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NGS technologies for detection of SARS-CoV-2 strains and mutations
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Manisha Choudhury, Ayushi Verma, Ankit Halder, Arup Acharjee
The studies on the genome of SARS-CoV-2 reveal that, like any other Betacoronaviruses, it comprises ORF1ab polyprotein at 5′-end and four major structural proteins, the spike surface glycoprotein, small envelope protein, matrix protein, and nucleocapsid protein (Phan 2020b). In terms of mutations, one of the studies revealed three deletions in the genomes of SARS-CoV-2; two deletions (comprising 3 and 24 nucleotides) were found in the ORF1ab polyprotein, and one deletion of 10 nucleotides was noticed in the 3′-end of the genome in the SARSCoV-2 samples from different countries. The other significant finding was that overall 93 mutations could be detected in the entire genome of SARS-CoV-2. The major nsp and structural protein-coding regions in the genome incurred missense mutations, the only exception being the envelope protein.
Coronavirus
Published in Suman Lata Tripathi, Kanav Dhir, Deepika Ghai, Shashikant Patil, Health Informatics and Technological Solutions for Coronavirus (COVID-19), 2021
The genome of coronaviruses basically comprises a set of genes in the invariant order 5’-replicase-S-E-M-N-3’, with the huge replicase gene that generally occupies the two-third of the coding capacity [23]. Following are the notable common features of genome structure among different coronaviruses: The 5′ end of the genome contains a leader sequence and untranslated region (UTR) ranging from 209 to 528 nucleotides in length. This region also contains similarly positioned short, AUG-initiated ORF, capable of encoding peptides of 3–11 amino acids [20].The 3′ end of the genome also contains the UTR ranging from 288 to 506 nucleotides in length. This region also possesses an octameric sequence of GGAAGAGC at 73–80 upstream from the 3′ poly-A tail [20,24].Every genome has one extremely large gene around 5′ terminal, Gene 1 (replicase gene), covering approximately two-third of the genome separated into two ORFs 1a and 1b. This replica gene is responsible for encoding nonstructural proteins that are known to have a role in proteolytic processing of polyprotein products of replicase gene, replication and transcription [subgenomic mRNA (sg mRNA) synthesis] of the viral genome [20,24,25]. Translation of ORF1a yields polyprotein (pp) 1a (~450 kDa) whereas the translation of ORF1b requires a programmed ribosomal frameshift event that takes place just upstream of the ORF1a stop codon and results in polyprotein (pp) 1ab (~750 kDa) [20,26]. The replicase-transcriptase is the only protein that is translated from the genome; the other products of all downstream ORFs are derived from sg mRNAs [26]. Figure 4.2 represents a schematic of the genome organization as found in coronaviruses concerning SARS-CoV, SARS-CoV-2 and MERS-CoV.
Dual-target one-step nested PCR for sensitive detection of SARS-CoV-2 nucleic acids
Published in Preparative Biochemistry & Biotechnology, 2022
Qijie Li, Yiqing Xia, Dunshui Liao, Hu Nie, Ming Zhang, Tinghua Wang, Jiayu Liao, Qingjie Xia
Studies postulate that numerous sub-genomic RNA is synthesized using the negative-strand RNA as a template after positive-strand RNA of SARS-CoV-2 enters the host cells. The ORF1ab gene is only transcribed from the full-length viral genome and thus only exists in the complete viral genome. In contrast, the N gene exists in both the full-length genome and other sub-genomic RNAs.[19] The transcriptional synthesis of the N gene is, however, higher than that of the ORF1ab gene. The DTO-N-PCR system designed herein was based on a dual-target for the ORF1ab and N gene to ensure a high detection efficiency. Notably, it was different from that of Cyril et al., Wang et al., and Carmen et al.,[10–12] whose systems contained only one primer pair for one gene of SARS-CoV-2. In addition, the SARS-CoV-2 variants B.1.1.7, B.1.351, P.1, and B.1.617.2, which are most widely spread and have the greatest influence, mainly have mutations in the S gene. Therefore, the accuracy and sensitivity of DTO-N-PCR in this paper may be not affected.
Nanoprotection from SARS-COV-2: would nanotechnology help in Personal Protection Equipment (PPE) to control the transmission of COVID-19?
Published in International Journal of Environmental Health Research, 2023
Zhi Xin Phuna, Bibhu Prasad Panda, Naveen Kumar Hawala Shivashekaregowda, Priya Madhavan
CoVs are classified under the family Coronaviridae, which is a monophyletic cluster in the order of Nidovirales. The subfamily Orthocoronavirinae contains another 4 genera, alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus. The CoV is an enveloped virus with a positive sense and single-stranded RNA (Hasöksüz et al. 2020). SARS-CoV-2 is a betacoronavirus, encoding a large and non-structural polyprotein (ORF1a/b) that is proteolytically cleaved to produce 15/16 proteins, 5 accessory proteins (ORF3a, ORF6, ORF7, ORF8 and ORF9), and 4 structural proteins. The structural proteins are vital in viral assembly and infections, where they consist of spike (S) surface glycoprotein, membrane (M) protein, envelope (E) protein and nucleocapsid (N) protein (Li et al. 2020) (Figure 1). The S glycoprotein belongs to a type 1 membrane glycoprotein with different functional domains near the amino (S1) and carboxy (S2) termini. The S1 subunit is associated with receptor binding functions, while S1 subunit is primarily responsible for mediating the viral and cellular membrane fusion (Duan et al. 2020). The M protein, on the other hand can bind to all other structural proteins, which contribute to the nucleocapsid’s stabilization and completion of viral assembly (Astuti and Ysrafil 2020). On the other hand, the N protein in SARS-CoV-2 can lead to dysregulation of cell cycle in order to offer a better environment for itself to bind with viral RNA to form ribonucleocapsid, thus promoting virus replication, transcription as well as translation (McBride et al. 2014; Cong et al. 2020). Moreover, the E protein is not only involved in viral assembly but it is also crucial for viral infection and pathogenesis by functioning as a gated ion channel (Sarkar and Saha 2020).
DeepCOVID-19: A model for identification of COVID-19 virus sequences with genomic signal processing and deep learning
Published in Cogent Engineering, 2022
Emmanuel Adetiba, Joshua A. Abolarinwa, Anthony A. Adegoke, Tunmike B. Taiwo, Oluwaseun T. Ajayi, Abdultaofeek Abayomi, Joy N. Adetiba, Joke A. Badejo
The ORF1ab gene is made up of ORF1a and ORF1b. The position of the ORF1ab gene is located closely to the starting codon of SARS-CoV-2 at position 251–21541 unlike SARS-CoV and MERS-CoV at 265–21486 and 279–21514, respectively (Biswas et al., 2020).