scholarly journals Time variation in the probability of failing to detect a case of polymerase chain reaction testing for SARS-CoV-2 as estimated from a viral dynamics model

2021 ◽  
Vol 18 (177) ◽  
Author(s):  
Keisuke Ejima ◽  
Kwang Su Kim ◽  
Shoya Iwanami ◽  
Yasuhisa Fujita ◽  
Ming Li ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Symptom Onset ◽  
High Sensitivity ◽  
Viral Dynamics ◽  
Dynamics Model ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Pcr Test ◽  
Over Time

Viral tests including polymerase chain reaction (PCR) tests are recommended to diagnose COVID-19 infection during the acute phase of infection. A test should have high sensitivity; however, the sensitivity of the PCR test is highly influenced by viral load, which changes over time. Because it is difficult to collect data before the onset of symptoms, the current literature on the sensitivity of the PCR test before symptom onset is limited. In this study, we used a viral dynamics model to track the probability of failing to detect a case of PCR testing over time, including the presymptomatic period. The model was parametrized by using longitudinal viral load data collected from 30 hospitalized patients. The probability of failing to detect a case decreased toward symptom onset, and the lowest probability was observed 2 days after symptom onset and increased afterwards. The probability on the day of symptom onset was 1.0% (95% CI: 0.5 to 1.9) and that 2 days before symptom onset was 60.2% (95% CI: 57.1 to 63.2). Our study suggests that the diagnosis of COVID-19 by PCR testing should be done carefully, especially when the test is performed before or way after symptom onset. Further study is needed of patient groups with potentially different viral dynamics, such as asymptomatic cases.

scholarly journals Clinical characteristics and viral load dynamics of COVID-19 in a mildly or moderately symptomatic outpatient sample

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258970
Author(s):  
Amanda Caplan ◽  
Kelly W. Bates ◽  
Carla Brioni ◽  
Aileen Santos ◽  
Linda M. Sabatini ◽  
...  
Keyword(s):  
Viral Load ◽  
Symptom Onset ◽  
Clinical Characteristics ◽  
Symptom Duration ◽  
Test Results ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Antibody Tests ◽  
Pcr Test

Background Studies of outpatients with mild or moderate COVID-19 are uncommon. We studied: 1) association of symptoms with reverse transcriptase polymerase chain reaction (RT-PCR) test results; and 2) association of initial RT-PCR cycle threshold (Ct) in relation to duration of RT-PCR positivity in outpatients with mild or moderate COVID-19. Methods This was a cohort study of outpatients with confirmed COVID-19 and at least one symptom. Participants had repeat nasopharyngeal swabs and symptom checklists every 3–5 days until two consecutive RT-PCR tests were negative. RT-PCR tests were used to assess viral load. Antibody tests for COVID-19 were performed at 2 weeks, 4 weeks, and 8 weeks after symptom onset. Results Twenty-five patients (nine females) were enrolled, ranging in age from 19–58 (median age 28 years). All patients reported at least one symptom, with a median of six symptoms per patient. Symptoms persisted for 6–67 days (median duration 18 days). In all 25 patients, blood samples collected a median of 13 days after symptom onset were positive for SARS-CoV-2 antibodies in 15 (60%). After a median of 28 days following symptom onset, 23/23 patients with available samples tested positive for antibodies. The longest duration of positive RT-PCR test was 49 days from first positive PCR test (Mean = 27.4, SD = 12.5, Median = 24). Initial Ct was significantly associated with longer duration (β = -1.3, SE = 0.3, p<0.01 per 1 cycle higher) of RT-PCR positivity. Conclusions In mildly or moderately ill COVID-19 outpatients, RT-PCT tests remained positive for as long as 49 days and test positivity and symptom duration correlated with initial viral load.

scholarly journals Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study

BMJ ◽  
2021 ◽  
pp. n1637 ◽  
Author(s):  
Marta García-Fiñana ◽  
David M Hughes ◽  
Christopher P Cheyne ◽  
Girvan Burnside ◽  
Mark Stockbridge ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Predictive Value ◽  
High Viral Load ◽  
Test Results ◽  
Chain Reaction ◽  
Viral Loads ◽  
Flow Test ◽  
Polymerase Chain ◽  
Lateral Flow Test

Abstract Objective To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. Design Observational cohort study. Setting Community LFT pilot at covid-19 testing sites in Liverpool, UK. Participants 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. Interventions Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. Main outcome measures Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. Results Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >10 6 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>10 4 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<10 4 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. Conclusions The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.

Death and COVID-19 Anxiety in Home-Quarantined Individuals Aged 65 and Over During the Pandemic

2021 ◽  
pp. 003022282110598
Author(s):  
Hümeyra Aslaner ◽  
Betül Özen ◽  
Zeliha K. Erten ◽  
Mebrure Beyza Gökçek
Keyword(s):  
Polymerase Chain Reaction ◽  
Death Anxiety ◽  
Short Form ◽  
Anxiety Score ◽  
Test Results ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Test Result ◽  
Pcr Test

Urgent measures were taken for those at the age of 65 and over who were at the risk group all over the world due to the COVID-19 pandemic. It is known that many individuals at the age of 65 and over have experienced anxiety due to the uncertainties. This study aimed to determine the anxiety and death anxiety in individuals aged 65 and over who were isolation at home due to being diagnosed with COVID-19 or being in contact during the pandemic process. The study is descriptive and cross-sectional. It was performed with 656 home-quarantined individuals aged between 65–80 years with positive or negative real-time polymerase chain reaction (RT-PCR) test result. A form including questions about the death anxiety and the Coronavirus Anxiety Scale Short Form prepared by the researchers were administered to the individuals by phone call. Of the participants, 49.5% were male. Median COVID-19 anxiety score was 4 (0–18). Anxiety scores of the male and female participants were similar. Participants with negative polymerase chain reaction (PCR) results and those with death anxiety had higher COVID anxiety scores. Death anxiety has increased by 1.661 times in male gender, 1.983 times in RT-PCR positivity and 0.146 times in the presence of symptoms. Individuals with positive COVID-19 test results or those aged 65 and over who had death anxiety and negative COVID-19 test result but who were in home-isolation due to being a contact had higher anxiety score. For this reason, those with death anxiety can be supported in line with their religious beliefs to reduce anxiety. Those with negative PCR test results in quarantine can be adequately informed about the COVID-19.

scholarly journals Streptococcus agalactiae mastitis of bovine detection by Polymerase Chain Reaction (PCR) test in AL-Diwanyia province

2013 ◽  
Vol 12 (2) ◽  
pp. 101
Author(s):  
Gh. K. A. Al-kuzaay ◽  
Q. H. Kshash
Keyword(s):  
Polymerase Chain Reaction ◽  
Streptococcus Agalactiae ◽  
Specific Primer ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Milk Samples ◽  
Bacteriological Testing ◽  
Polymerase Chain ◽  
Pcr Test

This study was conducted for exam 348 milk samples from (clinically mastitic and other healthy cows) in many areas in AL-Diwanyia province by using CMT and bacteriological testing , which appeared that (64.9%) as percentage of mastitis ( clinically 15.9% , subclinically 84.0% ) Streptococcus agalactiae mastitis 13.2% ( 26.6% clinically , 73.3 % subclinicaly) diagnose by PCR assay by using specific primer (16SrRNA). Streptococcus agalactiae (30 isolates) after classical methods applied for streptococcus agalactiae identification (86 isolates).

scholarly journals Evaluating the bacterial culture technique by Polymerase chain reaction for the diagnosis of Brucella abortus in milk of cows suspected with brucellosis.

2016 ◽  
Vol 40 (1) ◽  
pp. 5-8
Author(s):  
Bashar Sadeq Noomy
Keyword(s):  
Polymerase Chain Reaction ◽  
Brucella Abortus ◽  
Bacterial Culture ◽  
Culture Technique ◽  
Test Results ◽  
Chain Reaction ◽  
Culture Techniques ◽  
Milk Samples ◽  
Polymerase Chain ◽  
Pcr Test

      The aim of this study is to determine the sensitivity of bacterial culture technique in the detection of Brucella abortus in milk samples of aborted cows. Sixty samples of milk were collected from aborted cows during a period which did not exceed two months after the abortion. All of them were positive for rose bengal test. Results showed that Brucella abortus was isolated from 7 out of 60 (11.6%) from the milk of aborted cows, while PCR test showed that 32 out of 60 (53.3%) milk sample contained Brucella abortus. The specificity of culture techniques was 10%, but its sensitivity was only 21.8%. Beside the cautions in dealing with live Brucella abortus (as culture), it is also less sensitive than PCR, though it is better to use PCR technique in the diagnosis of brucellosis in aborted cows milk.

scholarly journals What Is the Predictive Value of a Single Nasopharyngeal SARS-CoV-2 PCR Swab Test in a Patient With COVID-Like Symptoms and/or Significant COVID-19 Exposure?

2020 ◽  
Vol 7 (10) ◽  
Author(s):  
Blessen George ◽  
James McGee ◽  
Eileen Giangrasso ◽  
Sheila Finkelstein ◽  
Susan Wu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Severe Acute Respiratory Syndrome ◽  
Predictive Value ◽  
Hospital Workers ◽  
Chain Reaction ◽  
Pcr Screening ◽  
Test Characteristics ◽  
Antibody Titers ◽  
Polymerase Chain ◽  
Pcr Test

Abstract Utilizing results of polymerase chain reaction (PCR) testing and subsequent antibody titers, we report on the test characteristics of a PCR screening test for severe acute respiratory syndrome coronavirus 2 among hospital workers. The PCR test was found to be 87% sensitive and 97% specific, with a positive predictive value of 0.98 and a negative predictive value of 0.80.

scholarly journals Performance of a Commercial Polymerase Chain Reaction Test for EndocervicalChlamydia trachomatisInfection in a University Hospital Population

1998 ◽  
Vol 6 (5) ◽  
pp. 224-229
Author(s):  
C. H. Livengood III ◽  
K. A. Boggess ◽  
J. W. Wrenn ◽  
A. P. Murtha
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Test ◽  
Laboratory Evaluation ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Predictive Values ◽  
Target Dna ◽  
Wide Range ◽  
Polymerase Chain ◽  
Pcr Test

Objectives:To examine the accuracy of a commercial polymerase chain reaction (PCR) test (Amplicor CTR, Roche Diagnostic Systems, Branchburg NJ) for identification of endocervical chlamydial infections through both laboratory evaluation and among a diverse teaching hospital patient population.Methods:Testing of reliable threshold inocula and reproducibility were carried out using laboratory stock organisms. Paired endocervical samples from patients with a wide range of indications were tested by PCR and an established culture procedure, and discrepant pairs were further analyzed to determine true results.Results:Laboratory evaluation suggested that one copy of target DNA from a viable organism consistently yielded a positive result, and test reproducibility was very good, with an overall coefficient of variation of 15%. Compared to true results in 1,588 paired clinical samples from 1,489 women with a 10% prevalence of infection, the PCR test and culture yielded respective sensitivities of 87.4% and 78.0%, and negative predictive values of 98.6% and 97.6%. Specificity and positive predictive value for both tests were 100%. Cost per specimen was nearly identical at $18.84 and $18.88 respectively. Polymerase inhibitors and organisms lacking target DNA were not found in false-negative PCR samples.Conclusion:This commercial PCR test is accurate, cost-competitive, and much faster than culture for diagnosis of endocervical chlamydia infections in our population of intermediate prevalence of chlamydial infection.

scholarly journals Viral RNA Shedding and Transmission Potential of Asymptomatic and Pauci-symptomatic COVID-19 Patients

2020 ◽  
Author(s):  
Arghadip Samaddar ◽  
Ravisekhar Gadepalli ◽  
Vijaya Lakshmi Nag ◽  
Sanjeev Misra ◽  
Pankaj Bhardwaj ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Viral Rna ◽  
Exhaled Breath ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Transmission Potential ◽  
Polymerase Chain ◽  
Pcr Test

Abstract We studied the pattern and duration of viral RNA shedding in 32 asymptomatic and 11 pauci-symptomatic coronavirus disease 2019 (COVID-19) cases. Viral RNA shedding in exhaled breath progressively diminished and became negative after six days of a positive reverse transcription polymerase chain reaction (RT-PCR) test. Therefore, the duration of isolation can be minimised to six days.

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