scholarly journals Insufficient Sensitivity of RNA Dependent RNA Polymerase Gene of SARS-CoV-2 Viral Genome as Confirmatory Test using Korean COVID-19 Cases

2020 ◽  
Author(s):  
Soyoun Kim ◽  
Dong-Min Kim ◽  
Baeckseung Lee
Keyword(s):  
Diagnostic Methods ◽  
Confirmatory Test ◽  
Test Results ◽  
Rt Pcr ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Pcr Method ◽  
Who Guideline ◽  
Rna Polymerase Gene ◽  
Insufficient Sensitivity

Since mid-December of 2019, coronavirus disease 2019 (COVID-19) has been spreading from Wuhan, China. As of February 21, total 75,773 confirmed cases worldwide have spread to more than two dozen countries. Transmission of COVID-19 can occur early in the course of infection since SARS-CoV-2 viral loads in asymptomatic patients are similar to that in the symptomatic patients. Therefore, more sensitive diagnostic methods are needed to detect early phase of the infection to prevent secondary or tertiary spreads. Here, we compare the RT-PCR confirmatory test results using two different SARS-CoV-2 viral RNAs from two Korean COVID-19 confirmed cases.RT-PCR method targeting the RdRP gene, which was recommended by WHO guideline, was less sensitive than targeting N genes (as per CDC guideline). Because many countries follow the WHO guideline, our findings may contribute to the early diagnosis of COVID-19.

scholarly journals Diagnostic performance of a novel digital immunoassay (RapidTesta SARS-CoV-2): a prospective observational study with 1,127 nasopharyngeal samples

2021 ◽  
Author(s):  
Hiromichi Suzuki ◽  
Yusaku Akashi ◽  
Atsuo Ueda ◽  
Yoshihiko Kiyasu ◽  
Yuto Takeuchi ◽  
...  
Keyword(s):  
Diagnostic Performance ◽  
Prospective Observational Study ◽  
Test Results ◽  
Antigen Test ◽  
Rt Pcr ◽  
Asymptomatic Patients ◽  
Pcr Method ◽  
Antigen Tests ◽  
Positive Line ◽  
Test Cassette

Introduction: Digital immunoassays are generally regarded as superior tests for the detection of infectious disease pathogens, but there have been insufficient data concerning SARS-CoV-2 immunoassays. Methods: We prospectively evaluated a novel digital immunoassay (RapidTesta SARS-CoV-2). Two nasopharyngeal samples were simultaneously collected for antigen tests and RT-PCR. Real-time RT-PCR for SARS-CoV-2, using a method developed by the National Institute of Infectious Diseases, Japan, served as the reference RT-PCR method. Results: During the study period, 1,127 nasopharyngeal samples (symptomatic patients: 802, asymptomatic patients: 325) were evaluated. For digital immunoassay antigen tests, the sensitivity was 78.3% (95% CI: 67.3%-87.1%) and the specificity was 97.6% (95% CI: 96.5%-98.5%). When technicians visually analyzed the antigen test results, the sensitivity was 71.6% (95% CI: 59.9%-81.5%) and the specificity was 99.2% (95% CI: 98.5%-99.7%). Among symptomatic patients, the sensitivity was 89.4% (95% CI; 76.9%-96.5%) with digital immunoassay antigen tests, and 85.1% (95% CI; 71.7%-93.8%) with visually analyzed the antigen test, respectively. Conclusions: The findings indicated that RapidTesta SARS-CoV-2 analysis with the DIA device had sufficient analytical performance for the detection of SARS-CoV-2 in nasopharyngeal samples. When positive DIA results are recorded without a visually recognizable red line at the positive line location on the test cassette, additional RT-PCR evaluation should be performed.

scholarly journals Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259908
Author(s):  
Laura Heireman ◽  
Steven Abrams ◽  
Peggy Bruynseels ◽  
Reinoud Cartuyvels ◽  
Lize Cuypers ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Age Group ◽  
Test Results ◽  
Rt Pcr ◽  
Median Viral Load ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Positivity Ratio ◽  
Second Wave

Introduction The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. Materials/Methods We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020–31 March 2021). Results In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20–30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20–40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. Conclusion There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20–30 year old individuals, indicating they could have been the hidden drivers of this wave.

Detection of SARs CoV-2 during initial phase of pandemic from population of banas kantha district of Gujarat-India with special emphasis on pooled samples

2021 ◽  
Vol 7 (4) ◽  
pp. 295-299
Author(s):  
Hiren Patel ◽  
Parijat N Goswami
Keyword(s):  
Viral Load ◽  
Age Groups ◽  
High Viral Load ◽  
Rt Pcr ◽  
Viral Loads ◽  
Corona Virus ◽  
Asymptomatic Patients ◽  
Care Workers ◽  
Pcr Method ◽  
Pharynx Swab

Corona virus (SARs CoV-2) has caused immense effect on morbidity and mortality of the population globally. We undertook this study as we are a part of one of the network laboratories of ICMR to test the patient’s sample by RT PCR for the ORF 1 ab gene of corona virus. : For a period of one and half months (14 April to 31 May 2020) we tested the nasopharynx and oro-pharynx swab samples sent to us in VTM from the assigned districts of Gujarat. All the samples were subjected to RT PCR method by following standard methods. Total of 9.04%(256/2833) population was positive and 4.73%(139/2833) belonged to age groups 21-40 and 2.33% (66/2833) to 41-60yrs. Above the age of 60yrs there were only 0.95% (22/2833) cases which were positive. It was advantageous to pool the samples. Out of the number of pools prepared, we reported around 80% negative and rest were positive in pools. The study also included association of viral load and infectivity. We found that 12% of the asymptomatic people and 5.1% of symptomatic individuals had high viral load. : It is seen that the incidence of Novel corona virus -19 detection by RT PCR is a reliable method and the establishment of the Ct value and infectivity of the patient to the health care workers and relatives needs to be taken care of. Also, the study presents asymptomatic patients having high viral loads being highly infective.

scholarly journals Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study

2021 ◽  
Vol 9 (4) ◽  
pp. 798
Author(s):  
Giorgia Caruana ◽  
Antony Croxatto ◽  
Eleftheria Kampouri ◽  
Antonios Kritikos ◽  
Onya Opota ◽  
...  
Keyword(s):  
Immunoglobulin A ◽  
University Hospital ◽  
Lower Sensitivity ◽  
Clinical Settings ◽  
Rt Pcr ◽  
Emergency Ward ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Asymptomatic Subjects ◽  
Antigen Testing

Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for patients’ cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q®, PanbioTM and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q®, PanbioTM and BD Veritor™, respectively, for viral loads above 105 copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/mL and 100% for viral loads above 107 copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.

scholarly journals Detection of Flavescence Dorée Phytoplasma in Grapevine by Reverse-Transcription PCR

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1496-1501 ◽  
Author(s):  
P. Margaria ◽  
C. Rosa ◽  
C. Marzachì ◽  
M. Turina ◽  
S. Palmano
Keyword(s):  
Reverse Transcription ◽  
Large Scale ◽  
Diagnostic Methods ◽  
Kappa Index ◽  
Rt Pcr ◽  
Flavescence Dorée ◽  
Reverse Transcription Pcr ◽  
Novel Method ◽  
Pcr Method ◽  
Polymerase Chain

Flavescence dorée (FD) is the most serious phytoplasma disease of grapevine. This report describes a novel method of detecting FD phytoplasma based on reverse-transcription polymerase chain reaction (RT-PCR) on 16S ribosomal RNA (16SrRNA) which will greatly improve mass screening of infected grapevines. A rapid protocol for extracting sap from whole leaves or midveins and successive one-tube amplification by RT-PCR was applied to grapevine samples with or without symptoms collected from different areas of Piedmont (northwestern Italy). Results were compared with those obtained using one of the current diagnostic methods that utilizes nested PCR on phytoplasma DNA-enriched preparations. A Cohen's kappa index of 0.76 indicated a substantial agreement between the two sets of results. The RT-PCR method has the advantage of being a rapid, reliable, and sensitive assay for large-scale screening of grapevines.

scholarly journals Monitoring and predicting viral dynamics in SARS-CoV-2-infected Patients

2020 ◽  
Author(s):  
Shaoqing Wen ◽  
Jianxue Xiong ◽  
Chang Sun ◽  
Barnaby Edward Young ◽  
David Chien Lye ◽  
...  
Keyword(s):  
Throat Swab ◽  
False Negative ◽  
Viral Dynamics ◽  
Test Results ◽  
Rt Pcr ◽  
Time Model ◽  
Viral Loads ◽  
Robust Model ◽  
Health Situation ◽  
The Mathematical Model

AbstractThis study is based on the a simple but robust model we developed urgently to accurately monitor and predict viral dynamics for each SARS-CoV-2-infected patient, given the limited number of RT-PCR tests and the complexity of each individual’s physical health situation. We used the mathematical model to monitor and predict the changes of viral loads from different nasal and throat swab of clinical specimens collected from diagnosed patients. We also tested this real-time model by using the data from the SARS-CoV-2-infected patients with different severity. By using this model (http://58.87.113.187:8080/), we can predict the viral dynamics of patients, minimize false-negative test results, and screen the patients who are at risk of testing positive again after recovery. We sincerely thank those who are on the front lines battling SARS-CoV-2 virus. We hope this model will be useful for SARS-CoV-2-infected patients.

Evaluation of the consistency of RT-PCR test results in nasopharyngeal and fecal specimens in patients with Covid-19 disease with gastrointestinal symptoms

2021 ◽  
Vol 15 (6) ◽  
pp. 1843-1846
Author(s):  
Mohammad Ebrahim Ghamarchehreh ◽  
Mohammad Mehdi Jahani ◽  
Zahra Nourollahzadeh
Keyword(s):  
Infectious Disease ◽  
Severe Acute Respiratory Syndrome ◽  
Gastrointestinal Symptoms ◽  
Taqman Probe ◽  
Clinical Samples ◽  
Test Results ◽  
Rt Pcr ◽  
Specific Primers ◽  
Pcr Method ◽  
Pcr Test

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Addition to respiratory manifestations, gastrointestinal symptoms have been observed in some patients with COVID-19. The aim of the present study was to investigate the simultaneous diagnosis of SARS-CoV-2 RNA by RT-PCR in nasopharyngeal and fecal specimens of patients with covid-19 with gastrointestinal symptoms. In the present study, 100 patients with COVID-19 disease with gastrointestinal symptoms were included. Isolation of viral RNA in nasopharyngeal and fecal samples performed using specific laboratory kits. Detection of COVID-19 in clinical samples conducted using TaqMan-probe Real Time PCR method with specific primers and probes (Pishtaz Teb RT-PCR kit, Iran). PCR test results showed that in 21% of patients with positive nasopharyngeal test, SARS ‐ CoV ‐ 2 RNA was detected. As a result, the compatibility of PCR test in the diagnosis of Covid-19 virus between nasopharyngeal and fecal results was 21%. Keywords: Covid-19, nasopharyngeal, fecal specimens, RT-PCR

Management of Pandemic Crisis: COVID-19

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 885-891
Author(s):  
Jayati Mehta ◽  
Sudhindra Baliga ◽  
Nilima Thosar ◽  
Nilesh Rathi ◽  
Shreyans Jain ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Public Health Workforce ◽  
Protective Equipment ◽  
Psychological Violence ◽  
Rt Pcr ◽  
Wuhan City ◽  
The Public ◽  
Asymptomatic Patients ◽  
Pcr Method ◽  
Physical And Psychological Violence

The world is threatened with a novel corona virus (COVID-19) which has posed an unpredictable challenge to the public health workforce. It originated from the Wuhan City of China and spread across the globe creating havoc among the public and healthcare workers which led to WHO declaring it to be pandemic. Transmission of this virus is through symptomatic and asymptomatic patients in the form of fomites produced while coughing or sneezing. This has led to a global crisis subsequently leading to the scarce availability of health care resources such as personal protective equipment, ventilators, ICU beds, medication. Healthcare workers have been a vital human resource in providing treatment and assistance to the infected patients though they were facing a high risk of themselves getting infected by the coronavirus. They suffered from fatigue, physical, and psychological violence as they tend to work for longer hours. Detection of infected patients was implemented, as the widely used RT- PCR method was accurate but took more time for the definite results. Hence, for quick results and to detect more number of infected patients, the rapid antigen test was conducted. Therefore, this virus has resulted in a greater impact on the economy and social development and this article of many infected countries.

scholarly journals Comparing lateral flow testing with a rapid RT-PCR method for SARS-CoV-2 detection in the UK

2021 ◽  
Author(s):  
Andrew Taylor ◽  
Ronan Calvez ◽  
Mark Atkins ◽  
Colin G Fink
Keyword(s):  
Scientific Evidence ◽  
Lateral Flow ◽  
Careful Examination ◽  
Rt Pcr ◽  
Laboratory Staff ◽  
Viral Loads ◽  
Pcr Method ◽  
Uk Government ◽  
Us Fda ◽  
The Uk

AbstractIn late 2019, SARS-CoV-2 emerged in the Wuhan province of China. Rapid global spread led to the Covid-19 pandemic. Rapid and accurate detection of SARS-CoV-2 has become a vitally important tool in controlling the spread of the virus. Lateral flow devices (LFDs) offer the potential advantage of speed and on-site testing. The sensitivity of these devices compared to the gold standard RT-PCR has been questioned. We compared the performance of the Innova lateral flow kit, recommended by the UK government, with our rapid in-house RT-PCR protocol using stored positive patient samples. The LFD device was found to be 6,000-10,000 times less sensitive than RT-PCR for the detection of SARS-CoV-2. Overall, the LFD detected 46.2% of the positives detected by RT-PCR. 50% of the LFD results were observed to be weak positives, only visible after careful examination by experienced laboratory staff. At lower viral loads, such as 10,000-100,000 RNA copies/ml, the LFD detected 22.2% of positives. In addition, two strong positives (3 and 1.5 million RNA copies/ml) were not detected by the LFD. The argument for use of LFD kits, despite their lack of sensitivity, is that they detect infectious virus and hence contagious individuals. At present, there is a lack of scientific evidence supporting this claim. The LFD used in the UK fails to identify individuals with considerable viral loads and has been subject to a class I recall by the US FDA but is still approved and recommended for use by the UK government. We believe that using LFD testing for assessing SARS-CoV-2 infection risk is a strategy which has risks that outweigh any benefits.

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