scholarly journals Analysis of Nucleotide Changes in RT-PCR Primer/Probe Binding Regions in SARS-CoV-2 Isolates Reported from Turkey

2021 ◽  
Vol 55 (3) ◽  
pp. 311-326
Author(s):  
Ayşe Banur Demir ◽  
Alihan Bulgurcu ◽  
Özgür Appak ◽  
Ayça Arzu Sayıner
Keyword(s):  
Rt Pcr ◽  
Binding Regions ◽  
Pcr Primer

scholarly journals Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

2020 ◽  
Author(s):  
Manu Vanaerschot ◽  
Sabrina A. Mann ◽  
James T. Webber ◽  
Jack Kamm ◽  
Sidney M. Bell ◽  
...  
Keyword(s):  
Diagnostic Sensitivity ◽  
N Gene ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Multiple Targets ◽  
Epidemiologic Evidence ◽  
Gene Assay ◽  
Pcr Primer

AbstractWe identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection.Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

Evaluation of several RT-PCR primer pairs for the detection of Apple stem pitting virus

2010 ◽  
Vol 168 (1-2) ◽  
pp. 242-247 ◽  
Author(s):  
B. Komorowska ◽  
T. Malinowski ◽  
L. Michalczuk
Keyword(s):  
Rt Pcr ◽  
Apple Stem ◽  
Apple Stem Pitting Virus ◽  
Stem Pitting ◽  
Pcr Primer

Development of an extraction and concentration procedure and comparison of RT-PCR primer systems for the detection of hepatitis A virus and norovirus GII in green onions

2006 ◽  
Vol 134 (1-2) ◽  
pp. 130-135 ◽  
Author(s):  
Evelyne Guévremont ◽  
Julie Brassard ◽  
Alain Houde ◽  
Carole Simard ◽  
Yvon-Louis Trottier
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Rt Pcr ◽  
Norovirus Gii ◽  
Pcr Primer

scholarly journals How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection?

2021 ◽  
pp. 114197
Author(s):  
Ahalieyah Anantharajah ◽  
Raphael Helaers ◽  
Jean-Philippe Defour ◽  
Nathalie Olive ◽  
Florence Kabera ◽  
...  
Keyword(s):  
Real Time ◽  
Rt Pcr ◽  
Primer Sets ◽  
The Right ◽  
Pcr Primer

Detection of false positives with a commonly used Norovirus RT-PCR primer set

2013 ◽  
Vol 56 (1) ◽  
pp. 84-85 ◽  
Author(s):  
Elke Wollants ◽  
Marc Van Ranst
Keyword(s):  
False Positives ◽  
Rt Pcr ◽  
Pcr Primer

scholarly journals Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays

2021 ◽  
Author(s):  
Takeru Nakabayashi ◽  
Yuki Kawasaki ◽  
Koichiro Murashima ◽  
Kazuya Omi ◽  
Satoshi Yuhara
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Detection Sensitivity ◽  
Genetic Mutations ◽  
Rt Pcr ◽  
Mutant Strains ◽  
Binding Regions ◽  
Control And Prevention ◽  
Pcr Assays ◽  
Silico Analysis

AbstractSeveral mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.

Detection of Nucleic Acids in Cells or Tissue Sections Using In situ Polymerase Chain Reaction (PCR)

1996 ◽  
Vol 54 ◽  
pp. 16-17
Author(s):  
J. R. Hully ◽  
K. R. Luehrsen ◽  
K. Aoyagi ◽  
C. Shoemaker ◽  
R. Abramson
Keyword(s):  
Nucleic Acids ◽  
Viral Infections ◽  
Anatomical Location ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Cellular Source ◽  
Gene Transcripts ◽  
Initial Description ◽  
In Cells

The development of PCR technology has greatly accelerated medical research at the genetic and molecular levels. Until recently, the inherent sensitivity of this technique has been limited to isolated preparations of nucleic acids which lack or at best have limited morphological information. With the obvious exception of cell lines, traditional PCR or reverse transcription-PCR (RT-PCR) cannot identify the cellular source of the amplified product. In contrast, in situ hybridization (ISH) by definition, defines the anatomical location of a gene and/or it’s product. However, this technique lacks the sensitivity of PCR and cannot routinely detect less than 10 to 20 copies per cell. Consequently, the localization of rare transcripts, latent viral infections, foreign or altered genes cannot be identified by this technique. In situ PCR or in situ RT-PCR is a combination of the two techniques, exploiting the sensitivity of PCR and the anatomical definition provided by ISH. Since it’s initial description considerable advances have been made in the application of in situ PCR, improvements in protocols, and the development of hardware dedicated to in situ PCR using conventional microscope slides. Our understanding of the importance of viral latency or viral burden in regards to HIV, HPV, and KSHV infections has benefited from this technique, enabling detection of single viral copies in cells or tissue otherwise thought to be normal. Clearly, this technique will be useful tool in pathobiology especially carcinogenesis, gene therapy and manipulations, the study of rare gene transcripts, and forensics.

1089: Prognostic Value of Molecular Staging of Bladder Cancer with RT -PCR Assay for KRT20: Results at 5 Year-Follow-up

2007 ◽  
Vol 177 (4S) ◽  
pp. 360-360
Author(s):  
Ana Agud ◽  
Maria J. Ribal ◽  
Lourdes Mengual ◽  
Mercedes Marin-Aguilera ◽  
Laura Izquierdo ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Prognostic Value ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Molecular Staging
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