scholarly journals Performance of Self-Collected Saliva Testing Compared with Nasopharyngeal Swab Testing for the Detection of SARS-CoV-2

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 895
Author(s):  
Florence Carrouel ◽  
Martine Valette ◽  
Hervé Perrier ◽  
Maude Bouscambert-Duchamp ◽  
Claude Dussart ◽  
...  
Keyword(s):  
Viral Load ◽  
Quantitative Pcr ◽  
Statistical Analyses ◽  
Fair Agreement ◽  
Quantitative Detection ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Noninvasive Techniques ◽  
Concordance Probability ◽  
Salivary Test

The aim of this study was to determine whether self-collected pure saliva (SCPS) is comparable to nasopharyngeal (NP) swabs in the quantitative detection of SARS-CoV-2 by RT-PCR in asymptomatic, mild patients with confirmed COVID-19. Thirty-one patients aged from 18 to 85 years were included between 9 June and 11 December 2020. A SCPS sample and a NP sample were taken for each patient. Quantitative PCR was performed to detect SARS-CoV-2 viral load. Results of SCPS vs NP samples testing were compared. Statistical analyses were performed. Viral load was significantly correlated (r = 0.72). The concordance probability was estimated at 73.3%. In symptomatic adults, SCPS performance was similar to that of NP swabs (Percent Agreement = 74.1%; p = 0.11). Thus, the salivary test based on pure oral saliva samples easily obtained by noninvasive techniques has a fair agreement with the nasopharyngeal one in asymptomatic, mild patients with a confirmed diagnosis of COVID-19.

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 A Direct Comparison of Enhanced Saliva to Nasopharyngeal Swab for the Detection of SARS-CoV-2 in Symptomatic Patients

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Gary W. Procop ◽  
Nabin K. Shrestha ◽  
Sherilynn Vogel ◽  
Kelly Van Sickle ◽  
Susan Harrington ◽  
...  
Keyword(s):  
Viral Load ◽  
Final Analysis ◽  
Nasopharyngeal Swab ◽  
Reference Standard ◽  
Rt Pcr ◽  
Viral Transport ◽  
Qualitative Detection ◽  
Diagnostic Panel ◽  
The One ◽  
Positive Agreement

ABSTRACT The ongoing coronavirus disease 2019 (COVID-19) pandemic has resulted in shortages of nasopharyngeal swabs (NPS) and viral transport media, necessitating the search for alternate diagnostic specimens, such as saliva. We directly compared matched saliva and NPS specimens from symptomatic patients suspected of having COVID-19. An enhanced saliva specimen (i.e., strong sniff, elicited cough, and collection of saliva/secretions) was collected without transport medium prior to collection of NPS from 224 patients with symptoms deemed consistent with COVID-19. Both specimens were tested with the CDC 2019 nCoV real-time RT-PCR diagnostic panel (4 February 2020 version), with the NPS result used as the reference standard. For the 216 patients included in the final analysis, there was 100% positive agreement (38/38 positive specimens) and 99.4% negative agreement (177/178 negative specimens). The one discrepant specimen had the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confirmed in the saliva specimen using an alternate FDA EUA assay. The overall mean difference in cycle threshold (CT) values for the positive NPS and saliva specimens was −3.61 (95% confidence interval [CI], −5.78 to −1.44; P = 0.002). An enhanced saliva specimen performed as well as NPS for the qualitative detection of SARS-CoV-2 in symptomatic patients, although the overall mean viral load in saliva was lower.

scholarly journals Development and application of a TaqMan-MGB real-time RT-PCR assay for the detection of porcine epidemic diarrhoea virus strains in China

2016 ◽  
Vol 60 (2) ◽  
pp. 127-133 ◽  
Author(s):  
Yi-Xuan Hou ◽  
Chun Xie ◽  
Kang Wang ◽  
Yu-Ting Zhao ◽  
Yang-Yang Xie ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
N Gene ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Conserved Sequence ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus ◽  
Quantitative Pcr Assay

AbstractIntroduction:A real-time RT-PCR method for identification and quantification of porcine epidemic diarrhoea virus (PEDV) strains in China was developed.Material and Methods:Based on the conserved sequence of the PEDV nucleocapsid (N) gene, a primer pair and probe were designed to establish a TaqMan-MGB real-time RT-PCR assay for quantitative detection of the virus. The sequence was cloned into the pMD18-T vector and a series of diluted recombinant plasmids were used to generate a standard curve with an R2 value of 0.999.Results:The developed quantitative PCR assay detected viral titres as low as 0.1 TCID50with high specificity and no cross-reaction with other porcine viruses (PoRV, TGEV, PRRSV, or CSFV). The intra-batch and inter-batch coefficients of variation were both less than 1%, which indicated good reproducibility. Thirty clinical diarrhoea samples obtained from pigs in Shanghai and Fujian were analysed using this quantitative PCR assay. Out of these samples, 93.3% were found to be PEDV positive.Conclusion:This approach is suitable for clinical sample identification and pathogenesis studies.

scholarly journals Correlation between cycle threshold and viral load through comparison of RT-PCR qualitative versus quantitative assay for SARS-CoV-2

2021 ◽  
Vol 36 (2) ◽  
Author(s):  
Angela Saraiello ◽  
Federica Ferrentino ◽  
Nunzia Cuomo ◽  
Maria Grimaldi ◽  
Erasmo Falco ◽  
...  
Keyword(s):  
Viral Load ◽  
Quantitative Assay ◽  
Quantitative Detection ◽  
Load Testing ◽  
Rt Pcr ◽  
Ct Value ◽  
Viral Load Monitoring ◽  
Load Monitoring ◽  
Qualitative Test ◽  
Qualitative Assay

Background and aims. Real-time reverse transcription polymerase chain reaction (RT-PCR) is the gold-standard assay to detect SARS-CoV-2, but it has limitations compared to viral load analysis. Quantitative detection improves surveillance, diagnosis, and prevention. We performed a comparative study of qualitative and quantitative tests for the diagnosis of COVID-19 on respiratory samples from patients screened for SARS-CoV-2 infection, and explored the correlation between viral load compared to the threshold cycle (Ct) value obtained in RT-PCR.Materials and methods. Sixty respiratory samples from patients affected by SARS-CoV-2 were subjected to both the qualitative (Allplex ™ 2019-nCoV Seegene) and the quantitative (Clonit® Quanty COVID-19) assays, and the relationship between viral load and Ct value was assessed by Spearman correlation analysis (ρ). In addition, the viral load of samples collected from a patient with symptomatic cancer was monitored. Results. The results show 100% agreement between the results obtained with quantitative assay and the reference standards, whereas 99.2% agreement was found for the qualitative test. A strong negative Spearman’s correlation between the Ct values of the N genes and RdRP gene was observed from qualitative assay values and viral loads.Conclusions. Quantitative assay has a higher sensitivity than qualitative assay, and viral load testing allows the clinicians to better orient themself in the choice of therapeutic treatment to be adopted. The constantly higher viral load of clinical cases considered, irrespective of the different therapies used, confirms that viral load monitoring could represent a great advantage in clinical practice.

scholarly journals Clinical evaluation of the Roche/SD Biosensor rapid antigen test with symptomatic, non-hospitalized patients in a municipal health service drive-through testing site

2020 ◽  
Author(s):  
Zsὁfia Iglὁi ◽  
Jans Velzing ◽  
Janko van Beek ◽  
David van de Vijver ◽  
Georgina Aron ◽  
...  
Keyword(s):  
Viral Load ◽  
Rapid Test ◽  
Contact Tracing ◽  
Gene Copy ◽  
Nasopharyngeal Swab ◽  
List Type ◽  
Antigen Test ◽  
Rt Pcr ◽  
Outbreak Management ◽  
Testing Site

AbstractBackgroundRapid detection of infectious individuals is essential in stopping the further spread of SARS-CoV-2. Although rapid antigen test is not as sensitive as the gold standard RT-PCR, the time to result is decreased by day(s), strengthening the effectiveness of contact tracing.MethodsThe Roche/SD Biosensor lateral flow antigen rapid test was evaluated in a mild symptomatic population at a large drive through testing site. A second nasopharyngeal swab was directly tested with the rapid test on site and results were compared to RT-PCR and virus culture. Date of onset and symptoms were analysed using data from a clinical questionnaire.ResultsWe included 970 persons with complete data. Overall sensitivity and specificity were 84.9% (CI95% 79.1-89.4) and 99.5% (CI95% 98.7-99.8) which translated into a positive predictive value of 97.5% (CI95% 94.0-99.5) under the current regional PCR positivity of 19.2%. Sensitivity for people with high loads of viral RNA (ct <30, 2.17E+05 E gene copy/ml) and who presented within 7 days since symptom onset increased to 95.8% (CI95% 90.5-98.2). Band intensity and time to result correlated strongly with viral load thus strong positive bands could be read before the recommended time. Around 98% of all viable specimen with ct <30 were detected successfully indicating that the large majority of infectious people can be captured with this test.ConclusionAntigen rapid tests can detect mildly symptomatic cases in the early phase of disease thereby identifying the most infectious individuals. Using this assay can have a significant value in the speed and effectiveness of SARS-CoV-2 outbreak management.SummaryPeople with early onset and high viral load were detected with 98.2% sensitivity.97% of individuals in which virus could be cultured were detected by the rapid test.This test is suitable to detect mild symptomatic cases.

scholarly journals Multicenter evaluation of the Panbio™ COVID-19 Rapid Antigen-Detection Test for the diagnosis of SARS-CoV-2 infection

2020 ◽  
Author(s):  
Paloma Merino-Amador ◽  
Jesús Guinea ◽  
Irene Muñoz-Gallego ◽  
Patricia González-Donapetry ◽  
Juan-Carlos Galán ◽  
...  
Keyword(s):  
Viral Load ◽  
Clinical Symptoms ◽  
False Negative ◽  
Rapid Test ◽  
Antigen Detection ◽  
Nasopharyngeal Swab ◽  
Diagnostic Strategy ◽  
Rt Pcr ◽  
University Hospitals ◽  
Kappa Score

AbstractThe standard RT-PCR assay for COVID-19 is laborious and time-consuming, limiting the availability of testing. Rapid antigen-detection tests are faster and less expensive; however, the reliability of these tests must be validated before they can be used widely. The objective of this study was to determine the reliability of the PanbioTM COVID-19 Ag Rapid Test Device (PanbioRT) (Abbott) for SARS-CoV-2 in nasopharyngeal swab specimens. This was a prospective multicenter study in ten Spanish university hospitals of patients from hospital units with clinical symptoms or epidemiological criteria for COVID-19. Patients whose onset of symptoms or exposure was more than 7 days earlier were excluded. Two nasopharyngeal exudate samples were taken to perform the PanbioRT and a diagnostic RT-PCR test. Among the 958 patients studied, 359 (37.5%) were positive by RT-PCR and 325 (33.9%) were also positive by the PanbioRT. Agreement was 95.7% (kappa score: 0.90). All 34 false-negative PanbioRT results were in symptomatic patients, with 23.5% of them at 6–7 days since the onset of symptoms and 58.8% presenting CT >30 values for RT-PCR, indicating a low viral load. Overall sensitivity and specificity for the PanbioRT were 90.5% and 98.8%, respectively. The PanbioRT provides good clinical performance as a point-of-care test, with even more reliable results for patients with a shorter clinical course of the disease or a higher viral load. While this study has had a direct impact on the national diagnostic strategy for COVID-19 in Spain, the results must be interpreted based on the local epidemiological context.

MOLECULAR DETECTION OF COVID -19 BY TRUENAT RT-PCR IN A TERTIARY CARE HOSPITAL IN DELHI NCR REGION

2021 ◽  
pp. 20-22
Author(s):  
Alosha Sharma ◽  
Maneesh Goyal ◽  
Ritu Agarwal ◽  
Neha Goel ◽  
Divyaansh Shridhar ◽  
...  
Keyword(s):  
Viral Load ◽  
Tertiary Care Hospital ◽  
Tertiary Care ◽  
Diagnostic Methods ◽  
Therapeutic Interventions ◽  
Nasopharyngeal Swab ◽  
Care Hospital ◽  
Age Group ◽  
Rt Pcr ◽  
Viral Lysis

Introduction: COVID-19 is a severe infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affected lives of millions of people , responsible for millions of death affecting health care systems worldwide seriously. To diagnose Aims and Objectives: COVID -19 infection in a tertiary care hospital using TrueNat RTPCR and to categorise and co - relate various Ct values with viral load. Material and Methods: Oropharyngeal and nasopharyngeal swab specimens were collected from the patients following standard protocols and were inserted into the viral lysis medium tube. Specimen is transferred from viral lysis medium to automatic extracted device for extraction of RNA and then into RT-PCR analyser for reaction to start automatically. Test detects the screening E gene and conrmatory RdRp /Orf1a gene and human RNase P. Of the 1025 patients subjected to COVID - 19- RTPCR 630 (61%) were male Results : s and 395 (39%) were females. 26% (269/1025) of patients were conrmed COVID positive and 72% (747/1025) were negative. Age group 21-30 showed maximum positive cases followed by age group 51-60 years. High viral load was seen in 41% cases whereas maximum no. of conrmed positive had low viral loads. Rapid and Conclusion: accurate diagnostic methods are required for early detection along with precautionary measures for timely therapeutic interventions and prophylaxis to control and prevent the Spread of highly contagious COVID-19.

scholarly journals Estimation of conjunctival swab and nasopharyngeal swab specimens for viral nucleic acid detection in Coronavirus disease 2019 patients to compare the viral load

2021 ◽  
Vol 4 ◽  
pp. 2
Author(s):  
Jaya Kaushik ◽  
Vikas Marwah ◽  
Ankita Singh ◽  
Y. V. K. Chaitanya ◽  
Rajeev Mohan Gupta ◽  
...  
Keyword(s):  
Viral Load ◽  
Nucleic Acid ◽  
Statistical Correlation ◽  
Nucleic Acid Detection ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Viral Nucleic Acid ◽  
Ocular Manifestations ◽  
Conjunctival Swab ◽  
Polymerase Chain

Objectives: The purpose of the study was to detect the presence of viral ribonucleic acid of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in conjunctival swab along with nasopharyngeal swab specimens of Coronavirus disease 2019 (COVID-19) patients. Material and Methods: Thirty COVID-19 patients with at least one sample positive for real-time reverse transcription-polymerase chain reaction for SARS-CoV-2 in nasopharyngeal swab with the presence or absence of ocular manifestations were included in the study. The conjunctival swab along with nasopharyngeal swab of each patient was collected and sent to microbiology lab for evaluation and analysis of viral nucleic acid to assess the viral load. Results: Out of 30 patients, 21 patients (70%) were males and the remaining nine patients (30%) were females. Mean age of the patients in the study was 44.80 ± 15.37 years. One patient had conjunctivitis as ocular manifestation. Two (6.7%) out of 30 patients were positive for RT-PCR SARS-CoV-2 in the conjunctival swab. There was no statistical correlation between nasopharyngeal swab and conjunctival swab positivity using Pearson’s correlation coefficient (r) = 0.010; P = 0.995 (>0.05). Conclusion: The results of the study revealed that SARS-CoV-2 can also be detected in conjunctival swabs of confirmed cases of COVID-19 patients. Although, in comparison to nasopharyngeal and throat swabs the rate of detection of SARS-CoV-2 in conjunctival swabs is relatively less, still diligent care and precautions should be practiced during the ophthalmic evaluation of COVID-19 patients.

scholarly journals Pooled Saliva Specimens for SARS-CoV-2 Testing

2020 ◽  
Author(s):  
Bidisha Barat ◽  
Sanchita Das ◽  
Valeria De Giorgi ◽  
David K. Henderson ◽  
Stacy Kopka ◽  
...  
Keyword(s):  
Viral Load ◽  
Screening Program ◽  
High Viral Load ◽  
Load Cycle ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Viral Loads ◽  
Viral Transport ◽  
Average Loss ◽  
Positive Agreement

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The percent positive agreement increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion®, and Roche COBAS® 6800. The average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

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