scholarly journals Comparison of Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Binding to ACE2 Receptors from Human, Pets, Farm Animals, and Putative Intermediate Hosts

2020 ◽  
Vol 94 (15) ◽  
Author(s):  
Xiaofeng Zhai ◽  
Jiumeng Sun ◽  
Ziqing Yan ◽  
Jie Zhang ◽  
Jin Zhao ◽  
...  
Keyword(s):  
Amino Acids ◽  
Severe Acute Respiratory Syndrome ◽  
Respiratory Tract ◽  
Binding Site ◽  
Protein S ◽  
Spike Protein ◽  
Farm Animals ◽  
Intermediate Hosts ◽  
Species Barrier ◽  
Interaction Sites

ABSTRACT The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in a pandemic. Here, we used X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptors allows the definition of residues important for binding. From the 20 amino acids in ACE2 that contact S, up to 7 can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or acquisition of N-glycosylation sites located near the S interface. Of note, pigs and dogs, which are not infected or are not effectively infected and have only a few changes in the binding site, exhibit relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with that from bat coronavirus strain RaTG13 (Bat-CoV-RaTG13) and pangolin coronavirus (Pangolin-CoV) strain hCoV-19/pangolin/Guangdong/1/2019 revealed that the latter contains only one substitution, whereas Bat-CoV-RaTG13 exhibits five. However, ACE2 of pangolin exhibits seven changes relative to human ACE2, and a similar number of substitutions is present in ACE2 of bats, raccoon dogs, and civets, suggesting that SARS-CoV-2 may not be especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-CoV-2. IMPORTANCE SARS-CoV-2 is threatening people worldwide, and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear, and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes, indicating that the species barrier might be low. Exceptions are dogs and especially pigs, which revealed relatively low ACE2 expression levels in the respiratory tract. Monitoring of animals is necessary to prevent the generation of a new coronavirus reservoir. Finally, our analysis also showed that SARS-CoV-2 may not be specifically adapted to any of its putative intermediate hosts.

scholarly journals Comparison of SARS-CoV-2 spike protein binding to human, pet, farm animals, and putative intermediate hosts ACE2 and ACE2 receptors

2020 ◽  
Author(s):  
Xiaofeng Zhai ◽  
Jiumeng Sun ◽  
Ziqing Yan ◽  
Jie Zhang ◽  
Jin Zhao ◽  
...  
Keyword(s):  
Amino Acids ◽  
Respiratory Tract ◽  
Binding Site ◽  
Spike Protein ◽  
Farm Animals ◽  
Upper Respiratory Tract ◽  
Intermediate Hosts ◽  
Species Barrier ◽  
Interaction Sites ◽  
Animal Source

ABSTRACTThe emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used recently released X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptor allows to define residues important for binding. From the 20 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S-binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites located near the S-interface. Of note, pigs and dogs which are not or not effectively infected, respectively, have only a few changes in the binding site have relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with viruses from bat and pangolin revealed that the latter contains only one substitution, whereas the bat virus exhibits five. However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-COV-2.IMPORTANCESARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. However, the lower expression of ACE2 in the upper respiratory tract of some pets and livestock means more research and monitoring should be done to explore the animal source of infection and the risk of potential cross-species transmission. Finally, the analysis also showed that SARS-CoV-2 may not specifically adapted to any of its putative intermediate hosts.

scholarly journals Conformational States of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Ectodomain

2006 ◽  
Vol 80 (14) ◽  
pp. 6794-6800 ◽  
Author(s):  
Fang Li ◽  
Marcelo Berardi ◽  
Wenhui Li ◽  
Michael Farzan ◽  
Philip R. Dormitzer ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Membrane Fusion ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Viral Entry ◽  
Protein S ◽  
Spike Protein ◽  
Fusion Peptides ◽  
Conformational States ◽  
Protease Cleavage

ABSTRACT The severe acute respiratory syndrome coronavirus enters cells through the activities of a spike protein (S) which has receptor-binding (S1) and membrane fusion (S2) regions. We have characterized four sequential states of a purified recombinant S ectodomain (S-e) comprising S1 and the ectodomain of S2. They are S-e monomers, uncleaved S-e trimers, cleaved S-e trimers, and dissociated S1 monomers and S2 trimer rosettes. Lowered pH induces an irreversible transition from flexible, L-shaped S-e monomers to clove-shaped trimers. Protease cleavage of the trimer occurs at the S1-S2 boundary; an ensuing S1 dissociation leads to a major rearrangement of the trimeric S2 and to formation of rosettes likely to represent clusters of elongated, postfusion trimers of S2 associated through their fusion peptides. The states and transitions of S suggest conformational changes that mediate viral entry into cells.

scholarly journals Mutating novel interaction sites in NRP1 reduces SARS-CoV-2 spike protein internalization

2021 ◽  
Author(s):  
Debjani Pal ◽  
Kuntal De ◽  
Tomithy Yates ◽  
Wellington Muchero
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Ribosomal Protein ◽  
Protein S ◽  
Spike Protein ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Interaction Sites ◽  
Viral Binding ◽  
Expression Of Genes ◽  
Neuropilin 1

The global pandemic of Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 has become a severe global health problem because of its rapid spread. Both angiotensin-converting enzyme 2 and neuropilin 1 provide initial viral binding sites for SARS-CoV-2. Here, we show that three cysteine residues located in a1/a2 and b1 domains of neuropilin 1 are necessary for SARS-CoV-2 spike protein internalization in human cells. Mutating cysteines C82, C104, and C147 altered neuropilin 1 stability and binding ability as well as cellular internalization and lysosomal translocation of the spike protein. This resulted in up to 4 times reduction in spike protein load in cells for the original, alpha, and delta SARS-CoV-2 variants even in the presence of the endogenous angiotensin-converting enzyme 2 receptors. Transcriptome analysis of cells transfected with mutated NRP1 revealed significantly reduced expression of genes involved in viral infection and replication, including eight members of the ribosomal protein L, ten members of ribosomal protein S, and five members of the proteasome β subunit family proteins. We also observed higher expression of genes involved in the suppression of inflammation and endoplasmic reticulum-associated degradation. These observations suggest that these cysteines offer viable targets for therapies against COVID-19.

scholarly journals Alpha-1 antitrypsin inhibits SARS-CoV-2 infection

2020 ◽  
Author(s):  
Lukas Wettstein ◽  
Carina Conzelmann ◽  
Janis A. Müller ◽  
Tatjana Weil ◽  
Rüdiger Groß ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Respiratory Tract ◽  
Bronchoalveolar Lavage ◽  
Airway Epithelium ◽  
Specific Inhibitor ◽  
Spike Protein ◽  
Human Airway ◽  
Human Airway Epithelium ◽  
Protein Library ◽  
Alpha 1 Antitrypsin

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). To identify factors of the respiratory tract that suppress SARS-CoV-2, we screened a peptide/protein library derived from bronchoalveolar lavage, and identified α1-antitrypsin (α1-AT) as specific inhibitor of SARS-CoV-2. α1-AT targets the viral spike protein and blocks SARS-CoV-2 infection of human airway epithelium at physiological concentrations. Our findings show that endogenous α1-AT restricts SARS-CoV-2 and repurposes α1-AT-based drugs for COVID-19 therapy.

scholarly journals Epidemiological associations with genomic variation in SARS-CoV-2

2021 ◽  
Author(s):  
Ali Rahnavard ◽  
Rebecca Clement ◽  
Nathaniel Stearrett ◽  
Marcos Pérez-Losada ◽  
Keith A. Crandall ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nonstructural Protein ◽  
Protein S ◽  
Disease Status ◽  
Virus Genome ◽  
Genomic Variation ◽  
Spike Protein ◽  
Genome Variation ◽  
Host Sex ◽  
Novel Coronavirus

Abstract The 2019 novel coronavirus (SARS-CoV-2) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. To diminish the short-term and long-term impacts of coronavirus (CoV), we investigated CoV differences at the nucleotide and protein level and CoV genomic variation associated with epidemiological variation and geography. We divided the CoV genome into 29 constituent regions for this analysis. Our results highlight the variation of CoV variants of lineage and show that nonstructural protein 3 (nsp3) and Spike protein (S) have the highest variation and greatest correlation with the viral whole-genome variation, which makes these two proteins potential targets for treatments. S protein variation is highly correlated with nsp3, nsp6, and 3'−to−5' exonuclease. Country of origin and time since the start of the pandemic were the most influential metadata in these differences. Host sex and age are the lowest in terms of explaining the virus genome variation. We quantified variation explained by regions of the CoV genome across different CoV viruses including, SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), other severe acute respiratory syndrome coronavirus SARS-CoV (SARS-related), and bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses (Bat-SL-CoV). We found that Spike protein and nsp3 explain most of the variation among these viruses; they are also among the genomic regions with the highest number of sites under natural selection. Our results provide a direction to prioritize genes associated with outcome predictors, including health, therapeutic, and vaccine outcomes, and to inform improved DNA tests for predicting disease status.

scholarly journals First Description of a Multisystemic and Lethal SARS-CoV-2 Variant of Concern P.1 (Gamma) Infection in a FeLV-Positive Cat: New Concerns Regarding Viral Re-emergence and Adaption to Pets

2021 ◽  
Author(s):  
Rodrigo Lima Carneiro ◽  
Jessica Pires Farias ◽  
Josilene Ramos Pinheiro ◽  
Jackson Farias ◽  
Andre Carloto Vielmo ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Leukemia Virus ◽  
Fatal Case ◽  
Genomic Analysis ◽  
High Load ◽  
Feline Leukemia Virus ◽  
Intermediate Hosts ◽  
Species Barrier ◽  
Pathological Analysis ◽  
New Hosts

Abstract Background: Coronaviruses are recognized for their ability to cross the species barrier and infect new hosts. The coronavirus disease 2019 (COVID-19) is caused by the new coronavirus SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). It remains unclear whether other animals, including pets, are crucial in the spread and maintenance of COVID-19 worldwide. Methods: In this study, we analysed the first fatal case of a SARS-CoV-2 and FeLV (Feline leukemia virus) co-infection of an eight-year-old male cat. We carried out a clinical evaluation, pathological analysis, and viral genomic analysis. Results: As main results, we observed an animal presenting severe acute respiratory syndrome and lesions in several organs, which led to animal’s death. The causative agent was confirmed to be SARS-CoV-2, variant of concern P.1 (Gamma). The virus presented a pattern of mutations potentially associated with feline infection. In addition, the virus was detected by RT-qPCR in the spleen, liver, heart, lungs, trachea, intestines and kidneys, indicating a multisystemic viral infection. The virus was found in a high load in the trachea, suggesting a capacity of transmitting the virus. Conclusion: Our data show that felines, such as FeLV-positive cats, are susceptible to SARS-CoV-2 infection, and may be intermediate hosts in this pandemic.

scholarly journals Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction

2015 ◽  
Vol 113 (05) ◽  
pp. 976-987 ◽  
Author(s):  
Sofia Somajo ◽  
Josefin Ahnström ◽  
Juan Fernandez-Recio ◽  
Magdalena Gierula ◽  
Bruno O. Villoutreix ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Tissue Factor ◽  
In Silico ◽  
Tissue Factor Pathway Inhibitor ◽  
Protein S ◽  
Protein Docking ◽  
Amino Acid Residues ◽  
Interaction Sites ◽  
Tissue Factor Pathway

SummaryProtein S functions as a cofactor for tissue factor pathway inhibitor (TFPI) and activated protein C (APC). The sex hormone binding globulin (SHBG)-like region of protein S, consisting of two laminin G-like domains (LG1 and LG2), contains the binding site for C4b-binding protein (C4BP) and TFPI. Furthermore, the LG-domains are essential for the TFPI-cofactor function and for expression of full APC-cofactor function. The aim of the current study was to localise functionally important interaction sites in the protein S LG-domains using amino acid substitutions. Four protein S variants were created in which clusters of surface-exposed amino acid residues within the LG-domains were substituted. All variants bound normally to C4BP and were fully functional as cofactors for APC in plasma and in pure component assays. Two variants, SHBG2 (E612A, I614A, F265A, V393A, H453A), involving residues from both LG-domains, and SHBG3 (K317A, I330A, V336A, D365A) where residues in LG1 were substituted, showed 50–60 % reduction in enhancement of TFPI in FXa inhibition assays. For SHBG3 the decreased TFPI cofactor function was confirmed in plasma based thrombin generation assays. Both SHBG variants bound to TFPI with decreased affinity in surface plasmon resonance experiments. The TFPI Kunitz 3 domain is known to contain the interaction site for protein S. Using in silico analysis and protein docking exercises, preliminary models of the protein S SHBG/TFPI Kunitz domain 3 complex were created. Based on a combination of experimental and in silico data we propose a binding site for TFPI on protein S, involving both LGdomains.

scholarly journals Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A

2019 ◽  
Vol 116 (7) ◽  
pp. 2681-2690 ◽  
Author(s):  
Ruben J. G. Hulswit ◽  
Yifei Lang ◽  
Mark J. G. Bakkers ◽  
Wentao Li ◽  
Zeshi Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Receptor Binding ◽  
Protein S ◽  
Protein Domain ◽  
Spike Protein ◽  
Ligand Docking ◽  
Respiratory Pathogens ◽  
Receptor Binding Site ◽  
Human Coronaviruses

Human betacoronaviruses OC43 and HKU1 are endemic respiratory pathogens and, while related, originated from independent zoonotic introductions. OC43 is in fact a host-range variant of the species Betacoronavirus-1, and more closely related to bovine coronavirus (BCoV)—its presumptive ancestor—and porcine hemagglutinating encephalomyelitis virus (PHEV). The β1-coronaviruses (β1CoVs) and HKU1 employ glycan-based receptors carrying 9-O-acetylated sialic acid (9-O-Ac-Sia). Receptor binding is mediated by spike protein S, the main determinant of coronavirus host specificity. For BCoV, a crystal structure for the receptor-binding domain S1A is available and for HKU1 a cryoelectron microscopy structure of the complete S ectodomain. However, the location of the receptor-binding site (RBS), arguably the single-most important piece of information, is unknown. Here we solved the 3.0-Å crystal structure of PHEV S1A. We then took a comparative structural analysis approach to map the β1CoV S RBS, using the general design of 9-O-Ac-Sia-binding sites as blueprint, backed-up by automated ligand docking, structure-guided mutagenesis of OC43, BCoV, and PHEV S1A, and infectivity assays with BCoV-S–pseudotyped vesicular stomatitis viruses. The RBS is not exclusive to OC43 and related animal viruses, but is apparently conserved and functional also in HKU1 S1A. The binding affinity of the HKU1 S RBS toward short sialoglycans is significantly lower than that of OC43, which we attribute to differences in local architecture and accessibility, and which may be indicative for differences between the two viruses in receptor fine-specificity. Our findings challenge reports that would map the OC43 RBS elsewhere in S1A and that of HKU1 in domain S1B.

scholarly journals Basic Coronavirus biology and vaccines for COVID-19

2021 ◽  
Vol 39 (4) ◽  
Author(s):  
Hernan Garcia-Ruiz ◽  
Katherine LaTourrette ◽  
Mayra Teresa Garcia-Ruiz
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Diagnostic Test ◽  
Drug Administration ◽  
Diagnostic Tests ◽  
Protein S ◽  
Antiviral Drugs ◽  
Genomic Variation ◽  
Spike Protein ◽  
Human Coronaviruses

<p><em>Severe acute respiratory syndrome coronavirus 2</em> (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Two mRNA vaccines based on the spike protein S have been authorized by the Food and Drug Administration. Antibody-based diagnostic test detect antibodies developed against protein S. Mutations in the genome of SARS-CoV-2 might compromise the precision of diagnostic tests and the efficacy of vaccines and antiviral drugs. We recently profiled genomic variation in human coronaviruses SARS[1]CoV, SARS-CoV-2, and <em>Middle East respiratory syndrome coronavirus</em> (MERS-CoV). As in all species of the genus Betacoronavirus, the genome is hyper variable, and mutations are not random. The most variable cistron codes for the spike S protein. Hyper variation in protein S has the potential to affect the efficacy of vaccines, the reliability of antibody-based diagnostic test, and predicts potential for repeated SARS-CoV-2 infections. Here we review the basics of coronavirus biology and genomic variation, and link them to diagnostic tests, vaccines, and antiviral drugs.</p>

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