energy Mix

 When oil shale rocks are heated (pyrolysed) in absence of oxygen it produces shale oil. The shale oil available technologies and production capacities in million bbl/year are the Enefit280, (1.7) VKG Petroter, (0.63), (while total Estonian companies production is 1.6) Brazilian Petrosix, (1.0) Fushun retorts processes, (0.9) and the newly installed ATP process in China in testing stage. The shale oil produced by these technologies is used as heavy fuel oil for heating purposes or ships fuels due to its physical properties and contaminants. The contribution of shale oil in the energy mix is increasing but up to now is insignificant

Kinetic modeling of liquid generation from oil shale in fixed bed retort

Kinetics of shale oil generation in a fixed bed retort is modeled using a second order rate equation. Samples from Ellajjun oil shale deposits are tested in 350-550 °C temperatures range. In each run, 400 g are charged to reactor and heated in a range of 2.2-10 °C min-1. Shale oil liquid is condensed at 0 ± 2 °C and its rate measured as function of time and temperature. Increasing heating rate from 2.2 to 10 °C min-1 decreased activation energy from 115 to 71.2 kJ mol-1 and frequency factor from 2.85 x 107 to 9.0 x 103 correspondingly. The generated data are modeled using Coats and Redfern differential and integral models. Good agreement has been obtained.Kinetic modeling Oil shale Heating rate Pyrolysis Fixed bed Shale oil

Neospora caninum infection in dairy cattle in Egypt: a serosurvey and associated risk factors

Abstract Neospora caninum (N. caninum) is one of the causative agents that causing cattle abortion, and severe economic losses. Due to the scarcity of data on N. caninum infection in Egyptian cattle, the purpose of this study was to estimate the seroprevalence and determine the risk factors for parasite infection. In four governorates in northern Egypt, 540 blood samples from cattle were taken, and tested using a commercial ELISA kit. The overall seroprevalence of N. caninum in examined cattle was 28.89%. A multivariate logistic regression model determined that age (OR = 2.63, P < 0.001), manual milking (OR = 1.39, P = 0.14), abortion history (OR = 2.78, P < 0.0001), repetition of estrus (OR = 2.31, P < 0.0001), and contact with dogs (OR = 2.57, P < 0.0001) were significant risk factors. The findings proved that N. caninum infection was one of the factors contributing to abortion and financial losses in dairy cattle in Egypt. Therefore, the application of sanitary security and control programs is very important in dairy farms

Serosurvey and associated risk factors for Neospora caninum infection in Egyptian water buffaloes (Bubalus bubalis)

Abstract Neosporosis is a parasitic disease that causes reproductive disorders in animals, making it a barrier to maximum efficiency. The purpose of this study was to determine the seroprevalence of Neospora caninum (N. caninum) antibodies in water buffaloes from four governorates in northern Egypt. A commercial indirect-ELISA test was used to detect antibodies against N. caninum in the serum of 450 water buffaloes. The total seroprevalence of N. caninum in water buffaloes from Egypt was 31.3%, and the highest prevalence was observed in Gharbia governorate. The identified risk factors for N. caninum infections in water buffaloes were sex (OR = 1.96, 95%CI: 1.22−4.17), buffaloes more than 4 years of age ( OR = 5.80, 95%CI: 2.26−14.86), abortion in second trimester (OR = 16.48, 95%%CI: 2.99−34.03), history of abortion (OR = 3.45, 95%CI: 1.58−7.52) and contact with dogs (OR = 2.55, 95%CI: 1.51−4.32). Thus, more studies are needed to determine the role of buffaloes in the epidemiology of neosporosis in Egypt

Prevalence of Cryptosporidium infection and associated risk factors in calves in Egypt

Abstract Cryptosporidium is one of the causative parasitic agents that causes gastrointestinal diseases in calves. The parasite poses a zoonotic risk to immunocompromised individuals and children. Thus, this study aimed to determine the prevalence of Cryptosporidium infection in calves in three Egyptian governorates situated in Nile Delta and assess the associated risk factors. The Cryptosporidium oocysts were detected in 81 out of 430 calves (18.84%). In addition, the univariant analysis showed that age, feeding source, hygienic status, presence of diarrhea and contact with other animals were significantly (P < 0.05) associated with Cryptosporidium prevalence in calves. Furthermore, the risk factors related with Cryptosporidium prevalence were age (OR 1.96, 95%CI 0.97–3.94), feeding on milk and pasture (OR 2.07, 95%CI 1.15–3.72), poor hygienic condition (OR 2.25, 95%CI 1.28–3.94), presence of diarrhea (OR 2.47, 95%CI 1.23–4.96) and contact with other domestic animals (OR 2.08, 95%CI 1.24–3.50). In addition, the PCR assay targeting 18srRNA showed that the most prevalent species among calves was C. parvum. Although additional researches are required to understand the most effective steps that farmers and veterinary professionals should take to decrease the occurrence of Cryptosporidium infection

Impact of the COVID-19 pandemic on patients with paediatric cancer in low-income, middle-income and high-income countries: a multicentre, international, observational cohort study

OBJECTIVES: Paediatric cancer is a leading cause of death for children. Children in low-income and middle-income countries (LMICs) were four times more likely to die than children in high-income countries (HICs). This study aimed to test the hypothesis that the COVID-19 pandemic had affected the delivery of healthcare services worldwide, and exacerbated the disparity in paediatric cancer outcomes between LMICs and HICs. DESIGN: A multicentre, international, collaborative cohort study. SETTING: 91 hospitals and cancer centres in 39 countries providing cancer treatment to paediatric patients between March and December 2020. PARTICIPANTS: Patients were included if they were under the age of 18 years, and newly diagnosed with or undergoing active cancer treatment for Acute lymphoblastic leukaemia, non-Hodgkin's lymphoma, Hodgkin lymphoma, Wilms' tumour, sarcoma, retinoblastoma, gliomas, medulloblastomas or neuroblastomas, in keeping with the WHO Global Initiative for Childhood Cancer. MAIN OUTCOME MEASURE: All-cause mortality at 30 days and 90 days. RESULTS: 1660 patients were recruited. 219 children had changes to their treatment due to the pandemic. Patients in LMICs were primarily affected (n=182/219, 83.1%). Relative to patients with paediatric cancer in HICs, patients with paediatric cancer in LMICs had 12.1 (95% CI 2.93 to 50.3) and 7.9 (95% CI 3.2 to 19.7) times the odds of death at 30 days and 90 days, respectively, after presentation during the COVID-19 pandemic (p<0.001). After adjusting for confounders, patients with paediatric cancer in LMICs had 15.6 (95% CI 3.7 to 65.8) times the odds of death at 30 days (p<0.001). CONCLUSIONS: The COVID-19 pandemic has affected paediatric oncology service provision. It has disproportionately affected patients in LMICs, highlighting and compounding existing disparities in healthcare systems globally that need addressing urgently. However, many patients with paediatric cancer continued to receive their normal standard of care. This speaks to the adaptability and resilience of healthcare systems and healthcare workers globally