Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus

Background: In developing countries, the necessary equipment for the diagnosis is only available in few central laboratories, which are less accessible and of limited capacity to test large numbers of incoming samples. Moreover, transport conditions of samples are inadequate and therefore lead to unreliable results. Objectives: The development of rapid, inexpensive, and simple test would allow mobile detection of viruses. Study Design: A suitcase laboratory “Diagnostics-in-a-Suitcase” (56 × 45.5 × 26.5 cm) containing all necessary reagents and devices to perform reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed. As an example, Two RT-RPA assays for the detection of hemagglutinin (H) and neuraminidase (N) genes of the novel avian influenza (H7N9) virus were established. Results: Sensitivities were 10 and 100 \{RNA\} molecules for the \{H7\} and the \{N9\} RT-RPA assays, respectively. Assays were performed at a single temperature (42 °C). Results were obtained within 2-7 minutes. The \{H7N9\} RT-RPA assays showed neither a cross-detection of any other respiratory viruses affecting humans and/or birds nor of the human or chicken genomes. All reagents were used, stored, and transported at ambient temperature, i.e. cold chain independent. In addition, the Diagnostics-in-a-Suitcase was operated by a solar power battery. Conclusions: The developed assay protocol and mobile setup performed well. Moreover, it can be easily implemented to perform diagnosis at airport, quarantine stations, or farms for rapid on-site viral nucleic acid detection

Efficient Screening of Long Oligonucleotides Against Hundred Thousands of SARS-CoV-2 Genome Sequences

An unprecedented use of high-throughput sequencing for routine monitoring of SARS-CoV-2 viruses in patient samples has created a dataset of over 6 million SARS-CoV-2 genomes. To monitor genomes, deposited in the GISAID database, and to track the continuous sequence evolution of molecular assay oligonucleotide target sequences. A simple pipeline tool for non-experts was developed to mine this database for nucleotide changes in oligonucleotides and tested with the long oligonucleotides of a Recombinase polymerase amplification (RPA) assay targeting the RNA-dependent RNA polymerase (RdRP) gene of the SARS-CoV-2. Results indicate the emergence of a single nucleotide change in the reverse oligonucleotide from 0.03 to 26.23% (January to May 2021) in Alpha variant genomes, which however reduced to 17.64% by September after which the Alpha variant was completely displaced by the Delta variant. For all other variants, no relevant nucleotide changes were observed. The oligonucleotide screening pipeline allows efficient screening of nucleotide changes in oligonucleotides of all sizes in minutes

Orogenic Gold in Transpression and Transtension Zones: Field and Remote Sensing Studies of the Barramiya–Mueilha Sector, Egypt

Multi-sensor satellite imagery data promote fast, cost-efficient regional geological mapping that constantly forms a criterion for successful gold exploration programs in harsh and inaccessible regions. The Barramiya–Mueilha sector in the Central Eastern Desert of Egypt contains several occurrences of shear/fault-associated gold-bearing quartz veins with consistently simple mineralogy and narrow hydrothermal alteration haloes. Gold-quartz veins and zones of carbonate alteration and listvenitization are widespread along the ENE–WSW Barramiya–Um Salatit and Dungash–Mueilha shear belts. These belts are characterized by heterogeneous shear fabrics and asymmetrical or overturned folds. Sentinel-1, Phased Array type L-band Synthetic Aperture Radar (PALSAR), Advanced Space borne Thermal Emission and Reflection Radiometer (ASTER), and Sentinel-2 are used herein to explicate the regional structural control of gold mineralization in the Barramiya–Mueilha sector. Feature-oriented Principal Components Selection (FPCS) applied to polarized backscatter ratio images of Sentinel-1 and PALSAR datasets show appreciable capability in tracing along the strike of regional structures and identification of potential dilation loci. The principal component analysis (PCA), band combination and band ratioing techniques are applied to the multispectral ASTER and Sentinel-2 datasets for lithological and hydrothermal alteration mapping. Ophiolites, island arc rocks, and Fe-oxides/hydroxides (ferrugination) and carbonate alteration zones are discriminated by using the PCA technique. Results of the band ratioing technique showed gossan, carbonate, and hydroxyl mineral assemblages in ductile shear zones, whereas irregular ferrugination zones are locally identified in the brittle shear zones. Gold occurrences are confined to major zones of fold superimposition and transpression along flexural planes in the foliated ophiolite-island arc belts. In the granitoid-gabbroid terranes, gold-quartz veins are rather controlled by fault and brittle shear zones. The uneven distribution of gold occurrences coupled with the variable recrystallization of the auriferous quartz veins suggests multistage gold mineralization in the area. Analysis of the host structures assessed by the remote sensing results denotes vein formation spanning the time–space from early transpression to late orogen collapse during the protracted tectonic evolution of the belt

Reverse transcription recombinase polymerase amplification assay for the detection of middle East respiratory syndrome coronavirus

The emergence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in the eastern Mediterranean and imported cases to Europe has alerted public health authorities. Currently, detection of MERS-CoV in patient samples is done by real-time RT-PCR. Samples collected from suspected cases are sent to highly-equipped centralized laboratories for screening. A rapid point-of-care test is needed to allow more widespread mobile detection of the virus directly from patient material. In this study, we describe the development of a reverse transcription isothermal Recombinase Polymerase Amplification (RT-RPA) assay for the identification of MERS-CoV. A partial nucleocapsid gene RNA molecular standard of MERS-coronavirus was used to determine the assay sensitivity. The isothermal (42°C) MERS-CoV RT-RPA was as sensitive as real-time RT-PCR (10 RNA molecules), rapid (3-7 minutes) and mobile (using tubescanner weighing 1kg). The MERS-CoV RT-RPA showed cross-detection neither of any of the RNAs of several coronaviruses and respiratory viruses affecting humans nor of the human genome. The developed isothermal real-time RT-RPA is ideal for rapid mobile molecular MERS-CoV monitoring in acute patients and may also facilitate the search for the animal reservoir of MERS-CoV

Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Avian Influenza Virus H9N2 HA Gene

The H9N2 subtype of avian influenza A virus (aIAV) is circulating among birds worldwide, leading to severe economic losses. H9N2 cocirculation with other highly pathogenic aIAVs has the potential to contribute to the rise of new strains with pandemic potential. Therefore, rapid detection of H9 aIAVs infection is crucial to control virus spread. A qualitative reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of aIAV subtype H9N2 was developed. All results were compared to the gold standard (real-time reverse transcription polymerase chain reaction (RT-PCR)). The RT-RPA assay was designed to detect the hemagglutinin (HA) gene of H9N2 by testing three pairs of primers and a probe. A serial concentration between 106 and 100 EID50 (50% embryo infective dose)/mL was applied to calculate the analytical sensitivity. The H9 RT-RPA assay was highly sensitive as the lowest concentration point of a standard range at one EID50/mL was detected after 5 to 8 min. The H9N2 RT-RPA assay was highly specific as nucleic acid extracted from H9 negative samples and from other avian pathogens were not cross detected. The diagnostic sensitivity when testing clinical samples was 100% for RT-RPA and RT-PCR. In conclusion, H9N2 RT-RPA is a rapid sensitive and specific assay that easily operable in a portable device for field diagnosis of aIAV H9N2

Shear-Related Gold Ores in the Wadi Hodein Shear Belt, South Eastern Desert of Egypt: Analysis of Remote Sensing, Field and Structural Data

Space-borne multispectral and radar data were used to comprehensively map geologi- cal contacts, lithologies and structural elements controlling gold-bearing quartz veins in the Wadi Hodein area in Egypt. In this study, enhancement algorithms, band combinations, band math (BM), Principal Component Analysis (PCA), decorrelation stretch and mineralogical indices were applied to Landsat-8 OLI, ASTER and ALOS PALSAR following a pre-designed flow chart. Together with the field observations, the results of the image processing techniques were exported to the GIS environment and subsequently fused to generate a potentiality map. The Wadi Hodein shear belt is a ductile shear corridor developed in response to non-coaxial convergence and northward escape tectonics that accompanied the final stages of terrane accretion and cratonization (~680–600 Ma) in the northern part of the Arabian–Nubian Shield. The evolution of this shear belt encompassed a protracted ~E–W shortening and recurrent sinistral transpression as manifested by east-dipping thrusts and high-angle reverse shear zones. Gold-mineralized shear zones cut heterogeneously de- formed ophiolites and metavolcaniclastic rocks and attenuate in and around granodioritic intrusions. The gold mineralization event was evidently epigenetic in the metamorphic rocks and was likely attributed to rejuvenated tectonism and circulation of hot fluids during transpressional deformation. The superposition of the NW–SE folds by NNW-trending, kilometer scale tight and reclined folds shaped the overall framework of the Wadi Hodein belt. Shallow NNW- or SSE-plunging mineral and stretching lineations on steeply dipping shear planes depict a considerable simple shear component. The results of image processing complying with field observations and structural analysis suggest that the coincidence of shear zones, hydrothermal alteration and crosscutting dikes in the study area could be considered as a model criterion in exploration for new gold targets

Risk Factors and Nutritional Assessment among Early Adolescent Girls with Iron Deficiency Anemia in Damanhour City

Background: The physical and physiological changes that occur in adolescents place a great demand on their nutrition and put them at risk for Iron Deficiency Anemia (IDA). Anemia in the adolescence causes reduced physical and mental capacity and diminished concentration in work and educational performance, and also poses a major threat to future safe motherhood in girls. Aims: this study aimed to identify the risk factors for IDA among school girls and to assess nutritional status of girl students with IDA in Damanhour city. Design: A case control study design was adopted to carry out this study. Setting: the study was conducted at 1 urban and 8 rural preparatory school girls. Subjects: The total number of the randomly selected girls was 240 preparatory school girls (120 girl student as cases who have anemia and the same number of girls recruited in control group). Tools: data was collected using three tools; tool (I) entitled adolescent girl's students profile structured interview questionnaire, tool (II) entitled nutritional practices of adolescent girl student's, and tool (III) namely anthropometric measurements tool. Results: according to multivariate analysis logistic regression girls’ students with low parent education, rural residence, and those with intestinal parasite infection were identified as predictors of IDA. Moreover, poor eating habits and menstrual history also played a significant role in the development of anemia. The relationship between academic performance and anemia was very significant in this study. Recommendations: Intensify supplementation and or food fortification programs to include iron for school age group. Conduct school’s breakfast program, carry out laboratory investigations for anemia, develop school nutrition education programs in curriculum and conduct national nutritional situation analysis survey. Key words: Early adolescent, Nutritional assessment, Risk factors, Iron Deficiency Anemia & Damanhour city

Facies analysis, glauconite distribution and sequence stratigraphy of the middle Eocene Qarara Formation, El-Minya area, Egypt

AbstractThe Qarara Formation consists mainly of shale at the base and overlain by limestone at the top. The formation is Middle Eocene (Lutetian) in age. Three sections located at the eastern bank of the Nile River in El-Minya Province have been measured, described, and sampled. These sections from north to south are: Gebel Qarara, El-Sheikh Fadl, and Gebel El-Ahmar.The main microfacies identified in the studied sections are: silty claystone, silty shale, fossiliferous glauconite, glauconitic (green) sand, glauconitic fossiliferous ironstone, glauconitic bioclastic wacke-packstone, glauconitic bioclastic lime-mudstone-wackestone. These microfacies have been deposited in shallow open marine environment.Collectively the studied rocks contain two principal facies: lower argillaceous facies and upper carbonate facies that separated by glauconitic fossiliferous ironstone bed. The lower argillaceous part represents highstand systems tract (HST), whereas the upper carbonate part represents transgressive systems tract (TST). The glauconitic fossiliferous ironstone bed is recognized as a sequence boundary (SB)

Molecular Detection of Feline Coronavirus Based on Recombinase Polymerase Amplification Assay

Feline coronavirus (FCoV) is endemic in cat populations worldwide. Persistently, subclinically infected cats play a significant role in spreading the infection. Testing fecal samples of cats may facilitate efforts to decrease the viral burden within a population. Real-time RT-PCR is highly sensitive and specific for the detection of FCoV but must be performed in a fully equipped laboratory. A simple and accurate assay is needed to identify FCoV at the point-of-need. The aim of this study was to develop a rapid FCoV detection assay based on isothermal amplification technology, i.e., reverse transcription-recombinase polymerase amplification (RT-RPA). Primers were designed to target the highly conserved 3′ untranslated region of the 7b gene. Running on a constant temperature of 42 °C, reverse transcription as well as DNA amplification and detection was achieved in a maximum of 15 min. A probit analysis revealed a detection limit of 58.5 RNA copies/reaction. For cross-detection, nucleic acids from 19 viruses were tested. Both RT-RPA and real-time RT-PCR showed cross-detection with canine coronavirus and transmissible gastroenteritis virus, but not with other pathogens. To evaluate clinical performance, RNA was extracted from 39 fecal samples from cats. All samples were tested simultaneously with real-time RT-PCR resulting in a RT-RPA sensitivity and specificity of 90.9% and 100%, respectively. RT-RPA can be considered a promising simple method for rapid detection of FCoV

Irisin in Adolescent Type 1 Diabetic Patients and its Relation to Diabetes Control and Atherosclerosis

AIM: The objective of this was to determine the role of irisin in adolescent type 1 diabetes (T1D) patients. METHODS: This study was conducted on 65 patients with T1D and 50 healthy individuals as control group. Serum irisin, glycosylated hemoglobin (HbA1c), lipid profile, oxidized low-density lipoprotein (OxLDL), urinary albumin/creatinine ratio; carotid intimal medial thickness (cIMT), and aortic intimal medial thickness (aIMT) were evaluated for all participant. RESULTS: HbA1c, lipid profile, albumin/creatinine ratio, OxLDL, irisin, aIMT and cIMT were significantly higher in diabetic patients. Irisin had a positive correlation with age of diabetic patients, onset of diabetes, mid arm circumference, waist/height ratio, body mass index, HbA1c, and cIMT. CONCLUSION: Irisin is a marker for detection of diabetes control and early detection of subclinical atherosclerosis. Irisin had a relation with obesity