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

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.

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

Wellcome Open Research ◽

10.12688/wellcomeopenres.16342.1 ◽

2020 ◽

Vol 5 ◽

pp. 254

Author(s):

Thomas C. Williams ◽

Elizabeth Wastnedge ◽

Gina McAllister ◽

Ramya Bhatia ◽

Kate Cuschieri ◽

...

Keyword(s):

Respiratory Tract ◽

Clinical Diagnosis ◽

Gold Standard ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Reverse Transcription Pcr ◽

Hospitalised Patients ◽

Increased Sensitivity ◽

Upper Respiratory ◽

Pcr Test

Background: This study aimed to determine the sensitivity and specificity of reverse transcription PCR (RT-PCR) testing of upper respiratory tract (URT) samples from hospitalised patients with coronavirus disease 2019 (COVID-19), compared to the gold standard of a clinical diagnosis. Methods: All URT RT-PCR testing for severe acute respiratory syndrome coronavirus-2 (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 a negative RT-PCR test 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. Results: Compared to the gold standard of a clinical diagnosis of COVID-19, the sensitivity of a single upper respiratory tract RT-PCR for COVID-19 was 82.2% (95% confidence interval 79.0-85.1%). The sensitivity of two upper respiratory tract 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; this may be an underestimate of the value of further testing as the majority of patients 93.0% (2999/3226) only had one or two URT RT-PCR tests. Conclusions: The sensitivity of a single RT-PCR test of URT samples 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 repeat testing.

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

10.1101/2020.07.19.20156869 ◽

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.

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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

Clinical Medicine ◽

10.7861/clinmed.2020-0555 ◽

2020 ◽

Vol 20 (6) ◽

pp. e209-e211 ◽

Cited By ~ 3

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

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The upper respiratory tract microbiome of hospitalised patients with community-acquired pneumonia of unknown aetiology: a pilot study

Pneumonia ◽

10.15172/pneu.2015.6/682 ◽

2015 ◽

Vol 6 (1) ◽

pp. 83-89

Author(s):

Timothy L. Wiemken ◽

Venkatakrishna Rao Jala ◽

Robert R. Kelley ◽

Paula Peyrani ◽

William A. Mattingly ◽

...

Keyword(s):

Pilot Study ◽

Respiratory Tract ◽

Community Acquired Pneumonia ◽

Upper Respiratory Tract ◽

Unknown Aetiology ◽

Hospitalised Patients ◽

Upper Respiratory

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Common upper respiratory tract problems in the elderly—A guide to clinical diagnosis and prudent prescription

South African Family Practice ◽

10.1080/20786204.2006.10873390 ◽

2006 ◽

Vol 48 (5) ◽

pp. 20-23 ◽

Cited By ~ 1

Author(s):

L Geffen

Keyword(s):

Respiratory Tract ◽

Clinical Diagnosis ◽

The Elderly ◽

Upper Respiratory Tract ◽

Upper Respiratory

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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 ◽

10.3390/medicina57030290 ◽

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.

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

10.21203/rs.3.rs-29834/v1 ◽

2020 ◽

Cited By ~ 1

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.

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

Eurosurveillance ◽

10.2807/1560-7917.es.2020.25.32.2001483 ◽

2020 ◽

Vol 25 (32) ◽

Cited By ~ 43

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.

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