False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications

Katz, Andrew P.; Civantos, Francisco; Sargi, Zoukaa; Leibowitz, Jason M.; Nicolli, Elizabeth A.; Weed, Donald T.; Moskovitz, Alexander E.; Civantos, Alyssa M.; Andrews, David; Martínez, Octavio; Thomas, Giovana R.

doi:10.1002/hed.26317

Cited by 41 publications

(54 citation statements)

References 28 publications

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“…For all these reasons, several publications have focused their attention on false negative results [ 6 , 7 ]. However, false positive results have been observed, even if less frequently, due to contaminations of commercial primers/probe sets or poor test specificity [ 8 , 9 ].…”

Section: Discussionmentioning

confidence: 99%

Detection of SARS-COV N2 Gene: Very low amounts of viral RNA or false positive?

Falasca

Sciandra

Carlo

et al. 2020

Journal of Clinical Virology

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Background The detection of a low amount of viral RNA is crucial to identify a SARS-CoV-2 positive individual harboring a low level of virus, especially during the convalescent period. However, the detection of one gene at high Cycle threshold (Ct) has to be interpreted with caution. In this study we address this specific issue and report our real-life experience. Study design A total of 1639 nasopharyngeal swabs (NPS) were analyzed with Xpert® Xpress SARS-CoV-2. Positive samples showing high Ct values (Ct>35) were concentrated by centrifugation and re-tested with Cepheid or other methods (RealStar SARS-CoV2 RT-PCR, Altona Diagnostics; GeneFinder COVID-19 Plus RealAmp Kit, Elitech). Results 1599 (97.5%) negative samples, 36 (2.3%) positive samples and 4 (0.2%) presumptive positive samples were detected. In 17 out of 36 positive patients, very low viral RNA copies were suspected since positivity was detected at high Ct. We confirmed positivity for patients who showed both E and N genes detected and for patients with only N detected but with Ct <39. On the contrary, samples with only gene N detected with Ct values >39 were found negative. NPS taken 24 hours after the first collection confirmed the negativity of the 12 samples. Clinical data sustained these results since only 2 of these 12 patients showed COVID-19-like symptoms. Conclusions These data support our consideration that detection of the N2 gene at high Ct needs to be interpreted with caution, suggesting that collaboration between virologists and clinicians is important for better understanding of results.

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Section: Discussionmentioning

confidence: 99%

Detection of SARS-COV N2 Gene: Very low amounts of viral RNA or false positive?

Falasca

Sciandra

Carlo

et al. 2020

Journal of Clinical Virology

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“…For the pools where 1 or more positives were identified the Ct values ranged 16.97 to 37.81 with median 30.43 (IQR: 25.68-32.90). False-positive results during pooled testing may arise as technical artifacts of degraded probe, primer/probe cross-reaction with non-SARS-CoV-2 sequences in some samples or technical cross-contamination/mislabeling during sample processing 24 .…”

Section: Resultsmentioning

confidence: 99%

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Agoti¹,

Mutunga²,

Lambisia³

et al. 2020

Wellcome Open Res

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Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

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“…• 7.1% from Katz et al [16] • 2.6% (CI 0.9-4.3%) from Albendin-Iglesias et al [15] Henceforth, two figures will be generally given, as a range. The pessimistic is the data of Ai (≡ P −#), and the optimistic is the data of Albendin-Iglesias (≡ O−#).…”

Section: Working Confusion Matrixmentioning

confidence: 99%

“…Likewise for the previous subsection, equation 9 yields Ni = 3336 infected people per day, slightly lower than the official count of 4007. Swedish state television reports daily intensive care admissions 16 at 190 per day at the time of writing, which is 5.6% of cases. The current death rate in Sweden is 19 per day, suggesting 0.6% mortality rate.…”

Section: Swedenmentioning

confidence: 99%

Error Rates in SARS-CoV-2 Testing Examined with Bayesian Inference

Bentley

2020

Preprint

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A literature review on SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) is used to construct a clinical test confusion matrix, including false positives and false negatives. This allows the simple correction of bulk test data results to estimate the actual infection rate, as demonstrated with examples. Then, the required sensitivity and specificity of a test are explored for the societal needs. It is indicated that many of the people with mild symptoms and positive test results are unlikely to be infected with SARS-CoV-2 in some regions. It is also concluded that current and foreseen alternative tests cannot be used to “clear” people as being non-infected. Recommendations are given that regional authorities must establish a programme to monitor operational test characteristics before launching large scale testing; and that large scale testing for tracing infection networks in some regions is not viable, but may be possible in a focused way that does not exceed the working capacity of the laboratories staffed by competent experts. At scale RT-PCR tests cannot be relied upon as the gold standard for SARS-CoV-2 diagnosis, instead clinical assessment supported by a range of expert diagnostic tests should be used.

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False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications

Cited by 41 publications

References 28 publications

Detection of SARS-COV N2 Gene: Very low amounts of viral RNA or false positive?

Detection of SARS-COV N2 Gene: Very low amounts of viral RNA or false positive?

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Error Rates in SARS-CoV-2 Testing Examined with Bayesian Inference

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