Synthesis and larvicidal efficacy of pyrazolopyrimidine derivatives conjugated with selenium nanoparticles against Culex pipiens L. and Musca domestica L. larvae.

The synthesized pyrazolopyrimidine derivatives conjugated with selenium nanoparticles were prepared via a reaction of pyrazolone 1 with aryl-aldehyde and malononitrile or 3-oxo-3-phenylpropanenitrile in the presence ammonium acetate or pipridine using an ultrasonic bath as a modified method in the organic synthesis for such materials. The structure of the synthesized compounds was elucidated through various techniques. All the synthesized pyrazolopyrimidines were used in the synthesis of selenium nanoparticles (SeNPs). These nanoparticles were confirmed using UV-spectra, Dynamic Light scattering and (TEM) techniques. The larvicidal efficiency;of the synthesized;compounds; was investigated against some strains such as Culex pipiens;and Musca domestica larvae. Bioassay test showed pyrazolopyrimide derivatives to exhibit an acceptable larvicidal;bio-efficacy. The derivative (3) exhibited;the highest;efficiency for more than; lab strains of both species. Moreover, C. pipiens larvae were more sensitive towards the examined compounds than M. domestica. The field;strain displayed lower affinity for the 2 folds compounds. Some biochemical changes were tracked through analysis of insect main metabolites (protein, lipid and carbohydrate), in addition to measuring the changes in seven enzymes after treatment. Generally, there was a reduction in the protein, lipids and carbohydrates after treatment with all tested compounds. Moreover, a decrement was noticed for acetylcholine esterase and glutathione;S-transferase; enzymes. There was an increment in the acid;phosphatase; and alkaline phosphatase. In addition, there was elevation in Phenoloxidase level but it noticed the declination in both Cytochrome P450 and Ascorbate peroxidase activity after treatment both flies with derivatives of selenium-nanoparticles in both lab and field strain. Generally, the experiments carried out indicate that antioxidant and detoxification enzymes may play a significant role in mechanism of action of our novel nanocompounds. The cytotoxicity of the synthesized compounds and conjugated with SeNPs showed enhanced compatibility with human normal fibroblast cell line (BJ1) with no toxic effect.

Plasma miRNA expression profile in pediatric pineal pure germinomas.

Background: Pure germinomas account for 40% of pineal tumors and are characterized by the lack of appreciable tumor markers, thus requiring a tumor biopsy for diagnosis. MicroRNAs (miRNA) have emerged as potential non-invasive biomarkers for germ cell tumors and may facilitate the non-invasive diagnosis of pure pineal germinomas. Material and methods: A retrospective chart review was performed on all patients treated at the Children's Cancer Hospital Egypt diagnosed with a pineal region tumor between June 2013 and March 2021 for whom a research blood sample was available. Plasma samples were profiled for miRNA expression, and DESeq2 was used to compare between pure germinoma and other tumor types. Differentially expressed miRNAs were identified. The area under the curve of the receive;r operating characteristic curve was constructed to evaluate diagnostic performance. Results: Samples from 39 pediatric patients were available consisting of 12 pure germinomas and 27 pineal region tumors of other pathologies, including pineal origin tumors [n = 17; pineoblastoma (n = 13) and pineal parenchymal tumors of intermediate differentiation (n = 4)] and others [n = 10; low-grade glioma (n = 6) and atypical teratoid rhabdoid tumor (n = 4)]. Using an adjusted p-value <0.05, three miRNAs showed differential expression (miR-143-3p, miR-320c, miR-320d; adjusted p = 0.0058, p = 0.0478, and p = 0.0366, respectively) and good discriminatory power between the two groups (AUC 90.7%, p < 0.001) with a sensitivity of 25% and a specificity of 100%. Conclusion: Our results suggest that a three-plasma miRNA signature has the potential to non-invasively identify pineal body pure germinomas which may allow selected patients to avoid the potential surgical complications.

Hilfer-Katugampola fractional stochastic differential inclusions with Clarke sub-differential.

The objective of this paper is to investigate the existence of mild solutions and optimal controls for a class of stochastic Hilfer-Katugampola fractional differential inclusions (SHKFDIs) with non-instantaneous impulsive (NIIs) that is strengthened by Brownian motion (BM) and the Clarke sub-differential. First, we establish a new set of sufficient conditions for the existence of mild solutions of the aforementioned fractional systems by using stochastic analysis, the Clarke sub-differential's characteristics, and the multi-valued fixed point theorem. Subsequently, by employing Balder's theorem, the existence of optimal control pairs for the considered system is investigated. Eventually, an example is provided to validate the obtained results.

New Medical Device and Therapeutic Approvals in Otolaryngology: State of the Art Review of 2022.

Objective: To review new drugs and devices relevant to otolaryngology approved by the Food and Drug Administration (FDA) in 2022. Data Sources: Publicly available FDA data on drugs and devices approved in 2022. Review Methods: A preliminary screen was conducted to identify drugs and devices relevant to otolaryngology. A secondary screen by members of the American Academy of Otolaryngology-Head and Neck Surgery's (AAO-HNS) Medical Devices and Drugs Committee differentiated between minor updates and new approvals. The final list of drugs and devices was sent to members of each subspecialty for review and analysis. Conclusion: A total of 1251 devices and 37 drugs were identified on preliminary screening. Of these, 329 devices and 5 drugs were sent to subspecialists for further review, from which 37 devices and 2 novel drugs were selected for further analysis. The newly approved devices spanned all subspecialties within otolaryngology. Many of the newly approved devices aimed to enhance patient experience, including over-the-counter hearing aids, sleep monitoring devices, and refined CPAP devices. Other advances aimed to improve surgical access, convenience, or comfort in the operating room and clinic. Implications for Practice: Many new devices and drugs are approved each year to improve patient care and care delivery. By staying up to date with these advances, otolaryngologists can leverage new innovations to improve the safety and quality of care. Given the recent approval of these devices, further studies are needed to assess long-term impact within the field of otolaryngology.

Encapsulated polycaprolactone with triazole derivatives and selenium nanoparticles as promising antiproliferative and anticancer agents.

Background and purpose: Polycaprolactone nanocapsules incorporated with triazole derivatives in the presence and absence of selenium nanoparticles were prepared and evaluated as antiproliferative and anticancer agents. Polycaprolactone nanoparticles were prepared using the emulsion technique. Experimental approach: The prepared capsules were characterized using FT-IR, TEM and DLS measurements. The synthesized triazolopyrimidine derivative in the presence and absence of selenium nanoparticles encapsulated in polycaprolactone was tested for its in vitro antiproliferative efficiency towards human breast cancer cell line (MCF7) and murine fibroblast normal cell line (BALB/3T3) in comparison to doxorubicin as a standard anticancer drug. Key results: The results indicated that encapsulated polycaprolactone with selenium nanoparticles (SeNPs) and triazole-SeNPs were the most potent samples against the tested breast cancer cell line (MCF7). On the other hand, all compounds showed weak or moderate activities towards the tested murine fibroblast normal cell line (BALB/3T3). Conclusion: As the safety index (SI) was higher than 1.0, it expanded the way for newly synthesized compounds to express antiproliferative efficacy against tumour cells. Hence, these compounds may be considered promising ones. However, they should be examined through further in-vivo and pharmacokinetic studies.

Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings.

Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii, 28 K. pneumoniae, and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species' BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the "harmful" BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.

Design and synthesis of new spirooxindole candidates and their selenium nanoparticles as potential dual Topo I/II inhibitors, DNA intercalators, and apoptotic inducers.

A new wave of dual Topo I/II inhibitors was designed and synthesised via the hybridisation of spirooxindoles and pyrimidines. In situ selenium nanoparticles (SeNPs) for some derivatives were synthesised. The targets and the SeNP derivatives were examined for their cytotoxicity towards five cancer cell lines. The inhibitory potencies of the best members against Topo I and Topo II were also assayed besides their DNA intercalation abilities. Compound 7d NPs exhibited the best inhibition against Topo I and Topo II enzymes with IC50 of 0.042 and 1.172 µM, respectively. The ability of compound 7d NPs to arrest the cell cycle and induce apoptosis was investigated. It arrested the cell cycle in the A549 cell at the S phase and prompted apoptosis by 41.02% vs. 23.81% in the control. In silico studies were then performed to study the possible binding interactions between the designed members and the target proteins.

A new wave of dual Topo I/II inhibitors was designed and synthesised via the hybridisation of spirooxindoles and pyrimidines.In situ selenium nanoparticles (SeNPs) for some derivatives were synthesised.Cytotoxicity, Topo I and Topo II inhibitory assays, and DNA intercalation abilities were evaluated.Compound 7d NPs showed the best Topo I and Topo II inhibition.Cell cycle arrest, apoptosis induction, and molecular docking studies were performed.

Novel pyrimidine Schiff bases and their selenium-containing nanoparticles as dual inhibitors of CDK1 and tubulin polymerase: design, synthesis, anti-proliferative evaluation, and molecular modelling.

Nanotechnology-based strategies can overcome the limitations of conventional cancer therapies. Hence, novel series of pyrimidine Schiff bases (4-9) were employed in the synthesis of selenium nanoparticle forms (4NPs-9NPs). All selenium nano-sized forms exerted greater inhibitions than normal-sized compounds, far exceeding 5-fluorouracil activity. Compound 4 showed effective anti-proliferative activity against MCF-7(IC50 3.14 ± 0.04 µM), HepG-2(IC50 1.07 ± 0.03 µM), and A549(IC50 1.53 ± 0.01 µM) cell lines, while its selenium nanoform 4NPs showed excellent inhibitory effects, with efficacy increased by 96.52%, 96.45%, and 93.86%, respectively. Additionally, 4NPs outperformed 4 in selectivity against the Vero cell line by 4.5-fold. Furthermore, 4NPs exhibited strong inhibition of CDK1(IC50 0.47 ± 0.3 µM) and tubulin polymerase(IC50 0.61 ± 0.04 µM), outperforming 4 and being comparable to roscovitine (IC50 0.27 ± 0.03 µM) and combretastatin-A4(IC50 0.25 ± 0.01 µM), respectively. Moreover, both 4 and 4NPs arrested the cell cycle at G0/G1 phase and significantly forced the cells towards apoptosis. Molecular docking demonstrated that 4 and 4NPs were able to inhibit CDK1 and tubulin polymerase binding sites.

Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability.

The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children's Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets.

Novel Electrospun Composite Membranes Based on Polyhydroxybutyrate and Poly(vinyl formate) Loaded with Protonated Montmorillonite for Organic Dye Removal: Kinetic and Isotherm Studies.

The use of biodegradable polyesters derived from green sources and their combination with natural abundantly layered aluminosilicate clay, e.g., natural montmorillonite, meets the requirements for the development of new sustainable, disposable, and biodegradable organic dye sorbent materials. In this regard, novel electrospun composite fibers, based on poly ß-hydroxybutyrate (PHB) and in situ synthesized poly(vinyl formate) (PVF), loaded with protonated montmorillonite (MMT-H) were prepared via electrospinning in the presence of formic acid, a volatile solvent for polymers and a protonating agent for the pristine MMT-Na. The morphology and structure of electrospun composite fibers were investigated through SEM, TEM, AFM, FT-IR, and XRD analyses. The contact angle (CA) measurements showed increased hydrophilicity of the composite fibers incorporated with MMT-H. The electrospun fibrous mats were evaluated as membranes for removing cationic (methylene blue) and anionic (Congo red) dyes. PHB/MMT 20% and PVF/MMT 30% showed significant performance in dye removal compared with the other matrices. PHB/MMT 20% was the best electrospun mat for adsorbing Congo red. The PVF/MMT 30% fibrous membrane exhibited the optimum activity for the adsorption of methylene blue and Congo red dyes.

miRNome of Child A hepatocellular carcinoma in Egyptian patients.

Introduction: Hepatocellular carcinoma (HCC) has different etiologies that contribute to its heterogeneity. In regards to the number of HCC patients, Egypt ranks third in Africa and fifteenth worldwide. Despite significant advancements in HCC diagnosis and treatment, the precise biology of the tumor is still not fully understood, which has a negative impact on patient outcomes. Methods: Advances in next-generation sequencing (NGS) have increased our knowledge of the molecular complexity of HCC. Results & discussion: In this research, 16 HCC and 6 tumor adjacent tissues (control) of Child A Egyptian patients were successfully profiled for the expression profile of miRNAs by NGS. Forty-one differentially expressed miRNAs (DEMs) were found by differential expression analysis, with 31 being upregulated and 10 being downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was then conducted on these differentially expressed miRNAs revealing that Sensitivity and specificity analysis showed that hsa-miR-4488, hsa-miR-3178, and hsa-miR-3182 were unique miRNAs as they are expressed in HCC tissues only. These miRNAs were all highly involved in AMPK signaling pathways. However, hsa-miR-214-3p was expressed in control tissues about eight times higher than in cancer tissues and was most abundant in "pathways in cancer and PI3K-Akt signaling pathway" KEGG terms. As promising HCC diagnostic markers, we here suggest hsa-miR-4488, hsa-miR-3178, hsa-miR-3182, and hsa-miR-214-3p. We further urge future research to confirm these markers' diagnostic and prognostic potential as well as their roles in the pathophysiology of HCC.

Biologic Therapies in Chronic Rhinosinusitis with Nasal Polyposis: Overview of Systematic Reviews and Updated Systematic Review.

Objectives: Chronic rhinosinusitis with nasal polyposis (CRSwNP) is a highly prevalent and challenging disease to manage. Several systematic reviews (SRs) have been carried out to evaluate the efficacy and safety of biologic therapies. We aimed to evaluate the current and available evidence of the biologics in treating CRSwNP. Data Source: Systematic Review of three electronic databases. Review Methods: Following the PRISMA Statement, the authors explored three main databases through February 2020 for pertinent SRs and meta-analyses (MAs) as well as experimental and observational studies. A Measurement Tool to Assess Systematic Reviews Version-2 (AMSTAR-2), was employed to evaluate the quality of methodology of SRs and MAs. Results: A Total of five SRs were included in this overview. The AMSTAR-2 final summary was moderate to critically low. Although conflicting findings were reported, anti-immunoglobulin E (Anti-IgE) and anti-interleukin-4 (Anti-IL-4) were superior to placebo for improving total nasal polyp (NP) score, particularly in patients with asthma. Findings of the included reviews revealed that both sinus opacification and the Lund-Mackay (LMK) total scores significantly improved after biologics use. Subjective quality-of-life (QoL) assessment provided by general and specific questionnaires illustrated favorable results of biologics for CRSwNP, whereas no significant adverse events were reported. Conclusion: The current findings support the use of biologics for CRSwNP patients. However, the evidence for their use in such patients should be cautiously adopted because of the questionable evidence. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-022-03144-8.

Value of Surgical and Nonsurgical Treatment for Sleep Apnea: A Closer Look at Health Care Utilization.

OBJECTIVE: To determine how surgery, continuous positive airway pressure (CPAP), and no treatment impact health care utilization in patients who have obstructive sleep apnea (OSA). STUDY DESIGN: This is a retrospective cohort study of patients between the ages of 18 and 65 that were diagnosed with OSA (9th International Classification of Diseases) from January 2007 to December 2015. Data were collected over 2 years, and prediction models were generated to evaluate trends over time. SETTING: A population-based study using real-world data and insurance databases. METHODS: A total of 4,978,649 participants were identified, all with at least 25 months of continuous enrollment. Patients with previous soft tissue procedures not approved for OSA (nasal surgery), or without continuous insurance coverage were excluded. A total of 18,050 patients underwent surgery, 1,054,578 were untreated, and 799,370 received CPAP. IBM Marketscan Research database was utilized to describe patient-specific clinical utilization, and expenditures, across outpatient, and inpatient services, and medication prescriptions. RESULTS: When the cost of the intervention was eliminated in the 2-year follow-up, the monthly payments of group 1 (surgery) were significantly less than group 3 (CPAP) in overall, inpatient, outpatient, and pharmaceutical payments (p < .001). The surgery group was associated with less cumulative payments compared to the other 2 groups when the cost of the intervention (CPAP or surgery) was eliminated in all comorbidities and age groups. CONCLUSION: Treating OSA with surgery can lessen overall health care utilization compared to no treatment and CPAP.

Synthesis and Molecular Docking Study of Novel Pyrimidine Derivatives against COVID-19.

A novel series of pyrido[2,3-d]pyrimidines; pyrido[3,2-e][1,3,4]triazolo; and tetrazolo[1,5-c]pyrimidines were synthesized via different chemical transformations starting from pyrazolo[3,4-b]pyridin-6-yl)-N,N-dimethylcarbamimidic chloride 3b (prepared from the reaction of o-aminonitrile 1b and phosogen iminiumchloride). The structures of the newly synthesized compounds were elucidated based on spectroscopic data and elemental analyses. Designated compounds are subjected for molecular docking by using Auto Dock Vina software in order to evaluate the antiviral potency for the synthesized compounds against SARS-CoV-2 (2019-nCoV) main protease M pro. The antiviral activity against SARS-CoV-2 showed that tested compounds 7c, 7d, and 7e had the most promising antiviral activity with lower IC50 values compared to Lopinavir, "the commonly used protease inhibitor". Both in silico and in vitro results are in agreement.

Integrated multiomics analysis to infer COVID-19 biological insights.

Three years after the pandemic, we still have an imprecise comprehension of the pathogen landscape and we are left with an urgent need for early detection methods and effective therapy for severe COVID-19 patients. The implications of infection go beyond pulmonary damage since the virus hijacks the host's cellular machinery and consumes its resources. Here, we profiled the plasma proteome and metabolome of a cohort of 57 control and severe COVID-19 cases using high-resolution mass spectrometry. We analyzed their proteome and metabolome profiles with multiple depths and methodologies as conventional single omics analysis and other multi-omics integrative methods to obtain the most comprehensive method that portrays an in-depth molecular landscape of the disease. Our findings revealed that integrating the knowledge-based and statistical-based techniques (knowledge-statistical network) outperformed other methods not only on the pathway detection level but even on the number of features detected within pathways. The versatile usage of this approach could provide us with a better understanding of the molecular mechanisms behind any biological system and provide multi-dimensional therapeutic solutions by simultaneously targeting more than one pathogenic factor.

Oral Losartan After Limited Mandibulectomy for Treatment of Desmoid-Type Fibromatosis.

Desmoid-type fibromatosis (DF) is a rare soft tissue lesion with an annual incidence of 2 to 4 per million population and peak incidence occurring at approximately 4.5 years of age. While benign, the tumor has a locally aggressive infiltrative growth pattern and a high rate of recurrence. Given the functional and aesthetic implications of excision and reconstruction in the facial skeleton, novel medical treatment options are highly desirable. We describe the case of a 3-year-old boy who presented with an enlarging, asymptomatic mass involving the left mandible. Biopsy revealed an immunohistochemical profile consistent with DF. Despite the high likelihood of recurrence, conservative, mandible-sparing en bloc resection and limited mandibulectomy were performed. Pathological and immunohistochemical analysis of the resection specimen revealed DF with grossly positive margins and elevated expression of angiotensin II type 1 receptor. Postoperative medical treatment with the angiotensin receptor blocker losartan was initiated. The patient remains medically stable and disease progression-free on repeat imaging at 20 months post-resection. We describe for the first time the successful use of the angiotensin blocker losartan following conservative surgery for management of DF.

Autophagic reprogramming of bone marrow-derived macrophages.

Macro-autophagy is a highly conserved catabolic process among eukaryotes affecting macrophages. This work studies the genetic regulatory network involving the interplay between autophagy and macrophage polarization (activation). Autophagy-related genes (Atgs) and differentially expressed genes (DEGs) of macrophage polarization (M1-M2) were predicted, and their regulatory networks constructed. Naïve (M0) mouse bone marrow-derived monocytes were differentiated into M1 and M2a. Validation of the targets of Smad1, LC3A and LC3B, Atg16L1, Atg7, IL-6, CD68, Arg-1, and Vamp7 was performed in vitro. Immunophenotyping by flow cytometry revealed three macrophage phenotypes: M0 (IL-6 + /CD68 +), M1 (IL-6 + /CD68 + /Arg-1 +), and M2a (CD68 + /Arg-1). Confocal microscopy revealed increased autophagy in both M1 and M2a and a significant increase in the pre-autophagosomes size and number. Bafilomycin A increased the expression of CD68 and Arg-1 in all cell lineages. In conclusion, our approach predicted the protein targets mediating the interplay between autophagy and macrophage polarization. We suggest that autophagy reprograms macrophage polarization via CD68, arginase 1, Atg16L1-1, and Atg16L1-3. The current findings provide a foundation for the future use of macrophages in immunotherapy of different autoimmune disorders.

SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.

A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.

Routine evaluation of tonsillectomy specimens: a cross-sectional survey of Canadian Otolaryngology: Head and Neck Surgeons.

BACKGROUND: Tonsillectomy is a commonly performed procedure in Canada. The rate of occult malignancy is rare in adult and pediatric populations. At present, no guidelines exist surrounding the need for routine histopathological evaluation of tonsil specimens when no malignancy is suspected. METHODS: We sent a confidential online survey to active members of the Canadian Society of Otolaryngology - Head and Neck Surgery (CSO-HNS) about their current tonsillectomy practice and beliefs surrounding the need for routine histopathological evaluation of tonsillectomy specimens when no malignancy is suspected. We used Opinio survey software for data collection and descriptive statistics. RESULTS: 95 participants completed our survey (response rate 19.3%). Most participants reported performing both adult and pediatric tonsillectomies. When no malignancy is suspected, participant responses were split between whether they send tonsil specimens in pediatrics only (4.2%), in adults only (31.6%), or not sending specimens (29.5%). Half of the participants reported that routinely sending specimens to rule out occult malignancy is an institutional policy. Approximately 75% of participants were in favour of removing this practice in both the pediatric and adult populations. CONCLUSION: Eliminating the practice of automatically sending tonsil specimens for histopathological evaluation when no malignancy is suspected was supported by the majority of study participants. This is in keeping with Choosing Wisely, a campaign designed to facilitate conversations about unnecessary medical tests and procedures. Institutional change is likely required in order to alter this practice.

Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients.

Klebsiella pneumoniae is considered a threat to public health especially due to multidrug resistance emergence. It is largely oligoclonal based on multi-locus sequence typing (MLST); in Egypt, ST 627 was recently detected. Despites the global dissemination of this ST, there is still paucity of information about it. Herein, we used 4 K. pneumoniae ST627 for whole genome sequencing utilizing an Illumina MiSeq platform. Genome sequences were examined for resistance and virulence determinants, capsular types, plasmids, insertion sequences, phage regions, and Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions using bioinformatic analysis. The molecular characterization revealed 15 and 65 antimicrobial resistance and virulence genes, respectively. Resistance genes such as tet(D), aph(3'')-Ib, aph(6)-Id, blaTEM-234, fosA, and fosA6; were mainly responsible for tetracycline, aminoglycoside, and fosfomycin resistance; respectively. The capsular typing revealed that the four strains are KL-24 and O1v1. One plasmid was found in all samples known as pC17KP0052-1 and another plasmid with accession no. NZ_CP032191.1 was found only in K90. IncFIB(K) and IncFII(K) are two replicons found in all samples, while ColRNAI replicon was found only in K90. Entero P88, Salmon SEN5, and Klebsi phiKO2 intact phage regions were identified. All samples harbored CRISPR arrays including CRISPR1 and CRISPR2. Our results shed light on critical tasks of mobile genetic elements in ST 627 in antibiotic resistance spreading.