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Epidemiology and Pathogenesis of COVID-19
Published in Hanadi Talal Ahmedah, Muhammad Riaz, Sagheer Ahmed, Marius Alexandru Moga, The Covid-19 Pandemic, 2023
Sidrah Tariq Khan, Sagheer Ahmed
The four structural proteins that make up the CoVs are the Spike Proteins (S1 and S2), nucleocapsid proteins, membrane proteins and envelop proteins. These viruses use the S1 spike proteins to attach themselves to the host cellular receptor ACE-2 and the S2 spike protein to fuse themselves to cellular membranes in order to penetrate inside the host cells. The spike proteins on this virus are of particular importance. These proteins give the virus its unique crown shape and range in size from 9–12 nm. The S1 spike protein has further been divided into A, B, and C domains. The SARS-Cov-2 virus mainly utilizes the S1 B domain to gain entry into the host cell. Apart from the structural proteins, 2/3rd of the total open reading frames (ORFs) comprises of the non-structural proteins (replicase complex, nsp 1–16) responsible for replication and transcription, and the remaining consists of accessory proteins. These together comprise the functional proteins of the SARS-CoV-2 virus (Figure 2.2).
The Journey through the Gene: a Focus on Plant Anti-pathogenic Agents Mining in the Omics Era
Published in Mahendra Rai, Chistiane M. Feitosa, Eco-Friendly Biobased Products Used in Microbial Diseases, 2022
José Ribamar Costa Ferreira-Neto, Éderson Akio Kido, Flávia Figueira Aburjaile, Manassés Daniel da Silva, Marislane Carvalho Paz de Souza, Ana Maria Benko-Iseppon
As claimed by Santos-Junior et al. (2020), two significant computational difficulties affect AMPs prospection in sequence-derived data: (i) predicting small genes in DNA/RNA sequences; (ii) the prediction of AMP activity for small genes. Regarding the prediction of small genes in DNA- or RNA-encoding small peptides, most gene prediction approaches exclude small ORFs (Open Reading Frames). The regular tools preserve the longest ORF, conventionalizing it as the coding for a given protein. Thus, specific peptide mining approaches have been developed (e.g., Ramada et al. 2017; Lin et al. 2019). Additionally, a few recent surveys have shown that long ORFs identification methods can be used to detect small ORFs. In this way, the results are subsequently filtered while revealing that small ORFs are biologically active across a range of functions (Miravet-Verde et al. 2019; Sberro et al. 2019).
Biosynthesis and Genetics of Lipopolysaccharide Core
Published in Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison, Endotoxin in Health and Disease, 2020
David E. Heinrichs, Chris Whitfield, Miguel A. Valvano
A WaaK homolog has been identified in N. meningitidis, where it is involved in the production of LOS (110). The deduced amino acid sequence of this protein shows 21% identity and 47% total similarity to the WaaK protein of Salmonella. However, the neisserial WaaK homolog shows very little similarity to the E. coli K-12 WaaU protein. Unfortunately, it is currently not known whether the neisserial waaK gene is capable of complementing either the waaK phenotype of Salmonella or the waaU phenotype of E. coli K-12. Sequence from the H. influenzae genome project (accession numbers U32734 and L42023) revealed an open reading frame whose deduced amino acid sequence indicates similarity, albeit over a small region, to the WaaU protein of E. coli K-12. Whether this open reading frame codes for a protein, and what its possible substrates are are unknown at this time.
Site-specialization of human oral Gemella species
Published in Journal of Oral Microbiology, 2023
Julian Torres-Morales, Jessica L. Mark Welch, Floyd E. Dewhirst, Gary G. Borisy
To build a Gemella pangenome, we accessed the National Center for Biotechnology Information (NCBI) database and downloaded all available genomes for strains of any named or unnamed species within the genus (SI Table S1). The set included genomes of human oral-associated Gemella species as well as several genomes from non-human and/or non-oral-associated species and 10 genomes identified only to genus level. As a quality control measure, from the total of 35 genomes available at NCBI, we removed five genomes that were not in RefSeq, constructing the pangenome from the remaining 30 RefSeq genomes. These genomes were derived from nine named species (n = 22), one not validly published, and seven entries that were identified only to genus level. We then used the analysis and visualization tool for ‘omics data, anvi’o [32], to organize the genomes into similarity groups based on the presence of homologous genes. Briefly, for each genome, open reading frames were predicted, and the resulting hypothetical genes were translated into amino acid sequences and grouped into gene clusters (groups of putative homologous genes) based on the level of amino acid similarity among them. Then, to visualize the pangenome, the gene clusters were hierarchically grouped by representation (presence/absence) across genomes to produce a gene cluster dendrogram, and the genomes were hierarchically grouped based on the frequency of the homologous genes within gene clusters to produce a genome dendrogram. These two dendrograms organize the pangenome structure of the Gemella genus.
Molecular diagnostic assays for COVID-19: an overview
Published in Critical Reviews in Clinical Laboratory Sciences, 2021
Parham Habibzadeh, Mohammad Mofatteh, Mohammad Silawi, Saeid Ghavami, Mohammad Ali Faghihi
SARS-CoV-2 belongs to the Coronaviridae family of the Nidovirales order [1]. The viral genome was first sequenced using deep meta-transcriptomic sequencing of the bronchoalveolar lavage fluid of a 41-year-old man who was admitted to the Central Hospital of Wuhan due to pneumonia of unknown etiology (Genbank: MN908947). The viral genome, which is approximately 30 kb in size, is a positive single-stranded RNA with a 5′-cap and a 3′-poly-A tail [7]. It contains 14 open reading frames (ORFs) encoding different replication, structural and nonstructural accessory proteins. At the 5′-terminal region of the genome, ORF1 and ORF2 encode 15 nonstructural proteins responsible for viral replication while the structural proteins, nucleocapsid (N), membrane protein (M), envelope protein (E), and spike protein (S), in addition to eight accessory proteins, are encoded by the 3′-terminal region [8,9] (Figure 1).
Perspective: diagnostic laboratories should urgently develop T cell assays for SARS-CoV-2 infection
Published in Expert Review of Clinical Immunology, 2021
Rohan Ameratunga, See-Tarn Woon, Anthony Jordan, Hilary Longhurst, Euphemia Leung, Richard Steele, Klaus Lehnert, Russell Snell, Anna E. S Brooks
Responses to the S glycoprotein may reflect cross-reactive T cell responses to HCoV and increase background proliferation [49]. In the event, there are overlapping responses between HCoV and SARS-CoV-2 during clinical validation of the assay, the relevant antigens could be altered (Figure 1) [59,72,73]. Proteins and peptides derived from other open reading frames (ORFs) could be used [62]. The N or M proteins or peptides might confer greater specificity for SARS-CoV-2 [62]. Furthermore, the large dynamic range of 3H thymidine uptake assays is likely to provide clear separation of background HCoV responses to those of SARS-CoV-2. A negative response most likely indicates absence of exposure to the virus. The possibility of immunodeficiency will be excluded by normal response to lectins and other antigens.