scholarly journals Investigation of revers-transcriptase polymerase chain reaction values of patients with COVID-19 findings in lung computed tomography results

2020 ◽  
Vol 9 (1) ◽  
pp. 41-48
Author(s):  
Ozüdogru Osman ◽  
Gunes Bolatli ◽  
Fatih Tas
Keyword(s):  
Polymerase Chain Reaction ◽  
Clinical Symptoms ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Alternative Approach ◽  
Polymerase Chain ◽  
Bilateral Lung ◽  
Patient’S History ◽  
Positive Results

It turned out that the cause of pneumonia cases that occurred in China was due to SARS-CoV-2. The aim is to compare chest computer tomography and Revers-Transcriptase Polymerase Chain Reaction methods used in the diagnosis of COVID-19 disease with each other and to evaluate this disease with risk factors. The study was carried out on 66 patients. Epidemiological history, clinical symptoms, chest CT and RT-PCR results of the cases were examined. RT-PCR results of 1, 4, and 7 days were evaluated for each case with positive chest CT results. Thirty-seven of them were found to be positive on day 1, 5 of them were found to be positive on day 4, and 2 of them were found to be positive on day seven from 52 patients whose RT-PCR results were examined. In the remaining 8 cases, no positive findings were found. The most common findings are; cough (78.8%), fever (55.8%), and shortness of breath (28.8%). It was observed that 51.9% of the cases had chronic disease history and 50% of the patients using cigarettes had bilateral lung involvement in their CT results. Seven cases received intensive care support, 3 cases were intubated. Two of the intubated cases were exitus (3,8%). The positive results of RT-PCR were found to be negative in most of the cases which have positive chest CT; suggests that chest CT is more reliable in making a diagnosis.  Therefore, evaluating chest CT results with RT-PCR can be an appropriate alternative approach in the diagnosis and treatment of disease. However, in order to be fully diagnosed, the patient's history, chronic diseases, age, symptoms, imaging, blood, and test findings must all be considered as a whole.

scholarly journals A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

scholarly journals The exact place of PCR and chest CT in screening, staging, and diagnosis of Covid-19: A meta-analysis

2020 ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

Abstract Introduction: Nowadays there is an ongoing acute respiratory outbreak causing by the novel highly contagious coronavirus (nCoV). There are two diagnostic protocol based on chest CT scan and quantitative reverse-transcription polymerase chain reaction (RT-PCR) which their diagnostic accuracy is under the debate. We designed this meta-analysis study to determine the diagnostic value of initial chest CT scan in patients with nCoV infection in comparison with RT- PCR.Search strategy and statistical analysis: Three main databases the PubMed (MEDLINE), Scopus, and EMBASE was systematically searched for all published literatures from January 1st, 2019, to the 27th march 2020 with key grouping of “COVID19 virus”, “2019 novel coronavirus”, “Wuhan coronavirus”, “2019-nCoV”, “X-Ray Computed Tomography”, “Polymerase Chain Reaction”, “Reverse Transcriptase PCR”, and “PCR Reverse Transcriptase”. All relevant case- series, cross-sectional, and cohort studies were selected. Data extraction was done in Excel 2007 (Microsoft Corporation, Redmond, CA) and their analysis was performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5.Result: From first recruited 668 articles we end up to the final 47 studies, which comprised a total sample size of 4238 patients. In compare to RT-PCR, the overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan were 86% (95% CI: 83% -90%), 43 % (95% CI: 26% -60%), 67% (95% CI: 57% -78%), and 84% (95% CI: 74% -95%) respectively. However the RT-PCR should be repeated for three times in order to give the 99% accuracy especially in negative samples.Conclusion: According to the acceptable sensitivity of chest CT scan, it can be employed complement to RT-PCR to diagnosis patients who are clinically suspicious for nCoV.

scholarly journals Chest CT versus RT-PCR for the Detection of COVID-19: Systematic Review and Meta-analysis

2020 ◽  
Author(s):  
Mohammad Karam ◽  
Sulaiman Althuwaikh ◽  
Mohammad Alazemi ◽  
Ahmad Abul ◽  
Amrit Hayre ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Systematic Review ◽  
Polymerase Chain Reaction ◽  
Meta Analysis ◽  
False Negative ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Chest Computed Tomography ◽  
Polymerase Chain

AbstractPurposeTo compare the performance of chest computed tomography (CT) scan versus reverse transcription polymerase chain reaction (RT-PCR) in the initial diagnostic assessment of coronavirus disease 2019 (COVID-19) patients.MethodsA systematic review and meta-analysis were performed as per the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. A search of electronic information was conducted to identify all relevant studies comparing the diagnostic performance of chest CT scan versus RT-PCR in COVID-19 suspected cases. Sensitivity, specificity and accuracy were primary outcome measures. Secondary outcome measures included other test performance characteristics, discrepant findings between both investigations and main chest CT findings. Random effects modelling was used for the analyses.ResultsEight non-randomised retrospective studies enrolling 1910 patients were identified. Chest CT was more sensitive but less specific than RT-PCR. Accuracy was not statistically significantly different between chest CT and RT-PCR for the identification and exclusion of COVID-19 cases (Odds Ratio [OR] = 0.40, P = 0.15) in the context of hospitalised patients in a pandemic. Chest CT was shown to detect patients with false-negative RT-PCR results and true positives. Ground-glass opacities and consolidations were the most common chest CT manifestations.ConclusionsChest CT is not superior to RT-PCR for the initial detection of COVID-19 and has more false positives. It is likely to be useful in confirming COVID-19 in patients with a suspicious clinical presentation, but who have a false-negative SARS-CoV-2 RT-PCR test.Key Points‐Chest computed tomography (CT) is more sensitive but less specific in detecting and excluding coronavirus disease 2019 (COVID-19) when compared to reverse transcription polymerase chain reaction (RT-PCR).‐Accuracy of chest CT is not significantly different from RT-PCR for COVID-19 cases.‐Chest CT can detect false-negative and true-positive RT-PCR cases.

scholarly journals Sensitive and specific cytokeratin 18 reverse transcription-polymerase chain reaction that excludes amplification of processed pseudogenes from contaminating genomic DNA

1997 ◽  
Vol 43 (12) ◽  
pp. 2244-2250 ◽  
Author(s):  
Peter Tschentscher ◽  
Christoph Wagener ◽  
Michael Neumaier
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Genomic Dna ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Cytokeratin 18 ◽  
Processed Pseudogenes ◽  
Polymerase Chain ◽  
Positive Results ◽  
Pcr Conditions

Abstract Processed pseudogenes of residual contaminating genomic DNA interfere with a sensitive detection of cytokeratin 18 (CK18) mRNA by reverse transcription and polymerase chain reaction (RT-PCR). This may cause false-positive results when CK18 mRNA is used as a marker for ectopic tumor cells in specimens from cancer patients. To establish a sensitive CK18 RT-PCR by excluding the amplification of processed pseudogenes, the following strategy was chosen: (a) CK18 pseudogene sequences were cloned from genomic DNA by PCR; (b) cDNA-specific primers were designed on the basis of mismatches between pseudogenes and cDNA; (c) PCR conditions were adjusted to reach maximum sensitivity and specificity. Epithelial cells (1–10) could be detected in 1 mL of blood. Among the numerous CK18 genes homologous to the transcribed gene, at least two different processed pseudogenes exist that are highly homologous to each other and to the exons of the transcribed CK18 gene.

scholarly journals The Clinical and Radiological Manifestations in Coronavirus Disease 2019 With Negative Nucleic Acid Results

2020 ◽  
Vol 7 (7) ◽  
Author(s):  
Guanjing Lang ◽  
Junwei Su ◽  
Wenrui Wu ◽  
Hong Zhao ◽  
Shihong Ying ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Chest Ct ◽  
Common Symptom ◽  
Negative Group ◽  
Rt Pcr ◽  
Positive Group ◽  
Epidemiological Features ◽  
Polymerase Chain ◽  
And Gender ◽  
Positive Results

Abstract Background Coronavirus disease 2019 (COVID-19) was a new emerging disease with high infectiousness. Its diagnosis primarily depended on real-time polymerase chain reaction (RT-PCR) results. This study investigated epidemiological, clinical, and radiological characteristics of COVID-19 with negative RT-PCR results before confirmation. Methods Patients with COVID-19 were enrolled and divided into 2 groups: a negative group with negative RT-PCR results before confirmation and a positive group with positive results at the first detection. Epidemiological and clinical features were compared. Dynamic chest computerized tomography (CT) images of the negative group were evaluated. Results Ninety-nine laboratory-confirmed patients with COVID-19 including 8 patients (8%) with negative RT-PCR results were included. Patients from the negative group had similar epidemiological features: the average age (50.25 ± 13.27 years in the negative group and 53.70 ± 16.64 years in the positive group) and gender distribution (males made up 50% of the negative group and 62.6% of the positive group) were comparable. No significant differences were observed in clinical symptoms between the 2 groups. We found that fever was the most common symptom for both groups, followed by cough, expectoration, chest distress, fatigue, and gastroenterological symptoms. Moreover, ground-glass opacities and consolidations were the main manifestation in chest CT of patients with COVID-19 with or without confirmed RT-PCR results. Conclusions Regardless of initial RT-PCR results, patients with COVID-19 had similar epidemiological, clinical, and chest CT features. Our study suggests value from early chest CT scans in COVID-19 screening and dynamic significance of radiology in disease monitoring should guide clinical decisions.

scholarly journals maxRatio improves the detection of samples with abnormal amplification profiles on QIAgen’s artus HIV-1 qPCR assay

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1030
Author(s):  
Luigi Marongiu ◽  
Eric B. Shain ◽  
Marianna Martinelli ◽  
Matteo Pagliari ◽  
Heike Allgayer
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Predictive Value ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Alternative Approach ◽  
External Standard ◽  
Polymerase Chain ◽  
Anti Hiv ◽  
Hiv 1

Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR. Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay’s standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs. Results: FP and maxRatio were highly comparable (Pearson’s ρ=0.994, Cohen’s  κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles. Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.

scholarly journals Comparison of chest HRCT severity score in PCR positive and PCR negative clinically suspected COVID-19 Patients

2021 ◽  
Vol 21 (4) ◽  
pp. 1558-66
Author(s):  
Hina Hanif Mughal ◽  
Syed Muhammad Jawad Zaidi ◽  
Hamza Waqar Bhatti ◽  
Madiha Maryum ◽  
Maria Khaliq ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Severity Score ◽  
Clinical Symptoms ◽  
False Negative ◽  
Left Lung ◽  
Lung Damage ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Severity Scores ◽  
Polymerase Chain

Background: The limitations and false-negative results of Real-time Polymerase chain reaction (RT PCR) in diagnosing COVID-19 infection demand the need for imaging modalities such as chest HRCT to improve the diagnostic accuracy andassess the severity of the infection. Objectives: The study aimed to compare the chest HRCT severity scores in RT-PCR positive and negative cases of COVID-19. Methods: This cross-sectional study included 50 clinically suspected COVID-19 patients. Chest HRCT and PCR testing of all 50 patients were done and the chest HRCT severity scores for each lung and bronchopulmonary segments were compared in patients with positive and negative PCR results. Chi-square and Mann Whitney U test were used to assess differences among study variables. Results: Chest HRCT severity score was more in PCR negative patients than in those with PCR positive results . However, the difference was not significant (p=0.11). There was a significant association in severity scores of the anterior basal segment of the left lung (p=0.022) and posterior segment upper lobe of right lung (p=0.035) with PCR results. This association was insignificantfor other bronchopulmonary segments (p>0.05). Conclusion: CR negativity does not rule out infection in clinically suspected COVID-19 patients. The use of chest HRCT helps to determine the extent of lung damage in clinically suspected patients irrespective of PCR results. Guidelines that consider clinical symptoms, chest HRCT severity score and PCR results for a confirmed diagnosis of COVID-19 in suspected patientsare needed. Keywords: Chest High resolution computed tomography (HRCT); COVID-19; Polymerase Chain Reaction (PCR).

scholarly journals Accuracy of chest computed tomography and reverse transcription polymerase chain reaction in diagnosis of 2019 novel coronavirus disease; a systematic review and meta-analysis

2021 ◽  
Vol 7 (2) ◽  
pp. e36-e36
Author(s):  
Kamyar Shokraee ◽  
Hossein Mahdavi ◽  
Parsa Panahi ◽  
Farnoosh Seirafianpour ◽  
Amir Mohammad Jahromizadeh ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Systematic Review ◽  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Chest Computed Tomography ◽  
Polymerase Chain

Introduction: This study aims to measure the diagnostic accuracy of chest computed tomography (CT) and reverse transcription polymerase chain reaction assay (RT-PCR) in COVID-19 in a systematic review and meta-analysis. Methods: PubMed, Scopus, Embase, and Google Scholar, WHO, SSRN, and MedRxiv have been searched on March 26, 2020 for all the alternative names of the disease and virus. Risk of bias assessment was based on QUADAS-2. Data from English-language studies after January 12, 2019 were pooled to calculate necessary diagnostic values and underwent diagnostic test accuracy, random-effects, proportions, and subgroup meta-analysis. Results: Pooled from 27 included studies, the sensitivity of chest CT was calculated 96.6%, specificity 22.5%, diagnostic odds ratio (DOR) 8.2, positive likelihood ratio (PLR) 1.2 (95% CI: 1.1-1.4), and negative likelihood ratio (NLR) 0.15 (95% CI: 0.1-0.3). The sensitivity for initial RT-PCR was 79.7%, the specificity 100%, and NLR 0.18. Conclusion: Considering the results, in order to diagnose COVID-19 (coronavirus disease 2019), it is recommended to initially performing chest CT to rule out the uninfected people. In suspicious cases, we suggest RT-PCR to confirm the disease. Performing serial RT-PCR instead of the one-time test is highly recommended, to let the viral loads reach the diagnostic levels, especially in cases of high clinical suspicion.

scholarly journals Development of a reverse transcription polymerase chain reaction for the detection of severe fever with thrombocytopenia syndrome virus from suspected infected animals

2020 ◽  
Author(s):  
Eun-sil Park ◽  
Osamu Fujita ◽  
Masanobu Kimura ◽  
Akitoyo Hotta ◽  
Koichi Imaoka ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Neutralizing Antibodies ◽  
Clinical Symptoms ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Primer Sets ◽  
Severe Fever

AbstractBackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV) causes severe hemorrhagic fever in humans and cats. Clinical symptoms of SFTS-infected cats resemble to those of SFTS patients and SFTS-contracted cats shows high levels of viral RNA loads in the serum and body fluids. Due to the risk of direct infection from SFTS-infected cats to human, it is important to diagnose SFTS-suspected animals.Methodology/Principle findingsFour primer sets were newly designed from consensus sequences constructed by 108 strains of SFTSV. A reverse transcription polymerase chain reaction (RT-PCR) with these four primer sets were successfully and specifically detected several clades of SFTSV. Their limits of detection are 1-10 copies/reaction. By this RT-PCR, 5 cat cases among 56 SFTS-suspected animal cases were diagnosed as SFTS. From these cats, IgM or IgG against SFTSV were detected by enzyme-linked immunosorbent assay (ELISA), but not neutralizing antibodies by plaque reduction neutralization titer (PRNT) test. This phenomenon is similar to those of fatal SFTS patients.Conclusion/SignificanceThis newly developed RT-PCR could detect SFTSV RNA of several clades from SFTS-suspected animals. In addition to ELISA and PRNT test, the useful laboratory diagnosis systems of SFTS-suspected animals has been made in this study.Author summaryThis study developed RT-PCR to detect SFTS animal cases. This assay could detect SFTSV RNA belonging to different clades. Cats diagnosed as SFTS had IgM or IgG, but not neutralizing antibodies. SFTS cat cases were distributed in the area where SFTS patients have been reported highly, indicating the establishment of the circulation of SFTSV in the environment. These diagnostic assays could be helpful tools to detect and not to miss SFTS animal cases.

scholarly journals Association between Clinical, Laboratory and CT Characteristics and RT-PCR Results in the Follow-up of COVID-19 patients

2020 ◽  
Author(s):  
Hang Fu ◽  
Huayan Xu ◽  
Na Zhang ◽  
Hong Xu ◽  
Zhenlin Li ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Clinical Laboratory ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Radiological Data ◽  
Polymerase Chain ◽  
Ct Features

AbstractBackgroundSince December 2019, more than 100,000 coronavirus disease 2019 (COVID-19) patients have been confirmed globally based on positive viral nucleic acids with real-time reverse transcriptase-polymerase chain reaction (RT-PCR). However, the association between clinical, laboratory and CT characteristics and RT-PCR results is still unclear. We sought to examine this association in detail, especially in recovered patients.MethodsWe analysed data from 52 confirmed patients who had been discharged with COVID-19. The clinical, laboratory, and radiological data were dynamically recorded and compared with the admission and follow-up RT-PCR results.ResultsIn this cohort, 52 admitted COVID-19 patients who had confirmed positive RT-PCR results were discharged after 2 rounds of consecutively negative RT-PCR results. Compared with admission levels, CRP levels (median 4.93 mg/L [IQR: 1.78-10.20]) decreased significantly (p<0.001). and lymphocyte counts (median 1.50×109/L [IQR: 1.11-1.88]) increased obviously after obtaining negative RT-PCR results (p<0.001). Additionally, substantially improved inflammatory exudation was observed on chest CT except for 2 progressed patients. At the two-week follow-up after discharge, 7 patients had re-positive RT-PCR results, including the abovementioned 2 progressed patients. Among the 7 patients, new GGO was demonstrated in 2 patients. There were no significant differences in CPR levels or lymphocyte counts when comparing the negative and re-positive PCT results (all p >0.05).ConclusionHeterogeneity between CT features and RT-PCR results was found in COVID-19, especially in some recovered patients with negative RT-PCR results. Our study highlights that both RT-PCR and chest CT should be considered as the key determinants for the diagnosis and management of COVID-19 patients.

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