Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

AbstractReverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.

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Real-World Clinical Performance of the Abbott Panbio with Nasopharyngeal, Throat and Saliva Swabs Among Symptomatic Individuals with COVID-19

10.21203/rs.3.rs-188293/v1 ◽

2021 ◽

Author(s):

William Stokes ◽

Byron M. Berenger ◽

Danielle Portnoy ◽

Brittney Scott ◽

Jonas Szelewicki ◽

...

Keyword(s):

Symptom Onset ◽

Clinical Performance ◽

Point Of Care ◽

Community Setting ◽

Rt Pcr ◽

Chain Reaction ◽

False Negatives ◽

Polymerase Chain ◽

Antigen Tests ◽

Health Canada

Abstract BACKGROUND Point of Care SARS-CoV-2 antigen tests, such as the Abbott Panbio, have great potential to help combat the COVID-19 pandemic. The Panbio is Health Canada approved for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of COVID-19 symptom onset(s). METHODS Symptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Paired nasopharyngeal (NP), throat, and saliva swabs were collected, with one paired swab tested immediately with the Panbio, and the other transported in universal transport media and tested using reverse-transcriptase polymerase chain reaction (RT-PCR). We also prospectively evaluated results from assessment centres. For those individuals, an NP swab was collected for Panbio testing and paired with RT-PCR results from parallel NP or throat swabs. RESULTS 145 individuals were included in the study. Collection of throat and saliva was stopped early due to poorer performance (throat sensitivity 57.7%, n = 61, and saliva sensitivity 2.6%, n = 41). NP swab sensitivity was 87.7% [n = 145, 95% confidence interval (CI) 81.0% − 92.7%]. There were 1,641 symptomatic individuals tested by Panbio in assessment centres, with 268/1641 (16.3%) positive for SARS-CoV-2. There were 37 false negatives and 2 false positives, corresponding to a sensitivity and specificity of 86.1% [95% CI 81.3% − 90.0%] and 99.9% [95% CI 99.5% − 100.0%], respectively. CONCLUSIONS The Panbio test reliably detects most cases of SARS-CoV-2 from adults in the community setting presenting within 7 days of symptom onset using nasopharyngeal swabs. Throat and saliva swabs are not reliable specimens for the Panbio.

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Evaluation of Sandwich Enzyme-Linked Immunosorbent Assay and Reverse Transcription Polymerase Chain Reaction for the Diagnosis of Foot-and-Mouth Disease

Intervirology ◽

10.1159/000517003 ◽

2021 ◽

pp. 1-6

Author(s):

Salman Khan ◽

Syed Asad Ali Shah ◽

Syed Muhammad Jamal

Keyword(s):

Polymerase Chain Reaction ◽

Viral Genome ◽

Foot And Mouth Disease ◽

Enzyme Linked Immunosorbent Assay ◽

Rt Pcr ◽

Chain Reaction ◽

Kappa Value ◽

Polymerase Chain ◽

Pcr Assays ◽

Level Of Agreement

Background: Foot-and-mouth disease (FMD) is an infectious and highly contagious disease of cloven-hoofed domestic and wild animals, causing heavy economic losses to the livestock industry. Rapid and reliable diagnosis of the disease is essential for the implementation of effective control measures. This study compared sandwich enzyme-linked immunosorbent assay (S-ELISA) and conventional reverse transcription polymerase chain reaction (RT-PCR) for the diagnosis of FMD. Methods: A total of 60 epithelial samples from suspected cases of FMD were tested using both S-ELISA and RT-PCR assays. The level of agreement between the assays was assessed by calculating the Kappa value. Results: S-ELISA detected 38 (63%) samples positive for FMD virus (FMDV). Being predominant, serotype O was detected in 22 (57.9%) of the total samples tested positive, whereas 9 (23.7%) and 7 (18.4%) samples were found positive for serotypes A and Asia-1, respectively. RT-PCR detected viral genome in 51 (85%) of the samples using pan-FMDV primers set, 1F/1R. Thirty-six samples were found positive and 7 negative by both the tests. The level of agreement between the tests was assessed by calculating the Kappa value, which was found to be fair (Kappa value = 0.303 and 95% CI = 0.089; 0.517) and significant (p = 0.009). However, 2 samples, which were found positive on S-ELISA tested negative on RT-PCR. This may be attributed to the presence of nucleotide mismatch(es) in the primer-binding sites that may have resulted in failure of amplification of the viral genome. The serotype-specific RT-PCR assays not only confirmed serotyping results of S-ELISA but were also able to establish serotype in 9 S-ELISA-negative but pan-FMDV RT-PCR-positive samples. Conclusions: The RT-PCR assay contributes significantly to establishing a quick, sensitive, and definitive diagnosis of FMD in resource-constrained countries. Samples giving negative results in S-ELISA should be tested in RT-PCR for the disease detection and virus typing.

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Perspective of Arguments in Public Health

Journal of Comprehensive Health ◽

10.53553/jch.v09i01.010 ◽

2021 ◽

Vol 9 (1) ◽

pp. 44-45

Author(s):

Dinesh Kumar

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Respiratory Symptoms ◽

False Negative ◽

Rt Pcr ◽

Chain Reaction ◽

Negative Report ◽

Polymerase Chain ◽

Time Of Admission ◽

Pcr Test

Recently, an argument was put forth because a symptomatic and positive patient for CoVID-19 turned tested negative after 7 days, so discharged from the hospital. Both at the time of admission and discharge real-time reverse transcriptase Polymerase Chain Reaction (RT-PCR) was done for testing of CoVID-19. Immediately, patient again developed respiratory symptoms and was admitted to hospital again. Amidst of current CoVID-19 pandemic, a question was asked “What is the specificity of the Real Time-Polymerase Chain Reaction (RT-PCR) test for COVID-19?” with an assumption that what if at the time of discharge the disease is present in patient but test turned out to be negative? In response to that a counter statement was posed that “It is the sensitivity that should be asked rather than specificity”. It was based on the implication of primary question that was implying false negative report of the RT-PCR. It means, since patient was discharged with negative result that could be false negative.

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Reducing False Negative PCR Test for COVID-19

International Journal of MCH and AIDS (IJMA) ◽

10.21106/ijma.421 ◽

2020 ◽

Vol 9 (3) ◽

pp. 408-410

Author(s):

Fatemeh Bahreini ◽

Rezvan Najafi ◽

Razieh Amini ◽

Salman Khazaei ◽

Saeid Bashirian

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

False Negative ◽

Rt Pcr ◽

Chain Reaction ◽

Creative Commons ◽

Negative Results ◽

False Negative Results ◽

Polymerase Chain ◽

Pcr Test

As the SARS-CoV-2 (COVID-19) pandemic spreads rapidly, there is need for a diagnostic test with high accuracy to detect infected individuals especially those without symptoms. Real-time polymerase chain reaction (RT-PCR) is a common molecular test for diagnosing SARS-CoV-2. If some factors are not taken into consideration when performing this test, it can have a relatively large number of false negative results. In this article, we discuss important considerations that could lead to false negative test reduction. Key words: • SARS-CoV-2 • COVID-19 • Real time polymerase chain reaction • RT-PCR test • Diagnosis • False negatives • Genetics • Emerging disease Copyright © 2020 Bahreini et al. Published by Global Health and Education Projects, Inc. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0)which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in this journal, is properly cited.

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False-Negative Nasopharyngeal Swab RT-PCR Assays in Typical COVID-19: Role of Ultra-low-dose Chest CT and Bronchoscopy in Diagnosis

European Journal of Case Reports in Internal Medicine ◽

10.12890/2020_001680 ◽

2020 ◽

Author(s):

Marco Marando ◽

Adriana Tamburello ◽

Pietro Gianella

Keyword(s):

Low Dose ◽

False Negative ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Oral Swab ◽

Negative Results ◽

False Negative Results ◽

Polymerase Chain ◽

Pcr Assays

On 11 March 2020, the WHO declared COVID-19 a pandemic and global health emergency. We describe the clinical features and role of ultra-low-dose chest computed tomography (CT) and bronchoscopy in the diagnosis of coronavirus disease (COVID-19). In our patient, who was highly suggestive clinically and radiologically for COVID-19, we had two false-negative results for nasopharyngeal and oral swab reverse-transcriptase polymerase chain reaction (RT-PCR) assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Eventually, we confirmed the diagnosis using bronchoscopy and bronchoalveolar lavage (BAL).

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Real-Time Polymerase chain reaction trends in COVID-19 patients

Pakistan Journal of Medical Sciences ◽

10.12669/pjms.37.1.3000 ◽

2020 ◽

Vol 37 (1) ◽

Author(s):

Dr Sana Abbas ◽

Aisha Rafique ◽

Dr Beenish Abbas ◽

Dr Rashid Iqbal

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Tertiary Care ◽

False Negative ◽

Polymerase Chain Reaction Test ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Chain Reaction ◽

Asymptomatic Patients ◽

Polymerase Chain

Objective: To assess trends of real-time Polymerase Chain Reaction test in Coronavirus infected Patients. Methods: This cross-sectional analytical study was conducted at Tertiary Care Institute, Rawalpindi from March 2020 to June 2020. All patients confirmed COVID positive by real-time Polymerase Chain Reaction (PCR) with recent travel history, close contact with known diagnosed patients and had symptoms of fever or upper respiratory tract with body aches. Nasopharyngeal swabs were taken and results generated within 48 hours. Positive PCR was admission criteria follow up was carried out at 7th and 8th day, with negative PCR were discharged. However, those who had persistent positive PCR on the 8th day were tested again on 11th and 12th day. Those with persistent positive results beyond 12th day were shifted to specialized quarantine centres. Results: A total of three hundred and ninety-two patients with mild to moderate illness, PCR positive for COVID 19 were included study with age range 9 - 45 and mean 33.22±7.98 years. A total of 8 (2%) patients were females and 384(98%) males. The duration of the negative test result was Mean ± Std. Deviation 9.05±2.00 with 7 – 8 days 152(38.8%)in and 11 – 12 days in 160(40.8%). PCR results on Day 7 and 8 were negative in 144(36.7%) patients whereas positive in 248(63.3%). PCR results on Day 11 and 12 were negative in 312(79.6%) patients whereas positive in 80 (20.4%). Conclusion: To conclude Real-Time Polymerase Chain Reaction (rT-PCR) inclines to give false negative results additionally can stay positive in asymptomatic patients for moderately longer-term. Hence decision to discharge ought to be intricately adjusted between RT-PCR, clinical judgement, radiological examinations, and biochemical assays. doi: https://doi.org/10.12669/pjms.37.1.3000 How to cite this:Abbas S, Rafique A, Abbas B, Iqbal R. Real-Time Polymerase chain reaction trends in COVID-19 patients. Pak J Med Sci. 2021;37(1):180-184. doi: https://doi.org/10.12669/pjms.37.1.3000 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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The Value of Pre-operative Testing for COVID-19 in Urological Patients

Journal of Endoluminal Endourology ◽

10.22374/jeleu.v3i3.98 ◽

2020 ◽

Vol 3 (3) ◽

pp. e29-e34

Author(s):

Vasileios Bonatsos ◽

Asif Raza

Keyword(s):

Gold Standard ◽

Diagnostic Tests ◽

Acute Infection ◽

World Health Organisation ◽

World Health ◽

Rt Pcr ◽

Chain Reaction ◽

The World ◽

Polymerase Chain ◽

Pcr Assays

According to the World Health Organisation there have been 30,055,710 confirmed COVID-19 cases and 933,433 confirmed deaths across 216 countries globally. The availability of the complete SARS-CoV-2 genome relatively early in the epidemic has enabled the development of tests for the diagnosis of COVID-19. There are two broad categories of SARS-CoV-2 diagnostic tests currently in use or development: (1) Real-time reverse transcriptase polymerase chain reaction (RT-PCR) tests and (2) serology tests. RT-PCR is considered the gold standard and preferred method of diagnosis of acute infection. There is, however, a plethora of laboratory-developed and commercial RT-PCR assays with different gene targets. We discuss the value of pre-operative testing for COVID-19 before urological surgery.

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High False-Negative Rate of HER2 Quantitative Reverse Transcription Polymerase Chain Reaction of the Oncotype DX Test: An Independent Quality Assurance Study

Journal of Clinical Oncology ◽

10.1200/jco.2011.34.7963 ◽

2011 ◽

Vol 29 (32) ◽

pp. 4279-4285 ◽

Cited By ~ 120

Author(s):

David J. Dabbs ◽

Molly E. Klein ◽

Syed K. Mohsin ◽

Raymond R. Tubbs ◽

Yongli Shuai ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Quality Assurance ◽

Reverse Transcription ◽

False Negative ◽

False Negative Rate ◽

Oncotype Dx ◽

Rt Pcr ◽

Chain Reaction ◽

Negative Rate ◽

Polymerase Chain

Purpose HER2 (ERBB2) status is an important prognostic and predictive marker in breast carcinoma. In recent years, Genomic Health (GHI), purveyors of the Oncotype DX test, has been separately reporting HER2 by reverse transcription polymerase chain reaction (RT-PCR) to oncologists. Because of the lack of independent evaluation, this quality assurance study was undertaken to define the concordance rate between immunohistochemistry (IHC)/fluorescent in situ hybridization (FISH) and GHI RT-PCR HER2 assay. Methods All patients at three participating laboratories (Magee-Womens Hospital [Pittsburgh, PA], Cleveland Clinic [Cleveland, OH], and Riverside Methodist Hospital [Columbus, OH]) with available HER2 RT-PCR results from GHI were included in this study. All IHC-positive and equivocal patient cases were further evaluated and classified by FISH at respective laboratories. Results Of the total 843 patient cases, 784 (93%) were classified as negative, 36 (4%) as positive, and 23 (3%) as equivocal at the three institutions using IHC/FISH. Of the 784 negative patient cases, 779 (99%) were also classified as negative by GHI RT-PCR assay. However, all 23 equivocal patient cases were reported as negative by GHI. Of the 36 positive cases, only 10 (28%; 95% CI, 14% to 45%) were reported as positive, 12 (33%) as equivocal, and 14 (39%) as negative. Conclusion There was an unacceptable false-negative rate for HER2 status with GHI HER2 assay in this independent study. This could create confusion in the decision-making process for targeted treatment and potentially lead to mismanagement of patients with breast cancer if only GHI HER2 information is used.

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Molecular analysis of t(11;19) breakpoints in childhood acute leukemias

Blood ◽

10.1182/blood.v87.11.4804.bloodjournal87114804 ◽

1996 ◽

Vol 87 (11) ◽

pp. 4804-4808 ◽

Cited By ~ 44

Author(s):

JE Rubnitz ◽

FG Behm ◽

AM Curcio-Brint ◽

RP Pinheiro ◽

AJ Carroll ◽

...

Keyword(s):

Acute Leukemia ◽

Myeloid Leukemia ◽

Lymphoblastic Leukemia ◽

Rt Pcr ◽

Chain Reaction ◽

Acute Leukemias ◽

Polymerase Chain ◽

Pcr Assays ◽

Childhood Acute Leukemia ◽

Acute Myeloid

MLL is fused to ENL or ELL in acute leukemias that contain t(ll;19)(q23;p13). Although ENL and ELL localize to chromosome 19, bands p13.3 and p13.1, respectively, these breakpoints are not always readily distinguished by standard cytogenetics. We therefore used reverse transcriptase-polymerase chain reaction (RT-PCR) assays to analyze 26 cases of childhood acute leukemia containing t(11;19) to determine the frequencies of ENL and ELL involvement. All 17 cases of acute lymphoblastic leukemia (ALL) had MLL/ENL fusion transcripts. By contrast, of the 9 cases of acute myeloid leukemia (AML) analyzed, 6 had MLL/ENL fusions, 2 had MLL/ELL fusions, and 1 case had no RT-PCR- detectable MLL fusion mRNA. These data suggest that the majority of 11;19 translocations involve ENL, whereas involvement of ELL is relatively uncommon in childhood acute leukemia and may be restricted to AML.

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Clinical significance of molecular detection of carcinoma cells in lymph nodes and peripheral blood by reverse transcription-polymerase chain reaction in patients with gastrointestinal or breast carcinomas.

Journal of Clinical Oncology ◽

10.1200/jco.1998.16.1.128 ◽

1998 ◽

Vol 16 (1) ◽

pp. 128-132 ◽

Cited By ~ 119

Author(s):

M Mori ◽

K Mimori ◽

H Ueo ◽

K Tsuji ◽

T Shiraishi ◽

...

Keyword(s):

Lymph Nodes ◽

Peripheral Blood ◽

Detection Rate ◽

Breast Carcinomas ◽

Rt Pcr ◽

Chain Reaction ◽

Blood Samples ◽

Polymerase Chain ◽

Cea Mrna ◽

Positive Results

PURPOSE This study evaluates the clinical significance of detection of carcinoembryonic antigen (CEA) mRNA in the dissected lymph nodes and peripheral blood samples of patients with gastrointestinal or breast carcinomas. PATIENTS AND METHODS A total of 406 lymph nodes obtained from 65 patients were analyzed by both histologic and molecular examination of CEA-specific reverse transcriptase-polymerase chain reaction (RT-PCR). Peripheral blood samples from another 102 patients were also analyzed by CEA-specific RT-PCR. Patients were followed up prospectively for 24 +/- 12 months. RESULTS Of 406 lymph nodes, the positive detection rate increased from 20% by histologic examination to 60% by RT-PCR examination. The recurrence rate was 40% in 15 cases showing positive results in both examinations, 14% in 29 cases showing histologically negative but RT-PCR positive results, and none in 21 cases showing negative results in both examinations. The positive detection rate for CEA mRNA in peripheral blood samples increased with advancing stage of disease. With respect to 62 curatively operated cases, CEA mRNA was detected in 12 cases. Four of these 12 cases developed metastatic disease after surgery whereas none of 50 cases negative by RT-PCR developed metastasis. CONCLUSION It has been shown that RT-PCR is a powerful tool to detect CEA mRNA in the lymph nodes or the peripheral blood. This is potentially very useful to determine high-risk patients for metastasis. Serial analysis is warranted to assess the long-term significance of this method and its therapeutic and prognostic implications.

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