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The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade
Abstract
In 2019, a new coronavirus (2019-nCoV) infecting Humans has emerged in Wuhan, China. Its genome has been sequenced and the genomic information promptly released. Despite a high similarity with the genome sequence of SARS-CoV and SARS-like CoVs, we identified a peculiar furin-like cleavage site in the Spike protein of the 2019-nCoV, lacking in the other SARS-like CoVs. In this article, we discuss the possible functional consequences of this cleavage site in the viral cycle, pathogenicity and its potential implication in the development of antivirals.
... Para abordar esta limitación, el Ministerio de Educación intervino y se instalaron canales de wi-fi. Sin embargo, no todos los estudiantes pudieron acceder a ellos, lo que indica que algunos aún se veían excluidos de la educación virtual debido a la falta de conectividad (Coutard et al., 2020). ...
... El uso de WhatsApp como plataforma principal y la comunicación directa a través de llamadas telefónicas demostraron ser alternativas efectivas para llegar a los estudiantes. Estas acciones reflejan la adaptabilidad y la búsqueda de soluciones durante una época de transformación educativa provocada por la pandemia Zhou et al., 2020;Coutard et al., 2020;Hassani y Sandali, 2020). ...
... Algunos estudiantes muestran una mayor responsabilidad y compromiso al realizar el reporte de manera inmediata, lo cual indica una buena organización y gestión del tiempo. Por otro lado, hay estudiantes que requieren más tiempo para completar y enviar sus evidencias, posiblemente debido a diversas razones como la carga de trabajo, la disponibilidad de recursos o la falta de organización (Huanca-Arohuanca, 2020; Coutard et al., 2020). ...
La mirada del estudiante suele ser diferente a los demás en cuanto a sus maestros se refiere y lo mismo ocurre con la mirada de sus docentes frente a sus alumnos, pero la pandemia se ha encargado de homogenizarlos a una sola mirada. El objetivo del estudio busca comprender las percepciones sobre el compromiso académico en docentes y estudiantes durante la pandemia en el colegio Carlos Oquendo de Amat, Cuyocuyo-Sandia, ya que, todos ellos conviven con todos los desafíos que implica una educación virtual en contextos difíciles. La metodología se desenvolvió bajo la investigación cualitativa de carácter interpretativo, con entrevistas semiestructuradas y con participación de cinco docentes dedicados a tiempo completo a la institución y cuatro estudiantes de la misma entidad. Los resultados revelaron que existe un grupo de docentes dedicados a otras actividades externas y estudiantes obligados a trabajar en los lavaderos de oro y en el agro. Se concluye que, todos los actores educativos están en la obligación de resolver la problemática atravesada por complejidades que presenta la enseñanza y aprendizaje durante la Covid-19.
... With the help of transmembrane protease serine 2 (TMPRSS2), Furin facilitates the entry of the SARS-CoV-2 into the host cell after binding through the Furin receptor. 12,13 A recent study has identified a Furin cleavage site within the Spike protein of the 2019-nCoV, missing within the other SARS-like CoVs, 14 and it may influence viral morbidity or mortality. Furin cleaves the SARS-CoV-2 spike glycoprotein (S), which is a crucial stage in the viral entry process. ...
COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) had an adverse effect globally because it caused a global pandemic with several million deaths. This virus possesses spike protein that is cleaved or activated by Furin-like protease enzymes occurring by mammalian lung or respiratory cells to enter the mammalian body. The addition of the Furin cleavage site in SARS-CoV-2 makes it a more infectious and emerging virus than its ancestor’s viruses. Phylogenetic relationships of coronavirus spike proteins have analyzed and mapped Furin recognition motif on the tree using bioinformatics tools such as GTEx, KEGG, GO, NCBI, PolyPhen-2, SNAP2, PANTHER, Hidden Markov Models (Fathmm), Phd-single-nucleotide polymorphism (SNP), I-TASSER, Modpred, Phobius, SIFT, iPTREE-STAB, and PROVEAN. During this study, it has been found that in certain regions, Furin SNPs have some relation with the susceptibility to SARS-CoV-2. Whereas in other regions, the effects are very negligible. Finally, our study demonstrates that Furin SNPs have a strong relationship with susceptibility to SARS-CoV-2. As it helps to cleave the spike protein of the virus, thus it can be targeted to inhibit at a particular site to prevent the SARS-CoV-2 from the entrance into the body.
... PRRA 684 insert between two adjacent Ser and Arg residues, resulting in a RXXR minimal FCS. This FCS, which does not fully match the canonical FCS motif RX(K/R)R (see [1]), has not been seen in other sarbecoviruses [3]; on the other hand, simple furin-like cleavage sites at S1/ S2 domains in other betacoronavirus spike glycoproteins ...
Objectives
SARS-CoV-2 spike (S) glycoprotein furin cleavage site is a key determinant of SARS-CoV-2 virulence and COVID-19 pathogencity. Located at the S1/S2 junction, it is unique among sarbecoviruses but frequently found among betacoronaviruses. Recent evidence suggests that this site includes two additional functional motifs: a pat7 nuclear localization signal and two flanking O -glycosites. However, a systematic genus and subgenus analysis of spike protein sequences bearing this polyfunctional sequence domain has been missing.
Data description
Here we report comprehensive sequence data to demonstrate that among spike proteins of genus Betacoronavirus and outside of the SARS-CoV-2 clade a fully analogous S1/S2 domain was found in only one other virus: the artificial MERS infectious clone MERS-MA30, described already in 2017, which was rationally selected from serial passage in genetically humanized mice. As the evolutionarily closest betacoronaviruses outside of the SARS-CoV-2 clade lack all its three functional motifs, these data extend—beyond natural evolution and zoonosis—the current view on SARS-CoV-2 pre-pandemic origins by presenting the analogous S1/S2 MERS-MA30 sequence domain as a precise molecular blueprint for SARS-CoV-2.
... One involves proteases activation for the fusion between the viral and host cell membranes, a process known as cell surface entry. Cellular proteases like transmembrane serine protease 2 (TMPRSS2) or furin cleave the S protein to separate receptor binding domain (RBD) and S2, activating S2's membrane-fusion capacity and starting the membrane-fusion process [4,5,11]. The other is referred to as endosomal entry. ...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19) pandemic and is continuously spreading globally. The continuous emergence of new SARS-CoV-2 variants keeps posing threats, highlighting the need for fast-acting, mutation-resistant broad-spectrum therapeutics. Protein translation is vital for SARS-CoV-2 replication, producing early non-structural proteins for RNA replication and transcription, and late structural proteins for virion assembly. Targeted blocking of viral protein translation is thus a potential approach to developing effective anti-SARS-CoV-2 drugs. SARS-CoV-2, as an obligate parasite, utilizes the host’s translation machinery. Translation-blocking strategies that target the SARS-CoV-2 mRNA, especially those that target its conserved elements are generally preferred. In this review, we discuss the current understanding of SARS-CoV-2 translation, highlighting the important conserved motifs and structures involved in its regulation. We also discuss the current strategies for blocking SARS-CoV-2 translation through viral RNA degradation or RNA element dysfunction.
Genetic Diversity of Coronaviruses (Volume 1) provides a comprehensive analysis of the genetic mutations and host interactions across three major coronaviruses—SARS-CoV, MERS-CoV, and SARS-CoV-2. This volume explores the evolutionary history, mutations, and emerging variants of these viruses, with a focus on understanding how they adapt to different hosts. The book is organized into three parts: Part I covers SARS-CoV, detailing its genetic mutations, host genetic diversity, and new variants. Part II focuses on MERS-CoV, offering insights into mutations and host adaptations. Part III addresses SARS-CoV-2, discussing its evolving variants and the role of host proteins. The book also discusses the connections between coronaviruses and neurological, epigenetic, and AI-related issues. Key Features: - In-depth analysis of genetic mutations in coronaviruses. - Exploration of host genetic diversity and virus adaptation. - Insight into emerging variants of SARS-CoV, MERS-CoV, and SARS-CoV-2. - Examination of host proteins' role in viral infections. - Discussion on the impact of AI and epigenetics on coronavirus research.
Genetic Diversity of Coronaviruses (Volume 1) provides a comprehensive analysis of the genetic mutations and host interactions across three major coronaviruses—SARS-CoV, MERS-CoV, and SARS-CoV-2. This volume explores the evolutionary history, mutations, and emerging variants of these viruses, with a focus on understanding how they adapt to different hosts. The book is organized into three parts: Part I covers SARS-CoV, detailing its genetic mutations, host genetic diversity, and new variants. Part II focuses on MERS-CoV, offering insights into mutations and host adaptations. Part III addresses SARS-CoV-2, discussing its evolving variants and the role of host proteins. The book also discusses the connections between coronaviruses and neurological, epigenetic, and AI-related issues. Key Features: - In-depth analysis of genetic mutations in coronaviruses. - Exploration of host genetic diversity and virus adaptation. - Insight into emerging variants of SARS-CoV, MERS-CoV, and SARS-CoV-2. - Examination of host proteins' role in viral infections. - Discussion on the impact of AI and epigenetics on coronavirus research.
Viral immunosuppression substantially affects the host immune response of infected patients and the protective efficacy of vaccines. Here, we found that the spike (S) protein, the major vaccine antigen of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strongly suppresses host innate immunity by inhibiting interferon-stimulated gene (ISG) expression through both S1 and S2 subunits. Mechanistically, the S protein inhibited the formation of the classic interferon-stimulated gene factor 3 (ISGF3) complex composed of STAT1, STAT2, and IRF9 by competing with STAT2 for binding to IRF9, thereby impeding the transcription of ISGs. A strong interaction between S and the STAT1/STAT2 proteins further traps the ISGF3 complex in the endoplasmic reticulum and hinders the nuclear translocation of ISGF3. Notably, the interferon-inhibitory mechanism of the S protein was universal among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, Middle East respiratory syndrome coronavirus (MERS-CoV), human coronavirus 229E (HCoV-229E), human coronavirus NL63 (HCoV-NL63), and human coronavirus HKU1 (HCoV-HKU1), through the most evolutionarily conserved region of S2 subunit. Taken together, the findings of this study reveal a new mechanism by which the coronavirus S protein attenuates the host antiviral immune response and provides new insights into the proper design of coronavirus S-based vaccines to prevent immunosuppressive effects.
IMPORTANCE
This study unveils a new mechanism by which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein attenuates the host’s antiviral immune response. The interferon-inhibitory mechanism of the S protein was universal among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1, through conserved S2 domains. Our study expands the understanding of SARS-CoV-2 and other human coronaviruses in evading antiviral immune strategies, which is very important for the design and optimization of vaccine antigens, thus providing a theoretical basis for human anti-coronavirus immunity and understanding the interaction between the host and coronavirus.
The recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002 to 2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational, and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV.
Backgrounds:
An ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number,R0, of 2019-nCoV in the early phase of the outbreak.
Methods:
Accounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate (γ), we estimated R0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI.
Findings:
The early outbreak data largely follows the exponential growth. We estimated that the meanR0 ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R0. CONCLUSION: The mean estimate ofR0 for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.
Background:
The initial cases of novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP.
Methods:
We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number.
Results:
Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9).
Conclusions:
On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.).
A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.
Some coronaviruses (CoVs) have an extra furin cleavage site (RRKR/S, furin-S2′ site) upstream of the fusion peptide in the spike protein, which plays roles in virion adsorption and fusion. Mutation of the S2′ site of QX genotype (QX-type) infectious bronchitis virus (IBV) spike protein (S) in a recombinant virus background results in higher pathogenicity, pronounced neural symptoms and neurotropism when compared with conditions in wild-type IBV (WT-IBV) infected chickens. In this study, we present evidence suggesting that recombinant IBV with a mutant S2′ site (furin-S2′ site) leads to higher mortality. Infection with mutant IBV induces severe encephalitis and breaks the blood–brain barrier. The results of a neutralization test and immunoprotection experiment show that an original serum and vaccine can still provide effective protection in vivo and in vitro. This is the first demonstration of IBV-induced neural symptoms in chickens with encephalitis and the furin-S2′ site as a determinant of neurotropism.
A wide variety of viruses exploit furin and other proprotein convertases (PCs) of the constitutive protein secretion pathway in order to regulate their cell entry mechanism and infectivity. Surface proteins of enveloped, as well as non-enveloped, viruses become processed by these proteases intracellularly during morphogenesis or extracellularly after egress and during entry in order to produce mature virions activated for infection. Although viruses also take advantage of other proteases, it is when some viruses become reactive with PCs that they may develop high pathogenicity. Besides reacting with furin, some viruses may also react with the PCs of the other specificity group constituted by PC4/PC5/PACE4/PC7. The targeting of PCs for inhibition may result in a useful strategy to treat infections with some highly pathogenic viruses. A wide variety of PC inhibitors have been developed and tested for their antiviral activity in cell-based assays.
Proteolytic cleavage regulates numerous processes in health and disease. One key player is the ubiquitously expressed serine protease furin, which cleaves a plethora of proteins at polybasic recognition motifs. Mammalian substrates of furin include cytokines, hormones, growth factors and receptors. Thus, it is not surprising that aberrant furin activity is associated with a variety of disorders including cancer. Furthermore, the enzymatic activity of furin is exploited by numerous viral and bacterial pathogens, thereby enhancing their virulence and spread. In this review, we describe the physiological and pathophysiological substrates of furin and discuss how dysregulation of a simple proteolytic cleavage event may promote infectious diseases and cancer. One major focus is the role of furin in viral glycoprotein maturation and pathogenicity. We also outline cellular mechanisms regulating the expression and activation of furin and summarise current approaches that target this protease for therapeutic intervention. The serine protease furin regulates numerous processes in health and disease and has become a promising target for the treatment of viral and bacterial infections, as well as cancer. This review provides an overview of proteins that are proteolytically processed by furin, with a major focus on the maturation of viral glycoproteins. It discusses cellular mechanisms regulating furin expression and describes how this protease may be targeted to treat infectious and noninfectious diseases.
The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.
Proprotein convertases (PCs) are serine proteases with an active role in the post-translational processing of numerous inactive proteins to active proteins including many substrates of paramount importance in cancer development and progression. Furin (PCSKC3), a well-studied member of this family, is overexpressed in numerous human and experimental malignancies. In the present communication we treated two furin-overexpressing non-small cell carcinoma (NSCLC) cell lines (Calu-6 andHOP-62) with the PC inhibitor CMK (Decanoyl-Arg-Val-Lys-Arg-chloromethylketone). This resulted in a diminished IGF-1R processing and a simultaneous decrease in cell proliferation of two NSCLC lines. Similarly, growth and proliferation of subcutaneous xenografts of both cell lines, were partially inhibited by an in vivo treatment with the same drug. These observations point to a potential role of PC inhibitors in cancer therapy. This article is protected by copyright. All rights reserved.