scholarly journals Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a Low-Prevalence Area of the United States

2020 ◽  
Vol 7 (9) ◽  
Author(s):  
Alexander J Lepak ◽  
Derrick J Chen ◽  
Ashley Buys ◽  
Linda Stevens ◽  
Nasia Safdar
Keyword(s):  
Demographic Data ◽  
Tertiary Care ◽  
False Negative ◽  
The United States ◽  
Inpatient Setting ◽  
Repeated Testing ◽  
Rt Pcr ◽  
Academic Center ◽  
Low Prevalence ◽  
Pcr Test

Abstract Background Multiple factors have led to an extremely high volume of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing. Concerns exist about sensitivity and false-negative SARS-CoV-2 RT-PCR testing results. We describe a retrospective observational study examining the utility of repeat nasopharyngeal (NP) SARS-CoV-2 RT-PCR testing at an academic center in a low-prevalence setting. Methods All patients within our health system with >1 NP SARS-CoV-2 RT-PCR test result were included. SARS-CoV-2 RT-PCR testing was performed according to 1 of 4 validated assays. Key clinical and demographic data were collected, including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible coronavirus disease 2019 or for asymptomatic screening. Results A total of 660 patients had >1 NP SARS-CoV-2 PCR test performed. The initial test was negative in 638. There were only 6 negative-to-positive conversions (0.9%). All 6 were outpatients undergoing a PUI workup 5–17 days after an initial negative result. In >260 inpatients with repeat testing, we found no instances of negative-to-positive conversion including those undergoing PUI or asymptomatic evaluation. Conclusions In a low-prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. The clinical sensitivity of NP RT-PCR testing may be higher than previously believed. These results have helped shape diagnostic stewardship guidelines, in particular guidance to decrease repeated testing in the inpatient setting to optimize test utilization and preserve resources.

scholarly journals Characteristics of Inpatients with False-Negative SARS-CoV-2 PCR Test Results

2021 ◽  
Vol 1 (S1) ◽  
pp. s56-s56
Author(s):  
Antigone Kraft ◽  
Jessica Ridgway ◽  
Erica Mackenzie ◽  
Aniruddha Hazra ◽  
Maggie Collison ◽  
...  
Keyword(s):  
False Negative ◽  
Inpatient Setting ◽  
Test Results ◽  
Repeated Testing ◽  
Radiographic Findings ◽  
Negative Test ◽  
Tomography Scan ◽  
Unnecessary Testing ◽  
Pcr Test ◽  
False Negative Test

Background: At our institution, the concern for false-negative nasopharyngeal testing for SARS-CoV-2 at the onset of illness led to a general policy of retesting inpatients at 48 hours. For such patients, 2 negative SARS-CoV-2 PCR test results were required prior to discontinuation of COVID-19 control precautions. To assess the utility of routine repeat testing We analyzed patients presenting to our hospital who initially tested negative for SARS-CoV-2 but were found to be positive on repeated testing. Methods: All inpatients with symptoms concerning for COVID-19 were tested via nasopharyngeal sample for SARS-CoV-2 by PCR on admission. Patients with continued symptoms and no alternative diagnosis were retested 48 hours later. Testing was performed using either the Roche cobas SARS-CoV-2 RT-PCR assay or the Cepheid Xpert Xpress SARS-CoV-2 test. Between March 17, 2020, and May 10, 2020, we retrospectively analyzed data from patients with false-negative SARS-CoV-2 PCR test results who were subsequently confirmed positive 48 hours later. We evaluated demographic information, days since symptom onset, symptomatology, chest imaging, vital sign trends, and the overall clinical course of each patient. Results: During the study period, 14,683 tests were performed, almost half (n = 7,124) were performed through the ED and in the inpatient setting. Of 2,283 patients who tested positive for SARS-CoV-2, only 19 (0.01%) initially tested negative. Patients with initial false-negative test results presented with symptoms that ranged from fever and dyspnea to fatigue and vomiting. Notably, few patients presented “early” in their disease (median, 6 days; range, 0–10 days). However, patients with initial false-negative PCR test results did seem to have consistent imaging findings, specifically bilateral bibasilar ground glass opacities on chest radiograph or computed tomography scan. Conclusions: Among inpatients with COVID-19, we found a very low rate of initial false-negative SARS-CoV-2 PCR test results, which were not consistently related to premature testing. We also identified common radiographic findings among patients with initially false-negative test results, which could be useful in triaging patients who may merit retesting. Based on these data, we revised our existing clearance criteria to allow for single-test removal of COVID-19 precautions. Evaluating subsequent reduction in unnecessary testing is difficult given changing community prevalence, increased census, and increased opening to elective procedures. However, given the significant percentage of ED and inpatient testing, removal of repeated testing has likely resulted in a reduction of several thousand unnecessary COVID-19 tests monthly.Funding: NoDisclosures: None

scholarly journals Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Viral Genome ◽  
False Negative ◽  
Rt Pcr ◽  
Rna Detection ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

scholarly journals First Report of Lolium latent virus in Ryegrass in the United States

Plant Disease ◽  
2006 ◽  
Vol 90 (4) ◽  
pp. 528-528 ◽  
Author(s):  
C. J. Maroon-Lango ◽  
J. Hammond ◽  
S. Warnke ◽  
R. Li ◽  
R. Mock
Keyword(s):  
United States ◽  
Lolium Perenne ◽  
The United States ◽  
Latent Virus ◽  
Hybrid Population ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
High Sequence Identity ◽  
Lolium Perenne L ◽  
Pcr Test

Initial reports of the presence of Lolium latent virus (LLV) in Lolium perenne L. and L. multiflorum Lam. breeding clones in Germany, the Netherlands, France (2), and recently the United Kingdom (3,4; described as Ryegrass latent virus prior to identification as LLV) prompted us to evaluate clonally propagated Lolium plants from the United States. Four genetically distinct plants (viz., MF22, MF48, MF125, and MF132) that have been maintained clonally for 5 years from a Lolium perenne × L. multiflorum hybrid population established in the United States exhibited either no symptoms or mild chlorotic flecking that coalesced to form chlorotic to necrotic streaking on the leaves. All four clonal plants tested positive using reverse transcription-polymerase chain reaction (RT-PCR) with the Potexvirus group PCR test (Agdia, Inc., Elkhart, IN), whereas all clones but MF48 tested positive using the Potyvirus group PCR test (Agdia, Inc.). No amplicons were obtained when the same plants were tested for tobamovirus, carlavirus, and closterovirus using appropriate virus group-specific primers. Cloning and sequencing of the potexviral amplicons revealed very high sequence identity with the comparable region of LLV-UK (GenBank Accession No. DQ333886), whereas those of the potyviral amplicons (GenBank Accession Nos. DQ355837 and DQ355838) were nearly identical with the comparable region of Ryegrass mosaic virus (RGMV), a rymovirus first reported from the United States in 1957 (1). Using indirect enzyme-linked immunosorbent assay (ELISA), extracts from all four Lolium clonal propagations tested positive for LLV using the antiserum raised to LLV-Germany (courtesy of Dr. Huth), whereas the potyvirus-positive results from RT-PCR of the three clones were confirmed using indirect ELISA with the broad spectrum potyvirus monoclonal antibody, PTY-1. LLV from singly or dually infected Lolium clones was transmitted to Nicotiana benthamiana Domin. but not to N. tabacum L. by mechanical inoculation. LLV was purified from infected N. benthamiana. Similar sized flexuous rods were observed using electron microscopy in leaf dip samples from Lolium clones and aliquots of the virions purified from N. benthamiana. References: (1) G. W. Bruehl et al. Phytopathology 47:517, 1957. (2) W. Huth et al. Agronomie 15:508, 1995. (3) R. Li et al. Asian Conf. Plant Pathol. 2:89, 2005. (4) C. Maroon-Lango et al. Int. Congr. Virol. 13:63, 2005.

scholarly journals High Proportion of Indeterminate Qua.jpegERON-TB Gold In-Tube Results in an Inpatient Population Is Related to Host Factors and Preanalytical Steps

2014 ◽  
Vol 1 (2) ◽  
Author(s):  
Valeria Fabre ◽  
Shmuel Shoham ◽  
Kathleen R. Page ◽  
Maunank Shah
Keyword(s):  
Skin Testing ◽  
Tertiary Care ◽  
Latent Tuberculosis ◽  
Host Factors ◽  
Inpatient Setting ◽  
Tuberculin Skin Testing ◽  
Sample Collection ◽  
Academic Center ◽  
Targeted Testing ◽  
Mitogen Response

Background.  Qua.jpegERON-TB Gold In-Tube test (QFT-GIT) can be used as an alternative to tuberculin skin testing (TST) for the targeted testing of latent tuberculosis. Due to many shortcomings with TST, QFT-GIT usage is increasing. QFT-GIT implementation in the inpatient setting remains unclear. Methods.  We retrospectively ide.jpegied patients admitted to a tertiary care academic center who received either a TST or a QFT-GIT in the 18 months prior to and after QFT-GIT implementation in March 2012. Risk factors associated with indeterminate results were evaluated. Results.  The proportion of inpatients receiving a test for tuberculosis infection doubled following QFT-GIT implementation (1.4% vs 2.9%). After QFT-GIT became available, 75% of tested people received a QFT-GIT and 25% received a TST. We found indeterminate test results in 19.8%. Independent predictors of indeterminate results were female sex (adjusted odds ratio [AOR], 1.64), lymphopenia (AOR, 2.21), hypoalbuminemia (AOR, 6.81) and sample collection by nonphlebotomists (AOR, 3.0, vs phlebotomists). Of patients who had indeterminate results, 42% had a subsequent indeterminate result on repeat testing. All indeterminate results were due to a low mitogen response. Conclusions.  QFT-GIT testing in the inpatient setting is associated with a high proportion of indeterminate results that is associated with host factors and preanalytical errors. Careful selection of patients to be tested and training on sample processing for QFT-GIT testing should be considered to decrease indeterminate results.

Delay in time from diagnosis to treatment in metastatic melanoma, lung, and colon cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e23186-e23186
Author(s):  
Muhammad Salman Faisal ◽  
Ahmed Khattab ◽  
Vida Jahangiri ◽  
Hira Shaikh ◽  
Soorih Shaikh ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Colon Cancer ◽  
Demographic Data ◽  
Tertiary Care ◽  
The United States ◽  
Definitive Treatment ◽  
Metastatic Colon Cancer ◽  
Female Ratio ◽  
Number Of Patients ◽  
Delay In Treatment

e23186 Background: Delay in cancer treatment is anxiety provoking both for the patient and clinician. We conducted the study to evaluate the patterns of delay in treatment of patients with metastatic colon cancer, lung cancer and melanoma from diagnosis to the initiation of the treatment, and to identify the causes of delay. Methods: In this retrospective study, patients with metastatic colon cancer, lung cancer and melanoma diagnosed between 01/01/2016 to 12/31/2016 in a tertiary care network in the United States were studied. Data was collected from electronic health record (EHR) database, ‘Epic’. Variables such as demographic data, including patient age and gender, and type of cancer, and treatment received were analyzed. The causes of the delay were also evaluated when available. Results: Total number of patients in the study was 288. Mean age was 68.3 years (median 69 years) and 36% were alive at the time of data analysis. Male to female ratio was 1.4:1. 66.7% people had lung cancer, 30% had colon cancer and 3% had melanoma. 67 (23.6%) of total analyzed patients had denied definitive treatment and chose to undergo palliative management. Of the rest, most started treatment with chemotherapy (39.5%), followed by surgery (22.6%) and then radiation (14.6%). With the time of pathological diagnosis of the tumor taken as the date of diagnosis, mean delay from the day of diagnosis to the start of treatment in this study population observed was 27.7 days. 67 patients (23.3%) had a delay of more than 30 days, with the most common reason being systemic factors in 39 patients (58.2%), followed by patient factors in 23 patients (34.3%) and physician factors in 5 patients (7.5%). On logistic regression analysis, time from diagnosis to treatment didn’t predict mortality (OR = 0.99, 95% CI P = 0.10(0.97-1.002). Conclusions: Delay in treatment is common and the system factors one of the common reasons as exhibited by our study. Time from diagnosis to treatment didn’t predict mortality.

scholarly journals Perspective of Arguments in Public Health

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.

scholarly journals Reducing False Negative PCR Test for COVID-19

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.

scholarly journals Diagnostic performance of the combined nasal and throat swab in patients admitted to hospital with suspected COVID-19

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kuan Ken Lee ◽  
◽  
Dimitrios Doudesis ◽  
Daniella A. Ross ◽  
Anda Bularga ◽  
...  
Keyword(s):  
Diagnostic Performance ◽  
Primary Outcome ◽  
Clinical Laboratory ◽  
Throat Swab ◽  
Tertiary Care ◽  
Secondary Outcome ◽  
Index Test ◽  
Repeated Testing ◽  
Rt Pcr ◽  
Serial Testing

Abstract Background Accurate diagnosis in patients with suspected coronavirus disease 2019 (COVID-19) is essential to guide treatment and limit spread of the virus. The combined nasal and throat swab is used widely, but its diagnostic performance is uncertain. Methods In a prospective, multi-centre, cohort study conducted in secondary and tertiary care hospitals in Scotland, we evaluated the combined nasal and throat swab with reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in consecutive patients admitted to hospital with suspected COVID-19. Diagnostic performance of the index and serial tests was evaluated for a primary outcome of confirmed or probable COVID-19, and a secondary outcome of confirmed COVID-19 on serial testing. The diagnosis was adjudicated by a panel, who recorded clinical, laboratory and radiological features blinded to the test results. Results We enrolled 1368 consecutive patients (median age 68 [interquartile range, IQR 53–80] years, 47% women) who underwent a total of 3822 tests (median 2 [IQR 1–3] tests per patient). The primary outcome occurred in 36% (496/1368), of whom 65% (323/496) and 35% (173/496) had confirmed and probable COVID-19, respectively. The index test was positive in 255/496 (51%) patients with the primary outcome, giving a sensitivity and specificity of 51.4% (95% confidence interval [CI] 48.8 to 54.1%) and 99.5% (95% CI 99.0 to 99.8%). Sensitivity increased in those undergoing 2, 3 or 4 tests to 60.1% (95% CI 56.7 to 63.4%), 68.3% (95% CI 64.0 to 72.3%) and 77.6% (95% CI 72.7 to 81.9%), respectively. The sensitivity of the index test was 78.9% (95% CI 74.4 to 83.2%) for the secondary outcome of confirmed COVID-19 on serial testing. Conclusions In patients admitted to hospital, a single combined nasal and throat swab with RT-PCR for SARS-CoV-2 has excellent specificity, but limited diagnostic sensitivity for COVID-19. Diagnostic performance is significantly improved by repeated testing.

scholarly journals Clinical Spectrum of COVID-19 in a Pediatric Mexican Population

2020 ◽  
Author(s):  
Edgar Bustos-Cordova ◽  
Daniela Castillo-García ◽  
Magdalena Cerón-Rodriguez ◽  
Nadia Soler-Quiñones
Keyword(s):  
Emergency Department ◽  
Pediatric Patients ◽  
Care Center ◽  
Tertiary Care ◽  
Signs And Symptoms ◽  
Clinical Spectrum ◽  
Tertiary Care Center ◽  
Rt Pcr ◽  
Excessive Crying ◽  
Pcr Test

Abstract ObjectiveFrom the beginning of the COVID-19 pandemic, it has become evident that the spectrum of manifestations in children is different from those seen in adults. In this study, we aimed to describe a broader clinical spectrum of COVID-19 in children.MethodsIn this descriptive, prospective study, we included confirmed pediatric patients with COVID-19 who presented to the emergency department of a pediatric tertiary care center from April to July 2020. All patients were confirmed by the SARS-CoV-2 RT-PCR test, and we analyzed 24 symptoms and 25 signs.ResultsWe analyzed 50 patients with COVID-19. From the evaluated signs and symptoms, the most common symptoms were fever, excessive crying and dry cough, digestive symptoms were frequently found (24%), and the most common signs were pharyngeal erythema and irritability.ConclusionClinicians should recognize that the clinical spectrum of COVID-19 in children is wider than previously described, often with nonspecific signs and symptoms, and digestive symptoms should raise suspicion.

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

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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