Morphology, Pathogenesis, Genome Organization, and Replication of Coronavirus (COVID-19)
Hanadi Talal Ahmedah, Muhammad Riaz, Sagheer Ahmed, Marius Alexandru Moga in The Covid-19 Pandemic, 2023
The connection between asymptomatic exposure and pre-symptomatic exposure of virus events and their distribution is not quite well understood. The RT-PCR test will diagnose whether the virus can be identified, but this will not tell us whether or not someone is infected [36]. Virulence in cell culture is used to determine whether or not a patient has been infected to a viral strain. In the lack of virus sample data, RT-PCR data such as viral load or cyclical thresholds (Ct) parameters were used as a guideline for spread possibility. The Ct is the total number of cycles needed to pass a certain limit in an RT-PCR signal [30]. This variable is not proportional to the number of targeted viral genome sequences or viral sample loaded, particularly when virus levels are low, as indicated by higher Ct measurement. The virus was not successfully eliminated unless Ct was smaller than 24 among 90 infected persons with COVID-19 infection, according to Bullard and colleagues [38]. The connection among COVID-19 virus RNA elimination and the mode of transmission remains unknown. The percentage of symptomless or pre-symptomatic exposure of COVID-19 infection is not apparent when compared to symptomatic infection [39].
The Evolution of COVID-19 Diagnostics
Debmalya Barh, Kenneth Lundstrom in COVID-19, 2022
CT examination has also been considered by various clinicians for the diagnosis of COVID-19 through the early screening and to assess the disease’s severity. This type of examination is very useful to deal with the disease and to detect lung lesions. However, there are major limitations of this technology, such as:The CT examination can be used for the specific detection of SARS-CoV-2 but only performed in few diagnostic centers and hospitals.Another shortcoming of the technology is that it cannot be used for field level or bedside diagnosis of COVID-19 disease. This is primary because of the requirement for sophisticated instruments and well-trained personnel to carry out the examination.
Artificial Intelligence Based COVID-19 Detection using Medical Imaging Methods: A Review
S. Prabha, P. Karthikeyan, K. Kamalanand, N. Selvaganesan in Computational Modelling and Imaging for SARS-CoV-2 and COVID-19, 2021
CT scan images are handy to identify the progression of GGO and mGGO in COVID-19 suspects over a time. Thereby, it provides a way of identifying different stages of COVID-19. The different stages of COVID-19 infections are classified based on the level of severity in the CT scan images. The amount of severity is calculated based on the number of multiple ground-glass opacities in both lungs. These chest CT severity scores are beneficial for clinicians to discover the different stages of COVID-19, such as mild, moderate, severethan classifying COVID-19 or normal (Ran et al. 2020). The researchers used the transfer-learning property a in Convolutional Neural Network (CNN) to classify the input sample into two classes: COVID-19 positive and other viral pneumonia. They achieved a maximum accuracy of 89.5%. The same algorithm gives 79.3% accuracy while testing with the external dataset.
SARS-CoV-2 RT-qPCR Ct values in saliva and nasopharyngeal swab samples for disease severity prediction
Published in Journal of Oral Microbiology, 2023
Kristina Snipaitiene, Birute Zablockiene, Rasa Sabaliauskaite, Kristina Zukauskaite, Elzbieta Matulyte, Tautvile Smalinskaite, Mindaugas Paulauskas, Rolandas Zablockis, Mantvydas Lopeta, Julius Gagilas, Alina Puriene, Ligita Jancoriene, Sonata Jarmalaite
Other interesting finding was that viral load reflected by Ct values in SSs was significantly higher than in NPSs, regardless of the severity of the disease. Low Ct value designates an elevated concentration of genetic material reflecting a higher viral load, typically correlated with a high infection risk [28]. The high value of Ct specifies a low concentration of viral genetic material with less infectivity risk; however, higher values may be seen in a later convalescent stage [29]. Both SSs and NPSs RT-qPCR Ct correlated clearly with duration of the disease in our study, with lower values in the first tests and higher in the third tests. Studies show [20,30,31] that the ACE2 receptor-rich minor salivary gland ductal epithelium and oral mucosal epithelium are the early targets for SARS-CoV-2 infection, and this fact could explain the high viral load in saliva at the early phases of infection. Thus, we may conclude that saliva samples are reliable materials for screening and detection of SARS-CoV-2.
Laboratory analysis of two Delta SARS-CoV-2 variant outbreaks in the Port of Antwerp
Published in Acta Clinica Belgica, 2022
Hélène L. F. Boogaerts, Patrick Smits, Guy Hans, Liza Bouly, Eline Coeck, Sarah Vandamme, Hilde Jansens, Herman Goossens, Veerle Matheeussen
To evaluate the duration of viral RNA shedding, nasopharyngeal swabs were taken every few days (5 times for vessel 1: day 1, 8, 12, 18 and 24 and 4 times for vessel 2: day 1, 7, 12 and 16). Due to practical considerations, the time lines for consecutive testing for both vessels differed somewhat. For the SARS-CoV-2 RNA positive samples, the CT values of the three different gene targets (ORF1ab, N1 and S) were documented. Low CT values indicating high viral loads in nasopharyngeal swabs are associated with a greater risk of transmission [8]. A CT value of ≥27.8 in our assay is equal to a viral load of <1.000 RNA copies/mL which is used as cut-off for infectiousness [9]. If a CT value increased above 27.8, and no symptoms or elevated temperature were present the patient was not tested further. In addition, the samples that were taken at day 7 from the vessel 2 crew, were sent to the Belgian COVID national reference laboratory (UZ Leuven) for viral culture. For these specific samples, swabs were not collected in RNA/DNA shield solution but in Universal Transport Medium (UTM, Copan). To evaluate if the B1.617.2 variant might be more transmissible than the B.1.1.7, the dataset of the PCR-positive crew members (n = 30) was compared to a dataset from January 2021 containing PCR results of 22 patients infected with the B.1.1.7 variant of which a retest at day 8 was performed. To analyze differences in delta CT values between the first test and retest for both variants a Mann Whitney U-test was performed using MedCalc v17.5.5 software.
Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test
Published in Expert Review of Molecular Diagnostics, 2022
Milad Shirvaliloo, Roghayeh Sheervalilou, Ehsan Ahmadpour, Saeid Safiri, Hossein Bannazadeh Baghi
To provide a better picture of the accuracy of these diagnostic nanobiosensors, we also extracted data regarding the lowest and highest cycle threshold (Ct) values of the correctly identified samples, either positive or negative. Ct value is a well-known indicator of sensitivity in RT-qPCR and is defined as the amplification cycle number that is required for a certain gene, e.g. the N gene of SARS-CoV-2, to exceed the threshold of positivity, and thus, result in a positive RT-qPCR test result. Generally, clinical samples with Ct values occurring in the range of 25–40 are considered to be positive or infected, though, this can be subject to change based on a number of other factors. There is an inverse relationship between Ct value and viral load, meaning that higher Ct values indicate lower concentrations of viral particles in the sample [34]. In this sense, the lower limit of Ct is an indicator of sensitivity, i.e. the performance of a diagnostic test at distinguishing patients based on a given viral load, which is technically desired to be lower to make the test more sensitive. Accordingly, the upper limit of Ct range delineates specificity, i.e. the performance of a diagnostic test at discerning patients with trace or minimal viral loads from healthy individuals.
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