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Background The most commonly utilized samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection using real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) are nasopharyngeal swabs (NPS) and oropharyngeal swabs. However, there are some drawbacks. For SARS-CoV-2 detection, induced sputum might be analyzed and may be equivalent to pharyngeal swabs. This study was done to assess the potential superiority of induced sputum over NPS for SARS-CoV-2 detection. Sixty symptomatic COVID-19 patients who attended Fayoum University Hospitals in Fayoum Governorate, Egypt, were included in this cross-sectional descriptive study. Paired NPS and induced sputum samples were collected from each subject on the third and tenth days after symptoms began for RT-qPCR SARS-COV2 diagnosis. Results At day 3, 52 (86.7%) of NPS and 48 (80.00%) of induced sputum specimens had positive RT-qPCR results with a significant statistical difference (P = 0.001). At day 10, 41 induced sputum samples (68.3%) were negative, while 19 (31.7%) were positive. Only three (5.0%) of the 19 positive induced sputum samples tested positive for NPS. NPS samples had a higher viral load than induced sputum samples at day 3 [25 (41.7%) vs. 23 (38.3%)]. At day 10, induced sputum samples had a higher viral load than NPS [9 (15.0%) vs. 6 (10.0%)]. A statistically significant positive correlation between the viral load value of the NPS and the induced sputum sample at day 3 (r = 0.497, p = 0.00) denoting similarity in the results of the two types of samples. By ROC analysis, the highest area under the curve for the overall CT value of the induced sputum was (0.604), with a statistically significant difference (p value = 0.0418). Conclusion In the early stages of the disease, induced sputum and NPS tests had comparable results, but NPS yielded more false negative results later in the disease course than an induced sputum sample, which yielded higher sample positivity and viral load than NPS. Furthermore, induced sputum collection is a straightforward, non-invasive, and risk-free method. As a result, induced sputum could be useful for COVID-19 confirmation in patients with radiologically or epidemiologically suspected COVID-19 who have a negative NPS or in difficult-to-diagnose COVID-19 patients.

Hepatocellular Carcinoma (HCC) is a universal health problem responsible for 8.2% of all cancer deaths. Numerous risk factors were documented to be contributed to HCC development with viral hepatitis C ranking as the major predisposing factor in Egypt. The presence of a detectable amount of long noncoding RNAs (lncRNAs) in the circulation is linked to the development and spread of tumors. LncRNAs NBAT-1 and FOXCUT expression levels were used as genetic markers for the detection of gastrointestinal tract cancers. We hypothesized that serum expression levels of NBAT-1 and FOXCUT are new biomarkers for HCC that are related to laboratory and pathological markers.This study included 165 hepatitis C virus (HCV)-related HCC Egyptian patients, 180 HCV-infected noncancer patients, and 180 healthy controls, the serum expression levels of NBAT-1 and FOXCUT were measured by using quantitative real-time polymerase chain reaction.This study's results include that medians (inter-quartile range [IQRs]) of NBAT-1 in HCC and HCV patients were (1.9 [0.87-4.94], 10.01 [7.34-13.29] respectively) which exhibited significantly higher expression than controls, while the medians (IQRs) of FOXCUT in HCC and HCV patients were (0.15 [0.04-0.52], 6.42 [2.49-10.10], respectively) that exhibited significantly lower expression than controls regarding HCC patients but significantly higher expression than controls regarding HCV patients. In comparing serum fold changes of NBAT-1 and FOXCUT between HCC patients and HCV patients; we obtained significantly higher levels of target genes in HCV patients (p 0.001) than in HCC patients. Also, a positive correlation was detected between NBAT-1 and FOXCUT in HCC group (r = 0.262, p = 0.001) and in HCV group (r = 0.937, p 0.001). Higher serum NBAT-1 and FOXCUT were significantly associated with better clinical and laboratory data of the disease. Multivariate regression analysis showed that FOXCUT was an independent predictor for HCC among HCV patients (p 0.001).Our study cited that NBAT-1 and FOXCUT could be considered new diagnostic serum biomarkers for HCC on top of HCV.

Neonatal sepsis is a lethal syndrome that necessitates prompt treatment to avoid disease complications. As a result, biomarkers that may either differentiate sepsis early or predict the outcome of sepsis are essential.The goal of this research was to find out the clinical weight of usingA total of 60 neonates with sepsis and 60 healthy neonates were involved in this study. Laboratory tests include complete blood count (CBC), random blood sugar (RBS), arterial blood gases (ABG), and serum C-reactive protein (CRP). Neonates with sepsis were assessed by the Score for Neonatal Acute Physiology II (SNAP II). The serum fold changes of the target miRNAs were determined using qRT-PCR and the 2The relative serum level of

Early diagnosis of tuberculosis continues to be a challenge for clinicians. The World Health Organization (WHO) guidelines recommend the application of GeneXpert MTB/RIF in extra-pulmonary tuberculosis (EPTB) diagnosis. This study aimed to test and compare the accuracy of the GeneXpert MTB/RIF assay to diagnose pulmonary tuberculosis (PTB) and EPTB, compared to bacterial culture and to composite reference standard (CRS). The GeneXpert assay diagnosed tuberculosis (TB) in 19.5 % of patients. With reference to bacterial culture, the sensitivity of this assay for detection of the pulmonary and extra-pulmonary specimens was perfect. For pulmonary specimens, on using CRS; the detected sensitivity and specificity of the GeneXpert assay were 78.3 % and 99.1 %, respectively. However, for extra-pulmonary specimens, the sensitivity and specificity of the GeneXpert assay were 37.1 % and 99 %, respectively. In the current study, the GeneXpert assay showed almost perfect agreement with the bacterial culture for TB diagnosis. The diagnostic accuracy of the GeneXpert assay was high in ruling in, but not in ruling out of EPTB.

Behçet's disease is a chronic relapsing and remitting autoimmune multisystem inflammatory disease characterised by oral aphthae, genital ulcers, skin lesions, gastrointestinal involvement, arthritis, vascular lesions and neurological manifestations. We hypothesised a link between rs57095329 of miR-146a and Behçet's disease, with further links with common clinical features.We tested our hypothesis in 130 Behçet's disease patients and 131 age and sex-matched healthy controls. Behcet's disease current activity index (BDCAI) was used to assess patients' disease activity status. MiR-146a (rs57095329) was genotyped in all participants using RT-PCR and results in patients analysed according to clinical features.The frequency of the GG and AG genotypes in rs57095329 were strongly associated with Behçet's disease (adjusted OR 8.05, 95% CI 3.63-17.82;The miR-146a (rs57095329) is associated with Behçet's disease and certain genotypes and alleles with oral ulcers, and with ocular and neurological manifestations.

BACKGROUND/AIMS Pediatric immune thrombocytopenia (ITP) is an autoimmune disease; whose etiology is not exactly understood and seems to be highly multifactorial. Long non-coding RNAs (lncRNAs) are key regulators of different actions, which contribute to the development of many autoimmune diseases. To gain a further understanding, we estimated the relative expression of lncRNAs Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and tumor necrosis factor-α (TNF-α) and heterogeneous nuclear ribonucleoprotein L (hnRNPL) immune-regulatory lncRNA (THRIL) in pediatric ITP. METHODS In this case-control study, analysis of the expression profiles of these lncRNAs in blood samples from children with ITP and healthy controls (HCs) using quantitative real-time PCR was done. The association of MALAT1 and THRIL with ITP clinical features and their potential usage as non-invasive circulating biomarkers for ITP diagnosis was also evaluated. The receiver operating characteristic curve was constructed, and an area under the curve was analyzed. RESULTS Both lncRNAs MALAT1 and THRIL were significantly upregulated in ITP patients in comparison to HCs ( p < .0001 and = .001 respectively). In addition, there was a positive significant correlation between the expression level of both biomarkers among patients (r = 0.745, p

Hepatitis B virus (HBV) infection is a significant health issue worldwide.. We attempted to fulfill the molecular mechanisms of epigenetic and genetic factors associated with chronic HBV (CHBV). Expression levels of the lncRNA growth arrest-specific 5 (GAS5) and miR-137 and their corresponding SNPs, rs2067079 (C/T) and rs1625579 (G/T) were analyzed in 117 CHBV patients and 120 controls to investigate the probable association between these biomarkers and CHBV pathogenesis in the Egyptian population. Serum expression levels of GAS5 and miR-137 were significantly down-regulated in cases vs controls. Regarding GAS5 (rs2067079), the mutant TT genotype showed an increased risk of CHBV (p p = 0.004). Regarding miR-137 rs1625579, the mutant genotype TT was reported as a risk factor for CHBV (p p = 0.007). Concerning miR-137 rs1625579, the mutant TT genotype was significantly associated with a lower serum expression level of miR-137 (p = 0.018). We revealed the dysregulated expression levels of GAS5 and miR-137 linked to their functioning SNPs were associated with CHBV risk and might act as potential therapeutic targets.

Background: Vitamin D had an important influence on the innate and adaptive immune system. 25-hydroxyvitamin D (25(OH)D) serum level is known to be the best predictor of vitamin D level. Objective is to determine the relationship between neonatal 25(OH)D level in early-onset sepsis (EOS) and its severity in term infants. Methods: This case-control study was performed on 50 septic neonates admitted to Fayoum University Hospitals' Neonatal Intensive Care Unit as a case group, and 50 healthy neonates as a control group. Each subject was subjected to a detailed history and meticulous general & systemic examinations. Laboratory assessment in form of complete blood count with differential counts, C-reactive protein (CRP), blood culture, and serum 25(OH)D level in infants and within 72 hours of life.Results: 25(OH)D levels in cases (4.91 ng/ml) were significantly lowered than those in controls (13.0 ng/ml) (p

Background: SARS-COV-2 pandemic is a serious health problem all over the world including Egypt, thus realizing the predictive factors and disease’s characteristics is an essential issue.Objectives: To evaluate the characteristics of laboratory-confirmed cases of SARS-CoV-2 infection in Fayoum governorate, Egypt, and to determine the predictive factors of disease severity.Methods: 140 patients confirmed with SARS-CoV-2 from the Fayoum governorate, Egypt, were collected in this descriptive multicenter study. The subtype classification of COVID-19 was according to the WHO guideline COVID-19 disease severity classification. Patients were divided into a asymptomatic/non-severe cases group and a severe/critical case group. Each patient was subjected to chest computed tomography (CT), clinical, and laboratory assessment in form of complete blood count, neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), liver function tests, urea, creatinine, C‐reactive protein (CRP), serum ferritin, and D- dimer. Results: Severe/critical patients were older (52.0±12.6) with a statistical significantly higher rate of diabetic mellitus, hypertension, and tuberculosis (TB) (p

Background Neonatal sepsis is a serious condition. Recent clinical studies have indicated that microRNAs (miRNAs) are key players in the pathogenesis of sepsis, which could be used as biomarkers for this condition. Patients and methods A total of 90 neonates with sepsis and 90 healthy neonates were enrolled in this study. qRT-PCR was performed to measure the expression levels of serum miR-34a-5p and miR-199a-3p. Results miR-34a-5p and miR-199a-3p serum levels were significantly reduced in neonates with sepsis compared with those in healthy neonates (P = 0.006 and P = 0.001, respectively). Significant correlations of miR-34a-5p and miR-199a-3p with each of TLC, RDW, RBS, and C-reactive protein (CRP) as well as SNAPII were observed, indicating their associations with the severity of neonatal sepsis. Conclusion miR-34a-5p and miR-199a-3p may be useful as novel biomarkers in neonatal sepsis and may provide a new direction for its treatment.

Colorectal cancer (CRC) represented the second cause of mortality among cancer patients. Long noncoding RNAs and microRNAs (miRNAs) serve as noninvasive biomarkers for CRC surveillance and introduce new therapeutic approaches. LINC00657 and miR-106a expression levels play a pivotal role in CRC. This study included 190 Egyptian subjects, and the expression levels of LINC00657 and miR-106a in serum were measured by using quantitative real-time polymerase chain reaction. We found that upregulation of LINC00657 and downregulation of miR-106a are significantly associated with the development of CRC. Also, a positive correlation was detected between their serum levels. In addition, serum LINC00657 can distinguish adenomatous polyposis (AP) patients and/or ulcerative colitis (UC) patients from controls. Also the miRNA-106a expression level discriminates AP but not UC from healthy individuals. Our study cited new diagnostic biomarkers for CRC, AP, and UC among Egyptians in addition to be noninvasive screening tools for CRC in both healthy subjects and those having precancerous lesions. © 2019 IUBMB Life, 71(9):1322-1335, 2019.

IntroductionBackground: The current study designed to analyze whether polymorphisms of miR-146a and miR-155 are related to Behçet’s disease (BD) in Egyptian population.Material and methodsMethods: A total of 96 unrelated BD patients and 100 healthy subjects were genotyped for miR-146a (rs2910164) and miR-155(rs767649) using real-time polymerase chain reaction.ResultsResults: the results showed significant elevation in the frequency of rs2910164 GG and CC genotypes in BD patients compared with controls (adjusted OR = 22.156, 95% CI (4.728-103.818); P < 0.001 and adjusted OR = 40.358, 95% CI (8.928 -182.440); P < 0.001, respectively). Also, rs2910164 G allele conferred a higher risk of developing BD (adjusted OR = 3.665, 95% CI (2.013-6.671); P < 0.001). MiR-146a (rs2910164) polymorphism was a risk factor for susceptibility to BD in dominant, recessive and additive models of inheritance(All P < 0.001), while, the miR-155(rs767649) polymorphism was a risk factor in recessive model only (P = 0.021). GG and CG genotypes of rs2910164 were associated with higher BDCAI activity and ocular involvement compared with CC genotype (P = 0.005 and P =0.004, respectively). Genotype AT of rs767649 was related to higher BDCAI activity (P = 0. 026) compared with TT or AA genotypes.ConclusionsConclusion: The miR-146a (rs2910164) and miR-155(rs767649) were likely to play an important role in Egyptian population to develop BD and also influence disease severity.

Different molecular assays for the detection of bacterial DNA in the peripheral blood represented a diagnostic tool for neonatal sepsis. We targeted to evaluate the role of 16S rRNA gene sequencing to screen for bacteremia to confirm suspected neonatal sepsis (NS) and compare with risk factors and septic screen testing. Sixty-two neonates with suspected NS were enrolled. White blood cells count, I/T ratio, C-reactive protein, blood culture and 16S rRNA sequencing were performed. Blood culture was positive in 26% of cases, and PCR was positive in 26% of cases. Evaluation of PCR for the diagnosis of NS showed sensitivity 62.5%, specificity 86.9%, PPV 62.5%, NPV 86.9% and accuracy of 79.7%. 16S rRNA PCR increased the sensitivity of detecting bacterial DNA in newborns with signs of sepsis from 26 to 35.4%, and its use can be limited to cases with the most significant risk factors and positive septic screen.