ChapterLiterature Review

Coronavirus Spike Protein and Tropism Changes

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Abstract

Coronaviruses (CoVs) have a remarkable potential to change tropism. This is particularly illustrated over the last 15 years by the emergence of two zoonotic CoVs, the severe acute respiratory syndrome (SARS)- and Middle East respiratory syndrome (MERS)-CoV. Due to their inherent genetic variability, it is inevitable that new cross-species transmission events of these enveloped, positive-stranded RNA viruses will occur. Research into these medical and veterinary important pathogens—sparked by the SARS and MERS outbreaks—revealed important principles of inter- and intraspecies tropism changes. The primary determinant of CoV tropism is the viral spike (S) entry protein. Trimers of the S glycoproteins on the virion surface accommodate binding to a cell surface receptor and fusion of the viral and cellular membrane. Recently, high-resolution structures of two CoV S proteins have been elucidated by single-particle cryo-electron microscopy. Using this new structural insight, we review the changes in the S protein that relate to changes in virus tropism. Different concepts underlie these tropism changes at the cellular, tissue, and host species level, including the promiscuity or adaptability of S proteins to orthologous receptors, alterations in the proteolytic cleavage activation as well as changes in the S protein metastability. A thorough understanding of the key role of the S protein in CoV entry is critical to further our understanding of virus cross-species transmission and pathogenesis and for development of intervention strategies.

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... Currently, seven human-infecting CoVs have been identified as early as the 1960s, namely: human CoV (HCoV)- 229E (1962), HCoV-OC43 (1967), severe acute respiratory syndrome (SARS)-CoV 1 (SARS1) (2002), HCoV-NL63 (2004), HCoV-HKU1 (2005), and Middle East respiratory syndrome (MERS)- CoV (2012) [all six are endemic to the human population] with SARS-CoV 2 (SARS2) (2019) being the latest CoV capable of infecting humans (Hamre and Procknow, 1966;Kapikian et al., 1969;Ksiazek et al., 2003;Fouchier et al., 2004;Woo et al., 2005;Zaki et al., 2012;Zhu et al., 2020). Moreover, the spike (a common structural protein among the CoVs) is classified as a class I viral fusion protein involved in host tropism, viral entry and pathogenesis, and host immune response induction (Lu et al., 2015;Millet and Whittaker, 2015;Hulswit et al., 2016;Li, 2016). Additionally, the spike has three segments, namely: the large ectodomain which is divided into the S1 receptor-binding subunit (involved in viral attachment) and S2 membrane-fusion subunit (assists virus-cell fusion) (Hulswit et al., 2016;Li, 2016), singlepass transmembrane anchor, and short intracellular tail (Li, 2016). ...
... Moreover, the spike (a common structural protein among the CoVs) is classified as a class I viral fusion protein involved in host tropism, viral entry and pathogenesis, and host immune response induction (Lu et al., 2015;Millet and Whittaker, 2015;Hulswit et al., 2016;Li, 2016). Additionally, the spike has three segments, namely: the large ectodomain which is divided into the S1 receptor-binding subunit (involved in viral attachment) and S2 membrane-fusion subunit (assists virus-cell fusion) (Hulswit et al., 2016;Li, 2016), singlepass transmembrane anchor, and short intracellular tail (Li, 2016). ...
... However, since it is probable that the protein structural dynamics along a receptor binding site may be composed of different atomic coordinates (particularly, protein length and structure) while having a similar binding surface (Di Rienzo et al., 2017) [consistent with what we observed (TM > 0.98) ( Figure 2B)], further structural comparison is merited which would mainly focus on both S1-CTD and S1-NTD of the VOC spike models. VOC S1-CTD and S1-NTD Models Are Structurally Comparable to the Original SARS2 and Endemic HCoV S1 subunit of CoV spike glycoproteins is made up of the C-terminal domain (S1-CTD) and N-terminal domain (S1-NTD) which in-turn have been associated to host cell binding (Hulswit et al., 2016;Li, 2016). To elucidate the structural similarities and differences within the SARS2 S1-CTD and S1-NTD, VOC S1-CTD and S1-NTD models were superimposed with models from the original SARS2 and endemic HCoV. ...
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Coronavirus disease 2019 (COVID-19) pandemic has been attributed to SARS-CoV-2 (SARS2) and, consequently, SARS2 has evolved into multiple SARS2 variants driving subsequent waves of infections. In particular, variants of concern (VOC) were identified to have both increased transmissibility and virulence ascribable to mutational changes occurring within the spike protein resulting to modifications in the protein structural orientation which in-turn may affect viral pathogenesis. However, this was never fully elucidated. Here, we generated spike models of endemic HCoVs (HCoV 229E, HCoV OC43, HCoV NL63, HCoV HKU1, SARS CoV, MERS CoV), original SARS2, and VOC (alpha, beta, gamma, delta). Model quality check, structural superimposition, and structural comparison based on RMSD values, TM scores, and contact mapping were all performed. We found that: 1) structural comparison between the original SARS2 and VOC whole spike protein model have minor structural differences (TM > 0.98); 2) the whole VOC spike models putatively have higher structural similarity (TM > 0.70) to spike models from endemic HCoVs coming from the same phylogenetic cluster; 3) original SARS2 S1-CTD and S1-NTD models are structurally comparable to VOC S1-CTD (TM = 1.0) and S1-NTD (TM > 0.96); and 4) endemic HCoV S1-CTD and S1-NTD models are structurally comparable to VOC S1-CTD (TM > 0.70) and S1-NTD (TM > 0.70) models belonging to the same phylogenetic cluster. Overall, we propose that structural similarities (possibly ascribable to similar conformational epitopes) may help determine immune cross-reactivity, whereas, structural differences (possibly associated with varying conformational epitopes) may lead to viral infection (either reinfection or breakthrough infection).
... Through viral bindings to SA surface moieties to be considered in detail below, SARS-CoV-2 agglutinates RBCs, as established in vitro [35], with such bindings also demonstrated clinically [36]. Hemagglutination also occurs for several other viral strains including other coronaviruses [35,[37][38][39][40][41][42][43][44][45][46][47][48], as demonstrated in the classic viral hemagglutination assay. In that assay, developed in the 1940s [38,[49][50][51] and refined later by Jonas Salk [52][53][54][55][56], virus particles are mixed with RBCs to form a hemagglutinated sheet [40,[57][58][59]. ...
... These matching glycans enable SARS-CoV-2 to hemagglutinate when mixed with human RBCs, as indeed demonstrated using the hemadsorption assay [35] (similar to the hemagglutination assay [106,107]). Hemagglutination occurs more generally in eight families of viruses, including other coronaviruses [35,[37][38][39][40][41][42][43][44][45][46][47][48]. Attachment of SARS-CoV-2 spike protein to RBCs was demonstrated directly through immunofluorescence analysis of RBCs from the blood of nine hospitalized COVID-19 patients [36]. ...
... After initial attachment, viral fusion to a host cell begins with linkage of the spike's receptor-binding domain (RBD), situated just below NTD on spike S1, to an ACE2 receptor on the host cell membrane. The S2 stalk then becomes engaged and viral replication proceeds [47,138,146]. The RBD, one on each of a spike's three monomers, constantly switches between open ("up") and closed ("down") configurations, the former enabling both ACE2 binding and immune surveillance, the latter blocking both of those functions [136,147]. ...
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Rouleaux (stacked clumps) of red blood cells (RBCs) observed in the blood of COVID-19 patients in three studies call attention to the properties of several enveloped virus strains dating back to seminal findings of the 1940s. For COVID-19, key such properties are: (1) SARS-CoV-2 binds to RBCs in vitro and also in the blood of COVID-19 patients; (2) although ACE2 is its target for viral fusion and replication, SARS-CoV-2 initially attaches to sialic acid (SA) terminal moieties on host cell membranes via glycans on its spike protein; (3) certain enveloped viruses express hemagglutinin esterase (HE), an enzyme that releases these glycan-mediated bindings to host cells, which is expressed among betacoronaviruses in the common cold strains but not the virulent strains, SARS-CoV, SARS-CoV-2 and MERS. The arrangement and chemical composition of the glycans at the 22 N-glycosylation sites of SARS-CoV-2 spike protein and those at the sialoglycoprotein coating of RBCs allow exploration of specifics as to how virally induced RBC clumping may form. The in vitro and clinical testing of these possibilities can be sharpened by the incorporation of an existing anti-COVID-19 therapeutic that has been found in silico to competitively bind to multiple glycans on SARS-CoV-2 spike protein.
... These new coronavirus types are primarily transmitted by aerosols and cause infections of the respiratory tract and atypical pneumonia. Their recurrent break into human populations in 2002-2003 (severe acute respiratory syndrome, SARS-CoV) and 2012 (Middle East respiratory syndrome (MERS-CoV)) has ended with the ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 [32]. Coronaviruses enter the infected cell by attaching to cell surface receptors. ...
... Coronaviruses (order Nidovirales, family Coronaviridae) are positive-sense singlestranded RNA (ssRNA) with large genomes (27 to 32 Kb in length) coiled inside a helical nucleocapsid. They belong to the subfamily Coronavirinae that includes four genera (alpha (α)-, beta (β)-, gamma (γ)-and delta (δ)-CoVs) [32,33]. Coronaviruses usually contain canonical structural proteins open reading frames (ORF) 1a and 1b, E (envelope protein), M (membrane protein), N (nucleocapsid protein) and S (spike protein) and some accessories proteins such as the membrane-anchored HE (hemagglutinin-esterase) protein expressed by betacoronaviruses [6]. ...
... Coronaviruses usually contain canonical structural proteins open reading frames (ORF) 1a and 1b, E (envelope protein), M (membrane protein), N (nucleocapsid protein) and S (spike protein) and some accessories proteins such as the membrane-anchored HE (hemagglutinin-esterase) protein expressed by betacoronaviruses [6]. [32]. Coronaviruses enter the infected cell by attaching to cell surface receptors. ...
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The emerging risk of viral diseases has triggered the search for preventive and therapeutic agents. Since the beginning of the COVID-19 pandemic, greater efforts have been devoted to investigating virus entry mechanisms into host cells. The feasibility of plasmonic sensing technologies for screening interactions of small molecules in real time, while providing the pharmacokinetic drug profiling of potential antiviral compounds, offers an advantageous approach over other biophysical methods. This review summarizes recent advancements in the drug discovery process of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) inhibitors using Surface Plasmon Resonance (SPR) biosensors. A variety of SPR assay formats are discussed according to the binding kinetics and drug efficacies of both natural products and repurposed drugs. Special attention has been given to the targeting of antiviral agents that block the receptor binding domain of the spike protein (RBD-S) and the main protease (3CLpro) of SARS-CoV-2. The functionality of plasmonic biosensors for high-throughput screening of entry virus inhibitors was also reviewed taking into account experimental parameters (binding affinities, selectivity, stability), potential limitations and future applications.
... Subsequently, SARS-CoV-2 related viruses' complete genomes were sequenced from bat samples collected before and after the SARS-CoV-2 outbreak in humans and previously collected pangolins samples (Zhou et al., 2020a(Zhou et al., , 2020b(Zhou et al., , 2021aWacharapluesadee et al., 2021;Lam et al., 2020;Xiao et al., 2020). On the other hand, all SARS-CoV-2-related bat and pangolin viruses, except RaTG13&BANAL-20-52, have the high genetic diversity with the SARS-CoV-2 spike gene (Zhou et al., 2020b(Zhou et al., , 2021aWacharapluesadee et al., 2021;York, 2021;Sarah Temmam et al., 2021), which is vital in determining virus entry, tissue tropism, host-range, human-human infection, and host immune responses Chi et al., 2020;Greaney et al., 2021;Suryadevara et al., 2021;Li, 2015Li, , 2016Hulswit et al., 2016). The SARS-CoV-2 spike protein is divided into a signal peptide, S1, and S2 subunits. ...
... Therefore, the less diversified S1-NTDs are considered a more reliable domain for the coronaviruses to bind the sugar receptors, thereby facilitating the S1-RBDs to search their high-affinity protein receptors (Li, 2015). Remarkably, the level of diversity and interaction of these domains with the host receptor is a critical determinant of the coronavirus host range, cross-species infection, tissue tropism, and host immune responses (Li, 2015(Li, , 2016Hulswit et al., 2016). However, over-the-counter studies have shown that genetic variation and evolution in SARS-CoV-2 S1-RBD are of more significant concern (Zhou et al., 2020b(Zhou et al., , 2021bWacharapluesadee et al., 2021;Wang et al., 2020;Wrobel et al., 2020;Ou et al., 2020). ...
... Subsequently, we were interested in understanding the spike gene's genetic diversity, a critical determinant of the coronavirus host range, tissue tropism, and host immune responses (Li, 2015(Li, , 2016Hulswit et al., 2016). To understand the spike gene genetic diversity, first, we performed phylogenetic and NBGMD analysis using 290 sequences. ...
Article
The clue behind the SARS-CoV-2 origin is still a matter of debate. Here, we report that SARS-CoV-2 has gained a novel spike protein S1–N-terminal domain (S1-NTD). In our CLuster ANalysis of Sequences (CLANS) analysis, SARS-CoV/SARS-CoV-2 S1-NTDs displayed a close relationship with OC43 and HKU1. However, in the complete and S1-NTD-free spike protein, SARS-CoV/SARS-CoV-2 revealed closeness with MERS-CoV. Further, we have divided the S1-NTD of SARS-CoV-2 related viruses into three distinct types (Type-I to III S1-NTD) and the S1-NTD of viruses associated with SARS-CoVs into another three classes (Type-A to C S1-NTD) using CLANS and phylogenetic analyses. In particular, the results of our study indicate that SARS-CoV-2, RaTG13, and BANAL-20-52 viruses carry Type-I-S1-NTD and other SARS-CoV-2-related-bat viruses have Type-II and III. In addition, it was revealed that the Pangolin-GX and Pangolin-Guangdong lineages inherited Type-I-like and Type–II–like S1-NTD, respectively. Then our CLANS study shows the potential for evolution of Type-I and Type-III S1-NTD from SARS-CoV-related viruses Type-A and Type-B S1-NTDs, respectively. Furthermore, our analysis clarifies the possibility that Type-II S1-NTDs may have evolved from Type-A-S1-NTD of SARS-CoV-related viruses through Type-I S1-NTDs. We also observed that BANAL-20-103, BANAL-20-236, and Pangolin-Guangdong-lineage viruses containing Type–II–like S1-NTD are very close to SARS-CoV-2 in spike genetic areas other than S1-NTD. Possibly, it suggests that the common ancestor spike gene of SARS-CoV-2/RaTG13/BANAL-20-52-like virus may have evolved by recombining the Pangolin-Guangdong/BANAL-20-103/BANAL-20-236-like spike gene to Pangolin-GX-like Type-I-like-S1-NTD in the unsampled bat or undiscovered intermediate host or possibly pangolin. These may then have evolved into SARS-CoV-2, RaTG13, and BANAL-20-52 virus spike genes by host jump mediated evolution. The potential function of the novel Type-I-S1-NTD and other types of S1-NTDs needs to be studied further to understand better its importance in the ongoing COVID-19 outbreak and for future pandemic preparedness.
... Activité nucléoside triphosphate hydrolase (NTP)ase Hélicase ARN [104] 35 domaines de fusion, le domaine transmembranaire ainsi que deux régions de répétition heptades. Le domaine S1 est très variable [105]. S s'associe en trimère avec les trois domaines S2 formant un trimère tandis que les domaines S1 forment une tête globulaire en « trèfle » [106] (voir Figure 6). ...
... 21 SM-CypI were screened for 104 their antiviral effect on feline coronavirus. Among them, the 83233 was highly potent 105 134 and exhibited a high selective index. Time-addition experiments were performed and 106 showed, that SM-CypI targeted an early stage of the virus cycle, after the attachment 107 step. ...
Thesis
Les Coronavirus (CoVs) forment une famille regroupant de nombreux virus qui peuvent infecter l’Homme et les animaux. Il n'existe actuellement aucun traitement spécifique des infections à coronavirus. Chez le chat, un des coronavirus félins, le virus de la péritonite infectieuse féline (FIPV) provoque une pathologie systématiquement létale. De par leur plasticité génomique et leur capacité à infecter de multiples espèces animales, mammifères ou oiseaux, les CoVs représentent une menace d’émergence continue. Les dernières émergences chez l'Homme du SARS-CoV, du MERS-CoV et plus récemment de SARS-CoV-2 sont le fruit de transmissions interspécifiques entre la faune sauvage et l'Homme. Des études récentes ont montré que les cyclophilines (CyP), des protéines cellulaires très conservées, sont indispensables au cycle réplicatif des CoVs mais les modes d’actions précis de ces protéines ne sont pas connus. Pour étudier le rôle des cyclophilines dans la réplication des coronavirus, nous avons utilisé de petites molécules inhibitrices des cyclophilines (SM-CypI) développées récemment, qui sont nonimmunosuppressives. Nous avons criblé 21 SM-CypI ainsi que la Cyclosporine A (CsA) comme inhibiteur de référence. Neuf SM-CypI avaient une activité inhibitrice de la réplication du FIPV supérieure à celle de la CsA. Sur les neuf molécules, trois ont été sélectionnées : la molécule nommée 83233, se révélant être le meilleur inhibiteur du virus FIPV, et les molécules 832 et 833 qui sont apparentées au 83233. Des expériences de temps d’addition où les molécules antivirales étaient appliquées à différents temps postinfection (1h, 3h, 6h, 9h et 12h) ou avant l’infection, ont montré que l’effet antiviral de ces molécules était maximal lorsqu’elles étaient appliquées au moment de l’infection ou 1h après. Dans toutes les autres conditions expérimentales, leur effet antiviral décroit. Nous avons ainsi déterminé que les cyclophilines étaient essentielles à une étape précoce de la réplication du coronavirus félin. Cette ou ces étapes correspondrai(ent) à la décapsidation et/ou la mise en place du complexe de réplication virale. Pour compléter notre étude sur les mécanismes d’action des cyclophilines, nous avons entrepris de déterminer quelles seraient les protéines virales pouvant interagir avec les cyclophilines cellulaires, en particulier la cyclophiline A. Ainsi, par la technique de ligation de proximité (Proximity Ligation Assay (PLA) en anglais), nous avons pu identifier que la protéine N du coronavirus félin interagissait avec la cyclophiline A féline. Cette interaction n’avait jusqu’à présent été montrée que sur des modèles de coronavirus et cyclophilines humaines, suggérant que les mécanismes d’interaction des cyclophilines avec les protéines des coronavirus pourraient être conservés. Pourtant, lors de tests d’inhibition effectués avec les SM-CypI sur le virus de la bronchite infectieuse aviaire, un gammacoronavirus, l’effet inhibiteur des molécules était modéré. Ces travaux ont permis d’apporter de nouvelles connaissances sur le rôle des cyclophilines dans la réplication des coronavirus et suggèrent que ce rôle pourrait être conservé au moins au sein des coronavirus infectant les mammifères. Nos données ont également permis d’identifier une cible thérapeutique intéressante, ainsi que des molécules présentant un effet antiviral majeur contre certains coronavirus, permettant d’envisager de nouvelles stratégies thérapeutiques.
... SARS-CoV, SARS-CoV-2, and MERS-CoV have different receptors that bind to the host cell because of the difference in S protein. 56,57 This suggests that the ability of different viruses to recognize and invade cells and the types of host cells infected will be different. ORF3 and ORF8 are related to inflammation and escape after virus infection, and the differences in ORF3 and ORF8 genes in the three coronaviruses may be related to different inflammatory mechanisms. ...
... 69 In contrast, although MERS-CoV infection of human primary T lymphocytes was abortive, apoptosis was induced via The core structure of the S2 gene of SARS-CoV is very similar, but the structure of the receptor-binding motif is quite different, so its receptor is dipeptidyl peptidase. 57 Compared with SARS-CoV, the receptor-binding domain sequence homology of S protein is 76%. 60 Its S protein also participates in the process of virus invasion by binding to the ACE2 receptor. ...
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Tong Liu,1,* Meng Feng,2,* Zexin Wen,3 Yijie He,1 Wei Lin,2 Min Zhang1 1Department of Medicine, Xizang Minzu University, Xianyang, Shaanxi, People’s Republic of China; 2School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People’s Republic of China; 3Department of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, People’s Republic of China*These authors contributed equally to this workCorrespondence: Min ZhangDepartment of Medicine, Xizang Minzu University, Xianyang, People’s Republic of ChinaTel +86 2918681997994Email zhangmin-wen@163.comWei LinSchool of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of ChinaTel +86 53115098926353Email linw1978@163.comAbstract: Cytokine storm (CS) is a significant cause of death in patients with severe coronavirus pneumonia. Excessive immune–inflammatory reaction, many inflammatory cell infiltration, and extreme increase of proinflammatory cytokines and chemokines lead to acute lung injury and acute respiratory distress syndrome (ARDS). This review compares the characters of cytokine storms and immune responses caused by three highly pathogenic and infectious coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and analyzes the possible mechanisms to guide clinical treatment in the future.Keywords: cytokines, coronavirus pneumonia, cytokine storm, immune evasion, interferon
... PRCV, a naturally occurring variant of TGEV, typifies how a modification in the N-terminal region of S1 can have a profound impact on tissue tropism. The S1 of PRCV has lost its N-terminal region through a deletion which resulted in the virus losing its sialic acid binding ability (reviewed by Hulswit et al. [12]) and this loss of function modified the tissue tropism of PRCV to predominately respiratory. ...
... Similar experimental data are not available for CCoV2bs; however, both pigs and dogs are known to have the same sialic acid receptors present on cells from similar anatomical regions [46]. The precise role of sialic acid binding in TGEV remains uncertain, with the possibility that it functions either as a co-receptor or protects the virus in the hostile conditions of the digestive tract [12]. Krempl et al. [37] have suggested that their experimentally mutated sites may play a structural role in sialic acid binding, rather than directly interacting with the sialic acid, suggesting that not only the specific sites, but adjacent sequence regions, such as the gapped sequence illustrated in alignment Figure 3, could be at play in this overall interaction. ...
Article
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A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related Alphacoronavirus 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain.
... The corona virus tropism is significantly determined by the spike (S) protein, which facilitates the infection by the virus, by aiding in its binding to the host cell surface (Hulswit et al., 2016). One of the important host cell membrane receptors are angiotensin-converting enzyme-2 (ACE2), which identifies the viral S protein and mediates its infection (Lan et al., 2020;Hoffmann et al., 2020). ...
... The corona viruses belong to the category of RNA viruses, which are not segmented, resulting in enzootic infections, especially in mammals and birds, which is extremely dangerous to the human kind (Wang et al., 2020a). The four structural proteins that the virus encompasses of are envelope (E), membrane (M), nucleocapsid (N) and spike (S) proteins, where the last one is a fundamental component to aid in the entry of SARS-CoV-2 into the host cell (Rota et al., 2003;Hulswit et al., 2016), via ACE-2, expressed in multiple tissues (Donoghue et al., 2000;Harmer et al., 2002). The spike (S) protein of SARS-CoV-2 is responsible for the viral entry into the host cell, where it is activated by proteases, mainly transmembrane serine protease 2 (TMPRSS2) (Hoffmann et al., 2020). ...
Article
The combat against the Corona virus disease of 2019 (COVID-19), has created a chaos among the healthcare institutions and researchers, in turn accelerating the dire need to curtail the infection spread. The already established entry mechanism, via ACE2 has not yet successfully aided in the development of a suitable and reliable therapy. Taking in account the constant progression and deterioration of the cases worldwide, a different perspective and mechanistic approach is required, which has thrown light onto the cluster of differentiation 147 (CD147) transmembrane protein, as a novel route for SARS-CoV-2 entry. Despite lesser affinity towards COVID-19 virus, as compared to ACE2, this receptor provides a suitable justification behind elevated blood glucose levels in infected patients, retarded COVID-19 risk in women, enhanced susceptibility in geriatrics, greater infection susceptibility of T cells, infection prevalence in non-susceptible human cardiac pericytes and so on. The manuscript invokes the title role and distribution of CD147 in COVID-19 as an entry receptor and mediator of endocytosis-promoted entry of the virus, along with the “catch and clump” hypothesis, thereby presenting its Fundamental significance as a therapeutic target for potential candidates, such as Azithromycin, melatonin, statins, beta adrenergic blockers, ivermectin, Meplazumab etc. Thus, the authors provide a comprehensive review of a different perspective in COVID-19 infection, aiming to aid the researchers and virologists in considering all aspects of viral entry, in order to develop a sustainable and potential cure for the 2019 COVID-19 disease.
... Previous research has highlighted that the S glycoprotein contributes towards both tissue and cellular tropism as well as virulence and host range [68][69][70][71][72]. This has been extensively documented throughout all the coronavirus genres (reviewed by Hulswit et al. [73] and Belouzard et al. [46]). Variance in tissue or host tropism can be the consequence of small or large changes within both the NTD and CTD regions [73,74]. ...
... This has been extensively documented throughout all the coronavirus genres (reviewed by Hulswit et al. [73] and Belouzard et al. [46]). Variance in tissue or host tropism can be the consequence of small or large changes within both the NTD and CTD regions [73,74]. For example, a large deletion in the S glycoprotein of Transmissible Gastroenteritis Virus (TGEV) resulted in the emergence of Porcine Respiratory Coronavirus (PRCV) [75][76][77], and two mutations, K479N and S487T within the S1-CTD resulted in interspecies transmission of SARS-CoV from palm civets to humans [78,79]. ...
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This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
... At present, it is known that COVID-19 is mainly spread through respiratory droplets and close contact and there is a possibility of aerosol transmission when exposed to a high concentration of aerosol for a long time in a relatively closed environment. Most CoVs share a similar viral structure and infection pathway [7][8][9][10]. COVID-19 is highly contagious and long-term latent, and the population is generally susceptible, which makes it difficult to control once it breaks out. ...
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Objective. The study aims to summarize and analyze the clinical and CT findings of severe COVID-19 patients. Methods. From February 11 to March 31, 2020, 61 COVID-19 patients in intensive care in the E1-3 ward of Tongji Hospital were analyzed retrospectively. Results. The main clinical manifestations were cough, expectoration in 56 cases (91.8%), shortness of breath, chest tightness in 48 cases (78.7%), fever in 61 cases (100%), muscle ache and weakness in 40 cases (65.6%), diarrhea or vomiting in 8 cases (13.1%), and headache in 4 cases (6.6%). After admission, the leukocyte count was normal in 40 cases (57.7%), higher in 9 cases (15.4%), and lower in 12 cases (26.9%). The lymphocyte count decreased in 53 cases (86.9%). CRP was increased in 29 cases (47.5%); PCT was increased in 15 cases (24.6%); ESR was increased in 38 cases (62.3%); D-dimer increased in 39 cases (63.9%); ALT/AST increased in 40 cases (65.6%); CK/CK-MB increased in 8 cases (13.1%); troponin I increased in 6 cases (9.8%); NT-proBNP increased in 35 cases (57.4%); IL-1 increased in 5 cases (8.2%); IL-2 receptor increased in 28 cases (45.9%); IL-6 increased in 23 cases (37.7%); IL-8 increased in 15 cases (24.6%); IL-10 increased in 12 cases (19.7%); and NTF increased in 22 cases (36.1%). The chest CT images showed that 38 cases (65.5%) of right lung lesions were more extensive than those of left lung lesions, 20 cases (34.5%) of left lung lesions were more extensive than those of right lung lesions, 42 cases (72.5%) of lower lobe lesions were more extensive than those of upper lobe lesions, 6 cases (10.3%) of upper lobe lesions were more extensive than those of lower lobe lesions, and 10 cases (17.2%) of upper and lower part lesions were roughly the same. Ground-glass opacity (GGO) was found in 12 cases (20.7%); GGO with focal consolidation in 38 cases (65.5%); small patchy edge fuzzy density increased in 24 cases (41.4%); large consolidation in 20 cases (34.5%); reticular or fibrous cord in 54 cases (93.1%); and air bronchogram in 8 cases (13.8%). Conclusions. COVID-19 patients in intensive care have no specific clinical manifestation and CT findings. However, analysis and summary of relevant data can help us assess the severity of the disease, decide the timing of treatment, and predict prognosis.
... The key element which is crucial in HCoV infection is the spike (S) protein surrounded by a lipid bilayer on the surface of the virus, from which trimer class I transmembrane glycoproteins protrude [28,29]. The spike (S) protein of SARS-CoV-2 mediates the recognition of the host-cell receptors and facilitates the cell attachment and the cell membrane fusion during the viral infection [30][31][32]. The trimeric S protein is located on the virion's surface and acts as the basic unit for the host-cell receptor recognition, and it is composed of two components, S1 and S2 subunits [33,34]. ...
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A novel human coronavirus prompted considerable worry at the end of the year 2019. Now, it represents a significant global health and economic burden. The newly emerged coronavirus disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the primary reason for the COVID-19 global pandemic. According to recent global figures, COVID-19 has caused approximately 243.3 million illnesses and 4.9 million deaths. Several human cell receptors are involved in the virus identification of the host cells and entering them. Hence, understanding how the virus binds to host-cell receptors is crucial for developing antiviral treatments and vaccines. The current work aimed to determine the multiple host-cell receptors that bind with SARS-CoV-2 and other human coronaviruses for the purpose of cell entry. Extensive research is needed using neutralizing antibodies, natural chemicals, and therapeutic peptides to target those host-cell receptors in extremely susceptible individuals. More research is needed to map SARS-CoV-2 cell entry pathways in order to identify potential viral inhibitors.
... This S2 subdomain is the probable target for cross-reactive antibodies (Lan et al. 2020). The S1 domain has two sub units-the N-terminal subdomain (NTD) that binds sialic acid and the C-terminal subdomain that binds a specific proteinaceous receptor (Hulswit et al. 2016). ...
Article
COVID-19 is a highly spreadable viral infection, reported first in Wuhan, China in December 2019 which spreads worldwide later. The pathogen of this disease is SARS-CoV virus. World Health Organization announced first the name of this new disease and declared this outbreak as a Public Health Emergency of International Concern. This disaster is the most polarising global pandemic after the World War II which causes significant economic, social, political disruption, and afflicts civilization throughout human history in the world. It becomes an unprecedented challenge for India. At the time of writing this review, some specific vaccines are available but due to mutations in virus, at present it is necessary to early analyse and implement supportive treatments of this infection. Therefore, a thorough investigation is urgently required to construct an outline for the inhibition and treatment of this disease. It is necessary to understand the pathogenic mechanisms, epidemiological characteristics and to detect possible drug targets. In the present article the existing knowledge of COVID-19 including epidemiological and clinical features, available medication and treatment options till date are summarized. In addition, an up-to-date synopsis of the ongoing research progress in designing safe and effective vaccines is also highlighted which will help the human being to combat against this disease and to completely control the pandemic finally. Lastly, some major concerns to be challenged and perspectives for the future development are discussed in this article which will help to give valuable insights into new research directions.
... This cleavage-mediated activation is complex and often involves multiple host proteases (Hulswit et al. 2016). For a detailed review of spike activation mechanisms, please see Whittaker et al. (2021). ...
Article
Compared to other known SARS-related coronaviruses (SARSr-CoVs), SARS-CoV-2 possesses a unique furin cleavage site (FCS) in its spike. This has stimulated discussion pertaining to the origin of SARS-CoV-2 because the FCS has been observed to be under strong selective pressure in humans and confers the enhanced ability to infect some cell types and induce cell-cell fusion. Furthermore, scientists have demonstrated interest in studying novel cleavage sites by introducing them into SARSr-CoVs. We review what is known about the SARS-CoV-2 FCS in the context of its pathogenesis, origin, and how future wildlife coronavirus sampling may alter the interpretation of existing data.
... Studies reported that SARS-CoV-2 RBD has a higher affinity for the ACE2 receptor than the RBD of SARS-CoV has due to key amino acid differences [1,8,26,27]. Besides its conserved nature, the S protein is crucial in the life cycle of CoVs as it contributes to receptor recognition, viral attachment, and entry [9,[25][26][27][35][36][37]. Other studies showed that S protein is involved in immune evasion [38] making it the primary target for vaccine and therapeutic studies. ...
Article
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Responsible for more than 4.9 million deaths so far, COVID-19, caused by SARS-CoV-2, is instigating devastating effects on the global health care system whose impacts could be longer for the years to come. Acquiring a comprehensive knowledge of host-virus interaction is critical for designing effective vaccines and/or drugs. Understanding the evolution of the virus and the impact of genetic variability on host immune evasion and vaccine efficacy is helpful to design novel strategies to minimize the effects of the emerging variants of concern (VOC). Most vaccines under development and/or in current use target the spike protein owning to its unique function of host receptor binding, relatively conserved nature, potent immunogenicity in inducing neutralizing antibodies, and being a good target of T cell responses. However, emerging SARS-CoV-2 strains are exhibiting variability on the spike protein which could affect the efficacy of vaccines and antibody-based therapies in addition to enhancing viral immune evasion mechanisms. Currently, the degree to which mutations on the spike protein affect immunity and vaccination, and the ability of the current vaccines to confer protection against the emerging variants attracts much attention. This review discusses the implications of SARS-CoV-2 spike protein mutations on immune evasion and vaccine-induced immunity and forward directions which could contribute to future studies focusing on designing effective vaccines and/or immunotherapies to consider viral evolution. Combining vaccines derived from different regions of the spike protein that boost both the humoral and cellular wings of adaptive immunity could be the best options to cope with the emerging VOC.
... Similarly in our recombinant network tree analysis, the Betacoronaviruses B (SARS-CoV2 and SARS-CoV) and Betacoronaviruses D (Bat-CoVs) shared common clades, although branched differently, however possible to be originated from bats. Incidence of such intra-species transmission happenings in birds and mammals might be manifested by the predominant occurrence of CoVs at a large scale (59). In terms of Gamma-CoVs, thought provoking trends were observed during phylogenetic analysis. ...
Article
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Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.
... Spike proteins assemble into homotrimers on the surface of virions, which gives CoVs a crown-like appearance [21]. The identity and distribution of the specific cellular receptor recognized by the S protein are the key factors that determine host species susceptibility and tissue tropism of the virus [22]. Since the S protein contains epitopes that induce strongly neutralizing antibodies, it is the most common target for CoV vaccines. ...
Article
Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.
... Either NTD or CTD domains can bind to distinct receptors and serve as the receptor-binding domain (RBD) [58]. However, the RBD of coronaviruses is located within the S1 subdomain of the spike protein, which might allow binding to different receptors [59]. For example, although the receptor-binding domain (RBD) of most coronaviruses is located in the CT, the RBD of murine hepatitis virus (MHV-A59) is located within the NTD of the S-protein [60][61][62][63][64][65]. ...
Article
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In December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China with serious impacts on global health and economy that is still ongoing. Although interspecies transmission of coronaviruses is common and well documented, each coronavirus has a narrowly restricted host range. Coronaviruses utilize different receptors to mediate membrane fusion and replication in the cell cytoplasm. The interplay between the receptor-binding domain (RBD) of coronaviruses and their coevolution are determinants for host susceptibility. The recently emerged SARS-CoV-2 caused the coronavirus disease 2019 (COVID-19) pandemic and has also been reported in domestic and wild animals, raising the question about the responsibility of animals in virus evolution. Additionally, the COVID-19 pandemic might also substantially have an impact on animal production for a long time. In the present review, we discussed the diversity of coronaviruses in animals and thus the diversity of their receptors. Moreover, the determinants of the susceptibility of SARS-CoV-2 in several animals, with special reference to the current evidence of SARS-CoV-2 in animals, were highlighted. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to mitigate the threat for both humans and animals.
... Either NTD or CTD domains can bind to distinct receptors and serve as the receptor-binding domain (RBD) [58]. However, the RBD of coronaviruses is located within the S1 subdomain of the spike protein, which might allow binding to different receptors [59]. For example, although the receptor-binding domain (RBD) of most coronaviruses is located in the CT, the RBD of murine hepatitis virus (MHV-A59) is located within the NTD of the S-protein [60][61][62][63][64][65]. ...
Article
Full-text available
In December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China with serious impacts on global health and economy that is still ongoing. Although interspecies transmission of coronaviruses is common and well documented, each coronavirus has a narrowly restricted host range. Coronaviruses utilize different receptors to mediate membrane fusion and replication in the cell cytoplasm. The interplay between the receptor-binding domain (RBD) of coronaviruses and their coevolution are determinants for host susceptibility. The recently emerged SARS-CoV-2 caused the coronavirus disease 2019 (COVID-19) pandemic and has also been reported in domestic and wild animals, raising the question about the responsibility of animals in virus evolution. Additionally, the COVID-19 pandemic might also substantially have an impact on animal production for a long time. In the present review, we discussed the diversity of coronaviruses in animals and thus the diversity of their receptors.
... The occurrence of a 290-nucleotide deletion (corresponding to the absence of BCoV ns4.9 and ns4.8) in HCoV-OC43 relative to the BCoV genome potentially supports the argument that an interspecies transmission event occurred from bovines to humans [88]. In addition, genetic recombination and viral mutations, especially gene recombination and mutations in the S protein, can promote the expansion of the host range [92]. In this study, using a sequence alignment analysis, no significant landmark differences were found in the amino acid sequences of the S protein between BCoV and bovine-like coronaviruses. ...
Article
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Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory disease in cattle. BCoV has also been reported to cause a variety of animal diseases and is closely related to human coronaviruses, which has attracted extensive attention from both cattle farmers and researchers. However, there are few comprehensive epidemiological reviews, and key information regarding the effect of S-gene differences on tissue tendency and potential cross-species transmission remain unclear. In this review, we summarize BCoV epidemiology, including the transmission, infection-associated factors, co-infection, pathogenicity, genetic evolution, and potential cross-species transmission. Furthermore, the potential two-receptor binding motif system for BCoV entry and the association between BCoV and SARS-CoV-2 are also discussed in this review. Our aim is to provide valuable information for the prevention and treatment of BCoV infection throughout the world.
... N-terminal subunit forms the globular head of spike protein and the C-terminal S2 region forms the stalk of the protein. These two subunits help the virus recognize and fuse with the host cell receptor hACE2 [4]. The SARS-CoV-2 consists of two overlapping open reading frames (ORF1a and ORF1b) which codes for two different polyproteins pp1a and pp1ab processed by 3CL protease and papain-like protease resulting in 16 different mature nonstructural proteins. ...
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Over the past year, owing to the emergent demand for the search for potential COVID-19 therapeutics, identifying alternative candidates from biological sources is one of the sustainable ways to reinforce the drug discovery process. Marine macroalgae have numerous advantages because of the richest availability of underexploited bioactive compounds. Polyphenolic compounds like phlorotannins obtained from brown macroalgae are reported as proven antiviral and immunostimulatory agents. Thus, the present study evaluated the possibility of phlorotannins as antagonists to the multiple target proteins essential for SARS-CoV-2 replication. Twenty different types of potent phlorotannins were targeted against druggable target proteins, viz., 3CLpro, RdRp, and Spro using AutoDock molecular docking, drug-likeness were assessed by ADMET profiling (QikProp module). Further, validated with 200 ns molecular dynamics (MD) simulation (Desmond module) for the top-ranked phlorotannins based on docking binding affinities. Among the twenty phlorotannins studied, eckol hexacetate, phlorofucofuroeckol, fucofuroeckol, and bifuhalol-hexacetate showed significant binding affinities across the selected targets. Besides, MD simulations highlighted Glu166, Gln189, Cys145, and Thr190 tetrad as potential interaction sites to inhibit 3CLpro's activity. Moreover, phlorotannins were confirmed to be druglike, with no major deviation observed in ADMET-profiling. Hence, phlorotannins could be therapeutic candidates against SARS-CoV-2. However, further investigations are needed to prove its efficacy as an antiviral agent. Conclusively, this study may envisage that the novel finding could notably impact the advancement of antiviral interventions for COVID-19 in the near future. Graphical Abstract
... The main surface protein of CoVs is the spike (S) protein that facilitates receptor binding and fusion of the viral lipid envelope with the host cell membrane. Receptor binding is facilitated by the S1 subunit while the S2 subunit is involved with fusion of the viral membrane with the cell membrane (Hoffmann et al., 2020b;Hulswit et al., 2016). For these two events to occur, the S protein needs to be post-transitionally modified by two different host proteases to become activated. ...
Article
The SARS-CoV-2 (SARS-CoV-2) virus has caused a worldwide pandemic because of the virus's ability to transmit efficiently human-to-human. A key determinant of infection is the attachment of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Because of the presumed zoonotic origin of SARS-CoV-2, there is no practical way to assess the susceptibility of every species to SARS-CoV-2 by direct challenge studies. In an effort to have a better predictive model of animal host susceptibility to SARS-CoV-2, we expressed the ACE2 and/or transmembrane serine protease 2 (TMPRSS2) genes from humans and other animal species in the avian fibroblast cell line, DF1, that is not permissive to infection. We demonstrated that expression of both human ACE2 and TMPRSS2 genes is necessary to support SARS-CoV-2 infection and replication in DF1 and a non-permissive sub-lineage of MDCK cells. Titers of SARS-CoV-2 in these cell lines were comparable to those observed in control Vero cells. To further test the model, we developed seven additional transgenic cell lines expressing the ACE2 and TMPRSS2 derived from Felis catus (cat), Equus caballus (horse), Sus domesticus (pig), Capra hircus (goat), Mesocricetus auratus (Golden hamster), Myotis lucifugus (Little Brown bat) and Hipposideros armiger (Great Roundleaf bat) in DF1 cells. Results demonstrate permissive replication of SARS-CoV-2 in cat, Golden hamster, and goat species, but not pig or horse, which correlated with the results of reported challenge studies. Cells expressing genes from either bat species tested demonstrated temporal replication of SARS-CoV-2 that peaked early and was not sustained. The development of this cell culture model allows for more efficient testing of the potential susceptibility of many different animal species for SARS-CoV-2 and emerging variant viruses.
... S glycoprotein mutations help escape the immune response and promote animal-human transmission through adaptation potentials (Zhang et al., 2006). The hypervariability of S glycoprotein is the main cause of changes in tissue tropism (Gallagher and Buchmeier, 2001;Hulswit et al., 2016). The deletion of about 216 or 227 amino acid residues in the N-terminus of S glycoprotein of TGEV has causally changed the enteric tissue tropism to a respiratory tissue tropism (named PRCV; Laude et al., 1993;Vaughn et al., 1995), which may be linked to the distribution of receptors over tissues or their different usage by different CoV strains (Whitworth et al., 2019). ...
Article
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Porcine hemagglutinating encephalomyelitis virus (PHEV) is a Betacoronavirus characterized by neurological symptoms and a worldwide prevalence. Although PHEV is one of the earliest discovered porcine coronaviruses, it remains poorly studied. The full-length genome of the earliest PHEV strain collected in 1970 in the United States (PHEV/67 N/US/1970) was determined in October 2020. Using this virus as a prototype, we comparatively analyzed all available PHEV full-length sequences during 1970–2015. In phylogenetic trees based on PHEV full-length or spike glycoprotein open reading frame genomic sequences, PHEV/67 N/US/1970 was sorted into a clade different from that of viruses isolated in the United States in 2015. Intriguingly, United States and Belgium viruses isolated in 2015 and 2005, respectively, revealed multiple deletion mutation patterns compared to the strain PHEV/67 N/US/1970, leading to a truncated or a non-functional NS2A coding region. In addition, the genomic similarity analysis showed a hypervariability of the spike glycoprotein coding region, which can affect at least eight potential linear B cell epitopes located in the spike glycoprotein. This report indicates that PHEVs in the United States underwent a significant genetic drift, which might influence PHEV surveillance in other countries.
... Another 2 mutations (A394G and K494I) were located within domain B, which was reported to have the highest variability across CoVs and correlates to the ability of different viruses to interact with distinct host receptors (Tortorici et al., 2019). Further, mutations in domain B were associated with changes in viral tropism and influenced animal-to-human transmission of SARS (Qu et al., 2005;Hulswit et al., 2016). Another 2 amino acid changes were in NSP3 and NSP6 within the ORF1a region. ...
Article
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The human coronavirus OC43 (HCoV-OC43) is one of the most common causes of common cold but can lead to fatal pneumonia in children and elderly. However, the available animal models of HCoV-OC43 did not show respiratory symptoms that are insufficient to assist in screening antiviral agents for respiratory diseases. In this study, we adapted the HCoV-OC43 VR-1558 strain by serial passage in suckling C57BL/6 mice and the resulting mouse-adapted virus at passage 9 (P9) contained 8 coding mutations in polyprotein 1ab, spike protein, and nucleocapsid protein. Pups infected with the P9 virus significantly lost body weight, and died within 5 dpi. In cerebral and pulmonary tissues, the P9 virus replication induced the production of G-CSF, IFN-γ, IL-6, CXCL1, MCP-1, MIP-1α, RANTES, IP-10, MIP-1β, and TNF-α, as well as pathological alterations including reduction of neuronal cells and typical symptoms of viral pneumonia. We found that the treatment of arbidol hydrochloride (ARB) or Qingwenjiere Mixture (QJM) efficiently improved the symptoms and decreased n gene expression, inflammatory response, and pathological changes. Furthermore, treating with QJM or ARB raised the P9-infected mice’ survival rate within a 15-day observation period. These findings suggested that the new mouse-adapted HCoV-OC43 model is applicable and reproducible for antiviral researches of HCoV-OC43.
... CoVs have an envelope spike protein (S) that mediates viral entry into cells and this is one of the key determinants of host and tissue tropisms (1). It has been well documented that SARS-CoV-2 uses angiotensin-converting enzyme receptor 2 (ACE2) as a receptor on the cell surface and that antibodies specific to the SARS-CoV-2 S inhibit its binding to ACE2 (2,3). ...
Article
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Antibody-dependent enhancement (ADE) of infection is generally known for many viruses. A potential risk of ADE in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has also been discussed since the beginning of the coronavirus disease 2019 (COVID-19) pandemic; however, clinical evidence of the presence of antibodies with ADE potential is limited. Here, we show that ADE antibodies are produced by SARS-CoV-2 infection and the ADE process can be mediated by at least two different host factors, Fcγ receptor (FcγR) and complement component C1q. Of 89 serum samples collected from acute or convalescent COVID-19 patients, 62.9% were found to be positive for SARS-CoV-2-specific IgG. FcγR- and/or C1q-mediated ADE were detected in 50% of the IgG-positive sera, whereas most of them showed neutralizing activity in the absence of FcγR and C1q. Importantly, ADE antibodies were found in 41.4% of the acute COVID-19 patients. Neutralizing activity was also detected in most of the IgG-positive sera, but it was counteracted by ADE in subneutralizing conditions in the presence of FcγR or C1q. Although the clinical importance of ADE needs to be further investigated with larger numbers of COVID-19 patient samples, our data suggest that SARS-CoV-2 utilizes multiple mechanisms of ADE. C1q-mediated ADE may particularly have a clinical impact since C1q is present at high concentrations in plasma and its receptors are ubiquitously expressed on the surfaces of many types of cells, including respiratory epithelial cells, which SARS-CoV-2 primarily infects. IMPORTANCE Potential risks of antibody-dependent enhancement (ADE) in the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been discussed and the proposed mechanism mostly depends on the Fc gamma receptor (FcγR). However, since FcγRs are exclusively expressed on immune cells, which are not primary targets of SARS-CoV-2, the clinical importance of ADE of SARS-CoV-2 infection remains controversial. Our study demonstrates that SARS-CoV-2 infection induces antibodies that increase SARS-CoV-2 infection through another ADE mechanism in which complement component C1q mediates the enhancement. Although neutralizing activity was also detected in the serum samples, it was counteracted by ADE in the presence of FcγR or C1q. Considering the ubiquity of C1q and its cellular receptors, C1q-mediated ADE may more likely occur in respiratory epithelial cells, which SARS-CoV-2 primarily infects. Our data highlight the importance of careful monitoring of the antibody properties in COVID-19 convalescent and vaccinated individuals.
... The Coronavirinae are classified into two subfamilies: Coronavirinae and Torovirinae. Based on the molecular structure and biological functions, the Coronavirinae are further divided into four genera: alpha-(α-), beta-(β-), gamma-(γ-), and delta-coronavirus (δ-CoV) (Hulswit et al., 2016;Payne 2017). To date, six human coronavirus species have been identified, namely, HCoV-NL63, HCoV-229E, HCoV-OC34, HCoV-HKU1, SARS-CoV, and MERS-CoV (Arden et al., 2005;Su et al., 2016;Zhang et al., 2018). ...
Article
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The ongoing pandemic coronavirus disease (COVID-19) caused by a novel corona virus, namely, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has had a major impact on global public health. COVID-19 cases continue to increase across the globe with high mortality rates in immunocompromised patients. There is still a pressing demand for drug discovery and vaccine development against this highly contagious disease. To design and develop antiviral drugs against COVID-19, the main protease (M pro) has emerged as one of the important drug targets. In this context, the present work explored Jadwar (Delphinium denudatum)-derived natural alkaloids as potential inhibitors against M pro of SARS-CoV-2 by employing a combination of molecular docking and molecular dynamic simulation-based methods. Molecular docking and interaction profile analysis revealed strong binding on the M pro functional domain with four natural alkaloids viz. panicutine (−7.4 kcal/mol), vilmorrianone (−7.0 kcal/mol), denudatine (−6.0 kcal/mol), and condelphine (−5.9 kcal/mol). The molecular docking results evaluated by using the MD simulations on 200 nanoseconds confirmed highly stable interactions of these compounds with the M pro. Additionally, mechanics/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energy calculations also affirmed the docking results. Natural alkaloids explored in the present study possess the essential drug-likeness properties, namely, absorption, distribution, metabolism, and excretion (ADME), and are in accordance with Lipinski's rule of five. The results of this study suggest that these four bioactive molecules, namely, condelphine, denudatine, panicutine, and vilmorrianone, might be effective candidates against COVID-19 and can be further investigated using a number of experimental methods.
... The accessory proteins are dispensable for replication but often have immunoevasive activities [7][8][9] . The main determinant of coronavirus tropism is the spike glycoprotein, which forms trimers on the surface of virions 10 . The spike protein consists of two subunits: the S1 subunit, which binds to the host entry receptor angiotensin-converting enzyme 2 (ACE2) 11 , and the S2 subunit, which mediates membrane fusion (Fig. 1b). ...
Article
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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating pandemic. Although most people infected with SARS-CoV-2 develop a mild to moderate disease with virus replication restricted mainly to the upper airways, some progress to having a life-threatening pneumonia. In this Review, we explore recent clinical and experimental advances regarding SARS-CoV-2 pathophysiology and discuss potential mechanisms behind SARS-CoV-2-associated acute respiratory distress syndrome (ARDS), specifically focusing on new insights obtained using novel technologies such as single-cell omics, organoid infection models and CRISPR screens. We describe how SARS-CoV-2 may infect the lower respiratory tract and cause alveolar damage as a result of dysfunctional immune responses. We discuss how this may lead to the induction of a ‘leaky state’ of both the epithelium and the endothelium, promoting inflammation and coagulation, while an influx of immune cells leads to overexuberant inflammatory responses and immunopathology. Finally, we highlight how these findings may aid the development of new therapeutic interventions against COVID-19. In this Review, Lamers and Haagmans explore recent clinical and experimental advances in understanding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis, interactions with host cells and the involvement of the immune system in the development of severe disease. Specifically, they focus on mechanisms underlying the development of COVID-19-associated acute respiratory distress syndrome.
... This protein projects through the viral envelope, is heavily glycosylated, and regulates host cell membrane receptor binding and fusion of the viral and cellular membrane. 49 The functions of the 11 accessory proteins encoded within the one-third closest to the 3' end of the SARS-CoV-2 genome are not fully understood. These accessory proteins are encoded by the ORF3a, ORF3b, ORF3c, ORF3d, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORC9c, and ORF10 genes. ...
Article
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As of 25 January 2022, over 349 million individuals have received a confirmed diagnosis of covid-19, with over 5.59 million confirmed deaths associated with the SARS-CoV-2 virus. The covid-19 pandemic has prompted an extensive global effort to study the molecular evolution of the virus and develop vaccines to prevent its spread. Although rigorous determination of SARS-CoV-2 infectivity remains elusive, owing to the continuous evolution of the virus, steps have been made to understand its genome, structure, and emerging genetic mutations. The SARS-CoV-2 genome is composed of several open reading frames and structural proteins, including the spike protein, which is essential for entry into host cells. As of 25 January 2022, the World Health Organization has reported five variants of concern, two variants of interest, and three variants under monitoring. Additional sublineages have since been identified, and are being monitored. The mutations harboured in these variants confer an increased transmissibility, severity of disease, and escape from neutralising antibodies compared with the primary strain. The current vaccine strategy, including booster doses, provides protection from severe disease. As of 24 January 2022, 33 vaccines have been approved for use in 197 countries. In this review, we discuss the genetics, structure, and transmission methods of SARS-CoV-2 and its variants, highlighting how mutations provide enhanced abilities to spread and inflict disease. This review also outlines the vaccines currently in use around the world, providing evidence for every vaccine's immunogenicity and effectiveness.
... however the strain isolated from cell culture harbored three additional mutations. Among these, we noticed a non-synonymous mutation (S A852V) in the gene encoding the Spike protein (S gene), that mediates receptor binding and fusion of the viral and cellular membrane (18), thus determining the ability of the virus to infect the cells and its transmissibility in the host (19). To date, several mutations in the S gene were reported, but it is still unclear whether these variations could influence viral infectivity, transmissibility or immune response (20). ...
Article
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. Several cases of persistent infection have been described, but there are few reports that compared the genetic variability among samples collected from the patient during infection. In the current study, we reported a viral genetic analysis of a diabetic male patient with Non-Hodgkin Lymphoma affected by persistent SARS-CoV-2 infection. We sequenced the patient-derived viral isolated both from oro/nasopharyngeal swab and VeroE6 cell line, collected from the same patient at different points of the infection. Due to the insufficient material of the second swab received, in order to obtain a complete coverage of the viral genome, it was convenient to perform a virus isolation after cell culture. Both genomes belonged to Pangolin Lineage B.1, Nextstrain clade 20A and GISAID clade G. The mutation spectrum predicted for the two viral genomes reveal three additionally mutations in the sequence of second sample when compared with mutations set identified in the first sample. Our findings show the evolution of the intra-host variability during the course of a long-lasting infection.
... Similar to other coronaviruses, the Spike protein is a trimeric class I transmembrane glycoprotein located on the surface of SARS-CoV-2 [55]. SARS-CoV-2 Spike protein is involved in receptor recognition, cell attachment, and fusion, making it crucial for viral entry and infectivity [56][57][58][59][60][61]. On the other hand, ORF1ab has been shown to have key roles in viral interaction with the innate immune response [62,63], viral replication [64], and viral RNA synthesis and processing [65,66]. ...
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Background: The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide during an unprecedented pandemic. Identification of the candidate viral epitopes is the first step in the design of vaccines against the viral infection. Several immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes that bind specifically with the major histocompatibility molecules class I (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. These alleles were also found with high frequency in other populations worldwide. Results: Molecular docking approach showed that using the co-crystallized MHC-I and T cell receptor (TCR) instead of using MHC-I structure only, significantly enhanced docking scores and stabilized the conformation, as well as the binding affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein sequence. This prediction has been confirmed by published experimentally validated and in silico predicted spike epitope. On the other hand, we predicted novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and antigenicity response with both MHC-I and TCR. Moreover, antigenicity, allergenicity, toxicity, and physicochemical properties of the predicted SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, showing high efficacy of the proposed epitopes as a vaccine candidate. Conclusion: Our predicted SARS-CoV-2 epitopes can facilitate vaccine development to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for further experimental validation. Our proposed molecular docking approach of exploiting both MHC and TCR structures can be used to identify potential epitopes for most microbial pathogens, provided the crystal structure of MHC co-crystallized with TCR.
... Protein-proofed single-cell RNA profiling (psc-RNA) studies reveal that ACE2, furin, and TMPRSS2 highly co-express in lung macrophages and AT2 followed by cardiomyocytes, stromal cells of the adrenal gland, testes, ovary, and thyroid, identifying tissue-dependent SARS-CoV-2 infection vulnerability [161]. Following furin-mediated S protein cleavage at the S1/S2 boundary results in two noncovalently associated proteins (S1 and S2) [48,49,91,162,163]. This process exposes a cleavage site on S2, which TMPRSS2 acts upon to activate the S protein, which initiates the fusion of the viral and cell membranes [56,162]. ...
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Objectives: The emergence of coronavirus disease 2019 (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health calamity unprecedented in the modern world. The disease spread worldwide, and to date, there have been over 230 million confirmed cases of COVID-19, including approximately 4.7 million deaths. Mutant variants of the virus have raised concerns about additional pandemic waves and threaten to reverse our progress thus far to limit the spread of the virus. These variants include Alpha, Beta, and Delta (first reported in December 2020 in the United Kingdom, South Africa, and India, respectively) and Gamma (reported in January 2021 in Brazil). In some cases, countries have even reported a rise in daily cases higher than the first wave in March 2020. Given the rapidly evolving nature of COVID-19 and subsequent new findings and updates each day, this review article aims to comprehensively summarize the etiology, pathophysiology, and clinical features of SARS-CoV-2 infection. Methods: A systematic review of the literature was performed in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to gain insight into the transmissibility, pathogenesis, entry factors, and immune response of COVID-19. Specifically, Pubmed and Google Scholar databases were searched to identify any relevant articles. References within the included articles were reviewed. Published articles related to search criteria from the onset of the COVID-19 pandemic to March 2022 were included. Results: Viral transmissibility is predominantly affected by the modes of transmission, various mutations on the nucleocapsid protein and endoRNAse, gender, age, and other factors. The pathophysiological mechanism is generally unknown, although the clinical manifestations such as headache, loss of smell and taste, vomiting, diarrhea, multiorgan failure, and dermatological and cardiovascular complications are well documented. The progression of infection depends on the immunopathological response and the innate/adaptive immunity. Conclusion: Our review has summarized the latest knowledge about SARS-CoV2. However, as the pandemic continues to spread across the continents, there is an urgent need for more research on potentially emerging coronaviruses and the development of a universal coronaviruses vaccine to put the pandemic behind us.
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A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.
Chapter
The well-established structure of SARS-CoV-2 proteins has opened the door for the drug development of the potent inhibitors. The interaction of spike proteins of the virus with human angiotensin converting enzyme (ACE-2) via receptor binding domain start the journey of the virus in the host cell. The entry of corona virus by endocytosis is followed by genomic replication, transcription and formation of the positive sense RNA. The assembling of genomic material with viral structure proteins, endoplasmic reticulum & golgi intermediate forms mature viron, which on exocytosis completes the SARS-CoV-2 life cycle. The entire cycle highlights the importance of different proteins involved in functioning and virulence of the virus. Targeting some of these proteins such as spike proteins, 3C like protease (3CL pro), papaine like protease (PL pro), helicase, RNA dependent RNA polymerase (RdRp) and N protein plays important role in the development of the antiviral drugs. Using computational approach the researchers are investigating important targets interaction with ligands (novel or existing) for the development of potent antiviral drugs. Number of existing FDA approved drug molecules are repurposed against 3CL pro, PL pro, RdRp and few of them, e.g. remdisivir, favipiravir and lvermectin, are currently used in clinical application against SARS-CoV-2. Numbers of small molecules libraries are also high through output screened for the identification of novel ligand molecule for new drug development. In the present chapter various approaches and strategies for the development of antiviral drugs using the computation tools has been highlighted for the main targets of SARS-CoV-2.
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El Comité Editorial de Biomédica ya aprobó para publicación este manuscrito, teniendo en cuenta los conceptos de los pares académicos que lo evaluaron. Se publica anticipadamente en versión pdf en forma provisional con base en la última versión electrónica del manuscrito pero sin que aún haya sido diagramado ni se le haya hecho la corrección de estilo. Siéntase libre de descargar, usar, distribuir y citar esta versión preliminar tal y como lo indicamos pero, por favor, recuerde que la versión impresa final y en formato pdf pueden ser diferentes.
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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new coronavirus discovered that appeared in Wuhan, China, in December 2019, causes COVID-19 disease which have resulted in cases similar to SARS-atypical pneumonia. Worldwide, around 116 million cases and 2.57 million deaths are reported with new cases and increasing mortality every day. To date, there is no specific commercial treatment to control the infection. Repurpose drugs targeting the angiotensin-converting enzyme 2 (ACE2) receptor represents an alternative strategy to block the binding of SARS-CoV-2 protein S and forestall virus adhesion, internalization, and replication in the host cell. Methods: We performed a rigid molecular docking using the receptor binding domain of the S1 subunit of S protein (RBD S1 )-ACE2 (PDB ID: 6VW1) interaction site and 1,283 drugs FDA approved. The docking score, frequency of the drug in receptor site, and interactions at the binding site residues were used as analyzing criteria. Results: This research yielded 40 drugs identified as a potential inhibitor of RBD S1 -ACE2 interaction. Among the inhibitors, compounds such as ipratropium, formoterol, and fexofenadine can be found. Specialists employ these drugs as therapies to treat chronic obstructive pulmonary disease, asthma and virtually any respiratory infection. Conclusions : Our results will serve as the basis for in vitro and in vivo studies to evaluate the potential use of those drugs to generate affordable and convenient therapies to treat COVID-19.
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Several animal species are susceptible to SARS-CoV-2 infection, as documented by case reports and serological and in vivo infection studies. However, the susceptibility of many animal species remains unknown. Furthermore, the expression patterns of SARS-CoV-2 entry factors, such as the receptor angiotensin-converting enzyme 2 (ACE2), as well as transmembrane protease serine subtype 2 (TMPRSS2) and cathepsin L (CTSL), cellular proteases involved in SARS-CoV-2 spike protein activation, are largely unexplored in most species. Here, we generated primary cell cultures from the respiratory tract of domestic and wildlife animals to assess their susceptibility to SARS-CoV-2 infection. Additionally, the presence of ACE2, TMPRSS2 and CTSL within respiratory tract compartments was investigated in a range of animals, some with unknown susceptibility to SARS-CoV-2. Productive viral replication was observed in the nasal mucosa explants and precision-cut lung slices from dogs and hamsters, whereas culture models from ferrets and multiple ungulate species were non-permissive to infection. Overall, whereas TMPRSS2 and CTSL were equally expressed in the respiratory tract, the expression levels of ACE2 were more variable, suggesting that a restricted availability of ACE2 may contribute to reduced susceptibility. Summarized, the experimental infection of primary respiratory tract cell cultures, as well as an analysis of entry-factor distribution, enable screening for SARS-CoV-2 animal reservoirs.
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The current situation of Coronavirus Disease 2019 (COVID-19) worldwide is still very severe. Presently, many breakthroughs have been accomplished in the research and development of drugs for the treatment of COVID-19, especially vaccines; however, some of the so-called COVID-19-specific drugs highlighted in the early stage failed to achieve the expected curative effect. There is no antiviral therapy available, by stimulating protective immunity vaccine is the best choice for the future management of infection. Therefore, we aimed to identify the latest developments in the research and development of these drugs and vaccines and provide a reference for the prevention and treatment of COVID-19.
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At the beginning of 2020, the pandemic caused by the SARS-CoV-2 virus led to the fast sequencing of its genome to facilitate molecular engineering strategies to control the pathogen’s spread. The spike (S) glycoprotein has been identified as the leading therapeutic agent due to its role in localizing the ACE2 receptor in the host’s pulmonary cell membrane, binding, and eventually infecting the cells. Due to the difficulty of delivering bioactive molecules to the intracellular space, we hypothesized that the S protein could serve as a source of membrane translocating peptides. AHB-1, AHB-2, and AHB-3 peptides were identified and analyzed on a membrane model of DPPC (dipalmitoylphosphatidylcholine) using molecular dynamics (MD) simulations. An umbrella sampling approach was used to quantify the energy barrier necessary to cross the boundary (13.2 to 34.9 kcal/mol), and a flat-bottom pulling helped to gain a deeper understanding of the membrane’s permeation dynamics. Our studies revealed that the novel peptide AHB-1 exhibited comparable penetration potential of already known potent cell-penetrating peptides (CPPs) such as TP2, Buforin II, and Frenatin 2.3s. Results were confirmed by in vitro analysis of the peptides conjugated to chitosan nanoparticles, demonstrating its ability to reach the cytosol and escape endosomes, while maintaining high biocompatibility levels according to standardized assays.
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Tauopathy is a term that has been used to represent a pathological condition in which hyperphosphorylated tau protein aggregates in neurons and glia which results in neurodegeneration, synapse loss and dysfunction and cognitive impairments. Recently, drug repositioning strategy (DRS) becomes a promising field and an alternative approach to advancing new treatments from actually developed and FDA approved drugs for an indication other than the indication it was originally intended for. This paradigm provides an advantage because the safety of the candidate compound has already been established, which abolishes the need for further preclinical safety testing and thus substantially reduces the time and cost involved in progressing of clinical trials. In the present review, we focused on correlation between tauopathy and common diseases as type 2 diabetes mellitus and the global virus COVID-19 and how tau pathology can aggravate development of these diseases in addition to how these diseases can be a risk factor for development of tauopathy. Moreover, correlation between COVID-19 and type 2 diabetes mellitus was also discussed. Therefore, repositioning of a drug in the daily clinical practice of patients to manage or prevent two or more diseases at the same time with lower side effects and drug-drug interactions is a promising idea. This review concluded the results of pre-clinical and clinical studies applied on antidiabetics, COVID-19 medications, antihypertensives, antidepressants and cholesterol lowering drugs for possible drug repositioning for management of tauopathy.
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Infectious bronchitis (IB) is an acute disease of chickens caused by a gammacoronavirus, infectious bronchitis virus (IBV). Infection of the nasal and tracheal mucosa causes a rapid loss of ciliated epithelium and impaired mucociliary clearance that predispose chickens to secondary bacterial infections. In poultry production, disease progression and severity are influenced by other live virus vaccines, immunosuppression, and coexisting pathogens. The digestive tract supports viral replication in the proventriculus, intestines, cloaca, and the bursa of Fabricius. Acute enteritis and stunted growth in young chickens are caused by an enterotropic IBV. IBV spreads systemically by infection of tracheal macrophages and blood monocytes, deep respiratory infections, and potentially ascending viral infection from the cloaca. Nephrotropic IBV causes severe disease in the kidney with necrosis of tubular epithelial cells, inflammation, and renal failure. Viral infection of the female reproductive tract in the first 2 weeks of life causes necrosis and scarring of the oviduct mucosa, resulting in a chronic cystic oviduct that precludes egg formation when the hen matures. Virus infection of mature hens causes necrosis and inflammation of the oviduct mucosa, leading to the deterioration of egg quality and transient interruption of egg production. In males, IBV infection of seminiferous tubules in the testicle and efferent ductules in the epididymis results in epididymitis and epididymal lithiasis, decreases in sperm production and fertility, and viral shed to semen, leading to venereal transmission. The role IBV in gastrointestinal and urogenital disease merits further study.
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Since the spread of COVID-19 pandemic, the world paid attention towards coronaviruses (CoVs) evolution and their diverged lineages, because many researches supposed that the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is evolutionary developed from a lineage of bats coronaviruses. This is due to the ability of some mutant CoVs to transmit from a host to different hosts. For this reason, there are many fears about the pathogenicity of the upcoming variants of CoVs. Thus, it is important to get a rapid and economic technique for typing a wide range of human and animals CoVs species for following up their mutants transmission. Therefore, the present study aims at approaching a simple design of DNA bar coding of a wide range of mammals CoVs (including alpha and beta CoVs), by universal amplification of a species-specific sequence inside a conserved gene (NSP12) followed by amplicon sequencing. The in silico evaluation involved 96 nucleotide sequences of different CoVs (18 alpha CoVs and 78 beta CoVs), and was applied experimentally into the lab on 5 human CoVs isolates; 3 of them belong to beta CoVs (OC43, MERS, and SARS-CoV-2) and 2 are alpha CoVs (229E and NL63). The results indicated that the designed universal primers are able to amplify 332 bp of a taxonomic region inside NSP12 coding sequence that facilitates the identification and classification of mammals CoVs upon the resulted phylogenetic tree. This article is protected by copyright. All rights reserved.
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Some key mutations of SARS-CoV-2 spike protein, such as D614G and P681R mutations, increase the transmission or pathogenicity by enhancing the cleavage efficacy of spike protein by furin. Loss of the furin cleavage motif of SARS-CoV-2 spike protein reduces the virulence and transmission, suggesting that furin is an attractive antiviral drug target.
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Motivation Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. Results This study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses. Availability The HVD is available at http://computationalbiology.cn/humanVirusBase/#/ Supplementary information Supplementary data are available at Bioinformatics online.
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COVID-19 associated acute kidney injury (COVID-AKI) is a common complication of SARS-CoV-2 infection in hospitalized patients. The susceptibility of human kidneys to direct SARS-CoV-2 infection and pharmacologic manipulation of the renin-angiotensin II signaling (RAS) pathway modulation of this susceptibility remain poorly characterized. Using induced pluripotent stem cell derived kidney organoids, SARS-CoV-1, SARS-CoV-2 and MERS-CoV tropism, defined by the paired expression of a host receptor (ACE2, NRP1 or DPP4) and protease (TMPRSS2, TMPRSS4, FURIN, CTSB or CTSL), was identified primarily amongst proximal tubule cells. Losartan, an angiotensin II receptor blocker being tested in COVID-19 patients, inhibited angiotensin II mediated internalization of ACE2, upregulated interferon stimulated genes (IFITM1 and BST2) known to restrict viral entry, and attenuated the infection of proximal tubule cells by SARS-CoV-2. Our work highlights the susceptibility of proximal tubule cells to SARS-CoV-2 and reveals a putative protective role for RAS inhibitors during SARS-CoV-2 infection.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the unprecedented coronavirus disease 2019 (COVID-19) pandemic. Critical cases of COVID-19 are characterized by the production of excessive amounts of cytokines and extensive lung damage, which is partially caused by the fusion of SARS-CoV-2-infected pneumocytes. Here, we found that cell fusion caused by the SARS-CoV-2 spike (S) protein induced a type I interferon (IFN) response. This function of the S protein required its cleavage by proteases at the S1/S2 and the S2' sites. We further showed that cell fusion damaged nuclei and resulted in the formation of micronuclei that were sensed by the cytosolic DNA sensor cGAS and led to the activation of its downstream effector STING. Phosphorylation of the transcriptional regulator IRF3 and the expression of IFNB, which encodes a type I IFN, were abrogated in cGAS-deficient fused cells. Moreover, infection with VSV-SARS-CoV-2 also induced cell fusion, DNA damage, and cGAS-STING-dependent expression of IFNB. Together, these results uncover a pathway underlying the IFN response to SARS-CoV-2 infection. Our data suggest a mechanism by which fused pneumocytes in the lungs of patients with COVID-19 may enhance the production of IFNs and other cytokines, thus exacerbating disease severity.
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Despite the recent announcement of the new pathogenic coronavirus to man, SARS-CoV2, a large number of publications are presented to the scientific community. An organized and systematic review of the epidemiological, etiological, and pathogenic factors of COVID-19 is presented. This is a systematic review using the databases MEDLINE, EMBASE, Web of Science, SCIELO; the descriptors coronavirus, SARS-CoV-2, etiology, epidemiology, pathophysiology, pathogenesis, COVID-19, with publications from December 2019 to January 2021, resulting in more than 800 publications and 210 selected. The data suggest that COVID-19 is associated with SAR-CoV-2 infection, with the transmission of contagion by fomites, salivary droplets, and other forms, such as vertical and fecal–oral. The bat and other vertebrates appear to be reservoirs and part of the transmission chain. The virus uses cell receptors to infect human cells, especially ACE2, like other coronaviruses. Heat shock proteins have different roles in the infection, sometimes facilitating it, sometimes participating in more severe conditions, when not serving as a therapeutic target. The available data allow us to conclude that COVID-19 is a pandemic viral disease, behaving as a challenge for public health worldwide, determining aggressive conditions with a high mortality rate in patients with risk factors, without treatment, but with the recent availability of the first vaccines.
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Some clinical studies have indicated activity of ivermectin, a macrocyclic lactone, against COVID-19, but a biological mechanism initially proposed for this anti-viral effect is not applicable at physiological concentrations. This in silico investigation explores potential modes of action of ivermectin and 14 related compounds, by which the infectivity and morbidity of the SARS-CoV-2 virus may be limited. Binding affinity computations were performed for these agents on several docking sites each for models of (1) the spike glycoprotein of the virus, (2) the CD147 receptor, which has been identified as a secondary attachment point for the virus, and (3) the alpha-7 nicotinic acetylcholine receptor (α7nAChr), an indicated point of viral penetration of neuronal tissue as well as an activation site for the cholinergic anti-inflammatory pathway controlled by the vagus nerve. Binding affinities were calculated for these multiple docking sites and binding modes of each compound. Our results indicate the high affinity of ivermectin, and even higher affinities for some of the other compounds evaluated, for all three of these molecular targets. These results suggest biological mechanisms by which ivermectin may limit the infectivity and morbidity of the SARS-CoV-2 virus and stimulate an α7nAChr-mediated anti-inflammatory pathway that could limit cytokine production by immune cells.
Chapter
Polyanions as polymers carrying multiple negative charges have been extensively studied with regard to their potential antiviral activity. Most studies to date focused on organic polyanionic polymers, both natural and synthetic. The inorganic polymer, polyphosphate (polyP), despite the ubiquitous presence of this molecule from bacteria to man, has attracted much less attention. More recently, and accelerated by the search for potential antiviral agents in the fight against the pandemic caused by the coronavirus SARS-CoV-2, it turned out that polyP disrupts the first step of the viral replication cycle, the interaction of the proteins in the virus envelope and in the cell membrane that are involved in the docking process of the virus with the target host cell. Experiments on a molecular level using the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the cellular angiotensin converting enzyme 2 (ACE2) receptor revealed that polyP strongly inhibits the binding reaction through an electrostatic interaction between the negatively charged centers of the polyP molecule and a cationic groove, which is formed by positively charged amino acids on the RBD surface. In addition, it was found that polyP, due to its morphogenetic and energy delivering activities, enhances the antiviral host innate immunity defense of the respiratory epithelium. The underlying mechanisms and envisaged application of polyP in the therapy and prevention of COVID-19 are discussed.
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Chloroquine was discovered in 1934 and since then it is used as an antimalarial drug saving millions of lives. Chloroquine and its analogue Hydroxychloroquine possess pleotropic pharmacological actions and are of proven value in multiple conditions ranging from protozoal to autoimmune diseases. Advantage with these drugs is their well-documented tolerability profile. In Severe Acute Respiratory Syndrome Corona virus-2 (SARS-CoV-2), these drugs in vitro showed promising results working at multiple sites ranging from prevention of entry of the virus into human cells, halting the multiplication by altering the pH of internal organelles towards basic side and via exocytosis. These drugs also act as immunomodulators to prevent flare up of cytokines and interleukin cascade, thus preventing multiple organ dysfunction syndrome. In this review we trend the journey of these drugs, how high hopes were pinned to their use but they failed to show any mortality benefit in hospitalized patients. However, still certain studies are underway to explore their role in prophylaxis or otherwise. Medline, Medscape, EMBASE, Cochrane database, Scopus and clinicaltrials.gov were searched using terms like “SARS-CoV-2”, “COVID-19”, “Chloroquine” and “Hydroxychloroquine”.
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SARS-CoV-2 was perceived in China which forms a pandemic within weeks and affected the whole world population. Unfortunately, some people who were already suffering from cancer were affected severely and had more disease severity. COVID-19 badly affected cancer diagnosis and treatment resulting in increased mortality rate. A major issue that cancer patients had to face was a lack of access to necessary health care. The “Renin-angiotensin-aldosterone system (RAAS)” plays a role in cancer development, it was observed that COVID-19 affects the functioning of RAAS by affecting the Angiotensin-Converting Enzyme -2 (ACE-2) receptor with the assistance of spike proteins to gain entrance into the cells. It was proved that the ACE 2 receptor is a major link between cancer and COVID-19. Cancer patients are very sensitive to COVID-19 due to “macrophages”. Macrophages induce inflammatory responses in both cancer and COVID-19 patients. It was also observed that COVID-19 may create a microenvironment for cancer development by increasing the activation of macrophages, and neutrophils as well as causing the overproduction of proinflammatory cytokines.
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HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in part by the coronavirus spike (S) protein, which binds cellular receptors and mediates membrane fusion. As the largest known class I fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. Here we present the 4.0 Å resolution structure of the trimeric HKU1 S protein determined using single-particle cryo-electron microscopy. In the pre-fusion conformation, the receptor-binding subunits, S1, rest above the fusion-mediating subunits, S2, preventing their conformational rearrangement. Surprisingly, the S1 C-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. These features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive S protein destabilization through receptor binding and proteolytic cleavage. These studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens.
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The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a mouse coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains.
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Bats have been recognized as the natural reservoirs of a large variety of viruses. Special attention has been paid to bat coronaviruses as the two emerging coronaviruses which have caused unexpected human disease outbreaks in the 21st century, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV), are suggested to be originated from bats. Various species of horseshoe bats in China have been found to harbor genetically diverse SARS-like coronaviruses. Some strains are highly similar to SARS-CoV even in the spike protein and are able to use the same receptor as SARS-CoV for cell entry. On the other hand, diverse coronaviruses phylogenetically related to MERS-CoV have been discovered worldwide in a wide range of bat species, some of which can be classified to the same coronavirus species as MERS-CoV. Coronaviruses genetically related to human coronavirus 229E and NL63 have been detected in bats as well. Moreover, intermediate hosts are believed to play an important role in the transmission and emergence of these coronaviruses from bats to humans. Understanding the bat origin of human coronaviruses is helpful for the prediction and prevention of another pandemic emergence in the future.
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Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s.)Ne report the phylogenetic relationship of swine enteric coronaviruses collected in Italy during 2007-2014 and identify a drastic shift in PEDV strain variability and a new swine enteric coronavirus generated by recombination of transmissible gastroenteritis virus and PEDV.
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The enteric disease of swine recognized in the early 1970s in Europe was initially described as "epidemic viral diarrhea" and is now termed "porcine epidemic diarrhea (PED)". The coronavirus referred to as PED virus (PEDV) was determined to be the etiologic agent of this disease in the late 1970s. Since then the disease has been reported in Europe and Asia, but the most severe outbreaks have occurred predominantly in Asian swine-producing countries. Most recently, PED first emerged in early 2013 in the United States that caused high morbidity and mortality associated with PED, remarkably affecting US pig production, and spread further to Canada and Mexico. Soon thereafter, large-scale PED epidemics recurred through the pork industry in South Korea, Japan, and Taiwan. These recent outbreaks and global re-emergence of PED require urgent attention and deeper understanding of PEDV biology and pathogenic mechanisms. This paper highlights the current knowledge of molecular epidemiology, diagnosis, and pathogenesis of PEDV, as well as prevention and control measures against PEDV infection. More information about the virus and the disease is still necessary for the development of effective vaccines and control strategies. It is hoped that this review will stimulate further basic and applied studies and encourage collaboration among producers, researchers, and swine veterinarians to provide answers that improve our understanding of PEDV and PED in an effort to eliminate this economically significant viral disease, which emerged or re-emerged worldwide.
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Middle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of the spike (S) gene in betacoronaviruses (betaCoVs) isolated from different mammals, in bat coronavirus populations, as well as in MERS-CoV strains from the current outbreak. Results indicated several positively selected sites located in the region comprising the two heptad repeats (HR1 and HR2) and their linker. Two sites (R652 and V1060) were positively selected in the betaCoVs phylogeny and correspond to mutations associated with expanded host range in other coronaviruses. During the most recent evolution of MERS-CoV, adaptive mutations in the HR1 (Q/R/H1020) arose in camels or in a previous host and spread to humans. We determined that different residues at position 1020 establish distinct inter- and intra-helical interactions and affect the stability of the six-helix bundle formed by the HRs. A similar effect on stability was observed for a nearby mutation (T1015N) that increases MERS-CoV infection efficiency in vitro. Data herein indicate that the heptad repeat region was a major target of adaptive evolution in MERS-CoV-related viruses; these results are relevant for the design of fusion inhibitor peptides with antiviral function.
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Importance: The ancestral origins of major human coronaviruses (HCoV) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We re-analyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic MERS-Coronavirus.
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Middle East respiratory syndrome coronavirus (MERS-CoV) currently spreads in humans and causes ∼36% fatality in infected patients. Believed to have originated from bats, MERS-CoV is genetically related to bat coronaviruses HKU4 and HKU5. To understand how bat coronaviruses transmit to humans, we investigated the receptor usage and cell entry activity of the virus-surface spike proteins of HKU4 and HKU5. We found that dipeptidyl peptidase 4 (DPP4), the receptor for MERS-CoV, is also the receptor for HKU4, but not HKU5. Despite sharing a common receptor, MERS-CoV and HKU4 spikes demonstrated functional differences. First, whereas MERS-CoV prefers human DPP4 over bat DPP4 as its receptor, HKU4 shows the opposite trend. Second, in the absence of exogenous proteases, both MERS-CoV and HKU4 spikes mediate pseudovirus entry into bat cells, whereas only MERS-CoV spike, but not HKU4 spike, mediates pseudovirus entry into human cells. Thus, MERS-CoV, but not HKU4, has adapted to use human DPP4 and human cellular proteases for efficient human cell entry, contributing to the enhanced pathogenesis of MERS-CoV in humans. These results establish DPP4 as a functional receptor for HKU4 and host cellular proteases as a host range determinant for HKU4. They also suggest that DPP4-recognizing bat coronaviruses threaten human health because of their spikes' capability to adapt to human cells for cross-species transmissions.
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The recently reported Middle East respiratory syndrome coronavirus (MERS-CoV) is phylogenetically closely related to the bat coronaviruses (BatCoVs) HKU4 and HKU5. However, the evolutionary pathway of MERS-CoV is still unclear. A receptor binding domain (RBD) in the MERS-CoV envelope-embedded spike protein specifically engages human CD26 (hCD26) to initiate viral entry. The high sequence identity in the viral spike protein prompted us to investigate if HKU4 and HKU5 can recognize hCD26 for cell entry. We found that HKU4-RBD, but not HKU5-RBD, binds to hCD26, and pseudotyped viruses embedding HKU4 spike can infect cells via hCD26 recognition. The structure of the HKU4-RBD/hCD26 complex revealed a hCD26-binding mode similar overall to that observed for MERS-RBD. HKU4-RBD, however, is less adapted to hCD26 than MERS-RBD, explaining its lower affinity for receptor binding. Our findings support a bat origin for MERS-CoV and indicate the need for surveillance of HKU4-related viruses in bats.
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The availability of a robust disease model is essential for the development of countermeasures for Middle East respiratory syndrome coronavirus (MERS-CoV). While a rhesus macaque model of MERS-CoV has been established, the lack of uniform, severe disease in this model complicates the analysis of countermeasure studies. Modeling of the interaction between the MERS-CoV spike glycoprotein and its receptor dipeptidyl peptidase 4 predicted comparable interaction energies in common marmosets and humans. The suitability of the marmoset as a MERS-CoV model was tested by inoculation via combined intratracheal, intranasal, oral and ocular routes. Most of the marmosets developed a progressive severe pneumonia leading to euthanasia of some animals. Extensive lesions were evident in the lungs of all animals necropsied at different time points post inoculation. Some animals were also viremic; high viral loads were detected in the lungs of all infected animals, and total RNAseq demonstrated the induction of immune and inflammatory pathways. This is the first description of a severe, partially lethal, disease model of MERS-CoV, and as such will have a major impact on the ability to assess the efficacy of vaccines and treatment strategies as well as allowing more detailed pathogenesis studies.
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Influenza hemagglutinin (HA), a homotrimeric glycoprotein crucial for membrane fusion, undergoes a large-scale structural rearrangement during viral invasion. X-ray crystallography has shown that the pre- and postfusion configurations of HA2, the membrane-fusion subunit of HA, have disparate secondary, tertiary, and quaternary structures, where some regions are displaced by more than 100 Å. To explore structural dynamics during the conformational transition, we studied simulations of a minimally frustrated model based on energy landscape theory. The model combines structural information from both the pre- and postfusion crystallographic configurations of HA2. Rather than a downhill drive toward formation of the central coiled-coil, we discovered an order-disorder transition early in the conformational change as the mechanism for the release of the fusion peptides from their burial sites in the prefusion crystal structure. This disorder quickly leads to a metastable intermediate with a broken threefold symmetry. Finally, kinetic competition between the formation of the extended coiled-coil and C-terminal melting results in two routes from this intermediate to the postfusion structure. Our study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the "spring-loaded" model proposed for the HA2 conformational transition.
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Unlabelled: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012. Recently, the MERS-CoV receptor dipeptidyl peptidase 4 (DPP4) was identified and the specific interaction of the receptor-binding domain (RBD) of MERS-CoV spike protein and DPP4 was determined by crystallography. Animal studies identified rhesus macaques but not hamsters, ferrets, or mice to be susceptible for MERS-CoV. Here, we investigated the role of DPP4 in this observed species tropism. Cell lines of human and nonhuman primate origin were permissive of MERS-CoV, whereas hamster, ferret, or mouse cell lines were not, despite the presence of DPP4. Expression of human DPP4 in nonsusceptible BHK and ferret cells enabled MERS-CoV replication, whereas expression of hamster or ferret DPP4 did not. Modeling the binding energies of MERS-CoV spike protein RBD to DPP4 of human (susceptible) or hamster (nonsusceptible) identified five amino acid residues involved in the DPP4-RBD interaction. Expression of hamster DPP4 containing the five human DPP4 amino acids rendered BHK cells susceptible to MERS-CoV, whereas expression of human DPP4 containing the five hamster DPP4 amino acids did not. Using the same approach, the potential of MERS-CoV to utilize the DPP4s of common Middle Eastern livestock was investigated. Modeling of the DPP4 and MERS-CoV RBD interaction predicted the ability of MERS-CoV to bind the DPP4s of camel, goat, cow, and sheep. Expression of the DPP4s of these species on BHK cells supported MERS-CoV replication. This suggests, together with the abundant DPP4 presence in the respiratory tract, that these species might be able to function as a MERS-CoV intermediate reservoir. Importance: The ongoing outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 701 laboratory-confirmed cases to date, with 249 fatalities. Although bats and dromedary camels have been identified as potential MERS-CoV hosts, the virus has so far not been isolated from any species other than humans. The inability of MERS-CoV to infect commonly used animal models, such as hamster, mice, and ferrets, indicates the presence of a species barrier. We show that the MERS-CoV receptor DPP4 plays a pivotal role in the observed species tropism of MERS-CoV and subsequently identified the amino acids in DPP4 responsible for this restriction. Using a combined modeling and experimental approach, we predict that, based on the ability of MERS-CoV to utilize the DPP4 of common Middle East livestock species, such as camels, goats, sheep, and cows, these form a potential MERS-CoV intermediate host reservoir species.
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We describe the isolation and sequencing of Middle East respiratory syndrome coronavirus (MERS-CoV) obtained from a dromedary camel and from a patient who died of laboratory-confirmed MERS-CoV infection after close contact with camels that had rhinorrhea. Nasal swabs collected from the patient and from one of his nine camels were positive for MERS-CoV RNA. In addition, MERS-CoV was isolated from the patient and the camel. The full genome sequences of the two isolates were identical. Serologic data indicated that MERS-CoV was circulating in the camels but not in the patient before the human infection occurred. These data suggest that this fatal case of human MERS-CoV infection was transmitted through close contact with an infected camel.
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Feline infectious peritonitis (FIP) continues to be one of the most researched infectious diseases of cats. The relatively high mortality of FIP, especially for younger cats from catteries and shelters, should be reason enough to stimulate such intense interest. However, it is the complexity of the disease and the grudging manner in which it yields its secrets that most fascinate researchers. Feline leukemia virus infection was conquered in less than two decades and the mysteries of feline immunodeficiency virus were largely unraveled in several years. After a half century, FIP remains one of the last important infections of cats for which we have no single diagnostic test, no vaccine and no definitive explanations for how virus and host interact to cause disease. How can a ubiquitous and largely non-pathogenic enteric coronavirus transform into a highly lethal pathogen? What are the interactions between host and virus that determine both disease form (wet or dry) and outcome (death or resistance)? Why is it so difficult, and perhaps impossible, to develop a vaccine for FIP? What role do genetics play in disease susceptibility? This review will explore research conducted over the last 5 years that attempts to answer these and other questions. Although much has been learned about FIP in the last 5 years, the ultimate answers remain for yet more studies.
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IMPORTANCE In most cases of Middle East respiratory syndrome (MERS), the route for human infection with the causative agent, MERS coronavirus (MERS-CoV), is unknown. Antibodies to and viral nucleic acids of MERS-CoV have been found in dromedaries, suggesting the possibility that they may serve as a reservoir or vector for human infection. However, neither whole viral genomic sequence nor infectious virus has been isolated from dromedaries or other animals in Saudi Arabia. Here, we report recovery of MERS-CoV from nasal swabs of dromedaries, demonstrate that MERS-CoV whole-genome consensus sequences from dromedaries and humans are indistinguishable, and show that dromedaries can be simultaneously infected with more than one MERS-CoV. Together with data indicating widespread dromedary infection in the Kingdom of Saudi Arabia, these findings support the plausibility of a role for dromedaries in human infection.
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The Middle East respiratory syndrome (MERS) is proposed to be a zoonotic disease; however, the reservoir and mechanism for transmission of the causative agent, the MERS coronavirus, are unknown. Dromedary camels have been implicated through reports that some victims have been exposed to camels, camels in areas where the disease has emerged have antibodies to the virus, and viral sequences have been recovered from camels in association with outbreaks of the disease among humans. Nonetheless, whether camels mediate transmission to humans is unresolved. Here we provide evidence from a geographic and temporal survey of camels in the Kingdom of Saudi Arabia that MERS coronaviruses have been circulating in camels since at least 1992, are distributed countrywide, and can be phylogenetically classified into clades that correlate with outbreaks of the disease among humans. We found no evidence of infection in domestic sheep or domestic goats. IMPORTANCE This study was undertaken to determine the historical and current prevalence of Middle East respiratory syndrome (MERS) coronavirus infection in dromedary camels and other livestock in the Kingdom of Saudi Arabia, where the index case and the majority of cases of MERS have been reported.
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Unlabelled: The Middle East respiratory syndrome coronavirus (MERS-CoV) recently spread from an animal reservoir to infect humans, causing sporadic severe and frequently fatal respiratory disease. Appropriate public health and control measures will require discovery of the zoonotic MERS coronavirus reservoirs. The relevant animal hosts are liable to be those that offer optimal MERS virus cell entry. Cell entry begins with virus spike (S) protein binding to DPP4 receptors. We constructed chimeric DPP4 receptors that have the virus-binding domains of indigenous Middle Eastern animals and assessed the activities of these receptors in supporting S protein binding and virus entry. Human, camel, and horse receptors were potent and nearly equally effective MERS virus receptors, while goat and bat receptors were considerably less effective. These patterns reflected S protein affinities for the receptors. However, even the low-affinity receptors could hypersensitize cells to infection when an S-cleaving protease(s) was present, indicating that affinity thresholds for virus entry must be considered in the context of host-cell proteolytic environments. These findings suggest that virus receptors and S protein-cleaving proteases combine in a variety of animals to offer efficient virus entry and that several Middle Eastern animals are potential reservoirs for transmitting MERS-CoV to humans. Importance: MERS is a frequently fatal disease that is caused by a zoonotic CoV. The animals transmitting MERS-CoV to humans are not yet known. Infection by MERS-CoV requires receptors and proteases on host cells. We compared the receptors of humans and Middle Eastern animals and found that human, camel, and horse receptors sensitized cells to MERS-CoV infection more robustly than goat and bat receptors. Infection susceptibility correlated with affinities of the receptors for viral spike proteins. We also found that the presence of a cell surface lung protease greatly increases susceptibility to MERS-CoV, particularly in conjunction with low-affinity receptors. This cataloguing of human and animal host cell factors allows one to make inferences on the distribution of MERS-CoV in nature.
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A novel human coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), has caused outbreaks of a SARS-like illness with high case fatality rate. The reports of its person-to-person transmission through close contacts have raised a global concern about its pandemic potential. Here we characterize the six-helix bundle fusion core structure of MERS-CoV spike protein S2 subunit by X-ray crystallography and biophysical analysis. We find that two peptides, HR1P and HR2P, spanning residues 998-1039 in HR1 and 1251-1286 in HR2 domains, respectively, can form a stable six-helix bundle fusion core structure, suggesting that MERS-CoV enters into the host cell mainly through membrane fusion mechanism. HR2P can effectively inhibit MERS-CoV replication and its spike protein-mediated cell-cell fusion. Introduction of hydrophilic residues into HR2P results in significant improvement of its stability, solubility and antiviral activity. Therefore, the HR2P analogues have good potential to be further developed into effective viral fusion inhibitors for treating MERS-CoV infection.