Comparison of two commercial molecular tests and a laboratory-developed modification of the CDC 2019-nCOV RT-PCR assay for the qualitative detection of SARS-CoV-2 from upper respiratory tract specimens

ABSTRACTWe compared the ability of 2 commercial molecular amplification assays [RealTime SARS-CoV-2 on the m2000 (Abbott) and ID NOW™ COVID-19 (Abbott)] and a laboratory-developed test [modified CDC 2019-nCoV RT-PCR assay with RNA extraction by eMag® (bioMérieux) and amplification on QuantStudio™ 6 or ABI 7500 Real-Time PCR System (Life Technologies)] to detect SARS-CoV-2 RNA in upper respiratory tract specimens. Discrepant results were adjudicated by medical record review. 200 nasopharyngeal swab specimens in viral transport medium (VTM) were collected from symptomatic patients between March 27 and April 9, 2020. Results were concordant for 167 specimens (83.5% overall agreement), including 94 positive and 73 negative specimens. The RealTime SARS-CoV-2 assay on the m2000 yielded 33 additional positive results, 25 of which were also positive by the modified CDC assay but not by the ID NOW™ COVID-19 assay. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by the ID NOW™ COVID-19 assay had a paired nasopharyngeal swab specimen collected in VTM and tested by the RealTime SARS-CoV-2 assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. Medical record review deemed all discrepant results to be true positives. The ID NOW™ COVID-19 test was the easiest to perform and provided a result in the shortest time: as soon as 5 minutes for positive and 13 minutes for negative result. The RealTime SARS-CoV-2 assay on the m2000 detected more cases of COVID-19 infection than the modified CDC assay or the ID NOW™ COVID-19 test.

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Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2

Journal of Clinical Microbiology ◽

10.1128/jcm.00938-20 ◽

2020 ◽

Vol 58 (8) ◽

Cited By ~ 12

Author(s):

Nicholas M. Moore ◽

Haiying Li ◽

Debra Schejbal ◽

Jennifer Lindsley ◽

Mary K. Hayden

Keyword(s):

Reverse Transcriptase ◽

Medical Record ◽

Medical Record Review ◽

Nasopharyngeal Swab ◽

Upper Respiratory Tract ◽

Pcr Assay ◽

Reverse Transcriptase Pcr ◽

Viral Transport Medium ◽

Record Review ◽

Swab Specimen

ABSTRACT We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. Discrepant results were adjudicated by medical record review. A total of 200 nasopharyngeal swab specimens in viral transport medium (VTM) were collected from symptomatic patients between 27 March and 9 April 2020. Results were concordant for 167 specimens (83.5% overall agreement), including 94 positive and 73 negative specimens. The ACOV assay yielded 33 additional positive results, 25 of which were also positive by the CDC COV assay but not by the IDNOW assay. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. Medical record review deemed all discrepant results to be true positives. The IDNOW test was the easiest to perform and provided a result in the shortest time but detected fewer cases of COVID-19. The ACOV assay detected more cases of COVID-19 than the CDC COV or IDNOW assays.

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A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay

10.1101/2020.09.25.20201541 ◽

2020 ◽

Author(s):

Wiebke Michel ◽

Jacqueline Farber ◽

Milica Dilas ◽

Ina Tammer ◽

Jannik Baar ◽

...

Keyword(s):

Respiratory Tract ◽

Test Performance ◽

Nasopharyngeal Swab ◽

Virus Concentration ◽

Upper Respiratory Tract ◽

Sterile Water ◽

Test Results ◽

Pcr Assay ◽

Previous Diagnosis ◽

Upper Respiratory

Objectives: The optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance. Methods: We tested asymptomatic persons with a previous diagnosis of COVID-19 and their household contacts. First, a mouthwash (gargling for at least 5 sec) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800 system with the Roche SARS-CoV-2 test. Results: Of 76 persons, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 (17%) of these infections but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs. Conclusions: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection.

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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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Clinical evaluation of a multiplex real-time RT-PCR assay for detection of SARS-CoV-2 in individual and pooled upper respiratory tract samples

Archives of Virology ◽

10.1007/s00705-021-05148-1 ◽

2021 ◽

Author(s):

Melissa Laverack ◽

Rebecca L. Tallmadge ◽

Roopa Venugopalan ◽

Brittany Cronk ◽

XiuLin Zhang ◽

...

Keyword(s):

Respiratory Tract ◽

Real Time ◽

Clinical Evaluation ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Pcr Assay ◽

Upper Respiratory

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A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay

Infection ◽

10.1007/s15010-021-01600-1 ◽

2021 ◽

Author(s):

Wiebke Michel ◽

Jacqueline Färber ◽

Milica Dilas ◽

Hans-Gert Heuft ◽

Ina Tammer ◽

...

Keyword(s):

Respiratory Tract ◽

Test Performance ◽

Nasopharyngeal Swab ◽

Virus Concentration ◽

Upper Respiratory Tract ◽

Sterile Water ◽

Pcr Assay ◽

Upper Respiratory ◽

Roche Cobas ◽

Close Contacts

Abstract Objectives The optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance. Methods In a large refugee facility, we retested individuals with a previous positive test for SARS-CoV-2 and their quarantined close contacts. All individuals were asymptomatic at the time of testing. First, a mouthwash (gargling for at least 5 s) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800® system with the Roche SARS-CoV-2 test. Results Of 76 individuals, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 of 76 (17%) infections, but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs. Conclusion Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection.

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Is it enough for COVID-19 screening test? Limitation of swab test and general characteristics of mild symptom patients

Science Progress ◽

10.1177/00368504211026152 ◽

2021 ◽

Vol 104 (2) ◽

pp. 003685042110261

Author(s):

Sungwoo Choi ◽

Hyo Jeong Choi ◽

Ho Jung Kim

Keyword(s):

Screening Test ◽

Community Treatment ◽

Upper Respiratory Tract ◽

Test Results ◽

Rt Pcr ◽

Pcr Assay ◽

Positive Rate ◽

Upper Respiratory ◽

Polymerase Chain ◽

Discharge Criteria

The most common method for SARS-CoV-2 testing is throat or nasal swabbing by real-time reverse transcription polymerase chain reaction (RT-PCR) assay. In South Korea, drive-through swab test is used for screening system and community treatment centers (CTCs), which admit and treat confirmed COVID-19 patients with mild symptoms, are being used. This retrospective study was conducted on patients admitted to a CTC on March 6, 2020. A total of 313 patients were admitted. The nasal and throat swabs were collected from the upper respiratory tract, and a sputum test was performed to obtain lower respiratory samples. The positive rate of the first set of test, sputum test was higher than that of the swab test ( p = 0.011). In the second set of test, 1 week after the first ones, the rate of positive swab tests was relatively high ( p = 0.026). In the first set of test, 66 of 152 (43.4%) patients showed 24-h consecutive negative swab test results, when the sputum test results were considered together, that number fell to 29 patients (19.1%) ( p < 0.001). Also, in the second set of test, 63 of 164 (38.4%) patients met the discharge criteria only when the swab test was considered; that number fell to 30 (18.3%) when the sputum test results were also considered ( p < 0.001). Using the swab test alone is insufficient for screening test and discharge decision. Patients who may have positive result in the sputum test can be missed.

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Conjunctivitis as a sign of persistent SARS-COV-2 infection? An observational study and report of late symptoms

European Journal of Ophthalmology ◽

10.1177/11206721211056594 ◽

2021 ◽

pp. 112067212110565

Author(s):

Jose Luis Vallejo-Garcia ◽

L Balia ◽

R Raimondi ◽

G Rustioni ◽

FI Camesasca ◽

...

Keyword(s):

Foreign Body ◽

Observational Study ◽

Respiratory Tract ◽

Recovery Phase ◽

Nasopharyngeal Swab ◽

Upper Respiratory Tract ◽

End Points ◽

Body Sensation ◽

Upper Respiratory ◽

Mean Time

Purpose To investigate if symptomatic conjunctivitis during the recovery phase of the disease could be associated to a persistent presence of SARS-CoV-2 in the upper respiratory tract. Secondary end points were to analyze the presence of SARS-CoV-2 in the conjunctiva of ocular symptomatic patients and to record the presence of ocular disturbances at this point of the disease. Methods An observational study including consecutive COVID19 patients treated at Humanitas Clinical and Research Hospital who were attending for nasopharyngeal swab to confirm the resolution of SARS-CoV-2 infection and end of isolation. We examined 129 consecutive patients from May to June 2020. The primary end point was to determine if symptomatic conjunctivitis at this point of the disease could be associated to a persistent presence of SARS-CoV-2 in the upper respiratory tract. Secondary end points were to analyze the presence of SARS-CoV-2 in the conjunctiva of ocular symptomatic patients and to record the presence of ocular disturbances at this point of the disease. Results One hundred twenty eight patients were included, 9.38% had conjunctivitis, none resulted positive to conjunctival PCR swab test, while two of them had positive nasopharyngeal result. Mean time elapsed since the first COVID-19 positive swab to the time of examination was 6 weeks ( ± 3). The only significant association was the presence of conjunctivitis with older age (65.3 ± 12.7 vs 56.7 + 13.5. p = 0.046). Nasopharyngeal swab resulted positive in 22 patients (17.19%). While 88 patients (68.2%) did not have any ocular complain during their COVID19 disease. The 40 patients (31.8%) reporting ocular disturbances complained about: redness (25.43%), tearing (19.53%), burning (18.35%), foreign body sensation (17.18%), itching (15.62%), and discharge (12.5%). Conclusion This study showed that late conjunctivitis cannot be considered as a marker of persistent infection when patients are sent to confirm the resolution of SARS-CoV-2 infection.

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A Case Report of Prolonged COVID-19 Positive RT-PCR for five months

10.21203/rs.3.rs-97733/v1 ◽

2020 ◽

Author(s):

Zeinab Siami ◽

Alireza Soleimani ◽

Armin Khavandegar

Keyword(s):

Assessment Tool ◽

Nasopharyngeal Swab ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Case Presentation ◽

Treatment Regimens ◽

Standard Assessment ◽

Appropriate Treatment ◽

Upper Respiratory ◽

Old Persian

Abstract Background: The COViD-19 gold standard assessment tool remained the RT-PCR of upper respiratory tract specimen extracted by the nasopharyngeal swab. A positive result would dwindle through a three-week course and, eventually, would be undetectable. The most prolonged period of detectable viral RNA was 37 days. Besides, COViD-19 RT-PCR remained positive for 74 days in a patient suffering from lymphoma Case presentation: In this study, we have presented a 56-year-old Persian male patient, a known case of lymphoma since 2015, who experiences many episodes of chemotherapy with a five-month positive RT-PCR COViD-19 laboratory test and finally was intubated and then died of opportunistic pulmonary infections. Conclusion: COViD-19 patients who have concurrent lymphoma failed to remove the virus thoroughly, despite providing appropriate treatment regimens.

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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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