scholarly journals Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy

2021 ◽  
Author(s):  
Ron M Kagan ◽  
Amy A Rogers ◽  
Gwynngelle A Borillo ◽  
Nigel J Clarke ◽  
Elizabeth M Marlowe
Keyword(s):  
Return To Work ◽  
Screening Program ◽  
False Negative ◽  
N Gene ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Specimen Collection ◽  
Asymptomatic Patients ◽  
Nasal Swabs ◽  
The Impact

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

scholarly journals Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Gwynngelle A Borillo ◽  
Ron M Kagan ◽  
Russell E Baumann ◽  
Boris M Fainstein ◽  
Lamela Umaru ◽  
...  
Keyword(s):  
Real Time ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Negative Results ◽  
Single Positive ◽  
Upper Respiratory ◽  
Respiratory Specimens

Abstract Background Nucleic acid amplification testing is a critical tool for addressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Specimen pooling can increase throughput and conserve testing resources but requires validation to ensure that reduced sensitivity does not increase the false-negative rate. We evaluated the performance of a real-time reverse transcription polymerase chain reaction (RT-PCR) test authorized by the US Food and Drug Administration (FDA) for emergency use for pooled testing of upper respiratory specimens. Methods Positive specimens were selected from 3 prevalence groups, 1%–3%, >3%–6%, and >6%–10%. Positive percent agreement (PPA) was assessed by pooling single-positive specimens with 3 negative specimens; performance was assessed using Passing-Bablok regression. Additionally, we assessed the distributions of RT-PCR cycle threshold (Ct) values for 3091 positive specimens. Results PPA was 100% for the 101 pooled specimens. There was a linear relationship between Ct values for pooled and single-tested specimens (r = 0.96–0.99; slope ≈ 1). The mean pooled Ct shifts at 40 cycles were 2.38 and 1.90, respectively, for the N1 and N3 targets. The median Cts for 3091 positive specimens were 25.9 (N1) and 24.7 (N3). The percentage of positive specimens with Cts between 40 and the shifted Ct was 1.42% (N1) and 0.0% (N3). Conclusions Pooled and individual testing of specimens positive for SARS-CoV-2 demonstrated 100% agreement, which demonstrates the viability of pooled specimens for SARS-COV-2 testing using a dual-target RT-PCR system. Pooled specimen testing can help increase testing capacity for SARS-CoV-2 with a low risk of false-negative results.

scholarly journals Real-Time Polymerase chain reaction trends in COVID-19 patients

2020 ◽  
Vol 37 (1) ◽  
Author(s):  
Dr Sana Abbas ◽  
Aisha Rafique ◽  
Dr Beenish Abbas ◽  
Dr Rashid Iqbal
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Tertiary Care ◽  
False Negative ◽  
Polymerase Chain Reaction Test ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Asymptomatic Patients ◽  
Polymerase Chain

Objective: To assess trends of real-time Polymerase Chain Reaction test in Coronavirus infected Patients. Methods: This cross-sectional analytical study was conducted at Tertiary Care Institute, Rawalpindi from March 2020 to June 2020. All patients confirmed COVID positive by real-time Polymerase Chain Reaction (PCR) with recent travel history, close contact with known diagnosed patients and had symptoms of fever or upper respiratory tract with body aches. Nasopharyngeal swabs were taken and results generated within 48 hours. Positive PCR was admission criteria follow up was carried out at 7th and 8th day, with negative PCR were discharged. However, those who had persistent positive PCR on the 8th day were tested again on 11th and 12th day. Those with persistent positive results beyond 12th day were shifted to specialized quarantine centres. Results: A total of three hundred and ninety-two patients with mild to moderate illness, PCR positive for COVID 19 were included study with age range 9 - 45 and mean 33.22±7.98 years. A total of 8 (2%) patients were females and 384(98%) males. The duration of the negative test result was Mean ± Std. Deviation 9.05±2.00 with 7 – 8 days 152(38.8%)in and 11 – 12 days in 160(40.8%). PCR results on Day 7 and 8 were negative in 144(36.7%) patients whereas positive in 248(63.3%). PCR results on Day 11 and 12 were negative in 312(79.6%) patients whereas positive in 80 (20.4%). Conclusion: To conclude Real-Time Polymerase Chain Reaction (rT-PCR) inclines to give false negative results additionally can stay positive in asymptomatic patients for moderately longer-term. Hence decision to discharge ought to be intricately adjusted between RT-PCR, clinical judgement, radiological examinations, and biochemical assays. doi: https://doi.org/10.12669/pjms.37.1.3000 How to cite this:Abbas S, Rafique A, Abbas B, Iqbal R. Real-Time Polymerase chain reaction trends in COVID-19 patients. Pak J Med Sci. 2021;37(1):180-184. doi: https://doi.org/10.12669/pjms.37.1.3000 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

scholarly journals Outcome of COVID-19 with Co-Existing Surgical Emergencies in Children: Our Initial Experiences and Recommendations

2020 ◽  
Author(s):  
Samiul Hasan ◽  
Md Ayub Ali ◽  
Umama Huq
Keyword(s):  
Health Care ◽  
Health Care Workers ◽  
Hypertrophic Pyloric Stenosis ◽  
Laboratory Data ◽  
Ethical Review ◽  
Infantile Hypertrophic Pyloric Stenosis ◽  
Rt Pcr ◽  
Asymptomatic Patients ◽  
Care Workers ◽  
The Impact

Abstract Background: COVID-19 has changed the practice of surgery vividly all over the world. This has already lead to a huge burden of rescheduled pediatric surgical cases worldwide. Though children are less likely to be infected and suffer less when infected, there is a growing fear among health care workers of being self-infected, which is limiting the surgical care of children globally. This study aims to share our experiences with the outcome of COVID-19 in children who had a co-existing surgical emergency, which might help the pediatric surgeons globally to mitigate the effect of COVID 19 on pediatric surgery.Methods: This is a retrospective observational study. We reviewed the epidemiological, clinical, and laboratory data of all patients admitted in our surgery department through the emergency department and later diagnosed to have COVID-19 by RT-PCR. During April 2020 – June 2020. A nasopharyngeal swab was taken from all patients irrespective of symptoms to detect SARS CoV 2 by RT-PCR to identify and isolate asymptomatic patients and patients with atypical symptoms. We divided the test positive patients into 4 age groups for the convenience of data analysis. Data were retrieved from hospital records and analyzed using SPSS (version 25) software. Ethical permission was taken from the hospital ethical review board.Results: Total patients were 32. Seven (21.9%) of them were neonates. Twenty-four (75%) patients were male. The predominant diagnosis was acute abdomen followed by infantile hypertrophic pyloric stenosis (IHPS), myelomeningocele, and intussusception. Only two patients had mild respiratory symptoms (dry cough). Fever was present in 13 (40.6%) patients. Fourteen (43.8%) patients required surgical treatment. The mean duration of hospital stay was 5.5 days. One neonate with ARM died in the post-operative ward due to cardiac arrest. No patient had hypoxemia or organ failure. Seven health care workers (5.51%) including doctors & nurses got infected with SARS Co V2 during this period.Conclusion: Our study has revealed a milder course of COVID-19 in children with minimal infectivity even when present in association with emergency surgical conditions. This might encourage a gradual restart to mitigate the impact of COVID-19 on children’s surgery.

scholarly journals Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

2020 ◽  
Vol 71 (15) ◽  
pp. 793-798 ◽  
Author(s):  
Fengting Yu ◽  
Liting Yan ◽  
Nan Wang ◽  
Siyuan Yang ◽  
Linghang Wang ◽  
...  
Keyword(s):  
Viral Load ◽  
Target Genes ◽  
Single Gene ◽  
Clinical Staging ◽  
N Gene ◽  
Quantitative Detection ◽  
Imaging Data ◽  
Rt Pcr ◽  
Viral Loads ◽  
Nasal Swabs

Abstract Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 323 samples from 76 COVID-19–confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based 2 target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. Results In 95 samples that tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy number of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). Four (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral loads ranging from 11.1 to 123.2 copies/test. The viral load of respiratory samples was then compared and the average viral load in sputum (17 429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, P < .001) and nasal swabs (651 ± 501 copies/test, P < .001). Furthermore, the viral loads in the early and progressive stages were significantly higher than that in the recovery stage (46 800 ± 17 272 vs 1252 ± 1027, P < .001) analyzed by sputum samples. Conclusions Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.

scholarly journals Nasopharyngeal Panbio COVID-19 antigen performed at point-of-care has a high sensitivity in symptomatic and asymptomatic patients with higher risk for transmission and older age

2021 ◽  
Author(s):  
Mar Masiá ◽  
Marta Fernández-González ◽  
Manuel Sánchez ◽  
Mar Carvajal ◽  
José Alberto García ◽  
...  
Keyword(s):  
Test Performance ◽  
Point Of Care ◽  
Rapid Test ◽  
High Sensitivity ◽  
Older Age ◽  
Antigen Test ◽  
Rt Pcr ◽  
Asymptomatic Patients ◽  
Clinical Scenarios ◽  
Nasal Swabs

Abstract Background Performance of point-of-care tests in different clinical scenarios and on different samples remains undetermined. We comprehensively evaluated the performance of the nasopharyngeal Panbio COVID-19 antigen Rapid-Test-Device. Method Prospective study including consecutive patients attending three primary care centers (PCC) and an emergency department. The antigen test was performed at point-of-care in nasopharyngeal and nasal swabs, and in saliva. Positive and negative percent agreement (PPA, NPA) were calculated with the RT-PCR assay as reference standard. Results Of 913 patients included, 296 (32.3%) were asymptomatic and 690 (75.6%) came from the PCC. Nasopharyngeal swabs were collected from 913, nasal swabs from 659, and saliva from 611 patients. RT-PCR was positive in 196 (21.5%) nasopharyngeal samples (NPS). Overall PPA (95% CI) in NPS was 60.5% (53.3-67.4), and it was lower in nasal swabs (44.7%) and saliva (23.1%). Test performance in NPS was largely dependent on the cycle threshold (Ct) in RT-PCR, with PPA of 94% for Ct≤25 and 80% for Ct<30. In symptomatic patients, the PPA was 95% for Ct≤25; 85% for Ct<30, and 89% for the symptom triad of fever, cough and malaise. Performance was also dependent on age, with PPA of 100% in symptomatic patients >50 years with Ct<25. In asymptomatic patients, the PPA was 86% for Ct<25. In all cases, NPA was 100%. Conclusion The nasopharyngeal Panbio COVID-19 antigen test performed at point-of-care has a good sensitivity in symptomatic patients with Ct<30 and older age. The test was useful to identify asymptomatic patients with lower Ct values.

scholarly journals Asymptomatic screening of SARS-CoV-2 (COVID-19) virus RNA using reverse transcriptase loop-mediated isothermal amplification (RT-LAMP)

2021 ◽  
Author(s):  
Rebecca Allsopp ◽  
Caroline Cowley ◽  
Ruth Barber ◽  
Carolyn Jones ◽  
Christopher Holmes ◽  
...  
Keyword(s):  
Diagnostic Performance ◽  
Screening Program ◽  
False Negative ◽  
Rna Extraction ◽  
Lamp Assay ◽  
Molecular Diagnostic ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Clinical Patient ◽  
The University

Abstract This study demonstrates the diagnostic performance of SARS-CoV-2 RT-LAMP assays, comparing the performance of genomic versus sub-genomic sequence target with subsequent application in an asymptomatic screening population. An RT-LAMP workflow was developed using synthetic positive control RNA and the diagnostic sensitivity and specificity was then determined using clinical patient samples processed through the diagnostic RT-PCR service within the University Hospitals of Leicester NHS Trust. 92 RT-PCR clinically positive and 88 RT-PCR clinically negative swab samples along with 78 clinically positive and 63 clinically negative saliva samples were equally detected at 100% DSe and 100% DSp for all samples reporting a Ct < 20. DSe for all samples reporting a Ct < 30 reduced slightly to around 95% (100% DSp) for both the single genomic (large open reading frame; orf1a) and dual sub-genomic (nucleocapsid plus envelope) targeting RT-LAMP assays. Lastly, the diagnostic performance of a saliva direct workflow was only about 50% that of the saliva RNA extraction workflow. Subsequently, a swab based RNA -RT-LAMP assay was implemented to ISO 15189:2012 standards supporting an advisory COVID-19 screening program for staff and students at the University of Leicester between October and December 2020. Within a 24-hour period, total nucleic acid extraction was followed by genomic target RT-LAMP plus an internal total RNA control to mitigate the possibility of false negative reporting. SARS-CoV-2 RT-LAMP positive samples were confirmed by an RT-PCR test in an NHS diagnostic laboratory and results were included within national statistics. Nine confirmed positive samples were detected in 1680 symptom free individuals (equivalent to 540 cases per 100,000) thus demonstrating the utility of RT-LAMP molecular diagnostic tool for the detection of SARS-CoV-2 in an asymptomatic population.

scholarly journals In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness

2021 ◽  
Vol 118 (49) ◽  
pp. e2111477118
Author(s):  
Ruian Ke ◽  
Carolin Zitzmann ◽  
David D. Ho ◽  
Ruy M. Ribeiro ◽  
Alan S. Perelson
Keyword(s):  
Dynamic Models ◽  
False Negative ◽  
Reproductive Number ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Viral Kinetics ◽  
Antigen Tests ◽  
The Impact ◽  
Kinetics Of

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person’s infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person’s infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

scholarly journals Nasopharyngeal Panbio COVID-19 antigen performed at point-of-care has a high sensitivity in symptomatic and asymptomatic patients with higher risk for transmission and older age

2020 ◽  
Author(s):  
Mar Masiá ◽  
Marta Fernández-González ◽  
Manuel Sánchez ◽  
Mar Carvajal ◽  
José Alberto García ◽  
...  
Keyword(s):  
Point Of Care ◽  
Real Life ◽  
Older Age ◽  
Antigen Test ◽  
Rt Pcr ◽  
Life Conditions ◽  
Asymptomatic Patients ◽  
Clinical Scenarios ◽  
Highly Sensitive ◽  
Nasal Swabs

ABSTRACTBackgroundPerformance of point-of-care tests in clinical practice remains undetermined. We aimed to evaluate the performance of the nasopharyngeal Panbio COVID-19 antigen Rapid Test Device in real-life conditions in different clinical scenarios.MethodProspective study conducted in three primary care centers (PCC) and an emergency department. The antigen test was performed at point-of-care in nasopharyngeal and nasal swabs, and in saliva. Positive and negative percent agreement (PPA, NPA) were calculated with the RT-PCR assay as reference standard.ResultsOf 913 patients included, 296 (32.3%) were asymptomatic and 690 (75.6%) came from the PCC. Nasopharyngeal swabs were collected from 913, nasal swabs from 659, and saliva from 611 patients. RT-PCR was positive in 196 (21.5%) nasopharyngeal samples (NPS). Overall PPA (95% CI) in NPS was 60.5% (53.3-67.4), and it was lower in nasal swabs (44.7%) and saliva (23.1%). Test performance in NPS was largely dependent on the cycle threshold (Ct) in RT-PCR, with PPA>90% for Ct≤25 and ≥80% for Ct<30. In symptomatic patients, the PPA was 95% for Ct≤25; ≥85% for Ct<30, and 89% for the symptom triad of fever, cough and malaise. Performance was also dependent on age, with PPA of 100% in symptomatic patients >50 years with Ct<25. In asymptomatic patients, the PPA was 86% for Ct<25. In all cases, NPA was 100%.ConclusionThe nasopharyngeal Panbio COVID-19 antigen test performed at point-of-care is highly sensitive in symptomatic patients, particularly with Ct<30 and older age. The test was useful to identify asymptomatic patients with lower Ct values and therefore with contagious risk.Key pointsThe nasopharyngeal Panbio-COVID-19 antigen test performed in real-life conditions at point-of-care is highly sensitive in symptomatic patients, particularly with Ct<30 and older age. The test is useful to identify asymptomatic patients with lower Ct values and therefore with contagious risk.

scholarly journals Impact of Pool Testing in Detection of Asymptomatic Patients with COVID-19

2020 ◽  
Vol 52 (1) ◽  
pp. e15-e16 ◽  
Author(s):  
David L Smalley ◽  
Patricia M Cisarik ◽  
James Grantham ◽  
William Cloud ◽  
R Brock Neil ◽  
...  
Keyword(s):  
Single Patient ◽  
Rt Pcr ◽  
Detection Capability ◽  
Chain Reaction ◽  
Asymptomatic Patients ◽  
Alternative Approaches ◽  
Polymerase Chain ◽  
Asymptomatic Individuals ◽  
Low Prevalence ◽  
The Impact

Abstract Objective During the current pandemic, COVID-19 has been detected in patients using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) that confirms the presence of SARS-CoV-2 RNA. The demand for increased testing, particularly for asymptomatic individuals required alternative approaches to single-patient RT-PCR testing, such as pooling. Methods This study explored the impact of dilution on the detectability of SARS-CoV-2 in asymptomatic patients using RT-PCR and demonstrated that pooling can be effective in low prevalence populations. Results The RT-PCR results for the 3:1, 5:1, and 7:1 aliquot samples showed little differences in CT values, confirming detection capability at these dilutions. Conclusion Based on the results of the present study, a pooled approach with up to 5:1 sample aliquots and using the current RT-PCR methodology likely will detect SARS CoV2 RNA among asymptomatic patients.

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