scholarly journals Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Christian A. Devaux ◽  
Lucile Pinault ◽  
Jérémy Delerce ◽  
Didier Raoult ◽  
Anthony Levasseur ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
3D Structure ◽  
Spike Protein ◽  
Linear Epitope ◽  
Angiotensin I ◽  
Vaccine Protection ◽  
Angiotensin I Converting Enzyme ◽  
Neuropilin 1 ◽  
Rapid Spread ◽  
The Impact

The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines.

scholarly journals Prediction and evolution of the molecular fitness of SARS-CoV-2 variants: Introducing SpikePro

2021 ◽  
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Immune Response ◽  
Neutralizing Antibodies ◽  
Molecular Mechanisms ◽  
Population Level ◽  
Critical Issue ◽  
Spike Protein ◽  
Human Immune Response ◽  
Human Immune ◽  
The Stability ◽  
The Impact

The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the viral transmissibility predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful instrument for the genomic surveillance of the SARS-CoV-2 virus, since it predicts in a fast and accurate way the emergence of new viral strains and their dangerousness. It is freely available in the GitHub repository github.com/3BioCompBio/SpikeProSARS-CoV-2.

scholarly journals Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

2020 ◽  
Author(s):  
Philip J.M. Brouwer ◽  
Tom G. Caniels ◽  
Karlijn van der Straten ◽  
Jonne L. Snitselaar ◽  
Yoann Aldon ◽  
...  
Keyword(s):  
Global Health ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Vaccine Design ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Treatment And Prevention ◽  
Antigenic Sites ◽  
Rapid Spread ◽  
Therapeutic Measures

AbstractThe rapid spread of SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated neutralizing antibodies from convalescent COVID-19 patients using a SARS-CoV-2 stabilized prefusion spike protein. Several of these antibodies were able to potently inhibit live SARS-CoV-2 infection at concentrations as low as 0.007 µg/mL, making them the most potent human SARS-CoV-2 antibodies described to date. Mapping studies revealed that the SARS-CoV-2 spike protein contained multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as previously undefined non-RBD epitopes. In addition to providing guidance for vaccine design, these mAbs are promising candidates for treatment and prevention of COVID-19.

scholarly journals Host range projection of SARS-CoV-2: South Asia perspective

2020 ◽  
Author(s):  
Rasel Ahmed ◽  
Rajnee Hasan ◽  
A.M.A.M Zonaed Siddiki ◽  
Md. Shahidul Islam
Keyword(s):  
South Asia ◽  
Bird Species ◽  
Farming System ◽  
Spike Protein ◽  
Intermediate Hosts ◽  
Angiotensin I ◽  
Predominant Species ◽  
Angiotensin I Converting Enzyme ◽  
Animal Hosts ◽  
Future Outbreak

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causing agent of Coronavirus Disease-2019 (COVID-19), is likely to be originated from bat and transmitted through intermediate hosts. However, the immediate source species of SARS-CoV-2 has not yet been confirmed. Here, we used diversity analysis of the angiotensin I converting enzyme 2 (ACE2) that serves as cellular receptor for SARS-CoV-2 and transmembrane protease serine 2 (TMPRSS2), which has been proved to be utilized by SARS-CoV-2 for spike protein priming. We also simulated the structure of receptor binding domain of SARS-CoV-2 spike protein (SARS-CoV-2 S RBD) with the ACE2s to investigate their binding affinity to determine the potential intermediate animal hosts that could spread the SARS-CoV-2 virus to humans in South Asia. We identified cow, buffalo, goat and sheep, which are predominant species in the household farming system in South Asia that can potentially be infected by SARS-CoV-2. All the bird species studied along with rat and mouse were considered less potential to interact with SARS-CoV-2. The interaction interfaces of SARS-CoV-2 S RBD and ACE2 protein complex suggests pangolin as a potential intermediate host in SARS-CoV-2. Our results provide a valuable resource for the identification of potential hosts for SARS-CoV-2 in South Asia and henceforth reduce the opportunity for a future outbreak of COVID-19.

scholarly journals Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

Science ◽  
2020 ◽  
Vol 369 (6504) ◽  
pp. 643-650 ◽  
Author(s):  
Philip J. M. Brouwer ◽  
Tom G. Caniels ◽  
Karlijn van der Straten ◽  
Jonne L. Snitselaar ◽  
Yoann Aldon ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Somatic Hypermutation ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Treatment And Prevention ◽  
Antigenic Sites ◽  
Rapid Spread ◽  
Gene Usage ◽  
Therapeutic Measures ◽  
Low Levels

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3, and VH1-24 gene usage. A subset of the antibodies was able to potently inhibit authentic SARS-CoV-2 infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention.

scholarly journals Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 611
Author(s):  
Badr M. Al-Shomrani ◽  
Manee M. Manee ◽  
Sultan N. Alharbi ◽  
Mussad A. Altammami ◽  
Manal A. Alshehri ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Middle East ◽  
Neutralizing Antibodies ◽  
3D Structure ◽  
Arabian Gulf ◽  
Cell Epitope ◽  
Middle East Respiratory Syndrome ◽  
Spike Protein ◽  
Dromedary Camel ◽  
Gulf Countries

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory illness in humans; the second-largest and most deadly outbreak to date occurred in Saudi Arabia. The dromedary camel is considered a possible host of the virus and also to act as a reservoir, transmitting the virus to humans. Here, we studied evolutionary relationships for 31 complete genomes of betacoronaviruses, including eight newly sequenced MERS-CoV genomes isolated from dromedary camels in Saudi Arabia. Through bioinformatics tools, we also used available sequences and 3D structure of MERS-CoV spike glycoprotein to predict MERS-CoV epitopes and assess antibody binding affinity. Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries. The 2019-nCov strain appears to have higher homology to both bat coronavirus and SARS-CoV than to MERS-CoV strains. The spike protein tree exhibited clustering of MERS-CoV sequences similar to the complete genome tree, except for one sequence from Qatar (KF961222). B cell epitope analysis determined that the MERS-CoV spike protein has 24 total discontinuous regions from which just six epitopes were selected with score values of >80%. Our results suggest that the virus circulates by way of camels crossing the borders of Arabian Gulf countries. This study contributes to finding more effective vaccines in order to provide long-term protection against MERS-CoV and identifying neutralizing antibodies.

scholarly journals Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 935
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Neutralizing Antibodies ◽  
Molecular Mechanisms ◽  
Population Level ◽  
Critical Issue ◽  
Spike Protein ◽  
Surveillance Programs ◽  
Human Immune Response ◽  
Human Immune ◽  
The Stability ◽  
The Impact

The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.

scholarly journals SARS-CoV-2 bearing a mutation at the S1/S2 cleavage site exhibits attenuated virulence and confers protective immunity

2021 ◽  
Author(s):  
Michihito Sasaki ◽  
Shinsuke Toba ◽  
Yukari Itakura ◽  
Herman M. Chambaro ◽  
Mai Kishimoto ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Neutralizing Antibodies ◽  
Body Weight Loss ◽  
Airway Epithelial Cells ◽  
Spike Protein ◽  
Furin Cleavage ◽  
Growth Property ◽  
S Gene ◽  
Furin Cleavage Site ◽  
The Impact

AbstractSevere Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) possesses a discriminative polybasic cleavage motif in its spike protein that is recognized by host furin protease. Proteolytic cleavage activates the spike protein and influences both the cellular entry pathway and cell tropism of SARS-CoV-2. Here, we investigated the impact of the furin cleavage site on viral growth and pathogensis using a hamster animal model infected with SARS-CoV-2 variants bearing mutations at the furin cleavage site (S gene mutants). In the airway tissues of hamsters, the S gene mutants exhibited a low growth property. In contrast to parental pathogenic SARS-CoV-2, hamsters infected with the S gene mutants showed no body weight loss and only a mild inflammatory response, indicating the attenuated variant nature of S gene mutants. We reproduced the attenuated growth of S gene mutants in primary differenciated human airway epithelial cells. This transient infection was enough to induce protective neutralizing antibodies crossreacting with different SARS-CoV-2 lineages. Consequently, hamsters inoculated with S gene mutants showed resistance to subsequent infection with both the parental strain and the currently emerging SARS-CoV-2 variants belonging to lineages B.1.1.7 and P.1. Together, our findings revealed that the loss of the furin cleavage site causes attenuation in the airway tissues of SARS-CoV-2 and highlights the potential benefits of S gene mutants as potential immunogens.

scholarly journals Impact of prior Dengue immunity on Zika vaccine protection in rhesus macaques and mice

2021 ◽  
Vol 17 (6) ◽  
pp. e1009673
Author(s):  
Rafael A. Larocca ◽  
Peter Abbink ◽  
John D. Ventura ◽  
Abishek Chandrashekar ◽  
Noe Mercado ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Protective Efficacy ◽  
Rhesus Macaques ◽  
Passive Transfer ◽  
Zikv Infection ◽  
Vaccine Protection ◽  
Denv Serotypes ◽  
Immunization Strategies ◽  
Specific Igg ◽  
The Impact

Pre-existing immunity to flaviviruses can influence the outcome of subsequent flavivirus infections. Therefore, it is critical to determine whether baseline DENV immunity may influence subsequent ZIKV infection and the protective efficacy of ZIKV vaccines. In this study, we investigated the impact of pre-existing DENV immunity induced by vaccination on ZIKV infection and the protective efficacy of an inactivated ZIKV vaccine. Rhesus macaques and mice inoculated with a live attenuated DENV vaccine developed neutralizing antibodies (NAbs) to multiple DENV serotypes but no cross-reactive NAbs responses to ZIKV. Animals with baseline DENV NAbs did not exhibit enhanced ZIKV infection and showed no overall reduction in ZIKV vaccine protection. Moreover, passive transfer of purified DENV-specific IgG from convalescent human donors did not augment ZIKV infection in STAT2 -/- and BALB/c mice. In summary, these results suggest that baseline DENV immunity induced by vaccination does not significantly enhance ZIKV infection or impair the protective efficacy of candidate ZIKV vaccines in these models. These data can help inform immunization strategies in regions of the world with multiple circulating pathogenic flaviviruses.

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