scholarly journals Testing of four-sample pools offers resource optimization without compromising diagnostic performance of real time reverse transcriptase-PCR assay for COVID-19

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251891
Author(s):  
Anirudh K. Singh ◽  
Ram Kumar Nema ◽  
Ankur Joshi ◽  
Prem Shankar ◽  
Sudheer Gupta ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Real Time ◽  
Diagnostic Performance ◽  
Turnaround Time ◽  
Positive Sample ◽  
Resource Optimization ◽  
Diagnostic Laboratory ◽  
Reverse Transcriptase Pcr ◽  
Pooled Testing ◽  
Sample Pooling

Quick identification and isolation of SARS-CoV-2 infected individuals is central to managing the COVID-19 pandemic. Real time reverse transcriptase PCR (rRT-PCR) is the gold standard for COVID-19 diagnosis. However, this resource-intensive and relatively lengthy technique is not ideally suited for mass testing. While pooled testing offers substantial savings in cost and time, the size of the optimum pool that offers complete concordance with results of individualized testing remains elusive. To determine the optimum pool size, we first evaluated the utility of pool testing using simulated 5-sample pools with varying proportions of positive and negative samples. We observed that 5-sample pool testing resulted in false negativity rate of 5% when the pools contained one positive sample. We then examined the diagnostic performance of 4-sample pools in the operational setting of a diagnostic laboratory using 500 consecutive samples in 125 pools. With background prevalence of 2.4%, this 4-sample pool testing showed 100% concordance with individualized testing and resulted in 66% and 59% reduction in resource and turnaround time, respectively. Since the negative predictive value of a diagnostic test varies inversely with prevalence, we re-tested the 4-sample pooling strategy using a fresh batch of 500 samples in 125 pools when the prevalence rose to 12.7% and recorded 100% concordance and reduction in cost and turnaround time by 36% and 30%, respectively. These observations led us to conclude that 4-sample pool testing offers the optimal blend of resource optimization and diagnostic performance across difference disease prevalence settings.

scholarly journals Evaluation of a Sample Pooling Strategy for Sars-cov-2 Using Real Time PCR

2021 ◽  
Author(s):  
Annet M Nankya ◽  
Luke Nyakarahuka ◽  
Stephen Balinandi ◽  
John Kayiwa ◽  
Julius Lutwama ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Virus Disease ◽  
Laboratory Diagnosis ◽  
Turnaround Time ◽  
Limited Resources ◽  
Asymptomatic Patients ◽  
Sample Pooling ◽  
Sample Testing ◽  
Pooling Strategy

Abstract Back ground: Corona Virus Disease 2019 (COVID 19) in Uganda was first reported in a male traveler from Dubai on 21st March, 2020 shortly after WHO had announced the condition as a global pandemic. Timely laboratory diagnosis of COVID -19 for all samples from both symptomatic and asymptomatic patients was observed as key in containing the pandemic and breaking the chain of transmission. However, there was a challenge of limited resources required for testing SARS-COV-2 in low and middle income countries. To mitigate this, a study was conducted to evaluate a sample pooling strategy for COVI-19 using real time PCR. The cost implication and the turn around time of pooled sample testing versus individual sample testing were also compared.Methods: In this study, 1260 randomly selected samples submitted to Uganda Virus Research Institute for analysis were batched in pools of 5, 10, and 15. The pools were then extracted using a Qiagen kit. Both individual and pooled RNA were screened for the SARS-COV-2 E gene using a Berlin kit. Results: Out of 1260 samples tested, 21 pools were positive in pools of 5 samples, 16 were positive in pools of 10 and 14 were positive in pools of 15 samples. The study also revealed that the pooling strategy helps to save a lot on resources, time and expands diagnostic capabilities without affecting the sensitivity of the test in areas with low SARS-COV-2 prevalence.Conclusion: This study demonstrated that the pooling strategy for COVID-19 reduced on the turnaround time and there was a substantial increase in the overall testing capacity with limited resources as compared to individual testing.

Validation of a Real-Time Reverse Transcriptase–PCR Assay for the Detection of H7 Avian Influenza Virus

2010 ◽  
Vol 5 (s1) ◽  
pp. e148-e149
Author(s):  
Janice Pedersen ◽  
Mary Lea Killian ◽  
Nichole Hines ◽  
Dennis Senne ◽  
Brundaban Panigrahy ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Avian Influenza ◽  
Reverse Transcriptase ◽  
Avian Influenza Virus ◽  
Real Time ◽  
Pcr Assay ◽  
Reverse Transcriptase Pcr

Development of asigDE-Based Real-Time Reverse-Transcriptase PCR for the Detection of ViableSalmonella enterica

2014 ◽  
Vol 11 (7) ◽  
pp. 537-544 ◽  
Author(s):  
Min Zhou ◽  
Jielin Yang ◽  
Xiujuan Zhou ◽  
Bin Liu ◽  
Daixin Liu ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Real Time ◽  
Reverse Transcriptase Pcr

scholarly journals Comparison of Rapid Antigen Test and Real-Time Reverse Transcriptase PCR for Diagnosing Novel Swine Influenza A (H1N1)

2010 ◽  
Vol 13 (3) ◽  
pp. 109 ◽  
Author(s):  
Aerin Kwon ◽  
Jae-Seok Kim ◽  
Han-Sung Kim ◽  
Wonkeun Song ◽  
Ji-Young Park ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Real Time ◽  
Influenza A ◽  
Swine Influenza ◽  
Antigen Test ◽  
Reverse Transcriptase Pcr ◽  
Influenza A H1n1

Novel Approach for Detecting Prohibited Species-Specific Central Nervous System Tissue Contamination in Meat by One-Step Real-Time Reverse Transcriptase PCR

2009 ◽  
Vol 72 (5) ◽  
pp. 1063-1069 ◽  
Author(s):  
M. M. NAGARAJAN ◽  
D. LONGTIN ◽  
C. SIMARD
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Reverse Transcriptase ◽  
Real Time ◽  
Compliance Monitoring ◽  
Reverse Transcriptase Pcr ◽  
Qrt Pcr ◽  
Tissue Contamination ◽  
One Step ◽  
Species Specific

The dissemination of prohibited species-specific central nervous system (CNS) tissue contamination in meat must be tracked to mitigate human health risk associated with bovine spongiform encephalopathy. The efficiency of compliance monitoring and risk control measures taken by concerned regulatory authorities at meat production facilities to avoid such contamination depends on the ability to detect CNS tissue with a reliable and adequately sensitive quantitative method. A rapid and convenient one-step real-time quantitative reverse transcriptase PCR (qRT-PCR) assay was developed based on the absolute quantification of glial fibrillary acidic protein (GFAP) mRNA as a marker for CNS tissue contamination in meat. The GFAP RNA quantity corresponding to a percentage of CNS tissue in artificially spiked meat was determined using an appropriate in vitro transcribed target GFAP RNA as a calibration standard in the assay. The assay had a linear dynamic range of 102 to 109 copies of target RNA and was able to detect 0.01% CNS contamination in meat. Further evaluation consisted of an analysis of 272 random meat cuts from carcasses and 109 ground meat samples received from a federally inspected abattoir and two meat processing facilities, respectively, over a 5-month period. The analyzed samples were all negative for CNS tissue contamination at an arbitrarily set lower threshold of 0.025%. Overall, the newly developed one-step qRT-PCR may be useful as an objective quantitative compliance monitoring tool and for setting an acceptable low tolerance threshold for such contamination in meat.

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