scholarly journals Two mutations in the SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk

2020 ◽  
Author(s):  
Georg Hahn ◽  
Chloe M. Wu ◽  
Sanghun Lee ◽  
Julian Hecker ◽  
Sharon M. Lutz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
Structural Changes ◽  
Potential Method ◽  
Host Cells ◽  
Host Susceptibility ◽  
Spike Protein ◽  
Highly Pathogenic ◽  
Polymerase Complex ◽  
Therapeutic Development

SARS-CoV-2 mortality has been extensively studied in relation to host susceptibility. How sequence variations in the SARS-CoV-2 genome affect pathogenicity is poorly understood. Whole-genome sequencing (WGS) of the virus with death in SARS-CoV-2 patients is one potential method of early identification of highly pathogenic strains to target for containment. We analyzed 7,548 single stranded RNA-genomes of SARS-CoV-2 patients in the GISAID database (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) and associated variants with reported patient's health status from COVID-19, i.e. deceased versus non-deceased. We probed each locus of the single stranded RNA of the SARS-CoV-2 virus for direct association with host/patient mortality using a logistic regression. In total, evaluating 29,891 loci of the viral genome for association with patient/host mortality, two loci, at 12,053bp and 25,088bp, achieved genome-wide significance (p-values of 4.09e-09 and 4.41e-23, respectively). Mutations at 25,088bp occur in the S2 subunit of the SARS-CoV-2 spike protein, which plays a key role in viral entry of target host cells. Additionally, mutations at 12,053bp are within the ORF1ab gene, in a region encoding for the protein nsp7, which is necessary to form the RNA polymerase complex responsible for viral replication and transcription. Both mutations altered amino acid coding sequences, potentially imposing structural changes that could enhance viral infectivity and symptom severity, and may be important to consider as targets for therapeutic development. Identification of these highly significant associations, unlikely to occur by chance, may assist with COVID-19 early containment of strains that are potentially highly pathogenic.

scholarly journals Mutations in SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk

2020 ◽  
Author(s):  
Christoph Lange ◽  
Georg Hahn ◽  
Chloe Wu ◽  
Sanghun Lee ◽  
Julian Hecker ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
Viral Genome ◽  
Structural Changes ◽  
Host Cells ◽  
Spike Protein ◽  
Polymerase Complex ◽  
Genome Wide ◽  
Therapeutic Development ◽  
Host Mortality

Abstract SARS-CoV-2 mortality has been extensively studied in relationship to a patient's predisposition to the disease. However, how sequence variations in the SARS-CoV-2 genome affect mortality is not understood. To address this issue, we used a whole-genome sequencing (WGS) association study to directly link death of SARS-CoV-2 patients with sequence variation in the viral genome. Specifically, we analyzed 3,626 single stranded RNA-genomes of SARS-CoV-2 patients in the GISAID database (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) with reported patient’s health status from COVID-19, i.e. deceased versus non-deceased. In total, evaluating 28,492 loci of the viral genome for association with patient/host mortality, two loci, 12,053bp and 25,088bp, achieved genome-wide significance (p-values of 1.24e-12, and 1.24e-26, respectively). Mutations at 25,088bp occur in the S2 subunit of the SARS-CoV-2 spike protein, which plays a key role in viral entry of target host cells. Additionally, mutations at 12,053bp are within the ORF1ab gene, in a region encoding for the protein nsp7, which is necessary to form the RNA polymerase complex responsible for viral replication and transcription. Both mutations altered amino acid coding sequences, potentially imposing structural changes that could enhance viral infectivity and symptom severity, and may be important to consider as targets for therapeutic development.

scholarly journals Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

2020 ◽  
Vol 117 (45) ◽  
pp. 28046-28055 ◽  
Author(s):  
Anum Glasgow ◽  
Jeff Glasgow ◽  
Daniel Limonta ◽  
Paige Solomon ◽  
Irene Lui ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Surface Display ◽  
Random Mutagenesis ◽  
Yeast Surface Display ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Protein ◽  
Yeast Surface

An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2–RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2–pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.

scholarly journals In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice

2021 ◽  
Author(s):  
Amruta Narayanappa ◽  
Elizabeth B Engler-Chiurazzi ◽  
Isabel C Murray-Brown ◽  
Timothy E Gressett ◽  
Ifechukwude J Biose ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Viral Entry ◽  
Therapeutic Potential ◽  
Host Cells ◽  
Spike Protein ◽  
Cell Infection ◽  
Integrin Alpha5beta1 ◽  
Chemokine Ligand

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an infectious disease that has spread worldwide. Current treatments are limited in both availability and efficacy, such that improving our understanding of the factors that facilitate infection is urgently needed to more effectively treat infected individuals and to curb the pandemic. We and others have previously demonstrated the significance of interactions between the SARS-CoV-2 spike protein, integrin alpha5beta1 and human ACE2 to facilitate viral entry into host cells in vitro. We previously found that inhibition of integrin alpha5beta1 by the clinically validated small peptide ATN-161 inhibits these spike protein interactions and cell infection in vitro. In continuation with our previous findings, here we have further evaluated the therapeutic potential of ATN-161 on SARS-CoV-2 infection in k18-hACE2 transgenic (SARS-CoV-2 susceptible) mice in vivo. We discovered that treatment with single- or repeated intravenous doses of ATN-161 (1 mg/kg) within 48 hours after intranasal inoculation with SARS-CoV-2 lead to a reduction of lung viral load, viral immunofluorescence and improved lung histology in a majority of mice 72 hours post-infection. Furthermore, ATN-161 reduced SARS-CoV-2-induced increased expression of lung integrin alpha 5 and alpha v (an alpha 5-related integrin that has also been implicated in SARS-CoV-2 interactions) as well as the C-X-C motif chemokine ligand 10 (Cxcl10), further supporting the potential involvement of these integrins, and the anti-inflammatory potential of ATN-161, respectively, in SARS-CoV-2 infection. To the best of our knowledge, this is the first study demonstrating the potential therapeutic efficacy of targeting integrin alpha5beta1 in SARS-CoV-2 infection in vivo and supports the development of ATN-161 as a novel SARS-CoV-2 therapy.

scholarly journals Antibody response to SARS-CoV-2 infection and BNT162b2 vaccine in Israel

2021 ◽  
Author(s):  
Guy Shapira ◽  
Ramzia Abu Hamad ◽  
Chen Weiner ◽  
Nir Rainy ◽  
Reut Sorek-Abramovich ◽  
...  
Keyword(s):  
Immune Response ◽  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Host Cells ◽  
Spike Protein ◽  
Igg Antibodies ◽  
Age And Gender ◽  
Specific Igg ◽  
And Gender ◽  
Specific Igg Antibodies

Neutralizing antibodies targeting the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) block viral entry to host cells, preventing disease and further spread of the pathogen. The presence of SARS-CoV-2 antibodies in serum is a reliable indicator of infection, used epidemiologically to estimate the prevalence of infection and clinically as a measurement of an antigen-specific immune response. In this study, we analyzed serum Spike protein-specific IgG antibodies from 26,170 samples, including convalescent individuals who had coronavirus disease 2019 (COVID-19) and recipients of the BNT162b2 vaccine. We find distinct serological patterns in COVID-19 convalescent and vaccinated individuals, correlated with age and gender and the presence symptoms.

scholarly journals Ubiquitous genomic fragment in human 2019-nCoV viruses in the spike-protein, also encoding a novel 87 aa protein, completely missing in all other coronaviruses

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Viral Entry ◽  
Host Cells ◽  
Spike Protein ◽  
Genomic Fragment ◽  
Sequencing Data ◽  
Epitope Region ◽  
Reading Frame ◽  
Spike Gene ◽  
And Function ◽  
Highly Virulent

The origins of the highly virulent coronavirus isolated from Wuhan (Hubei, China) are uncertain, as are the reasons for its highly virulent nature (human-to-human transmission before the onset of symptoms). Here, 29 genomes of 2019-nCoV in GISAID reveals a genomic fragment which is present in all 2019-nCoV genomes, (and also in the recent Nanopore sequencing data from a family [1]), and absent in other species. The only entry in GISAID from bats (BatCoV-RaTG13) is a mystery (it does not have any publications linked to it), but is very close to human 2019-nCoV. Mutations in the viral genome need to translate in changes in protein sequences (and function) in order modulate its virulence. This genomic fragment is in the N-terminal of the spike-protein (98-228), a known-epitope region and implicated in viral entry into host cells. Interestingly, this region also encodes a novel 87 novel protein, with a shifted open-reading frame (a phenomenon common in viruses). The genomic fragment will help in faster diagnosis (excluding all other coronaviruses), while the protein information will aid in vaccine or inhibitor design. Note, there are no other fragments which have this property - present in nCov and absent in others. Coincidentally, amino acids ‘17-240 were deleted from the N-terminal domain of the TGEV Spike gene’ using CRISPR, an experiment carried out in Wuhan [2].

scholarly journals An engineered stable mini-protein to plug SARS-Cov-2 Spikes

2020 ◽  
Author(s):  
Maria Romano ◽  
Alessia Ruggiero ◽  
Flavia Squeglia ◽  
Rita Berisio
Keyword(s):  
Viral Entry ◽  
Structural Data ◽  
Host Cells ◽  
Spike Protein ◽  
Helical Conformation ◽  
The Novel ◽  
Angiotensin Converting Enzyme 2 ◽  
Different Types ◽  
Novel Virus ◽  
High Yields

AbstractThe novel betacoronavirus SARS-CoV-2 is the etiological agent of the current pandemic COVID-19. Like other coronaviruses, this novel virus relies on the surface Spike glycoprotein to access the host cells, mainly through the interaction of its Receptor Binding Domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with binding of the SARS-CoV-2 Spike protein to ACE2 have a great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 Spike protein and the host ACE2 receptor, we here engineered a mini-protein with the aim of creating a soluble and stable Spike interactor. This mini-protein, which was recombinantly produced in high yields, possesses a stable α helical conformation and is able to interact with the RBD of glycosylated Spike protein from SARS-CoV-2 with nanomolar affinity, as measured by microscale thermophoresis. By plugging the Spike protein, our mini-protein constitutes a valid tool for the development of treatments against different types of coronavirus.

SARS-CoV-2 S Protein Binding hACE2: Viral Entry, Pathogenesis, Prognosis, and Potential Therapeutic Targets

2020 ◽  
Author(s):  
Lobna Al-Zaidan ◽  
Sarra Mestiri ◽  
Afsheen Raza ◽  
Maysaloun Merhi ◽  
Varghese Inchakalody ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Viral Entry ◽  
Respiratory Illness ◽  
Host Cells ◽  
Host Susceptibility ◽  
Unknown Etiology ◽  
Viral Binding ◽  
Binding Interface ◽  
Novel Coronavirus ◽  
Severe Respiratory Illness

Pneumonia cases of unknown etiology in Wuhan, China, were reported to the WHO on 31st of December 2019. Later the pathogen was reported to be a novel coronavirus designated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is a novel pathogenic beta coronavirus that infects humans causing severe respiratory illness. However, multifarious factors can contribute to the susceptibility to COVID-19 related morbidity and mortality such as age, gender and underlying comorbidities. Importantly, SARS-CoV and SARS-CoV-2 entry into the host cells is mediated via ACE2 receptor. However, ACE2 receptor binding affinity to SARS-CoV-2 is 4 folds higher than that to SARS-CoV. Identification of different aspects such as binding affinity, differential antigenic profiles of spike glycoproteins, and ACE2 polymorphisms might influence the investigation of potential therapeutic strategies targeting SARS-CoV-2/ACE2 binding interface. Here we aim to elaborate on SARS-CoV-2 S1/ACE2 ligand that facilitates viral internalization as well as to highlight the differences between SARS-CoVs binding affinity to ACE2. We also discuss the possible immunogenic sequences of spike glycoprotein and the effect of ACE2 polymorphism on viral binding/infectivity and host susceptibility to disease. Furthermore, targeting of ACE2 will be discussed to understand its role in therapeutics.

Emergence and Reemergence of Human Coronaviruses: Spike Protein as the Potential Molecular Switch and Pharmaceutical Target

2020 ◽  
Vol 26 ◽  
Author(s):  
Fahim Ahmad ◽  
Mohammad A. Kamal ◽  
Babu L. Tekwani
Keyword(s):  
Molecular Switch ◽  
Host Cells ◽  
Host Susceptibility ◽  
Spike Protein ◽  
Comparative Genomic ◽  
Host Switching ◽  
Continuous Exposure ◽  
Recent Emergence ◽  
Multiple Strains ◽  
Spike Proteins

Background: Recent emergence of COVID-19 caused by a new human coronavirus (CoV) strain (SARS-CoV2), which originated from the China, poses future emergence of additional CoVs. In most of the cases of emergence of human CoVs bats, palm civets, raccoon dogs and camels have been identified as the sources of human infections and reservoir hosts. A review of comparative genomic and phenotypic characteristics of human CoV strains vis-à-vis their comparison with the corresponding animal isolates shall provide the clues regarding the potential genomic, phenotypic and molecular factors responsible for host-switching, which may lead to prospective emergence and reemergence of human CoV outbreaks in future. Methods: The seven known human strains of CoV were analyzed for the host and viral factors responsible for human outbreaks. The molecular factors responsible for host-susceptibility, virulence and pathogenesis were reviewed to predict emergence and re-emergence of additional human CoV strains. CoV spike protein was evaluated as a potential viral receptor for host switching and the target for pharmaceutical design. Results: Review of the factors associated with host-susceptibility, virulence and pathogenesis of seven known human CoV strains present significant possibilities for emergence of new CoV strain(s), leading to more human outbreaks. Continuous exposure of animals’ handlers to the infected animals, environmental changes, improper sanitations, nondisposal of the solid waste and resumption of exotic animals markets provide favorable conditions for “host switching” and emergence of new and potentially more virulent human CoV strains. Mutations in target genes (like spike protein), which facilitate the viral entry into the host-cells, provide potential “molecular switch” for preferences of new hostreceptors, genetic diversity, genetic-recombination and high virulence. Additionally, the clinical and environmental factors, asymptomatic carriers, paucity of efficacious vaccines & therapeutics, inefficient disease management and infection control measures, lack of public awareness, and effective communication of information about more virulent human-adapted virus isolates are critical factors for emergence of new and virulent SARS-CoV strains with high mortality and varied incubation period in the near future. Small molecules binding with conserved druggable regions of the CoV spike proteins may be effective against multiple strains of CoVs. Conclusions: High propensity of mutations and “molecular adaptations” in coronaviruses create the hot spots and high potential for “host switching” leading to emergence of more virulent strains human CoVs. The public/global health agencies, medical communities and research scientists should be prepared for emergence and reemergence of new human CoV strain(s) leading to potential disease outbreaks. The inhibitors binding with conserved druggable regions of spike proteins from multiple strains CoV may have utility as broad-spectrum antiviral drugs to combat future emergence of CoVs.

Sign in / Sign up

Export Citation Format

Share Document