scholarly journals Deep Learning Analysis Improves Specificity of SARS-CoV-2 Real Time PCR

Author(s):  
David J. Alouani ◽  
Roshani R.P. Rajapaksha ◽  
Mehul Jani ◽  
Daniel D. Rhoads ◽  
Navid Sadri

Real time polymerase chain reaction (RT-PCR) is widely used to diagnose human pathogens. RT-PCR data is traditionally analyzed by estimating the threshold cycle (CT) at which the fluorescence signal produced by emission of a probe crosses a baseline level. Current models used to estimate the CT value are based on approximations that do not adequately account for the stochastic variation of the fluorescence signal that is detected during RT-PCR. Less common deviations become more apparent as the sample size increases, as is the case in the current SARS-CoV-2 pandemic. In this work we employ a method independent of CT value to interpret to RT-PCR data. In this novel approach we built and trained a deep learning model, qPCRdeepNet, to analyze the fluorescent readings obtained during RT-PCR. We describe how this model can be deployed as a quality assurance tool to monitor results interpretation in real-time. The model’s performance with the TaqPath COVID19 Combo Kit, widely used for SARS-CoV-2 detection, is described. This model can be applied broadly for the primary interpretation of RT-PCR assays and potentially replace the CT interpretive paradigm.

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske

2020 ◽  
pp. 175717742097679
Author(s):  
Kordo Saeed ◽  
Emanuela Pelosi ◽  
Nitin Mahobia ◽  
Nicola White ◽  
Christopher Labdon ◽  
...  

Background: We report an outbreak of SARS coronavirus-2 (SARS-CoV-2) infection among healthcare workers (HCW) in an NHS elective healthcare facility. Methodology: A narrative chronological account of events after declaring an outbreak of SARS-CoV-2 among HCWs. As part of the investigations, HCWs were offered testing during the outbreak. These were: (1) screening by real-time reverse transcriptase polymerase chain reaction (RT- PCR) to detect a current infection; and (2) serum samples to determine seroprevalence. Results: Over 180 HCWs were tested by real-time RT-PCR for SARS-CoV-2 infection. The rate of infection was 15.2% (23.7% for clinical or directly patient-facing HCWs vs. 4.8% in non-clinical non-patient-facing HCWs). Of the infected HCWs, 57% were asymptomatic. Seroprevalence (SARS-CoV-2 IgG) among HCWs was 13%. It was challenging to establish an exact source for the outbreak. The importance of education, training, social distancing and infection prevention practices were emphasised. Additionally, avoidance of unnecessary transfer of patients and minimising cross-site working for staff and early escalation were highlighted. Establishing mass and regular screening for HCWs are also crucial to enabling the best care for patients while maintaining the wellbeing of staff. Conclusion: To our knowledge, this is the first UK outbreak report among HCWs and we hope to have highlighted some key issues and learnings that can be considered by other NHS staff and HCWs globally when dealing with such a task in future.


Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 20
Author(s):  
Reynaldo Villarreal-González ◽  
Antonio J. Acosta-Hoyos ◽  
Jaime A. Garzon-Ochoa ◽  
Nataly J. Galán-Freyle ◽  
Paola Amar-Sepúlveda ◽  
...  

Real-time reverse transcription (RT) PCR is the gold standard for detecting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), owing to its sensitivity and specificity, thereby meeting the demand for the rising number of cases. The scarcity of trained molecular biologists for analyzing PCR results makes data verification a challenge. Artificial intelligence (AI) was designed to ease verification, by detecting atypical profiles in PCR curves caused by contamination or artifacts. Four classes of simulated real-time RT-PCR curves were generated, namely, positive, early, no, and abnormal amplifications. Machine learning (ML) models were generated and tested using small amounts of data from each class. The best model was used for classifying the big data obtained by the Virology Laboratory of Simon Bolivar University from real-time RT-PCR curves for SARS-CoV-2, and the model was retrained and implemented in a software that correlated patient data with test and AI diagnoses. The best strategy for AI included a binary classification model, which was generated from simulated data, where data analyzed by the first model were classified as either positive or negative and abnormal. To differentiate between negative and abnormal, the data were reevaluated using the second model. In the first model, the data required preanalysis through a combination of prepossessing. The early amplification class was eliminated from the models because the numbers of cases in big data was negligible. ML models can be created from simulated data using minimum available information. During analysis, changes or variations can be incorporated by generating simulated data, avoiding the incorporation of large amounts of experimental data encompassing all possible changes. For diagnosing SARS-CoV-2, this type of AI is critical for optimizing PCR tests because it enables rapid diagnosis and reduces false positives. Our method can also be used for other types of molecular analyses.


2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Isabella Castiglioni ◽  
Davide Ippolito ◽  
Matteo Interlenghi ◽  
Caterina Beatrice Monti ◽  
Christian Salvatore ◽  
...  

Abstract Background We aimed to train and test a deep learning classifier to support the diagnosis of coronavirus disease 2019 (COVID-19) using chest x-ray (CXR) on a cohort of subjects from two hospitals in Lombardy, Italy. Methods We used for training and validation an ensemble of ten convolutional neural networks (CNNs) with mainly bedside CXRs of 250 COVID-19 and 250 non-COVID-19 subjects from two hospitals (Centres 1 and 2). We then tested such system on bedside CXRs of an independent group of 110 patients (74 COVID-19, 36 non-COVID-19) from one of the two hospitals. A retrospective reading was performed by two radiologists in the absence of any clinical information, with the aim to differentiate COVID-19 from non-COVID-19 patients. Real-time polymerase chain reaction served as the reference standard. Results At 10-fold cross-validation, our deep learning model classified COVID-19 and non-COVID-19 patients with 0.78 sensitivity (95% confidence interval [CI] 0.74–0.81), 0.82 specificity (95% CI 0.78–0.85), and 0.89 area under the curve (AUC) (95% CI 0.86–0.91). For the independent dataset, deep learning showed 0.80 sensitivity (95% CI 0.72–0.86) (59/74), 0.81 specificity (29/36) (95% CI 0.73–0.87), and 0.81 AUC (95% CI 0.73–0.87). Radiologists’ reading obtained 0.63 sensitivity (95% CI 0.52–0.74) and 0.78 specificity (95% CI 0.61–0.90) in Centre 1 and 0.64 sensitivity (95% CI 0.52–0.74) and 0.86 specificity (95% CI 0.71–0.95) in Centre 2. Conclusions This preliminary experience based on ten CNNs trained on a limited training dataset shows an interesting potential of deep learning for COVID-19 diagnosis. Such tool is in training with new CXRs to further increase its performance.


Plant Disease ◽  
2013 ◽  
Vol 97 (5) ◽  
pp. 641-644 ◽  
Author(s):  
Manphool S. Fageria ◽  
Mathuresh Singh ◽  
Upeksha Nanayakkara ◽  
Yvan Pelletier ◽  
Xianzhou Nie ◽  
...  

The current-season spread of Potato virus Y (PVY) was investigated in New Brunswick, Canada, in 11 potato fields planted with six different cultivars in 2009 and 2010. In all, 100 plants selected from each field were monitored for current-season PVY infections using enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) assay. Average PVY incidence in fields increased from 0.6% in 2009 and 2% in 2010 in the leaves to 20.3% in 2009 and 21.9% in 2010 in the tubers at the time of harvest. In individual fields, PVY incidence in tubers reached as high as 37% in 2009 and 39% in 2010 at the time of harvest. Real-time RT-PCR assay detected more samples with PVY from leaves than did ELISA. A higher number of positive samples was also detected with real-time RT-PCR from growing tubers compared with the leaves collected from the same plant at the same sampling time. PVY incidence determined from the growing tubers showed a significant positive correlation with the PVY incidence of tubers after harvest. Preharvest testing provides another option to growers to either top-kill the crop immediately to secure the seed market when the PVY incidence is low or leave the tubers to develop further for table or processing purposes when incidence of PVY is high.


Author(s):  
Tossaporn Santad ◽  
Piyarat Silapasupphakornwong ◽  
Worawat Choensawat ◽  
Kingkarn Sookhanaphibarn

F1000Research ◽  
2015 ◽  
Vol 2 ◽  
pp. 99
Author(s):  
Érica L. Fonseca ◽  
Ana Carolina Paulo Vicente

The gene cassettes found in class 1 integrons are generally promoterless units composed by an open reading frame (ORF), a short 5’ untranslated region (UTR) and a 3’ recombination site (attC). Fused gene cassettes are generated by partial or total loss of the attC from the first cassette in an array, creating, in some cases, a fusion with the ORF from the next cassette. These structures are rare and little is known about their mechanisms of mobilization and expression. The aim of this study was to evaluate the dynamic of mobilization and transcription of the gcu14-blaGES-1/aacA4 gene cassette array, which harbours a fused gene cassette represented by blaGES-1/aacA4. The cassette array was analyzed by Northern blot and real-time reverse transcription-polymerase chain reaction (RT-PCR) in order to assess the transcription mechanism of blaGES-1/aacA4 fused cassette. Also, inverse polymerase chain reactions (PCR) were performed to detect the free circular forms of gcu14, blaGES-1 and aacA4. The Northern blot and real time RT-PCR revealed a polycistronic transcription, in which the fused cassette blaGES-1/aacA4 is transcribed as a unique gene, while gcu14 (with a canonical attC recombination site) has a monocistronic transcription. The gcu14 cassette, closer to the weak configuration of cassette promoter (PcW), had a higher transcription level than blaGES-1/aacA4, indicating that the cassette position affects the transcript amounts. The presence of ORF-11 at attI1, immediately preceding gcu14, and of a Shine-Dalgarno sequence upstream blaGES-1/aacA4 composes a scenario for the occurrence of array translation. Inverse PCR generated amplicons corresponding to gcu14, gcu14-aacA4 and gcu14-blaGES-1/aacA4 free circular forms, but not to blaGES-1 and aacA4 alone, indicating that the GES-1 truncated attC is not substrate of integrase activity and that these genes are mobilized together as a unique cassette. This study was original in showing the transcription of fused cassettes and in correlating cassette position with transcription.


Author(s):  
Rajeev Kumar Jain ◽  
Nagaraj Perumal ◽  
Rakesh Shrivastava ◽  
Kamlesh Kumar Ahirwar ◽  
Jaya Lalwani ◽  
...  

Introduction: The whole world is facing an ongoing global health emergency of COVID-19 disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Real-Time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) is a gold standard in the detection of SARS-CoV-2 infection. Presently, many single tube multiple gene target RT-PCR kits have been developed and are commercially available for Coronavirus Disease 2019 (COVID-19) diagnosis. Aim: To evaluate the performance of seven COVID-19 RT-PCR kits (DiagSure, Meril, VIRALDTECT II, TruPCR, Q-line, Allplex and TaqPath) which are commercially available for COVID-19 RT-PCR diagnosis. Materials and Methods: This observational study was conductedat the State Virology Laboratory (SVL), Gandhi Medical College, Bhopal, Madhya Pradesh, India. Seven commercially available kits have been evaluated on the basis of: (i) number of SARS-CoV-2 specific gene target; (ii) human housekeeping genes as internal control; (iii) RT-PCR run time; and (iv) kit performances to correctly detect SARS-CoV-2 positive and negative RNA samples. A total of 50 RNA samples (left over RNA) were included, master mix preparation, template addition and RT-PCR test has been performed according to kits literature. At the end of PCR run, mean and standard deviation of obtained cut-off of all kits were calculated using Microsoft Excel. Results: All seven RT-PCR kits performed satisfactory regarding the reproducibility and they could correctly identify 30 positive and 20 negative RNA samples. RNA samples (group C) having low viral loads with a high Cycle threshold (Ct) value (>30) were also detected by all these seven kits. Obtained Ct values of each group was in parallel range in comparison with the initial testing Ct values. Kits were found to be superior which contains primers and probes for three SARS-CoV-2 specific gene targets, have human housekeeping gene as internal control and taking less time to complete RT-PCR. Conclusion: All seven COVID-19 RT-PCR kits included in this study demonstrated satisfactory performance and can be used for the routine molecular diagnosis of COVID-19 disease.


2021 ◽  
Author(s):  
Gaurav Chachra ◽  
Qingkai Kong ◽  
Jim Huang ◽  
Srujay Korlakunta ◽  
Jennifer Grannen ◽  
...  

Abstract After significant earthquakes, we can see images posted on social media platforms by individuals and media agencies owing to the mass usage of smartphones these days. These images can be utilized to provide information about the shaking damage in the earthquake region both to the public and research community, and potentially to guide rescue work. This paper presents an automated way to extract the damaged building images after earthquakes from social media platforms such as Twitter and thus identify the particular user posts containing such images. Using transfer learning and ~6500 manually labelled images, we trained a deep learning model to recognize images with damaged buildings in the scene. The trained model achieved good performance when tested on newly acquired images of earthquakes at different locations and ran in near real-time on Twitter feed after the 2020 M7.0 earthquake in Turkey. Furthermore, to better understand how the model makes decisions, we also implemented the Grad-CAM method to visualize the important locations on the images that facilitate the decision.


2021 ◽  
Author(s):  
Jannes Münchmeyer ◽  
Dino Bindi ◽  
Ulf Leser ◽  
Frederik Tilmann

<p><span>The estimation of earthquake source parameters, in particular magnitude and location, in real time is one of the key tasks for earthquake early warning and rapid response. In recent years, several publications introduced deep learning approaches for these fast assessment tasks. Deep learning is well suited for these tasks, as it can work directly on waveforms and </span><span>can</span><span> learn features and their relation from data.</span></p><p><span>A drawback of deep learning models is their lack of interpretability, i.e., it is usually unknown what reasoning the network uses. Due to this issue, it is also hard to estimate how the model will handle new data whose properties differ in some aspects from the training set, for example earthquakes in previously seismically quite regions. The discussions of previous studies usually focused on the average performance of models and did not consider this point in any detail.</span></p><p><span>Here we analyze a deep learning model for real time magnitude and location estimation through targeted experiments and a qualitative error analysis. We conduct our analysis on three large scale regional data sets from regions with diverse seismotectonic settings and network properties: Italy and Japan with dense networks </span><span>(station spacing down to 10 km)</span><span> of strong motion sensors, and North Chile with a sparser network </span><span>(station spacing around 40 km) </span><span>of broadband stations. </span></p><p><span>We obtained several key insights. First, the deep learning model does not seem to follow the classical approaches for magnitude and location estimation. For magnitude, one would classically expect the model to estimate attenuation, but the network rather seems to focus its attention on the spectral composition of the waveforms. For location, one would expect a triangulation approach, but our experiments instead show indications of a fingerprinting approach. </span>Second, we can pinpoint the effect of training data size on model performance. For example, a four times larger training set reduces average errors for both magnitude and location prediction by more than half, and reduces the required time for real time assessment by a factor of four. <span>Third, the model fails for events with few similar training examples. For magnitude, this means that the largest event</span><span>s</span><span> are systematically underestimated. For location, events in regions with few events in the training set tend to get mislocated to regions with more training events. </span><span>These characteristics can have severe consequences in downstream tasks like early warning and need to be taken into account for future model development and evaluation.</span></p>


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