scholarly journals Detection of SARS-CoV-2 by real time Reverse Transcriptase-Polymerase Chain Reaction assay in pleural effusion

2021 ◽  
pp. 201
Author(s):  
Keyword(s):  
Polymerase Chain Reaction ◽  
Pleural Effusion ◽  
Reverse Transcriptase ◽  
Pleural Fluid ◽  
Interstitial Pneumonia ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Pleural Involvement

SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) is a novel coronavirus identified for the first time in Wuhan (China) in 2019, responsible of the current pandemic infection known as Coronavirus-19 disease (COVID-19). Wide range of clinical presentation of COVD -19 has been observed, from asymptomatic carriers to ARDS. The common signs and symptoms of SARS-CoV-2 infection include fever, fatigue, dry cough, and dyspnoea; the severity of the disease is due to the impairment of the respiratory function. The radiological findings include a large variety of lesions; bilateral interstitial pneumonia is the most concerning presentation of COVID-19. Pleural involvement has been described in a minority of cases: pleural thickening had been observed in 32% of cases whereas pleural effusion is uncommon being described in only 5%. Furthermore, pleural involvement has been significantly associated with a worse prognosis. Coronavirus 2 (SARS-CoV-2), beyond the nasopharyngeal swab, has been detected in other samples; up to now, data about RT-PCR specific results in the pleural fluid of patients suffering from coronavirus disease 2019 5 (COVID-19) are very limited. The current gold standard for diagnosis is nucleic acid detection by real time Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) in nasopharyngeal swab. In this report, a case of a positive RT-PCR for Sars-Cov-2 in the pleura fluid and in the naso- pharyngeal swab of a patient affected by bilateral interstitial pneumonia and severe respiratory failure is described. As the presence of SARS-Cov-2 in the pleural fluid seems to be associated to a poor prognosis, physicians should carry out the specific RT-PCR assay both in the nasopharyngeal swab and in the pleural sample also when the fluid amount is very scarce and not recognizable in the chest X ray. Furthermore, the analysis of multiple samples allows to increase the test reliability.

scholarly journals High Resolution CHEST CT(HRCT) Evaluation in Patients Hospitalized with COVID-19 Infection

2020 ◽  
Author(s):  
Maulin Patel ◽  
Junad Chowdhury ◽  
Matthew Zheng ◽  
Osheen Abramian ◽  
Steven Verga ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
High Resolution ◽  
Diagnostic Accuracy ◽  
Reverse Transcriptase ◽  
Retrospective Analysis ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Bottom Line ◽  
Polymerase Chain

AbstractIntroductionCurrently the main diagnostic modality for COVID-19 (Coronavirus disease-2019) is reverse transcriptase polymerase chain reaction (RT-PCR) via nasopharyngeal swab which has high false negative rates. We evaluated the performance of high-resolution computed tomography (HRCT) imaging in the diagnosis of suspected COVID-19 infection compared to RT-PCR nasopharyngeal swab alone in patients hospitalized for suspected COVID-19 infection.MethodsThis was a retrospective analysis of 324 consecutive patients admitted to Temple University Hospital. All hospitalized patients who had RT-PCR testing and HRCT were included in the study. HRCTs were classified as Category 1, 2 or 3. Patients were then divided into four groups based on HRCT category and RT-PCR swab results for analysis.ResultsThe average age of patients was 59.4 (±15.2) years and 123 (38.9%) were female. Predominant ethnicity was African American 148 (46.11%). 161 patients tested positive by RT-PCR, while 41 tested positive by HRCT. 167 (52.02%) had category 1 scan, 63 (19.63%) had category 2 scan and 91 (28.35%) had category 3 HRCT scans. There was substantial agreement between our radiologists for HRCT classification (κ = 0.64). Sensitivity and specificity of HRCT classification system was 77.6 and 73.7 respectively. Ferritin, LDH, AST and ALT were higher in Group 1 and D-dimers levels was higher in Group 3; differences however were not statistically significant.ConclusionDue to its high infectivity and asymptomatic transmission, until a highly sensitive and specific COVID-19 test is developed, HRCT should be incorporated into the assessment of patients who are hospitalized with suspected COVID-19.Key PointsKey QuestionCan High Resolution CT chest (HRCT) improve diagnostic accuracy of current Nasopharyngeal swab in suspected COVID-19 patients?Bottom LineIn this retrospective analysis, our novel HRCT classification identified 20% of all COVID-19 patients who had negative nasopharyngeal reverse transcriptase polymerase chain reaction (RT-PCR) tests but had HRCT findings consistent with COVID-19 pneumonia. These patients were ruled out for other infections and laboratory markers were similar to other RT-PCR positive patientsWhy Read onOur new HRCT classification when combined with RT-PCR can improve diagnostic accuracy while promptly improving triaging in COVID-19 patients.

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 Use of immunodot blot and multiplex reverse transcriptase-polymerase chain reaction in dengue virus detection in macerates of Aedes aegypti larvae

2012 ◽  
Vol 3 (1) ◽  
pp. 13
Author(s):  
Aline T.A. Chagas ◽  
Michelle D. Oliveira ◽  
Jose M.S. Mezencio ◽  
Eduardo A.M. Silva ◽  
Leandro L. Oliveira ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Aedes Aegypti ◽  
Dengue Virus ◽  
Reverse Transcriptase ◽  
Epidemiological Surveillance ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Denv Serotypes ◽  
Polymerase Chain ◽  
Pcr Techniques

The <em>Dengue virus</em> is the main arbovirus that affects man in terms of morbidity and mortality. The detection of the virus is very important for epidemiological surveillance, so here we propose to standardize and compare the immunodot blot (IDB) and multiplex reverse transcriptase-polymerase chain reaction (M-RT-PCR) techniques to detect and characterize the dengue virus (DENV) serotypes in samples of <em>Aedes aegypti</em> larvae. Thus, the IDB and M-RT-PCR techniques were standardized using macerated samples of larvae collected in nature. The use of monoclonal antibodies in IDB has not shown great results, but DENV detection through this method was possible using polyclonal antibodies. The distinction of serotypes 1, 2 and 3 was carried out by M-RT-PCR.

scholarly journals Deteksi Molekuler Virus Dengue dan Chikungunya pada Nyamuk Aedes spp. di Kecamatan Cilongok

2020 ◽  
Vol 2 (2) ◽  
pp. 181
Author(s):  
Dwi Iva Fitriana ◽  
Endang Srimurni Kusmintarsih ◽  
Trisnowati Budi Ambarningrum
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

DBD dan chikungunya merupakan salah satu penyakit yang masih menjadi masalah di Indonesia. Kecamatan Cilongok merupakan salah kecamatan endemis DBD dan pernah mengalami KLB chikungunya. Deteksi virus pada nyamuk sebelum menginfeksi manusia penting sebagai peringatan dini dalam upaya pencegahan wabah di daerah endemis. Tujuan penelitian ini adalah mengetahui infeksi virus Dengue dan Chikungunya pada nyamuk Aedes spp. yang ditangkap. Penelitian ini dilakukan di empat desa di Kecamatan Cilongok yang meliputi Desa Cilongok, Pernasidi, Kalisari, dan Jatisaba, pengambilan sampel dilakukan secara purposive. Deteksi virus Dengue dan Chikungunya pada nyamuk dilakukan menggunakan metode Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR). Hasil positifitas virus dianalisis secara deskriptif untuk menggambarkan potensi transmisi virus. Hasil penelitian menunjukkan bahwa nyamuk Aedes spp. yang tertangkap tidak mengandung virus Dengue dan Chikungunya.  

scholarly journals Outcome of COVID-19 in Solid Organ Malignancies: Experience From a Tertiary Cancer Center in Eastern India

2021 ◽  
pp. 1374-1379
Author(s):  
Somnath Roy ◽  
Joydeep Ghosh ◽  
Sandip Ganguly ◽  
Debapriya Mondal ◽  
Deepak Dabkara ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Median Duration ◽  
Cancer Center ◽  
Nasopharyngeal Swab ◽  
Solid Organ ◽  
Chain Reaction ◽  
Unique Challenge ◽  
Risk Of Death ◽  
Polymerase Chain

PURPOSE The COVID-19 pandemic has imposed a unique challenge to oncology patients. Outcome data on COVID-19 in patients with cancer from the Indian subcontinent are scarce in the literature. We aimed to evaluate the outcome of patients with COVID-19 on active systemic anticancer therapy. MATERIALS AND METHODS This is a retrospective study of patients with solid organ malignancies undergoing systemic therapy with a diagnosis of COVID-19 between March 2020 and February 2021. COVID-19 was diagnosed if a reverse transcriptase polymerase chain reaction assay from oropharyngeal or nasopharyngeal swab was positive for severe acute respiratory syndrome coronavirus 2. The objectives were to evaluate the outcome of COVID-19 and factors predicting the outcome. RESULTS A total of 145 patients were included with a median age of 58 years (range, 20-81 years). Treatment was curative in 60 (42%) patients. Of all symptomatic cases (n = 88, 61%), 50 had mild, 27 had moderate and 19 had severe COVID-19–related symptoms as per WHO criteria. Fifty (34%) patients required hospitalization with a median duration of hospital stay of 12 days (range, 4-25 days); five patients required intensive care unit admission. The rest were treated with home isolation and did not require further hospitalization. Twenty-two (15%) patients died, and the risk of death was significantly associated with severity of symptoms (odds ratio, 91.3; 95% CI, 9.1 to 919.5, P = .0001) but not with any other clinical factors. Drug holiday was given to 63 (44%) patients with a median duration of 25 days (range, 7-88 days). The median duration to reverse transcriptase polymerase chain reaction–negative was 16 days (range, 7-62 days). CONCLUSION COVD-19–related death rate was 15% among patients with solid organ malignancies. The severity of the symptoms was related to mortality. The majority of patients with mild symptoms were treated at home isolation.

scholarly journals The utility of real-time polymerase chain reaction in detecting Coccidioides immitis among clinical specimens in the Central California San Joaquin Valley

2018 ◽  
Vol 57 (6) ◽  
pp. 688-693 ◽  
Author(s):  
Dominic Dizon ◽  
Marilyn Mitchell ◽  
Bernadette Dizon ◽  
Robert Libke ◽  
Michael W Peterson
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Pleural Fluid ◽  
Clinical Setting ◽  
Predictive Value ◽  
Coccidioides Immitis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Acute Pneumonia ◽  
Polymerase Chain

AbstractCoccidioidomycosis, the fungal infection caused by dimorphic Coccidioides species, is typically diagnosed by histopathologic identification of spherules, by culture, or by serology. These tests are reliable but time-intensive, delaying diagnosis and treatment. Rapid real-time polymerase chain reaction (RT-PCR) can be performed and was validated to identify Coccidioides immitis using an in-house developed assay for the Becton Dickinson molecular instrument (BD MAXTM). These studies were performed using patient samples that had been shown to be positive on previously set up fungal cultures. To evaluate this new RT-PCR test in the clinical setting, we conducted a retrospective chart review of patients (N = 1160) who underwent Coccidioides PCR (Cocci PCR) on clinical samples between March 1, 2014, and Dec 31, 2016. We abstracted clinical, microbiologic, serologic, radiographic, treatment, and follow-up data. Specimens of cerebrospinal fluid (CSF), bronchioalveolar lavage fluid (BAL), lung tissue biopsy (LTB), sputum, and pleural fluid were evaluated to determine sensitivity and specificity. Of the 113 specimens that tested positive for Cocci PCR, all had clinical disease defined by traditional clinical criteria, yielding 100% specificity. Overall sensitivity was 74% versus 46% for fungal culture and was available in 4 hours rather than 1–2 weeks. Sensitivities varied by source material and clinical setting. CSF had a sensitivity of 59%, BAL for acute pneumonia 91%, sputum for acute pneumonia 94%, pleural fluid 86%, but LTB for lung nodules only 44%. Overall positive predictive value (PPV) was 100%, while negative predictive value (NPV) was 96%, but again this varied by specimen and clinical setting. Our experience with clinical testing of >1160 specimens over 2–3 years shows we can utilize this technology to improve our ability to diagnose disease but that the sensitivity varies by specimen source and clinical setting.

scholarly journals A reverse transcriptase-polymerase chain reaction detects heterogeneous chimeric mRNAs in leukemias with 11q23 abnormalities

Blood ◽  
1994 ◽  
Vol 83 (10) ◽  
pp. 2912-2921 ◽  
Author(s):  
K Yamamoto ◽  
M Seto ◽  
S Iida ◽  
H Komatsu ◽  
N Kamada ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Response To Therapy ◽  
Chromosome 9 ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Single Clone ◽  
Sensitivity Studies ◽  
Polymerase Chain ◽  
11Q23 Abnormalities

Abstract The MLL gene involved in 11q23 translocations found in the majority of infantile leukemias and some secondary leukemias makes fusion transcripts with genes such as LTG4 (chromosome 4), LTG9 (chromosome 9), and LTG19 (chromosome 19) as a result of reciprocal translocation. We have examined 25 cases of leukemias with 11q23 abnormalities by Southern blot analysis and the reverse transcriptase-polymerase chain reaction (RT-PCR). Using various primer pairs, chimeric mRNAs could be amplified in 6 of 7 leukemias with t(4;11), 6 of 8 leukemias with t(9;11) including secondary leukemia, 8 of 9 leukemias with t(11;19), and 1 with a deletion at 11q23. The chimeric mRNAs were heterogeneous and differential usage of the MLL exons was found, irrespective of the partner chromosomes. Sensitivity studies showed that a single clone with chimeric mRNA in 10(4) to 10(5) cells could be detected. These findings show that the present RT-PCR settings provide a rapid, accurate, and sensitive tool for diagnosing leukemias with 11q23 translocations and for monitoring response to therapy in these patients.

Detection of Occult Melanoma Cells in Paraffin-Embedded Histologically Negative Sentinel Lymph Nodes Using a Reverse Transcriptase Polymerase Chain Reaction Assay

2001 ◽  
Vol 19 (5) ◽  
pp. 1437-1443 ◽  
Author(s):  
Giuseppe Palmieri ◽  
Paolo A. Ascierto ◽  
Antonio Cossu ◽  
Nicola Mozzillo ◽  
Maria L. Motti ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Prognostic Significance ◽  
Primary Melanoma ◽  
Disease Stage ◽  
Occult Metastasis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Polymerase Chain

PURPOSE: Detection of occult metastasis before the development of clinical disease could allow more accurate staging, appropriate follow-up procedures, and adjuvant therapies in patients with malignant melanoma (MM). The sentinel lymph node (SLN) has been proposed as a reliable predictor of metastatic disease in the lymphatic basin draining the primary melanoma. In this study, we screened both paraffin-embedded SLNs and peripheral-blood (PB) samples from MM patients at various stage of disease using a multimarker reverse transcriptase polymerase chain reaction (RT-PCR) assay. The prognostic significance of the presence of PCR-positive markers was also evaluated. PATIENTS AND METHODS: Total RNA was obtained from paraffin-embedded SLN sections and PB samples of 75 MM patients. RT-PCR was performed using tyrosinase and MelanA/MART1 as melanoma-associated markers. Radiolabeled PCR products were analyzed on denaturing polyacrylamide gels. RESULTS: Good sensitivity of the RT-PCR assay on archival tissues was demonstrated after comparison of RT-PCR results on frozen and paraffin-embedded SLNs from 16 MM patients. Significant correlation between the disease stage and marker expression in both PB and SLN samples was observed; the highest value was for patients who were positive for both markers in SLN (P = .006). Progression of disease was significantly associated with the total number of PCR-positive markers in both PB (P = .034) and SLN (P = .001) samples. CONCLUSION: Although sensitivity is lowered by the use of paraffin-embedded specimens, our data indicate that RT-PCR analysis of serial sections from archival SLNs may be helpful in improving detection of occult micrometastases, thus improving staging of patients with melanoma.

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