scholarly journals Improvement of Diagnostic System in a Real-Time RT-PCR “AmpliSens EBOV (ZAIRE)-FL” Format for Zaire ebolavirus RNA Detection

2015 ◽  
pp. 55-57 ◽  
Author(s):  
V. G. Dedkov ◽  
M. V. Safonova ◽  
S. A. Bodnev ◽  
A. S. Kabanov ◽  
V. A. Safronov ◽  
...  
Keyword(s):  
Real Time ◽  
Diagnostic System ◽  
Rt Pcr ◽  
Rna Detection ◽  
Zaire Ebolavirus

A new dual-targeting real-time RT-PCR assay for hepatitis D virus RNA detection

2018 ◽  
Vol 92 (2) ◽  
pp. 112-117 ◽  
Author(s):  
Yan Wang ◽  
Jeffrey S. Glenn ◽  
Mark A. Winters ◽  
Li-ping Shen ◽  
Ingrid Choong ◽  
...  
Keyword(s):  
Real Time ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Rna Detection ◽  
Hepatitis D ◽  
Hepatitis D Virus ◽  
Dual Targeting ◽  
Virus Rna

scholarly journals Development of a Diagnostic System for Novel Influenza A(H7N9) Virus Using a Real-Time RT-PCR Assay in Japan

2015 ◽  
Vol 68 (2) ◽  
pp. 113-118 ◽  
Author(s):  
Ikuyo Takayama ◽  
Hitoshi Takahashi ◽  
Mina Nakauchi ◽  
Shiho Nagata ◽  
Masato Tashiro ◽  
...  
Keyword(s):  
Real Time ◽  
Influenza A ◽  
Diagnostic System ◽  
H7n9 Virus ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Novel Influenza A

scholarly journals SARS-CoV-2 variants in Paraguay: Detection and surveillance with a readily modifiable, multiplex real-time RT-PCR

2021 ◽  
Author(s):  
Magaly Martinez ◽  
Phuong-Vi Nguyen ◽  
Maxwell Su ◽  
Fatima Cardozo ◽  
Adriana Valenzuela ◽  
...  
Keyword(s):  
Real Time ◽  
Sanger Sequencing ◽  
Lower Cost ◽  
Population Level ◽  
Nanopore Sequencing ◽  
Receptor Binding Domain ◽  
Rt Pcr ◽  
High Quality ◽  
Rna Detection ◽  
Detection Of Mutations

Objectives The objective of the current study was to develop a lower-cost and scalable protocol to identify and monitor SARS-CoV-2 variants in Paraguay by pairing real-time RT-PCR detection of spike mutations with amplicon Sanger sequencing and whole-genome Nanopore sequencing. Methods 201 acute-phase nasopharyngeal samples from SARS-CoV-2-positive individuals were tested with two rRT-PCRs: 1) N2RP assay to confirm SARS-CoV-2 RNA detection (CDC N2 target), and 2) the Spike SNP assay to detect mutations in the spike receptor binding domain. The assay was performed with probes to identify mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Results All samples were positive for SARS-CoV-2 in the N2RP assay (mean Ct, 20.8; SD 5.6); 198/201 (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%) and most consistent with P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%); and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). Results were confirmed by Sanger sequencing in 181/181 samples (100%) with high-quality amplicon sequences, and variant calls were consistent with Nanopore sequencing in 29/29 samples. Conclusions The Spike SNP assay provides accurate detection of mutations associated with SARS-CoV-2 variants. This can be implemented in laboratories performing rRT-PCR to improve population-level surveillance for these mutations and inform the judicious use of scarce sequencing resources.

scholarly journals Development and Testing of a Method for Detecting Lujo Virus RNA by Reverse Transcription and Real Time Polymerase Chain Reaction

2021 ◽  
pp. 110-115
Author(s):  
E. V. Naidenova ◽  
V. G. Dedkov ◽  
D. A. Agafonov ◽  
A. M. Senichkina ◽  
M. V. Safonova ◽  
...  
Keyword(s):  
Real Time ◽  
Internal Control ◽  
Biological Samples ◽  
Control Sample ◽  
Virus Genome ◽  
Positive Control ◽  
Control Panel ◽  
Rt Pcr ◽  
Rna Detection ◽  
Virus Rna

The aim of the study was to develop and assess the efficacy of a method for Lujo virus RNA detection in clinical and biological samples using one-step real-time RT-PCR.Materials and methods. In order to select the conservative regions of the genome, we utilized the available in GenBank database Lujo virus sequences (https://www.ncbi. nlm.nih.gov/genbank) aligned in BioEdit 7.2.5 software package ( (IbisBiosciences, USA). To conduct one-round RTPCR, reverse transcriptase and TaqF-polimerase were used. Recombinant Escherichia coli strain, XL1-Blue, containing pGEM-T plasmid with inserted synthetically-generated fragment of the virus genome, was produced to make positive control sample (PCS). Constructed recombinant plasmids were used for creating RNA-containing PCS with protective protein shell of MS2-phage. Determination of specificity of the developed method was performed with the help of control panel of RNA and DNA of 23 viral strains related to 10 families; the sensitivity – the panel of biological samples artificially contaminated with PCS. Further testing was carried out at the premises of laboratory of the Russian-Guinean Center for Epidemiology and Prevention of Infectious Diseases (Kindia, Republic of Guinea) on 265 blood sera from practically healthy persons, 110 blood sera of cattle, 83 suspensions of ticks, and 165 suspensions of organs of small mammals collected in the territory of Guinea.Results and discussion. Two conservative polymerase gene fragments have been chosen as targets for Lujo virus RNA detection using RT-PCR. The combination of primers and probes has been experimentally selected, optimum composition of reaction mixture for PCR and mode of RT-PCR set-up established, as well as control samples C+, internal control, positive control sample developed. Sensitivity of the proposed method is 5·103  GE /ml, specificity – 100 %. 

Comparison of real-time RT-PCR assays for hepatitis E virus RNA detection

2013 ◽  
Vol 58 (1) ◽  
pp. 36-40 ◽  
Author(s):  
Camelia Mokhtari ◽  
Eric Marchadier ◽  
Stephanie Haïm-Boukobza ◽  
Asma Jeblaoui ◽  
Sophie Tessé ◽  
...  
Keyword(s):  
Real Time ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Rt Pcr ◽  
Rna Detection ◽  
Virus Rna ◽  
Pcr Assays

Bluetongue Virus RNA Detection by Real-Time RT-PCR in Post-Vaccination Samples from Cattle

2013 ◽  
Vol 62 (2) ◽  
pp. 157-162 ◽  
Author(s):  
I. De Leeuw ◽  
M. Garigliany ◽  
G. Bertels ◽  
T. Willems ◽  
D. Desmecht ◽  
...  
Keyword(s):  
Real Time ◽  
Bluetongue Virus ◽  
Rt Pcr ◽  
Rna Detection ◽  
Post Vaccination ◽  
Virus Rna

Establishment of an in-house one-step real-time RT-PCR assay for detection of Zaire ebolavirus

2017 ◽  
Vol 59 (4) ◽  
pp. 51-55
Author(s):  
Xuan Su Hoang ◽  
Thi Thu Hang Dinh ◽  
Van Tong Hoang ◽  
Huu Tho Ho ◽  
Tien Sy Bui ◽  
...  
Keyword(s):  
Real Time ◽  
Rt Pcr ◽  
Pcr Assay ◽  
One Step ◽  
Zaire Ebolavirus

A Single-tube real-time RT-PCR assay for RNA detection and quantification of genetically diverse HIV including rare HIV-1 non-m groups and HIV-2

2014 ◽  
Vol 29 (4) ◽  
pp. 179-185
Author(s):  
M. A. Prasolova ◽  
M. K. Ivanov ◽  
N. M. Gashnikova ◽  
E. S. Netesova ◽  
G. M. Dymshits
Keyword(s):  
Real Time ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Rna Detection ◽  
Single Tube ◽  
Hiv 1 ◽  
Detection And Quantification

scholarly journals Development of the kit for diagnostics of COVID-19 by real time RT-PCR

2020 ◽  
Author(s):  
AK Shuryaeva ◽  
TV Malova ◽  
EE Davydova ◽  
YuA Savochkina ◽  
EV Bogoslovskaya ◽  
...  
Keyword(s):  
Real Time ◽  
Diagnostic System ◽  
High Specificity ◽  
Test System ◽  
Analytical Sensitivity ◽  
Rt Pcr ◽  
The Russian Federation ◽  
Diagnostic Sensitivity And Specificity ◽  
Respiratory Coronavirus ◽  
The City

Late in December 2019, an outbreak of an unknown coronavirus, later identified as SARS-CoV- 2, emerged in the city of Wuhan, China. It causes a dangerous respiratory coronavirus disease in humans - COVID-19. Objective. To detect cases of the disease and prevent its spread across the Russian Federation it is necessary to create an effective diagnostic test system. Material and methods. Based on the analysis of the alignment of the SARS-CoV-2 nucleotide sequences, primers and a probe for RT-PCR were selected, and the analysis conditions were optimized. Results. The diagnostic system was developed and registered in the shortest possible time in real-time RT-PCR format for detecting SARS-CoV-2 coronavirus RNA in smears from the nasopharynx and oropharynx, sputum and feces. The high specificity of the system was verified on a representative set of viruses and microorganisms, the analytical sensitivity was 1x103 copies / ml in smears from the mucous membrane of the nasopharynx and oropharynx and sputum, 5x104 copies / ml in fecal samples. Diagnostic sensitivity and specificity established during clinical trials on samples from patients with confirmed COVID-19 infection, from patients with a different etiology of a disease and clinically healthy people were to 100% (range 94.2-100% with a confidence level of 95%).

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