The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design

Abstract Background Tracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity. Methods Here, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations. Results Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs. Conclusions This work provides a framework able to track down SARS-CoV-2 genomic variability.

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The SARS CoV-2 spike domain, RGD and integrin binding effect-relationship for vaccine design strategy

Annals of Proteomics and Bioinformatics ◽

10.29328/journal.apb.1001014 ◽

2021 ◽

Vol 5 (1) ◽

pp. 027-041

Author(s):

M Luisetto ◽

G Tarro ◽

Edbey Khaled ◽

N Almukthar ◽

L Cabianca ◽

...

Keyword(s):

Vaccine Design ◽

Design Strategy ◽

Spike Protein ◽

Pathological Effect ◽

Technical Data ◽

Binding Effect ◽

New Strategy ◽

Rare Side Effect ◽

New Generation

Related the need to search new strategy in vaccine design in order to reduce also some rare effect like trombosys for some registered products it is interesting the role played by the SPIKE RGD domain. The binding with molecules like Fibronectin is a process that must to be deeply investigated. A better understanding in this process can be used to improve safety of the new generation of COVID vaccine. The rare effect like thrombosis recognized by regulatory agency produced a modification of technical data sheet of some vaccine so the phenomena Is interesting to be more investigated. Spike protein and its domains are involved in producing pathological effect of the COVID-19 disease. What it is interesting is that some pathological effect of this pathology are similar to some rare side effect produced by some COVID-19 vaccine classes. After a review of interesting literature related this topics is submitted an experimental projects able to verify in vitro the spike procoaugulant property.

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Vaccine design based on 16 epitopes of SARS‐CoV‐2 spike protein

Journal of Medical Virology ◽

10.1002/jmv.26596 ◽

2020 ◽

Author(s):

Jinlei He ◽

Fan Huang ◽

Jianhui Zhang ◽

Qiwei Chen ◽

Zhiwan Zheng ◽

...

Keyword(s):

Vaccine Design ◽

Spike Protein

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Cleavage of spike protein of SARS coronavirus by protease factor Xa is associated with viral infectivity

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2007.05.092 ◽

2007 ◽

Vol 359 (1) ◽

pp. 174-179 ◽

Cited By ~ 57

Author(s):

Lanying Du ◽

Richard Y. Kao ◽

Yusen Zhou ◽

Yuxian He ◽

Guangyu Zhao ◽

...

Keyword(s):

Factor Xa ◽

Spike Protein ◽

Viral Infectivity ◽

Sars Coronavirus

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An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity

10.1101/2021.04.02.438288 ◽

2021 ◽

Cited By ~ 1

Author(s):

Chihiro Motozono ◽

Mako Toyoda ◽

Jiri Zahradnik ◽

Terumasa Ikeda ◽

Akatsuki Saito ◽

...

Keyword(s):

Receptor Binding ◽

Cellular Immunity ◽

Human Leukocyte ◽

Spike Protein ◽

Viral Infectivity ◽

Receptor Binding Domain ◽

Viral Receptor ◽

Leukocyte Antigen ◽

Immune Resistance ◽

Naturally Occurring

SummaryDuring the current SARS-CoV-2 pandemic that is devastating the modern societies worldwide, many variants that naturally acquire multiple mutations have emerged. Emerging mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has recently been investigated, that to human leukocyte antigen (HLA)-restricted cellular immunity remains unaddressed. Here we demonstrate that two recently emerging mutants in the receptor binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429) and Y453F (in B.1.298), can escape from the HLA-24-restricted cellular immunity. These mutations reinforce the affinity to viral receptor ACE2, and notably, the L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication. Our data suggest that the HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes, and the escape from cellular immunity can be a further threat of the SARS-CoV-2 pandemic.Graphical Abstract

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

10.1101/2020.05.12.088716 ◽

2020 ◽

Cited By ~ 29

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.

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The SARS-CoV-2 spike protein primes inflammasome-mediated interleukin-1- beta secretion in COVID-19 patient-derived macrophages

10.21203/rs.3.rs-30407/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sebastian J. Theobald ◽

Alexander Simonis ◽

Christoph Kreer ◽

Matthias Zehner ◽

Julia Fischer ◽

...

Keyword(s):

Innate Immunity ◽

Drug Treatment ◽

Ex Vivo ◽

Interleukin 1 ◽

Vaccine Design ◽

Spike Protein ◽

Inflammasome Activation ◽

Interleukin 1 Beta ◽

Viral Control

Abstract Innate immunity triggers responsible for viral control or hyperinflammation in COVID- 19 are largely unknown. Here we show that the SARS-CoV-2 spike protein primes inflammasome activation and interleukin 1-beta (IL-1β) secretion in macrophages derived from COVID-19 patients but not in macrophages from healthy SARS-CoV-2 naïve controls. Chemical NLRP3 inhibition blocks spike protein-induced IL-1β secretion ex vivo. These findings can accelerate research on COVID-19 vaccine design and drug treatment.

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SARS-CoV-2 spike P681R mutation enhances and accelerates viral fusion

10.1101/2021.06.17.448820 ◽

2021 ◽

Author(s):

Akatsuki Saito ◽

Hesham Nasser ◽

Keiya Uriu ◽

Yusuke Kosugi ◽

Takashi Irie ◽

...

Keyword(s):

Cell Fusion ◽

Viral Genome ◽

Neutralizing Antibody ◽

Spike Protein ◽

Human Society ◽

Viral Infectivity ◽

Viral Fusion ◽

Antibody Resistance ◽

Cell Cell

During the current SARS-CoV-2 pandemic, a variety of mutations have been accumulated in the viral genome, and at least five variants of concerns (VOCs) have been considered as the hazardous SARS-CoV-2 variants to the human society. The newly emerging VOC, the B.1.617.2 lineage (delta variant), closely associates with a huge COVID-19 surge in India in Spring 2021. However, its virological property remains unclear. Here, we show that the B.1.617 variants are highly fusogenic and form prominent syncytia. Bioinformatic analyses reveal that the P681R mutation in the spike protein is highly conserved in this lineage. Although the P681R mutation decreases viral infectivity, this mutation confers the neutralizing antibody resistance. Notably, we demonstrate that the P681R mutation facilitates the furin-mediated spike cleavage and enhances and accelerates cell-cell fusion. Our data suggest that the P681R mutation is a hallmark characterizing the virological phenotype of this newest VOC, which may associate with viral pathogenicity.

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A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells

10.1101/2020.10.23.347534 ◽

2020 ◽

Cited By ~ 1

Author(s):

Drake M. Mellott ◽

Chien-Te Tseng ◽

Aleksandra Drelich ◽

Pavla Fajtová ◽

Bala C. Chenna ◽

...

Keyword(s):

Protease Inhibitor ◽

Host Cell ◽

Cysteine Protease ◽

Cleavage Site ◽

Cathepsin L ◽

Cysteine Proteases ◽

Protein Processing ◽

Spike Protein ◽

Cysteine Protease Inhibitor ◽

Viral Infectivity

ABSTRACTK777 is a di-peptide analog that contains an electrophilic vinyl-sulfone moiety and is a potent, covalent inactivator of cathepsins. Vero E6, HeLa/ACE2, Caco-2, A549/ACE2, and Calu-3, cells were exposed to SARS-CoV-2, and then treated with K777. K777 reduced viral infectivity with EC50 values of inhibition of viral infection of: 74 nM for Vero E6, <80 nM for A549/ACE2, and 4 nM for HeLa/ACE2 cells. In contrast, Calu-3 and Caco-2 cells had EC50 values in the low micromolar range. No toxicity of K777 was observed for any of the host cells at 10-100 μM inhibitor. K777 did not inhibit activity of the papain-like cysteine protease and 3CL cysteine protease, encoded by SARS-CoV-2 at concentrations of ≤ 100 μM. These results suggested that K777 exerts its potent anti-viral activity by inactivation of mammalian cysteine proteases which are essential to viral infectivity. Using a propargyl derivative of K777 as an activity-based probe, K777 selectively targeted cathepsin B and cathepsin L in Vero E6 cells. However only cathepsin L cleaved the SARS-CoV-2 spike protein and K777 blocked this proteolysis. The site of spike protein cleavage by cathepsin L was in the S1 domain of SARS-CoV-2, differing from the cleavage site observed in the SARS CoV-1 spike protein. These data support the hypothesis that the antiviral activity of K777 is mediated through inhibition of the activity of host cathepsin L and subsequent loss of viral spike protein processing.SIGNIFICANCEThe virus causing COVID-19 is highly infectious and has resulted in a global pandemic. We confirm that a cysteine protease inhibitor, approved by the FDA as a clinical-stage compound, inhibits SARS-CoV-2 infection of several human and monkey cell lines with notable(nanomolar) efficacy. The mechanism of action of this inhibitor is identified as a specific inhibition of host cell cathepsin L. This in turn inhibits host cell processing of the coronaviral spike protein, a step required for cell entry. Neither of the coronaviral proteases are inhibited, and the cleavage site of spike protein processing is different from that reported in other coronaviruses. Hypotheses to explain the differential activity of the inhibitor with different cell types are discussed.

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