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Morphology, Pathogenesis, Genome Organization, and Replication of Coronavirus (COVID-19)
Published in Hanadi Talal Ahmedah, Muhammad Riaz, Sagheer Ahmed, Marius Alexandru Moga, The Covid-19 Pandemic, 2023
Sadia Javed, Bahzad Ahmad Farhan, Maria Shabbir, Areeba Tahseen, Hanadi Talal Ahmedah, Marius Moga
There is the on N-protein that allow to form Nucleocapsid protein that it binds to the positive-sense RNA of Coronavirus [14]. N-protein have an important part in the transcriptional function and pathogenesis of Viral +ssRNA sequence and the expression of N-protein enhance the process of replication and recover the cDNA clones effectively [75]. It contains of two separate sites, CTD, and the NTD and the, both regions that binds positive sense RNAs in vitro. Perfect RNA binding has been proposed to contain assistance from both domains [76, 77] the N protein is also strongly bonded by phosphorylation [78], and it is proposed that this phosphorylation will cause some types of deformation that enhance the non-viral versus viral RNA attraction to bind each other. In a Beads of-string change in the confirmation, Nucleocapsid-protein bound to the viral positive-sense RNA. There are two groups of N-protein RNA substrates (NRSs): the genomic packing signal and the N-protein RNA substrates (NRSs) [79, 80]. The viral RNA packing signal is significantly connected to the other type of domain or C-terminal RNA binding domain [81]. nsp3 also attached with N-protein [77, 82]. This is the main constituent of the complex of replicase enzyme, and the Myoprotein interactions directly help to attach the RNA viral genomic sequence to the reverse transcriptase, and the condensed viral genomic sequence into particulates shown in Figure 1.6 [83].
COVID-19
Published in Stephen T. Sinatra, Mark C. Houston, Nutritional and Integrative Strategies in Cardiovascular Medicine, 2022
COVID-19 is a corona virus also known as SARS-CoV-2 that causes an infectious disease characterized by intense respiratory symptoms, fever, cough, headache, fatigue, and loss of taste and smell.1 While initial studies suggested that the first known case occurred in Wuhan, China in December 2019, later analyses of data suggest it actually occurred in October of 2019.2 The disease subsequently spread worldwide resulting in the pandemic that we are still dealing with today. The official name of the virus is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strain.3 This virus strain is closely related to the original SARS-CoV-1 that occurred in Foshan, China in 2002–2004, but significantly less related to the 2012 Middle East respiratory syndrome virus (MERS-CoV).4 The COVID-19 virus is very similar to the MERS and SARS-CoV-1 viruses. The components of the virus include a membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N), and the spikeprotein (S) (Figure 15.1).5
The Evolution of COVID-19 Diagnostics
Published in Debmalya Barh, Kenneth Lundstrom, COVID-19, 2022
Praveen Rai, Ballamoole Krishna Kumar, Deekshit Vijaya Kumar, Prashant Kumar, Anoop Kumar, Shashi Kumar Shetty, Biswajit Maiti
As per the WHO recommendation, the most widely used nucleic acid–based test for the detection of SARS-CoV-2 is RT-qPCR [19]. Several RT-qPCR assays targeting different genes of the SARS-CoV-2 genome, such as RdRp, N, E, and S genes, and ORF1b or ORF8 regions, have been used for the detection of SARS-CoV-2 from clinical samples. However, the WHO recommends an RT-qPCR-based assay targeting the E gene for screening the RdRp gene to confirm SARS-CoV-2. While the US Centers for Disease Control and Prevention (CDC) recommends an RT-qPCR assay based on two nucleocapsid protein genes (N1, N2) [19], to minimize the chances of false-positive results, CDC has developed a new RT-qPCR diagnostic panel including No Template Control (NTC) and Human Specimen Control (HSC). The method has also undergone tremendous modifications to improve the sensitivity, specificity, and feasibility of the technique. A multiplex RT-qPCR has been developed recently, targeting different regions of SARS-CoV-2 and seasonal influenza virus simultaneously with a limited quantification range between 5 and 10 copies per reaction for influenza and SARS-CoV-2, respectively [20]. Furthermore, a significant improvement has been made in the technique to achieve the results with greater accuracy in a short period of time at a low cost to detect SARS-CoV-2 RNA directly from samples without involving an extraction procedure [21]. The HID-RT-PCR (Heat Inactivated Direct-RT-PCR) developed in this study had an accuracy, sensitivity and specificity of 98.8%, with a limit of detection of 0.009 TCID50/ml for the ORF1 and 0.003 TCID50/ml for E genes.
Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in the Human Eye
Published in Ocular Immunology and Inflammation, 2023
Alireza Kamalipour, Mohammad Ali Ashraf, Sasan Moghimi, Afagh Moattari, Mohammad Javad Ashraf, Farhad Abbasi, Farzan Azodi, Shadi Oboudi, Neda Pirbonyeh, Maryam Mokhtaryan, Amirhossein Roshanshad, Jiun L. Do, Robert N. Weinreb
The real-time RT-PCR assay was done to amplify highly conserved genes of SARS-CoV-2 with the novel coronavirus (2019-nCoV) primer (PCR-Fluorescence Probing). The used primer and probe were made by Metabion company.35 Nucleocapsid protein (N gene) was used for the first-line screening assay, and RNA-dependent RNA polymerase (RdRp gene) was used for the confirmatory assay. The used master mix was made by Invitrogen company (SuperScript™ III Platinum ® One-Step qRT-PCR System with Platinum Taq DNA polymerase, Lot No. 1312837). The assays were performed on the Applied Biosystems (ABI, 7500) real-time PCR system. PCR test channels include FAM (ORF-1ab region) and VIC (N gene) channels to test 2019-nCoV nucleic acid, and ROX channel to test internal control (RNase P gene).
COVID-19—from emerging global threat to ongoing pandemic crisis
Published in Baylor University Medical Center Proceedings, 2022
Karen B. Brust, Vinayika Papineni, Cristie Columbus, Alejandro C. Arroliga
Point-of-care testing (rapid tests) are available through antigen testing under emergency use authorization (EUA). Rapid tests detect the presence of the SARS-CoV-2 nucleocapsid protein through immunochromatography methods. Although the results are ready in minutes, rapid testing is not as sensitive as PCR, leading to a chance of false-negatives.7 The Food and Drug Administration (FDA) recommends confirmatory reverse transcription PCR testing of positive antigen tests in asymptomatic people and negative antigen test results in symptomatic people.8 Of the 48 antigen tests available under EUA, 17 are sold over the counter for home testing. Examples of over-the-counter testing include the Abbott and Ellume tests that can detect antigen positivity in 15 and 20 minutes, respectively.8 The Abbott Binax NOW antigen self-test identifies positive results correctly 84.6% of the time and negative results correctly 98.5% of the time, based on at-home clinical studies.8
Histopathology of Third Trimester Placenta from SARS-CoV-2-Positive Women
Published in Fetal and Pediatric Pathology, 2022
Mai He, Priya Skaria, Kasey Kreutz, Ling Chen, Ian S. Hagemann, Ebony B. Carter, Indira U. Mysorekar, D. Michael Nelson, John Pfeifer, Louis P. Dehner
Coronavirus disease 2019 (COVID-19) is caused by infection of SARS-CoV-2, a member of the betacoronavirus family. SARS-CoV-2 is a 30 kb enveloped, positive sense, single-stranded RNA virus. The virus consists of four structural proteins (spike surface glycoprotein, envelope protein, membrane protein, and nucleocapsid protein) and nonstructural proteins. The spike protein consists of two functional subunits. The S1 subunit is responsible for binding to the host cell receptor and the S2 subunit is utilized for the fusion of the viral and cellular membranes [1, 2]. Studies showed that the spike protein for SARS-CoV-2 binds to angiotensin converting enzyme 2 (ACE2), which is also a functional receptor for SARS-CoV. ACE2 expression is high in lung, heart, ileum, kidney and bladder. Thus, SARS-CoV-2 virus primarily affects the respiratory system, although other organ systems may also be involved [1].