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

Induction of defense responses in common bean plants by arbuscular mycorrhizal fungi

Interaction between arbuscular mycorrhizal fungi as a bio-agent and Rhizoctonia root rot disease of common bean plant was investigated in this study under natural conditions in pot experiment. A mixture of Egyptian formulated AM (Multi-VAM) in suspension form (1x10(6)unitL(-1) in concentration) was used at dilution of 5mlL(-1) water. The results demonstrated that colonization of bean plants with AM fungi significantly increased growth parameters, yield parameters and mineral nutrient concentrations and reduced the negative effects on these parameters as well as both disease severity and disease incidence. Different physical and biochemical mechanisms have been shown to play a role in enhancement of plant resistance against Rhizoctonia solani, namely, improved plant nutrition, improved plant growth, increase in cell wall thickening, cytoplasmic granulation, and accumulation of some antimicrobial substances (phenolic compounds and defense related enzymes)

Construction of ovine GH-pmKate2N expression vector and its uptake by ovine spermatozoa using different methods

This study aims to produce transgenic ovine spermatozoa bearing Ossimi sheep growth hormone (Os_GH) cDNA using different methods. The complete coding sequence of Os_GH has been registered in GenBank accession no. KP221575. The sequence of Os_GH cDNA has been subcloned into pmkate2-N expression vectors to construct Os_GH-pmKate2-N vector. Five groups of sperm uptake were submitted. All groups were incubated at 37 °C for 1 h: Control (sperm cells were incubated without vector), Traditional incubation (sperm cells were incubated with vector), Heat shock (sperm cells were incubated with vector at 4 °C for 20 min and heated for 2 min at 42 °C), Heat shock + Dimethyl sulfoxide (DMSO) (sperm cells were incubated with vector and supplemented with 3% of DMSO and then submitted to heat shock regime) and DMSO (sperm cells were incubated with vector and supplemented with 3% DMSO). The sperm genomic DNA in groups was extracted. The Os_GH-pmKate2-N vector was introduced efficiently into the head of sperm cells in all treated groups. Adding DMSO either with or without heat shock increased the sperm uptake. The progressive motility was reduced (P < 0.05) by 29.9% in heat shock group compared to the control. Adding DMSO improved (P < 0.05) the total and progressive motilities by 8.2% and 19.8%, respectively in heat shock group compared to the heat shock group without DMSO. The results documented the ability of ovine spermatozoa to uptake the exogenous vector. Also, sperm incubation with 3% DMSO is the best method to introduce the exogenous vector into spermatozoa without notable adverse effects on sperm motilities

Functional evaluation of a modified Studer ileal neobladder

Objectives: To evaluate the results of using a shorter ileal segment (40 cm only) in reconstructing Studer ileal neobladder after radical cystectomy. Subjects and methods: Radical cystectomy and modified Studer ileal neobladder was performed in 60 patients for invasive bladder cancer. Only 40 cm of the ileum was used; 32 cm segment for constructing the body of the neobladder, while the remaining 8 cm as an isoperistaltic intact limb for ureteral reimplantation. After one year, evaluation included clinical, laboratory, radiographic and urodynamic studies to determine the functional and oncological outcomes. Results: Early complications occurred in 5 patients (8.6%). According to the modified Clavien system, two patients had grade I complications, IIIb occurred in one patient and two patients had grade V complications. Late complications (8.6%) included incisional hernia in 2 patients, deep venous thrombosis, bilateral uretero-ileal anastomotic stricture and intestinal obstruction each occurred in one patient. At one year, daytime and nighttime continence was 93.1% and 89.7%, respectively. Reflux was observed in 6 patients (10.3%) which was unilateral in 3 patients and bilateral in 3 without affecting the renal functions. Neobladder pressure was 7–18 cmH2O at half capacity and 13–38 cmH2O at full capacity with no uninhibited contractions. Conclusion: Minimizing the length of the ileum for Studer neobladder reconstruction is feasible and with acceptable results

The innovation of AI-based software in oral diseases: clinical-histopathological correlation diagnostic accuracy primary study

Abstract Background Machine learning (ML) through artificial intelligence (AI) could provide clinicians and oral pathologists to advance diagnostic problems in the field of potentially malignant lesions, oral cancer, periodontal diseases, salivary gland disease, oral infections, immune-mediated disease, and others. AI can detect micro-features beyond human eyes and provide solution in critical diagnostic cases. Objective The objective of this study was developing a software with all needed feeding data to act as AI-based program to diagnose oral diseases. So our research question was: Can we develop a Computer-Aided Software for accurate diagnosis of oral diseases based on clinical and histopathological data inputs? Method The study sample included clinical images, patient symptoms, radiographic images, histopathological images and texts for the oral diseases of interest in the current study (premalignant lesions, oral cancer, salivary gland neoplasms, immune mediated oral mucosal lesions, oral reactive lesions) total oral diseases enrolled in this study was 28 diseases retrieved from the archives of oral maxillofacial pathology department. Total 11,200 texts and 3000 images (2800 images were used for training data to the program and 100 images were used as test data to the program and 100 cases for calculating accuracy, sensitivity& specificity). Results The correct diagnosis rates for group 1 (software users), group 2 (microscopic users) and group 3 (hybrid) were 87%, 90.6, 95% respectively. The reliability for inter-observer value was done by calculating Cronbach’s alpha and interclass correlation coefficient. The test revealed for group 1, 2 and 3 the following values respectively 0.934, 0.712 & 0.703. All groups showed acceptable reliability especially for Diagnosis Oral Diseases Software (DODS) that revealed higher reliability value than other groups. However, The accuracy, sensitivity & specificity of this software was lower than those of oral pathologists (master’s degree). Conclusion The correct diagnosis rate of DODS was comparable to oral pathologists using standard microscopic examination. The DODS program could be utilized as diagnostic guidance tool with high reliability & accuracy