scholarly journals The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Alexander L. Greninger ◽  
Keith R. Jerome
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Real Time Pcr ◽  
Medical Center ◽  
Rt Pcr ◽  
University Of Washington ◽  
Clinical Laboratories ◽  
To Come ◽  
The Many ◽  
The University

ABSTRACT In early March 2020, the University of Washington Medical Center clinical virology laboratory became one of the first clinical laboratories to offer testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When we first began test development in mid-January, neither of us believed there would be more than 2 million confirmed SARS-CoV-2 infections nationwide or that we would have performed more than 150,000 real-time PCR (RT-PCR) tests, with many more to come. This article will be a chronological summary of how we rapidly validated tests for SARS-CoV-2, increased our testing capacity, and addressed the many problems that came up along the way.

scholarly journals Genome Sequence of a Minacovirus Strain from a Farmed Mink in The Netherlands

2021 ◽  
Vol 10 (8) ◽  
Author(s):  
Kirsty T. T. Kwok ◽  
Myrna M. T. de Rooij ◽  
Felisita F. Sinartio ◽  
Lidwien A. M. Smit ◽  
Marion P. G. Koopmans ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
The Netherlands ◽  
Real Time ◽  
Genome Sequence ◽  
Deep Sequencing ◽  
Real Time Pcr ◽  
Fecal Sample ◽  
Viral Genome ◽  
Rt Pcr ◽  
Content Type

ABSTRACT We report the genome sequence of a Minacovirus strain identified from a fecal sample from a farmed mink (Neovison vison) in The Netherlands that was tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using real-time PCR (RT-PCR). The viral genome sequence was obtained using agnostic deep sequencing.

scholarly journals Comorbidities and risk factors for COVID-19 in a group of Iraqi patients confirmed by real-time PCR test

2021 ◽  
Vol 4 (1) ◽  
pp. 1-5
Author(s):  
Z Abbas ◽  
F Manhal
Keyword(s):  
Diabetes Mellitus ◽  
Risk Factors ◽  
Real Time ◽  
Real Time Pcr ◽  
Medical Center ◽  
Rt Pcr ◽  
Respiratory Disorders ◽  
The Impact ◽  
Pcr Test

The aim of the study was to identify characteristic risk factors predisposing to coronavirus disease 2019 (COVID-19) outbreak in a group of Iraqi patients in Baghdad City.  In this study, we included a total of 13411 persons who had been tested for COVID-19, supervised by Al-Razi Medical Center in Baghdad City during the period from June 20 to November 13, 2020. Cases were tested and divided into two groups according to the result of real-time RT-PCR test for COVID-19.   A total of 1781 positive cases were detected with confirmed COVID-19. Comorbidities in the study patients were identified as hypertension, diabetes mellitus and respiratory disorders. Hypertension was the most common comorbidity in COVID-19 patients followed by diabetes mellitus.  The results of this study showed that patients with comorbidities were significantly associated with positive RT-PCR results related to COVID-19. It was concluded that understanding the comorbidities enhance defining patients with COVID-19 at higher risk. Further research is needed to confirm and clarify the impact of the association of co-morbidities that accompany COVID-19.

scholarly journals DO INDONESIAN GOVERNMENT DEPLOY RELIABLE AMMUNITION FOR COVID-19 MASS TEST? A COMPARISON OF REAL-TIME PCR KITS

2021 ◽  
pp. 75-77
Author(s):  
NELLY MARISSA ◽  
SALMIATY ◽  
SARI HANUM ◽  
EVAN FEBRIANSYAH ◽  
NUR RAMADHAN ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Real Time Pcr ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Great Ability ◽  
Commercial Kits ◽  
Mass Test ◽  
Amplification Procedure

Objective: This study aimed to compare the level of reliability of three commercial real-time PCR kits in determining clinical samples. Methods: A total of 40 swabs samples which were previously tested positive, were re-test using the BioCov-19 RT-PCR kit, Sansure coronavirus disease 19 (COVID-19) nucleic acid diagnostic kit, and Kogen PowerCheck with Thermocycler (Roche). The amplification procedure is carried out based on the manual for each kit. Results: Sansure COVID-19 nucleic acid diagnostic was able to detect 40 samples with positive severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) results detected in both genes, while the PowerChek™ 2019-nCoV real-time PCR kit able to detect 35 samples showed that SARS-COV-II was detected in both genes, and the BioCoV-19 RT-PCR Kit brand kit able to detect 34 samples showed positive SARS-COV-2 results in both genes. Conclusion: The three commercial kits show great ability detection, so that they can be used to detect the presence of SARS-COV-II in clinical samples, and also in mass screening.

scholarly journals Inter-laboratory comparison of three different real-time PCR assays for the detection of Pneumocystis jiroveci in bronchoalveolar lavage fluid samples

2006 ◽  
Vol 55 (9) ◽  
pp. 1229-1235 ◽  
Author(s):  
Catharina F. M. Linssen ◽  
Jan A. Jacobs ◽  
Pieter Beckers ◽  
Kate E. Templeton ◽  
Judith Bakkers ◽  
...  
Keyword(s):  
Bronchoalveolar Lavage ◽  
Real Time ◽  
Real Time Pcr ◽  
Bronchoalveolar Lavage Fluid ◽  
Medical Center ◽  
Tertiary Care ◽  
Lavage Fluid ◽  
The Other ◽  
Pneumocystis Jiroveci ◽  
Pcr Assays

Pneumocystis jiroveci pneumonia (PCP) is an opportunistic infection affecting immunocompromised patients. While conventional diagnosis of PCP by microscopy is cumbersome, the use of PCR to diagnose PCP has great potential. Nevertheless, inter-laboratory validation and standardization of PCR assays is lacking. The aim of this study was to evaluate the inter-laboratory agreement of three independently developed real-time PCR assays for the detection of P. jiroveci in bronchoalveolar lavage fluid samples. Therefore, 124 samples were collected in three tertiary care laboratories (Leiden University Medical Center, Maastricht Infection Center and Radboud University Nijmegen Medical Centre) and were tested by both microscopy and real-time PCR. Of 41 samples positive for P. jiroveci by microscopy, 40 were positive in all three PCR assays. The remaining sample was positive in a single assay only. Out of 83 microscopy-negative samples, 69 were negative in all three PCR assays. The other 14 samples were found positive, either in all three assays (n=5), in two (n=2) or in one of the assays (n=7). The data demonstrate high inter-laboratory agreement among real-time PCR assays for the detection of P. jiroveci.

Complement C3 Genotyping of Slow and Fast Variants by Real Time PCR-High Resolution Melting

2012 ◽  
Vol 10 (3) ◽  
pp. 329-334 ◽  
Author(s):  
D.M. Valero-Hervás ◽  
P. Morales ◽  
M.J. Castro ◽  
P. Varela ◽  
M. Castillo-Rama ◽  
...  
Keyword(s):  
High Resolution ◽  
Real Time ◽  
Real Time Pcr ◽  
High Resolution Melting ◽  
Low Cost ◽  
Complement C3 ◽  
Amplification Refractory Mutation System ◽  
Rt Pcr ◽  
Dna Amount ◽  
Mutation System

“Slow” and “Fast” C3 complement variants (C3S and C3F) result from a g.304C>G polymorphism that changes arginine to glycine at position 102. C3 variants are associated with complement-mediated diseases and outcome in transplantation. In this work C3 genotyping is achieved by a Real Time PCR - High Resolution Melting (RT-PCR-HRM) optimized method. In an analysis of 49 subjects, 10.2% were C3FF, 36.7% were C3SF and 53.1% were C3SS. Allelic frequencies (70% for C3S and 30% for C3F) were in Hardy-Weinberg equilibrium and similar to those published previously. When comparing RT-PCR-HRM with the currently used Tetraprimer-Amplification Refractory Mutation System PCR (T-ARMS-PCR), coincidence was 93.8%. The procedure shown here includes a single primer pair and low DNA amount per reaction. Detection of C3 variants by RT-PCR-HRM is accurate, easy, fast and low cost, and it may be the method of choice for C3 genotyping.

scholarly journals Increased Expression of the Pro-Protein Convertase Furin Predicts Decreased Survival in Ovarian Cancer

2007 ◽  
Vol 29 (4) ◽  
pp. 289-299
Author(s):  
Robert E. Page ◽  
Andrés J. P. Klein-Szanto ◽  
Samuel Litwin ◽  
Emmanuelle Nicolas ◽  
Raid Al-Jumaily ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Tumor Progression ◽  
Real Time ◽  
Cell Lines ◽  
Cancer Cell ◽  
Real Time Pcr ◽  
Ovarian Tumor ◽  
Cancer Cell Lines ◽  
Rt Pcr ◽  
Primary Tumors

Background: Proprotein convertases (PCs) are serine proteases that after restricted proteolysis activate many proteins that play a crucial role in cancer such as metalloproteinases, growth factors and growth factor receptors, adhesion molecules, and angiogenic factors. Although the expression of several PCs is increased in many tumors, their expression in primary ovarian tumors has not been studied in detail. We sought to determine if there was an association between the expression of the ubiquitously expressed PCs, furin, PACE-4, PC-5 and PC-7, and ovarian tumor progression. Methods: We assessed their expression by RT-PCR, Real-time PCR, Western blot, and immunohistochemistry using cells derived from normal human ovarian surface epithelium (HOSE) and cancer cell lines as well as ovarian epithelial cancer specimens (45 RT-PCR/Real-time PCR, and 120 archival specimens for Immunohistochemistry). Results: We found that furin expression was restricted to the cancer cell lines. In contrast, PACE-4 and PC-7 showed expression only in normal HOSE cells lines. Furthermore, furin was predominantly expressed in primary tumors from patients who survived for less than five years. The other PCs are either expressed in the group of survivors (PC-7 and PACE4) or expressed in low amounts (PC-5). Conclusions: Our studies point to a clear relationship between furin and ovarian cancer. In addition, these results show that furin exhibits the closest association with ovarian cancer among the ubiquitously expressed PCs, arguing against the redundancy of these proteases. In summary, furin may constitute a marker for ovarian tumor progression and could contribute to predict the outcome of this disease.

scholarly journals RT-PCR for COVID-19: Diagnosis Made Easy

BioMedica ◽  
2020 ◽  
Vol 36 (2S) ◽  
pp. 115-120
Author(s):  
Osheen Sajjad ◽  
Aiman Shahzad ◽  
Saqib Mahmood
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Detection Method ◽  
Current Knowledge ◽  
Detection Methods ◽  
Rt Pcr ◽  
Corona Virus ◽  
Positive Sense ◽  
Affected Person ◽  
Sampling Procedures

<p>Coronavirus disease COVID-19, caused by Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV2), is highly contagious and has been a pandemic since March 2020. The SARS-CoV-2 is an enveloped, single-stranded, positive-sense RNA viruswhich spreadsthrough air droplets by sneezing and coughing from affected person. The diagnosis of the COVID-19 remains a challenge to the scientists since the genome of the SARS-CoV-2 was novel and varying. Various studies have reported the validated procedures for sampling and the detection method of SARS-CoV-2. This mini-review provides a brief introduction of the SARS-CoV-2 features and the current knowledge for the recommended COVID19 detection methods including sampling procedures and real time SARS-CoV-2 genome detection.</p>

scholarly journals COVID-19 Admission Screening, and Assessment of Infectiousness at an Academic Medical Center, Iowa 2020

2021 ◽  
pp. 1-19
Author(s):  
Mohammed Alsuhaibani ◽  
Takaaki Kobayashi ◽  
Alexandra Trannel ◽  
Stephanie Holley ◽  
Oluchi J. Abosi ◽  
...  
Keyword(s):  
Medical Center ◽  
Academic Medical Center ◽  
Clinical History ◽  
Rt Pcr ◽  
University Of Iowa ◽  
Past Infection ◽  
Admission Screening ◽  
Academic Medical ◽  
The University ◽  
Positive Results

Abstract Objective: Patients admitted to the hospital may unknowingly carry SARS-CoV-2 and hospitals have implemented SARS-CoV-2 admission screening. However, because SARS-CoV-2 RT-PCR may remain positive for months after infection, positive results may represent active or past infection. We determined the prevalence and infectiousness of patients who were admitted for reasons unrelated to COVID-19 but tested positive on admission screening. Methods: We conducted an observational study at the University of Iowa Hospitals & Clinics from July 7 to October 25, 2020. All patients admitted without suspicion of COVID-19 infection were included and medical records of those with a positive admission screening test were reviewed. Infectiousness was determined using patient history, PCR cycle threshold (Ct) value, and serology. Results: A total of 5,913 patients were screened and admitted for reasons unrelated to COVID-19. Of these, 101 had positive admission RT-PCR results. Thirty-six patient were excluded because they had respiratory signs/symptoms on admission on chart review. Sixty-five patients (1.1%) did not have respiratory symptoms. A total of 55 patients had Ct values available and were included in this analysis. The median age was 56 years, and (51%) were male. Our assessment revealed that 23 patients (42%) were likely infectious. The median duration of in-hospital isolation was five days for those likely infectious and two days for those deemed non-infectious. Conclusions: COVID-19 infection was infrequent among patients admitted for reasons unrelated to COVID-19. An assessment of the likelihood of infectiousness using clinical history, RT-PCR Ct values, and serology may help discontinue isolation and conserve resources.

scholarly journals Μελέτη του μεταβολισμού του σιδήρου στον σκελετικό μυ

2012 ◽  
Author(s):  
Αικατερίνη Πολονύφη
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
T Test ◽  
Rt Pcr ◽  
Densitometric Analysis ◽  
Paired T Test

Ο μεταβολισμός του σιδήρου δεν είναι επαρκώς μελετημένος στον σκελετικό ιστό σε αντίθεση με τον ηπατικό. Σκοπός της μελέτης είναι η σύγκριση της έκφρασης των γονιδίων του μεταβολισμού του σιδήρου στον ανθρώπινο σκελετικό και ηπατικό ιστό. Συλλέχτηκαν βιοψίες μυϊκού και ηπατικού ιστού από έξι φυσιολογικά άτομα. Επιλέχθηκαν να μελετηθούν12 γονίδια που εμπλέκονται στο μεταβολισμό του σιδήρου για την εισαγωγή σιδήρου στο κύτταρο, αποθήκευση και εξαγωγή του καθώς και δύο μόρια ρύθμισης της ομοιοστασίας του σιδήρου: εισαγωγή σιδήρου [οι υποδοχείς της τρανσφερρίνης (TfR1 και TfR2), το μόριο HFE, ο μεταφορέας δισθενών μετάλλων (DMT1,DMT1nonIRE), και το σιδεροφόρο μόριο λιποκαλίνη (NGAL)], αποθήκευση σιδήρου [η βαριά αλυσίδα της φερριτίνης (FTH1)] και εξαγωγή σιδήρου [η φερροπορτίνη (IREG1), η ηφαιστίνη (HEPH) και η σερουλοπλασμίνη (CP)] καθώς και δύο μόρια ρύθμισης της ομοιοστασίας του σιδήρου [η εψιδίνη (HAMP) και η αιμοτζουβελίνη (HJV)]. Ακολούθησαν αλυσιδωτές αντιδράσεις της πολυμεράσης, RT-PCR και ημιποσοτικοποίηση των επιπέδων έκφρασης των γονιδίων με τη μέθοδο της πυκνομετρίας (Densitometric Analysis). Τα αποτελέσματα εκφράζονται με βάση το ποσοστό επί τοις εκατό του γονιδίου της β-ακτίνης. Το γονίδιο της β-ακτίνης χρησιμοποιήθηκε για την κανονικοποίηση των επιπέδων έκφρασης, ως γονίδιο αναφοράς της μελέτης. Αναδεικνυόμενες διαφορές συγκριτικής έκφρασης μεγαλύτερες του 20%, των μελετημένων γονιδίων του μεταβολισμού του σιδήρου με ημιποσοτικοποίηση, αναλύθηκαν περαιτέρω με την μέθοδο της PCR σε αληθινό χρόνο (Real time PCR, qPCR) και ποσοτικοποιήθηκαν (LightCycler, Roche). Η στατιστική ανάλυση των αποτελεσμάτων ποσοτικοποίησης έγινε με το one paired t test και τα αποτελέσματα είναι στατιστικά σημαντικά (p<0,05). H συγκριτική μελέτη μεταξύ ανθρώπινου ηπατικού και σκελετικού ιστού στα επιλεγμένα 12 γονίδια έδειξε ότι: 1. Περισσότερα απο τα γονίδια: HJV, TFR1, HFE, DMT1, DMT1nonIRE, NGAL, HEPH, IREG1 ,DMT1(IRE) , DMT1nonIRE, FTH1 εκφράζονται και στους δύο ιστούς με ποσοστό έκφρασης >70% των επιπέδων έκφρασης της βακτίνης. 2. Εξαίρεση αποτελούν τα HAMP, CP και TfR2 που απουσιάζουν ή παρουσιάζουν ελάχιστη έκφραση (<10% των επιπέδων έκφρασης της βακτίνης) στο σκελετικό μυ αντίστοιχα. 3. Ενώ τα HJV και HEPH παρουσιάζουν μεγαλύτερη έκφραση των επιπέδων mRNA στο σκελετικό μύ συγκριτικά με το ήπαρ (SM/L=2,65±1,1(p<0,05) και SM/L=1,5±0,06(p<0,05 αντίστοιχα στην Q-PCR). (Εικόνα 1). Η εργασία αυτή αφορά φυσιολογικές καταστάσεις ανθρώπινων ιστών, δίνει όμως σημαντικά ερεθίσματα για αντίστοιχες μελέτες του μεταβολισμού του σιδήρου σε παθολογικές καταστάσεις. Υπογραμμίζει δε την σπουδαιότητα του σκελετικού μυϊκού ιστού και την ανάλογη συμμετοχή του στη ομοιοστασία του σιδήρου. Οι ποσοτικές διαφορές που παρατηρούνται στην έκφραση γονιδίων που εμπλέκονται σε διάφορα κυτταρικά μονοπάτια αναδεικνύουν την ανάγκη περαιτέρω έρευνας του κυτταρικού μεταβολισμού στο σκελετικό ιστό.

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