Factors associated with real-time RT-PCR cycle threshold values among medically attended influenza episodes

2015 ◽  
Vol 88 (4) ◽  
pp. 719-723 ◽  
Author(s):  
Sarah Spencer ◽  
Jessie Chung ◽  
Mark Thompson ◽  
Pedro A. Piedra ◽  
Alan Jewell ◽  
...  
Keyword(s):  
Real Time ◽  
Threshold Values ◽  
Rt Pcr ◽  
Factors Associated ◽  
Cycle Threshold

scholarly journals Preanalytical Issues and Cycle Threshold Values in SARS-CoV-2 Real-Time RT-PCR Testing: Should Test Results Include These?

ACS Omega ◽  
2021 ◽  
Author(s):  
Ilka Engelmann ◽  
Enagnon Kazali Alidjinou ◽  
Judith Ogiez ◽  
Quentin Pagneux ◽  
Sana Miloudi ◽  
...  
Keyword(s):  
Real Time ◽  
Test Results ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold

scholarly journals Cycle Threshold Values in the Context of Multiple RT-PCR Testing for SARS-CoV-2

2021 ◽  
Vol Volume 14 ◽  
pp. 1311-1317
Author(s):  
Daniel Romero-Alvarez ◽  
Daniel Garzon-Chavez ◽  
Franklin Espinosa ◽  
Edison Ligña ◽  
Enrique Teran ◽  
...  
Keyword(s):  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold

scholarly journals Assessment of Commercial DNA Cleanup Kits for Elimination of Real-Time PCR Inhibitors in the Detection of Cyclospora cayetanensis in Cilantro

2020 ◽  
Vol 83 (11) ◽  
pp. 1863-1870
Author(s):  
ANGELA ASSURIAN ◽  
HELEN MURPHY ◽  
ALICIA SHIPLEY ◽  
HEDIYE NESE CINAR ◽  
ALEXANDRE DA SILVA ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
False Negative ◽  
Threshold Values ◽  
Cyclospora Cayetanensis ◽  
Cycle Threshold ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Inhibitor ◽  
Zymo Research

ABSTRACT Inhibited reactions have occasionally been observed when cilantro samples were processed for the detection of Cyclospora cayetanensis using quantitative real-time PCR (qPCR). Partial or total inhibition of PCR reactions, including qPCR, can occur, leading to decreased sensitivity or false-negative results. If inhibition occurs, this implies the need for additional purification or cleanup treatments of the extracted DNA to remove inhibitors prior to molecular detection. Our objective was to evaluate the performance of five commercial DNA cleanup kits (QIAquick purification kit from Qiagen [kit 1], OneStep PCR inhibitor removal by Zymo Research [kit 2], NucleoSpin genomic DNA cleanup XS from Macherey-Nagel [kit 3], DNA IQ system by Promega [kit 4], and DNeasy PowerPlant pro kit from Qiagen [5]) to minimize qPCR inhibition using the U.S. Food and Drug Administration–validated Bacteriological Analytical Manual (BAM) Chapter 19b method for detection of C. cayetanensis in cilantro samples containing soil. Each of the five commercial DNA cleanup kits evaluated was able to reduce the qPCR internal amplification control cycle threshold values to those considered to be normal for noninhibited samples, allowing unambiguous interpretation of results in cilantro samples seeded at both a high oocyst level (200 oocysts) and a low oocyst level (10 oocysts). Of the five kits compared, kits 1, 2, and 3 did not show significant differences in the detection of C. cayetanensis, while significantly higher cycle threshold values, indicating lower recovery of the target DNA, were observed from kits 4 and/or 5 in samples seeded with 200 and 10 oocysts (P < 0.05). This comparative study provides recommendations on the use of commercial cleanup kits which could be implemented when inhibition is observed in the detection of C. cayetanensis in cilantro samples using the BAM Chapter 19b method. HIGHLIGHTS

scholarly journals The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients

2021 ◽  
Author(s):  
Elisa Teyssou ◽  
Cathia Soulie ◽  
Benoit Visseaux ◽  
Sidonie Lambert-Niclot ◽  
Valentine Ferre ◽  
...  
Keyword(s):  
Viral Load ◽  
Newly Diagnosed ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
The World

The 501Y.V2 and the 501Y.V1 SARS-CoV-2 variants emerged and spread rapidly into the world. We analysed the RT-PCR cycle threshold values of 643 nasopharyngeal samples of COVID-19 patients at diagnosis and found that the 501Y.V2 variant presented an intermediate viral load between the 501Y.V1 and the historical variants.

scholarly journals Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

2021 ◽  
Author(s):  
Yun Lin ◽  
Bingyi Yang ◽  
Sarah Cobey ◽  
Eric Lau ◽  
Dillon Adam ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Temporal Distribution ◽  
Time Estimation ◽  
Population Level ◽  
Reproductive Number ◽  
Threshold Values ◽  
Illness Onset ◽  
Cycle Threshold ◽  
Viral Loads

Abstract Many locations around the world have used real-time estimates of the time-varying effective reproductive number (\({R}_{t}\)) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of \({R}_{t}\) are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the incubation period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral loads among confirmed cases can provide insights into epidemic trajectory. Here, we analyzed viral load data on confirmed cases during two local epidemics in Hong Kong, identifying a strong correlation between temporal changes in the distribution of viral loads (measured by cycle threshold values) and estimates of \({R}_{t}\) based on case counts. We demonstrate that cycle threshold values could be used to improve real-time \({R}_{t}\) estimation, enabling more timely tracking of epidemic dynamics.

scholarly journals Sampling site for SARS-CoV-2 RT-PCR—An intrapatient four-site comparison from Tampere, Finland

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260184
Author(s):  
Dominik Kerimov ◽  
Pekka Tamminen ◽  
Hanna Viskari ◽  
Lauri Lehtimäki ◽  
Janne Aittoniemi
Keyword(s):  
Informed Consent ◽  
Study Design ◽  
Nasal Swab ◽  
Sampling Site ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Significant Difference ◽  
Nasal Swabs ◽  
Written Informed Consent

Background SARS-CoV-2 diagnosis relies on the performance of nasopharyngeal swabs. Alternative sample sites have been assessed but the heterogeneity of the studies have made comparing different sites difficult. Objectives Our aim was to compare the performance of four different sampling sites for SARS-CoV-2 samples with nasopharynx being the benchmark. Study design COVID-19 positive patients were recruited prospectively, and samples were collected and analysed for SARS-CoV-2 with RT-PCR from all four anatomical sites in 43 patients, who provided written informed consent. Results All anterior nasal and saliva samples were positive, while two oropharyngeal samples were negative. There was no significant difference in the cycle threshold values of nasopharyngeal and anterior nasal samples while saliva and oropharynx had higher cycle threshold values. Conclusions Anterior nasal swab performs as good as nasopharynx swab with saliva also finding all the positives but with higher cycle threshold values. Thus, we can conclude that anterior nasal swabs can be used for SARS-CoV-2 detection instead of nasopharyngeal swabs if the situation would require so.

Comparison of Real Time PCR Cycle Threshold Values in Symptomatic and Asymptomatic COVID-19 Patients

2021 ◽  
Vol 55 (3) ◽  
pp. 435-444
Author(s):  
Harun Gülbudak ◽  
Şinasi Karvar ◽  
Gizem Soydan ◽  
Seda Tezcan Ülger ◽  
Özlem Kandemir ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Threshold Values ◽  
Cycle Threshold

scholarly journals Determination of cut-off cycle threshold values in routine RT–PCR assays to assist differential diagnosis of norovirus in children hospitalized for acute gastroenteritis

2015 ◽  
Vol 143 (15) ◽  
pp. 3292-3299 ◽  
Author(s):  
N. V. TRANG ◽  
M. CHOISY ◽  
T. NAKAGOMI ◽  
N. T. M. CHINH ◽  
Y. H. DOAN ◽  
...  
Keyword(s):  
Differential Diagnosis ◽  
Real Time ◽  
Acute Gastroenteritis ◽  
Bimodal Distribution ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Prevalence Studies ◽  
Cycle Threshold ◽  
Asymptomatic Children ◽  
Enteric Infections

SUMMARYNorovirus (NV) is an important cause of acute gastroenteritis in children, but is also frequently detected in asymptomatic children, which complicates the interpretation of NV detection results in both the clinical setting and population prevalence studies. A total of 807 faecal samples from children aged <5 years hospitalized for acute gastroenteritis were collected in Thai Binh, Vietnam, from January 2011 to September 2012. Real-time RT–PCR was used to detect and quantify NV-RNA in clinical samples. A bimodal distribution of cycle threshold (Ct) values was observed in which the lower peak was assumed to represent cases for which NV was the causal agent of diarrhoea, whereas the higher peak was assumed to represent cases involving an alternative pathogen other than NV. Under these assumptions, we applied finite-mixture modelling to estimate a threshold of Ct <21·36 (95% confidence interval 20·29–22·46) to distinguish NV-positive patients for which NV was the likely cause of diarrhoea. We evaluated the validity of the threshold through comparisons with NV antigen ELISA results, and comparisons of Ct values in patients co-infected with rotavirus. We conclude that the use of an appropriate cut-off value in the interpretation of NV real-time RT–PCR results may improve differential diagnosis of enteric infections, and could contribute to improved estimates of the burden of NV disease.

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