scholarly journals Better Diagnostic Modality for COVID-19: CT Chest or RT - PCR? - A Systematic Review

BioMedica ◽  
2020 ◽  
Vol 36 (2S) ◽  
pp. 169-174
Author(s):  
Seemi Tanvir ◽  
Ayesha Fazal ◽  
Sadia Sajjad ◽  
Shabbir Ahmed
Keyword(s):  
Systematic Review ◽  
Literature Search ◽  
Web Of Science ◽  
Review Paper ◽  
Diagnostic Methods ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Diagnostic Modality ◽  
Diagnostic Potential ◽  
Polymerase Chain

<p><strong>Background and Objective:</strong> A set of new studies is offering perspective and guidance on the differences between using Real Time Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and chest Computerized tomography (CT) in terms of sensitivity and specificity. This review paper addresses the comparative diagnostic potential of CT chest and RT-PCR for COVID-19. <strong>Method: </strong>An online literature search was carried out from Jan. 2020 to Apr. 2020 from Google -Scholar, Web of Science, Science Direct and PubMed using the MeSH key words. Twenty-five articles were retrieved. Articles with incomplete information and covering other factors like ethnicity were excluded and only the articles with comparison between two clinical diagnostic methods were included. Avoiding the duplication of issues, 5 articles were finally selected for review. <strong>Result:</strong> This review observed 98% pooled sensitivity of CT-chest being much higher than that of RT-PCR (75%). <strong>Conclusion:</strong> Patients with suspicion of COVID-19 should be screened using CT scan chest as a more sensitive technique.</p>

Accuracy of real-time polymerase chain reaction to detect Schistosoma mansoni – infected individuals from an endemic area with low parasite loads

Parasitology ◽  
2020 ◽  
Vol 147 (10) ◽  
pp. 1140-1148
Author(s):  
Fernanda do Carmo Magalhães ◽  
Samira Diniz Resende ◽  
Carolina Senra ◽  
Carlos Graeff-Teixeira ◽  
Martin Johannes Enk ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Schistosoma Mansoni ◽  
Real Time ◽  
Diagnostic Methods ◽  
Control Measures ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Cross Sectional ◽  
Intestinal Schistosomiasis ◽  
Polymerase Chain

AbstractDue to the efforts to control schistosomiasis transmission in tropical countries, a large proportion of individuals from endemic areas present low parasite loads, which hinders diagnosis of intestinal schistosomiasis by the Kato-Katz (KK) method. Therefore, the development of more sensitive diagnostic methods is essential for efficient control measures. The aim was to evaluate the accuracy of a real-time polymerase chain reaction (RT-PCR) to detect Schistosoma mansoni DNA in fecal samples of individuals with low parasite loads. A cross-sectional population-based study was conducted in a rural community (n = 257) in Brazil. POC-CCA® was performed in urine and feces were used for RT-PCR. In addition, fecal exams were completed by 18 KK slides, saline gradient and Helmintex techniques. The combined results of the three parasitological tests detected schistosome eggs in 118 participants (45.9%) and composed the consolidated reference standard (CRS). By RT-PCR, 117 out of 215 tested samples were positive, showing 91.4% sensitivity, 80.2% specificity and good concordance with the CRS (kappa = 0.71). RT-PCR identified 86.9% of the individuals eliminating less than 12 eggs/g of feces, demonstrating much better performance than POC-CCA® (50.8%). Our results showed that RT-PCR is a valuable alternative for the diagnosis of intestinal schistosomiasis in individuals with very low parasite loads.

scholarly journals Methods of Diagnosis a Preferential Advantage in COVID-19: A Mini Review

2021 ◽  
pp. 173-179
Author(s):  
Neha Saini ◽  
Prem Pandey ◽  
Mandar Shirolkar ◽  
Atul Kulkarni
Keyword(s):  
Polymerase Chain Reaction ◽  
Severe Acute Respiratory Syndrome ◽  
Review Article ◽  
Diagnostic Methods ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Health Crisis ◽  
The World ◽  
Polymerase Chain ◽  
Novel Coronavirus

Humanity is going through never seen before health crisis due to the outbreak of novel coronavirus or Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). There are 24.02 million cases and 0.82 million deaths worldwide as of 26th August 2020 due to deadly infection of COVID-19. The disease has been spreading exponentially (R-naught number: 3) and has challenged even the best healthcare infrastructure in the world. With the progression of the disease, the countries shifted the focus from cure to diagnosis and containment to flatten the curve. The review shows that the disease is spreading exponentially while the resources are still limited. We focus upon the probable vectors of the virus, different diagnostic methods with advantages & limitations, and the way forward. This review article covers the different diagnostic methods with more advantages, limitations, and the future sneak-peek into the forthcoming developments for the diagnostic processes such as RT-PCR (Reverse Transcription Polymerase chain reaction).

scholarly journals Systematic Review and Meta-analysis of Real-time Polymerase Chain Reaction assay for the detection of COVID-19 from clinical samples in low-and middle-income countries: Protocol

2021 ◽  
Author(s):  
Emmanuel Oladipo Babafemi
Keyword(s):  
Systematic Review ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Meta Analysis ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Middle Income ◽  
Polymerase Chain

Abstract Background: COVID-19 has spread globally since its discovery in Hubei province, China in December 2019 and became pandemic in 2020. COVID-19 is a new betacoronavirus and a variant of severe acute respiratory syndrome coronavirus 2 (SARA- CoV-2). Rapid, accurate and reliable diagnosis of COVID-19 will prevent the spread and allow for appropriate management. The main objective of this systematic review is to identify, appraise and summarise the published evidence on the diagnostic performance and effectiveness of SARS-CoV-2 virus in the diagnosis of current or previous COVID-19 using real-time polymerase chain reaction (RT-PCR) assay in low-and middle-income countries (LMICs). Methods: We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL for published studies for the diagnosis of COVID-19 using real-time polymerase chain reaction assay in LMICs There will be no restriction regarding the language, date of publication, and publication status. We will include retrospective, cross-sectional and cohort observational studies will be included in the review. Selection of studies, data extraction and management, assessment of risk of bias, and quality of evidence will be performed by two independent reviewers (EB and BC). A third researcher (GM) will be consulted in case of discrepancies. Depending on the availability and quality of the data, a meta-analysis will be performed. Otherwise, findings will be qualitatively reported. Discussion: To our knowledge, this is the first systematic review and meta-analysis to assess the uptake of RT-PCR assay for SARS-CoV-2 detection from clinical samples in human in LMICs. This review will make available evidence on the uptake, accuracy, approach, and interpretation of results of this assay in the context of COVID-19 diagnosis which will meet an urgent need, considering the diagnostic challenges of RT-PCR assay for COVID-19 diagnosis in humans. Systematic review registration: PROSPERO CRD42021271894

scholarly journals Real-time fluorogenic reverse transcription polymerase chain reaction assay for the specific detection of Bagaza virus

2012 ◽  
Vol 24 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Dolores Buitrago ◽  
Ana Rocha ◽  
Cristina Tena-Tomás ◽  
Marta Vigo ◽  
Montserrat Agüero ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Reverse Transcription ◽  
Diagnostic Methods ◽  
Nucleotide Sequencing ◽  
Alectoris Rufa ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Field Samples ◽  
Polymerase Chain

In September 2010, an outbreak of disease in 2 wild bird species (red-legged partridge, Alectoris rufa; ring-necked pheasant, Phasianus colchicus) occurred in southern Spain. Bagaza virus (BAGV) was identified as the etiological agent of the outbreak. BAGV had only been reported before in Western Africa (Central African Republic, Senegal) and in India. The first occurrence of BAGV in Spain stimulated a demand for rapid, reliable, and efficacious diagnostic methods to facilitate the surveillance of this disease in the field. This report describes a real-time reverse transcription polymerase chain reaction (RT-PCR) method based on a commercial 5’-Taq nuclease-3’ minor groove binder DNA probe and primers targeting the Bagaza NS5 gene. The method allowed the detection of BAGV with a high sensitivity, whereas other closely related flaviviruses ( Usutu virus, West Nile virus, and Japanese encephalitis virus) were not detected. The assay was evaluated using field samples of red-legged partridges dead during the outbreak ( n = 11), as well as samples collected from partridges during surveillance programs ( n = 81). The results were compared to those obtained with a pan-flaviviral hemi-nested RT-PCR followed by nucleotide sequencing, which was employed originally to identify the virus involved in the outbreak. The results obtained with both techniques were 100% matching, indicating that the newly developed real-time RT-PCR is a valid technique for BAGV genome detection, useful in both diagnosis and surveillance studies.

scholarly journals The optimal diagnostic methods for COVID-19

Diagnosis ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 349-356 ◽  
Author(s):  
Tinotenda A. Harahwa ◽  
Thomas Ho Lai Yau ◽  
Mae-Sing Lim-Cooke ◽  
Salah Al-Haddi ◽  
Mohamed Zeinah ◽  
...  
Keyword(s):  
Treatment Plan ◽  
Ct Scanning ◽  
Diagnostic Methods ◽  
X Rays ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Global Spread ◽  
Polymerase Chain ◽  
Direct Confirmation ◽  
Limited Sensitivity

AbstractAs the world continues to study and understand coronavirus disease (COVID-19), existing investigations and tests have been used to try and detect the virus to slow viral transmission and its global spread. A ‘gold-standard’ investigation has not yet been identified for detection and monitoring. Initially, computed tomography (CT) was the mainstay investigation as it shows the disease severity and recovery, and its images change at different stages of the disease. However, CT has been found to have limited sensitivity and negative predictive value in the early stages of the disease, and the value of its use has come under debate due to whether its images change the treatment plan, the risk of radiation, as well as its practicality with infection control. Therefore, there has been a shift to the use of other imaging modalities and tests, such as chest X-rays and ultrasound. Furthermore, the use of nucleic acid-based testing such as reverse-transcriptase polymerase chain reaction (RT-PCR) have proven useful with direct confirmation of COVID-19 infection. In this study, we aim to review and analyse current literature to compare RT-PCR, immunological biomarkers, chest radiographs, ultrasound and chest CT scanning as methods of diagnosing COVID-19.

scholarly journals Nucleic Acid Testing of SARS-CoV-2

2021 ◽  
Vol 22 (11) ◽  
pp. 6150
Author(s):  
Hee-Min Yoo ◽  
Il-Hwan Kim ◽  
Seil Kim
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Reverse Transcription ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Nucleic Acid Testing ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.

scholarly journals Exploring the Clinical Utility of Gustatory Dysfunction (GD) as a Triage Symptom Prior to Reverse Transcription Polymerase Chain Reaction (RT-PCR) in the Diagnosis of COVID-19: A Meta-Analysis and Systematic Review

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1315
Author(s):  
Khang Wen Pang ◽  
Sher-Lyn Tham ◽  
Li Shia Ng
Keyword(s):  
Systematic Review ◽  
Polymerase Chain Reaction ◽  
Likelihood Ratio ◽  
Reverse Transcription ◽  
Meta Analysis ◽  
Significant Heterogeneity ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Background: The diagnosis of COVID-19 is made using reverse transcription polymerase chain reaction (RT-PCR) but its sensitivity varies from 20 to 100%. The presence of gustatory dysfunction (GD) in a patient with upper respiratory tract symptoms might increase the clinical suspicion of COVID-19. Aims: To perform a systematic review and meta-analysis to determine the pooled sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR−) and diagnostic odds ratio (DOR) of using GD as a triage symptom prior to RT-PCR. Methods: PubMed and Embase were searched up to 20 June 2021. Studies published in English were included if they compared the frequency of GD in COVID-19 adult patients (proven by RT-PCR) to COVID-19 negative controls in case control or cross-sectional studies. The Newcastle-Ottawa scale was used to assess the methodological quality of the included studies. Results: 21,272 COVID-19 patients and 52,298 COVID-19 negative patients were included across 44 studies from 21 countries. All studies were of moderate to high risk of bias. Patients with GD were more likely to test positive for COVID-19: DOR 6.39 (4.86–8.40), LR+ 3.84 (3.04–4.84), LR− 0.67 (0.64–0.70), pooled sensitivity 0.37 (0.29–0.47) and pooled specificity 0.92 (0.89–0.94). While history/questionnaire-based assessments were predictive of RT-PCR positivity (DOR 6.62 (4.95–8.85)), gustatory testing was not (DOR 3.53 (0.98–12.7)). There was significant heterogeneity among the 44 studies (I2 = 92%, p < 0.01). Conclusions: GD is useful as a symptom to determine if a patient should undergo further testing, especially in resource-poor regions where COVID-19 testing is scarce. Patients with GD may be advised to quarantine while repeated testing is performed if the initial RT-PCR is negative. Funding: None.

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.

Diagnostic determination of Norovirus infection as one of the major causes of infectious diarrhea in HIV patients using a multiplex polymerase chain reaction assay

2019 ◽  
Vol 30 (6) ◽  
pp. 550-556 ◽  
Author(s):  
Siyuan Yang ◽  
Min Li ◽  
Jingwei Cheng ◽  
Gang Wan ◽  
Yunao Zhou ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Polymerase Chain Reaction ◽  
Diagnostic Methods ◽  
Enterotoxigenic Escherichia Coli ◽  
Rt Pcr ◽  
Infectious Diarrhea ◽  
Chain Reaction ◽  
Hiv Patients ◽  
Stool Specimens ◽  
Polymerase Chain

Although infectious diarrhea is one of the most common complications in human immunodeficiency virus (HIV)-infected patients, robust diagnostic methods for determining potential pathogens are still limited in the clinic. Norovirus, a type of calicivirus, has been shown to be the most common cause of gastroenteritis. Here, we used multiplex polymerase chain reaction as a diagnostic tool to verify Norovirus as the diarrhea-related pathogen in HIV-infected patients with unknown etiological information. Stool specimens obtained from 81 HIV-infected patients with diarrhea were analyzed by BioFire FilmArray Gastrointestinal (GI) panel. Among 26 HIV-infected patients with unknown etiological information, we detected Norovirus in 14 stool specimens of these patients with 100% sensitivity and specificity as confirmed by reverse transcription polymerase chain reaction (RT-PCR), and one specimen showed both Norovirus and enterotoxigenic Escherichia coli infection. Among the remaining 55 patients with verified Clostridium difficile infection, nine patients also detected positive for Norovirus infection. In conclusion, using FilmArray GI panel and RT-PCR, we determined that Norovirus infection as one of the main pathogens responsible for diarrhea in HIV patients.

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