scholarly journals Amplification of human β‐glucuronidase gene for appraising the accuracy of negative SARS‐CoV‐2 RT‐PCR results in upper respiratory tract specimens

2020 ◽  
Vol 93 (1) ◽  
pp. 48-50 ◽  
Author(s):  
Eliseo Albert ◽  
Blanca Ferrer ◽  
Ignacio Torres ◽  
Alicia Serrano ◽  
María J. Alcaraz ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Upper Respiratory

scholarly journals Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study

2020 ◽  
Author(s):  
Islam Hamed ◽  
Nesreen Shaban ◽  
Marwan Nassar ◽  
Sam Love ◽  
Martin D Curran ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Limit Of Detection ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Multi Centre Study ◽  
Upper Respiratory

Introduction Samples for diagnostic tests for SARS-CoV-2 can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum or tracheal aspirate or broncho-alveolar lavage - BAL). Data from different testing sites indicates different rates of positivity. Reverse-transcriptase polymerase chain reaction (RT-PCR) allows for semi-quantitative estimates of viral load as time to crossing threshold (Ct) is inversely related to viral load. Objectives The objective of our study was to evaluate SARS-CoV2 RNA loads between paired nasopharyngeal (NP) and deep lung (endotracheal aspirate or BAL) samples from critically ill patients. Methods SARS-CoV-2 RT-PCR results were retrospectively reviewed for 51 critically ill patients from 5 intensive care units in 3 hospitals ; Addenbrookes Hospital Cambridge (3 units), Royal Papworth Cambridge (1 unit), and Royal Sunderland Hospital (1 unit). At the times when paired NP and deep lung samples were obtained, one patient had been on oxygen only, 6 patients on non-invasive ventilation, 18 patients on ECMO, and 26 patients mechanically ventilated. Results Results collected showed significant gradient between NP and deep lung viral loads. Median Ct value was 29 for NP samples and 24 for deep lung samples. Of 51 paired samples, 16 were negative (below limit of detection) on NP swabs but positive (above limit of detection) on deep lung sample, whilst 2 were negative on deep sample but positive on NP (both patients were on ECMO). Conclusions It has been suggested that whilst SARS-CoV1 tends to replicate in the lower respiratory tract, SARS-CoV2 replicates more vigorously in the upper respiratory tract. These data challenge that assumption. These data suggest that viral migration to, and proliferation in, the lower respiratory tract may be a key factor in the progression to critical illness and the development of severe acute respiratory syndrome (SARS). Factors which promote this migration should be examined for association with severe COVID-19. From a practical point of view, patients with suspected severe COVID-19 should have virological samples obtained from the lower respiratory tract where-ever possible, as upper respiratory samples have a significant negative rate.

scholarly journals The clinical sensitivity of a single SARS-CoV-2 upper respiratory tract RT-PCR test for diagnosing COVID-19 using convalescent antibody as a comparator

2020 ◽  
Vol 20 (6) ◽  
pp. e209-e211 ◽  
Author(s):  
Abigail Holborow ◽  
Hibo Asad ◽  
Lavinia Porter ◽  
Poppy Tidswell ◽  
Claire Johnston ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Clinical Sensitivity ◽  
Upper Respiratory ◽  
Pcr Test

scholarly journals SARS-CoV-2 Detection in Fecal Sample from a Patient with Typical Findings of COVID-19 Pneumonia on CT but Negative to Multiple SARS-CoV-2 RT-PCR Tests on Oropharyngeal and Nasopharyngeal Swab Samples

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 290
Author(s):  
Barbara Brogna ◽  
Carlo Brogna ◽  
Mauro Petrillo ◽  
Adriana Modestina Conte ◽  
Giulio Benincasa ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Clinical Symptoms ◽  
Nasopharyngeal Swab ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Negative Results ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
Pcr Test

Reverse transcriptase polymerase chain reaction (RT-PCR) negative results in the upper respiratory tract represent a major concern for the clinical management of coronavirus disease 2019 (COVID-19) patients. Herein, we report the case of a 43-years-old man with a strong clinical suspicion of COVID-19, who resulted in being negative to multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR tests performed on different oropharyngeal and nasopharyngeal swabs, despite serology having confirmed the presence of SARS-CoV-2 IgM. The patient underwent a chest computed tomography (CT) that showed typical imaging findings of COVID-19 pneumonia. The presence of viral SARS-CoV-2 was confirmed only by performing a SARS-CoV-2 RT-PCR test on stool. Performing of SARS-CoV-2 RT-PCR test on fecal samples can be a rapid and useful approach to confirm COVID-19 diagnosis in cases where there is an apparent discrepancy between COVID-19 clinical symptoms coupled with chest CT and SARS-CoV-2 RT-PCR tests’ results on samples from the upper respiratory tract.

scholarly journals Viral load in upper respiratory tract of COVID-19 patients detected by digital PCR

2020 ◽  
Author(s):  
Jiankang Zhao ◽  
Haibo Li ◽  
Hui Li ◽  
Qiaoling Wu ◽  
Ke Wu ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Digital Pcr ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Lung Lesions ◽  
Viral Loads ◽  
Ct Value ◽  
Upper Respiratory ◽  
Close Contacts

Abstract Background: Upper respiratory tract specimens are widely applicable for the diagnosis of COVID-19. To date, no study has analyzed the actual viral loads in upper respiratory tract and its relationship with the severity of lung lesions, Ct value of RT-PCR and transmission capacity in COVID-19 patients.Methods: We retrospectively enrolled nine COVID-19 patients. Clinical data and close contacts of these patients were investigated. Respiratory samples were tested for SARS-CoV-2 with both normal RT-PCR and droplet digital PCR.Results: All the COVID-19 patients complicated with pneumonia. Viral loads in nasopharyngeal swabs were accurately quantified, and they had no direct correspondence with the severity of lung lesions. The Cycle Threshold (Ct) value of RT-PCR was approximately consistent with the absolute quantification of digital PCR. The spearman correlation coefficient between them was -0.952 with P value < 0.001. Close contacts of patients with very low viral load or no detected virus were not infected.Conclusions: Viral loads in nasopharyngeal swabs, could not predict the severity of lung lesions revealed by CT in COVID-19 patients. The infectious capacity of patients with low or absent viral load in upper respiratory tract was relatively weak, and wearing mask might be helpful for lower its spread.

scholarly journals Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020

2020 ◽  
Vol 25 (32) ◽  
Author(s):  
Anika Singanayagam ◽  
Monika Patel ◽  
Andre Charlett ◽  
Jamie Lopez Bernal ◽  
Vanessa Saliba ◽  
...  
Keyword(s):  
Viral Load ◽  
Severe Acute Respiratory Syndrome ◽  
Respiratory Tract ◽  
Symptom Onset ◽  
Infectious Virus ◽  
Upper Respiratory Tract ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Upper Respiratory

Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus.

scholarly journals Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study

2020 ◽  
Author(s):  
Thomas C Williams ◽  
Elizabeth Wastnedge ◽  
Gina McAllister ◽  
Ramya Bhatia ◽  
Kate Cuschieri ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Clinical Diagnosis ◽  
Gold Standard ◽  
Upper Respiratory Tract ◽  
Repeated Testing ◽  
Rt Pcr ◽  
Hospitalised Patients ◽  
Human Rnase ◽  
Increased Sensitivity ◽  
Upper Respiratory

ABSTRACTObjectivesTo determine the sensitivity and specificity of RT-PCR testing of upper respiratory tract (URT) samples from hospitalised patients with COVID-19, compared to the gold standard of a clinical diagnosis.MethodsAll URT RT-PCR testing for SARS-CoV-2 in NHS Lothian, Scotland, United Kingdom between the 7th of February and 19th April 2020 (inclusive) was reviewed, and hospitalised patients were identified. All URT RT-PCR tests were analysed for each patient to determine the sequence of negative and positive results. For those who were tested twice or more but never received a positive result, case records were reviewed, and a clinical diagnosis of COVID-19 allocated based on clinical features, discharge diagnosis, and radiology and haematology results. For those who had negative URT RT-PCR tests but a clinical diagnosis of COVID-19, respiratory samples were retested using a multiplex respiratory panel, a second SARS-CoV-2 RT-PCR assay, and a human RNase P control.ResultsCompared to the gold standard of a clinical diagnosis of COVID-19, the sensitivity of an initial URT RT-PCR for COVID-19 was 82.2% (95% confidence interval 79.0-85.1%). Two consecutive URT RT-PCR tests increased sensitivity to 90.6% (CI 88.0-92.7%). A further 2.2% and 0.9% of patients who received a clinical diagnosis of COVID-19 were positive on a third and fourth test.ConclusionsThe sensitivity of a single RT-PCR test of an URT sample in hospitalised patients is 82.2%. Sensitivity increases to 90.6% when patients are tested twice. A proportion of cases with clinically defined COVID-19 never test positive on URT RT-PCR despite repeated testing.

scholarly journals Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Wendy A. Szymczak ◽  
D. Yitzchak Goldstein ◽  
Erika P. Orner ◽  
Roger A. Fecher ◽  
Raquel T. Yokoda ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Gastrointestinal Symptoms ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Additional Source ◽  
Percent Agreement ◽  
Stool Specimens ◽  
Upper Respiratory ◽  
Group 2 ◽  
Acceptable Agreement

ABSTRACT The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either were nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% confidence interval [CI]: 81.1% to 98.2%), and negative percent agreement was 96% (95% CI: 89% to 0.99%). Four discrepant specimens (Cepheid positive only, n = 2; Hologic positive only, n = 2) exhibited average cycle threshold (CT) values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR-positive, nasopharyngeal/oropharyngeal PCR-negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract.

scholarly journals Amplification of human β-glucoronidase gene for appraising the accuracy of negative SARS-CoV-2 RT-PCR results in upper respiratory tract specimens

2020 ◽  
Author(s):  
Eliseo Albert ◽  
Blanca Ferrer ◽  
Ignacio Torres ◽  
Alicia Serrano ◽  
Maria Jesus Alcaraz ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Operating Characteristic ◽  
False Negative ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Roc Curve Analysis ◽  
True Negative ◽  
Negative Results ◽  
Upper Respiratory ◽  
Polymerase Chain

Real-time reverse transcription polymerase-chain reaction (RT-PCR) is the mainstay of Covid-19 diagnosis. False-negative RT-PCR results may hamper clinical management of patients and hinder the adoption of epidemiological measures to control the pandemic. The current study was aimed at assessing whether amplification of β-glucoronidase (GUSB) gene would help estimate the accuracy of SARS-CoV-2 RT-PCR negative results in upper respiratory tract (URT) specimens. URT specimens that tested negative by SARS-CoV-2 RT-PCR displayed higher GUSB RT-PCR cycle thresholds (CT) (P=0.070) than those testing positive (median, 30.7; range, 27.0-40.0, and median 29.7; range 25.5-36.8, respectively), this reflecting poorer cellularity. Receiver operating characteristic (roc) curve analysis indicated that a CT threshold of 31.2 discriminated best between positive and negative SARS CoV-2 RT-PCRs (area under a curve, 0.66; 95% CI, 0.50-0.81; P=0.08). This cut-off yielded a true negative ratio of 89% and accuracy of 70%. The data suggested that amplification of the GUSB gene by RT-PCR may help to appraise the accuracy of negative SARS-CoV-2 RT-PCR results in patients in whom Covid-19 is eventually diagnosed.

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