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Pangolins Harbor SARS-CoV-2-Related Coronaviruses
Published in William C. Cockerham, Geoffrey B. Cockerham, The COVID-19 Reader, 2020
Several recent studies reported the identification of SARS-CoV-2-related viruses in Malayan pangolins, native in Southeast Asia, that were smuggled into Southern China [3–7]. Pangolins (or scaly anteaters) are mammals that belong to the order of Pholidota, with one extant family (Manidae) and three genera (Manis, Phataginus, and Smutsia) [10]. As a source of food and traditional Asian medicines, pangolins are among the most illegally traded mammals in the world [10]. A number of pangolin species have been assessed to be endangered or critically endangered by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Two distinct clusters of SARS-CoV-2-related viruses were identified in pangolin samples obtained by anti-smuggling operations in the Guangxi (GX) and Guangdong (GD) provinces of China (Figure 4.1A). Interestingly, the GD pangolin CoVs have a higher amino acid identity (97.4%) with SARSCoV-2 than does the bat CoV RaTG13 (89.2%) in the receptor-binding domain (RBD) [3–7]. In the remainder of the genome, RaTG13 exhibits a higher sequence identity with SARS-CoV-2 than do the GD pangolin CoVs. This pattern can be explained by either recombination or convergent evolution [3–7]. Phylogenetic analysis based on the synonymous sites of RBD, whose evolution is less likely to be influenced by natural selection, shows that RaTG13 is more closely related to SARS-CoV-2 than are the GD pangolin CoVs (Figure 4.1B), indicating that the high amino acid similarity between the GD pangolin CoVs and SARS-CoV-2 in the RBD might be due to convergent evolution [3].
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
Corona viral genome is positive sense non-segmented RNA and have more similarity with SARS-CoV. The genome of the virus is determined to be 96.2% similar to the SARS CoV sequence of RaTG13. It is considered that Bat is the natural host for All types of CoVs, and it is assumed that it could traveled to humans and cause infection in humans through an unknown intermediate host like SARS CoV-2 [40]. This virulence is then transferred from human to human through coughing or sneezing that produce droplets or aerosol formation in the air and can be entered to other person by inhaling, as these viruses primarily cause respiratory infection in the throat and lungs. In the respiratory cells, their present receptor site on their cell allows the virus to enter the cell and cause the infection in these lungs’ cells [41]. There-fore, there are many modes of transmission of corona viral infections like by touching the exposed sites and then touching eye, mouth, and nose with contaminated bare hands, air droplets by coughing and sneezing and inhaling aerosols contaminated with virus, pregnant mother to child and eating viral exposed animal host to human and cause mild respiratory illness to serious illness and disturbance in breathing and even cause the death at this serious condition (Figure 1.2) [42]. There are variety of mode of transmission of this viral infection and because of respiratory illness it is very easy to transmit though air in the critical pandemic condition it is crucial to take much hard steps for government to take. For the prevention of this pandemic condition, it is necessary to use N95 masks and surgical masks to get rid of SARS CoV-2 [42].
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
SARS-CoV-2 is a new member of the genus Betacoronavirus in the Coronaviridae family of the order Nidovirales [6]. SARS-CoV-2 and other two human CoVs, SARS- CoV and MERS-CoV, have most likely originated from bats and have been transmitted to humans through intermediates, with pangolin being the potential intermediate for SARS-CoV-2. Whole-genome analysis reveals that SARS-CoV-2 is 79% similar to SARS-CoV and 50% similar to MERS-CoV. It is 96.2% similar to the RaTG13 bat coronavirus, which indicates that RaTG13 could be the origin of SARS-CoV-2 [7]. SARS-CoV-2 like other CoVs has a crown-shaped appearance through the uniform distribution of spike proteins on the virion surface as observed by electron microscopy (Figure 6.1). SARS-CoV-2 is an enveloped virus with a non-segmented positive-sense ssRNA genome of 29,891 bases encoding 9,860 amino acids. The genome encodes four structural proteins, namely the spike protein (S), the Envelope protein (E), the Nucleoprotein (N) and the Membrane protein (M), in addition to six accessory and sixteen non-structural proteins. The trimeric S glycoprotein is responsible for host cell tropism and entry into the target cells via the angiotensin-converting enzyme 2 (ACE2) receptor. The S glycoprotein consists of two subunits (S1and S2) and shows a structural difference from the S protein of other similar CoVs by having a furin cleavage site (S1/S2) rich in basic amino acid residues (SPRRARSVAS), which favors efficient viral entry into host cells [3]. There are six crucial amino acid residues in the Receptor-Binding Domain (RBD) of the S protein, responsible for viral attachment to the ACE2 receptor on the host cells. Five of them are different between SARS-CoV and SARS-CoV-2, while all six are identical for SARS-CoV-2 and Pangolin CoV, which suggest that pangolin is the intermediate host [8]. Other structural proteins, such as the N and E proteins, are relatively more conserved between SARS-CoV and SARS-CoV-2, with a sequence identity of 89.6% and 96%, respectively [7].
Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2022
Matteo Pavan, Davide Bassani, Mattia Sturlese, Stefano Moro
Concerning the second structural alteration, in the native SARS-CoV-2 structure Asn180 is involved in a double interaction with the sidechain of two charged residues, namely Asp176 and Arg105. Both of these interactions happen with the backbone of Asn180 and do not involve its sidechain, which is stretched towards the solvent. Intriguingly, in this case, the newly discovered bat coronaviruses all present a hydrophobic residue at position 180: in all these cases, no loss of native interaction happens, coherently with the fact that they do not involve the sidechain of residue 180 and only occur through its backbone. Once again, RaTG13 is the most diverse one, being the only analysed bat coronavirus that presents a polar amino acid (a threonine) at this position. As previously mentioned, the sidechain of residue 180 is not involved in any structurally relevant interaction, and therefore the presence of a hydroxyethyl sidechain does not give a particular advantage to this virus strain. Furthermore, as is the case for Pro96, this structural modification is also located in a solvent-exposed, non-structured loop region, indicating that no critical harm to the protease integrity should be provoked by this alteration.
New and developing diagnostic platforms for COVID-19: A systematic review
Published in Expert Review of Molecular Diagnostics, 2020
Nidhi Chauhan, Shringika Soni, Abhinandan Gupta, Utkarsh Jain
Like other coronaviruses, SARS-CoV-2 is an enveloped positive-sense single-stranded RNA (ssRNA+) virus, and belongs to Coronaviridae family, Coronvirinae subfamily and Nidovirales order [9]. On the basis of genetic criteria, SARS-CoV-2 is indexed into alpha (α), beta (β), gamma (γ), and delta (δ); among these, genera α- and β-coronaviruses infects mammals while γ- and δ-coronaviruses effect pigs and birds [10]. This coronavirus type has also shown close phylogenetic relationship with bat CoV RaTG13 (96.2%) and SARS-CoV (79.5%) [10]. The small membrane protein (SM), nucleocapsid protein (N), spike protein (S) and membrane glycoprotein (M) are major functional proteins of SARS-CoV-2 virus, which are highly susceptible to respiratory system and thereby induce infection [11]. Thus, genome sequencing and evolutionary analysis of coronaviruses were suspected to be of bat primary origin for SARS-CoV-2 and they were transmitted to humans through an unknown intermediate. To date, all clinical manifestations are not cleared with COVID-19 cases. However, mild symptoms including cough, fever and sore throat are common which further may lead to severe organ failure, septic shock, severe pneumonia, pulmonary edema, and Acute Respiratory Distress Syndrome (ARDS), collectively resulting in death of the SARS-CoV-2 infected patients [12,13].
The COVID-19 pandemic
Published in Critical Reviews in Clinical Laboratory Sciences, 2020
Marco Ciotti, Massimo Ciccozzi, Alessandro Terrinoni, Wen-Can Jiang, Cheng-Bin Wang, Sergio Bernardini
Structural studies carried out on the SARS-CoV-2 RBD/ACE2 complex showed that SARS-CoV-2 RBD binds ACE2 with higher affinity than SARS-CoV RBD. Indeed, SARS-CoV-2 RBD forms a larger binding interface and more contacts with ACE2 than SARS-CoV RBD [78]. From a structural point of view, there is a significant difference in the conformation of the loops in the ACE2 binding ridge that may explain this difference in receptor binding affinity between the two viruses. The SARS-CoV loop contains a three-residue motif, proline-proline-alanine, while SARS-CoV-2 and bat coronavirus RaGT13 contain a four-residue motif, glycine-valine/glutamine-glutamate/threonine-glycine. Due to these structural differences, the ridge in the SARS-CoV-2 RBD makes more contacts with the N-terminal helix of ACE2. The importance of this structure in determining the higher binding affinity of SARS-CoV-2 RBD for the ACE2 receptor was confirmed by mutations studies. Mutations at position 481–487, 493 and 501 of SARS-CoV-2, where the amino acids were mutated to those in SARS-CoV, reduced the surface of the SARS-CoV-2 spike available for binding to ACE2 [78]. The authors also showed that bat RaTG13 is able to bind ACE2. RaTG13 contains a four-residue motif in the ACE2 binding-ridge that is similar to SARS-CoV-2, suggesting that SARS-CoV-2 may have evolved from this virus or a bat-related coronavirus. Amino acid changes L486F and Y493Q from RaTG13 to SARS-CoV-2 facilitate ACE2 binding and support the idea that these changes enabled bat to human transmission. Also, L455 and N501, present both in RaTG13 and SARS-CoV-2, contribute to ACE2 binding and perhaps to bat to human transmission [78].