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1.
J Proteome Res ; 2020 Sep 11.
Article in English | MEDLINE | ID: covidwho-759561

ABSTRACT

Progress of the omics platforms widens their application to diverse fields, including immunology. This enables a deeper level of knowledge and the provision of a huge amount of data which management and fruitful integration with the past evidence requires a steadily growing computational effort. In this light, immunoinformatics emerges as a new discipline placed in-between the traditional lab-based investigations and the computational analysis of the biological data. Immunoinformatics make use of tailored bioinformatics tools and data repositories to facilitate the analysis of data from a plurality of disciplines and help driving novel research hypothesis and in silico screening investigations in a fast, reliable and cost-effective manner. Such computational immuno proteomics studies may as well prepare and guide lab-based investigations, representing a valuable technology for the investigation of novel pathogens, to tentatively evaluate specificity of diagnostic products, to forecast on potential adverse effects of vaccines and to reduce the use of animal models. The present manuscript provides an overview of the COVID-19 pandemics and reviews the state of the art of the omics technologies employed in fighting SARS-CoV-2 infections. A comprehensive description of the immunoinformatics approaches and its potential role in contrasting COVID-19 pandemics is provided.

2.
Microbes Infect ; 2020 Sep 03.
Article in English | MEDLINE | ID: covidwho-744191

ABSTRACT

The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.

3.
Microbes Infect ; 22(4-5): 182-187, 2020.
Article in English | MEDLINE | ID: covidwho-626674

ABSTRACT

Envelope protein of coronaviruses is a structural protein existing in both monomeric and homo-pentameric form. It has been related to a multitude of roles including virus infection, replication, dissemination and immune response stimulation. In the present study, we employed an immunoinformatic approach to investigate the major immunogenic domains of the SARS-CoV-2 envelope protein and map them among the homologue proteins of coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Also, when not available, we predicted the envelope protein structural folding and mapped SARS-CoV-2 epitopes. Envelope sequences alignment provides evidence of high sequence homology for some of the investigated virus specimens; while the structural mapping of epitopes resulted in the interesting maintenance of the structural folding and epitope sequence localization also in the envelope proteins scoring a lower alignment score. In line with the One-Health approach, our evidences provide a molecular structural rationale for a potential role of taxonomically related coronaviruses in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies.


Subject(s)
Betacoronavirus/metabolism , Computational Biology/methods , Coronavirus Infections/immunology , Coronavirus Infections/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Viral Envelope Proteins/immunology , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Betacoronavirus/immunology , Epitope Mapping , Gene Expression Regulation, Viral , Humans , Models, Molecular , One Health , Pandemics , Phylogeny , Protein Conformation , Sequence Alignment , Sequence Analysis, Protein
4.
Microbes Infect ; 22(4-5): 182-187, 2020.
Article in English | MEDLINE | ID: covidwho-346567

ABSTRACT

Envelope protein of coronaviruses is a structural protein existing in both monomeric and homo-pentameric form. It has been related to a multitude of roles including virus infection, replication, dissemination and immune response stimulation. In the present study, we employed an immunoinformatic approach to investigate the major immunogenic domains of the SARS-CoV-2 envelope protein and map them among the homologue proteins of coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Also, when not available, we predicted the envelope protein structural folding and mapped SARS-CoV-2 epitopes. Envelope sequences alignment provides evidence of high sequence homology for some of the investigated virus specimens; while the structural mapping of epitopes resulted in the interesting maintenance of the structural folding and epitope sequence localization also in the envelope proteins scoring a lower alignment score. In line with the One-Health approach, our evidences provide a molecular structural rationale for a potential role of taxonomically related coronaviruses in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies.


Subject(s)
Betacoronavirus/metabolism , Computational Biology/methods , Coronavirus Infections/immunology , Coronavirus Infections/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Viral Envelope Proteins/immunology , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Betacoronavirus/immunology , Epitope Mapping , Gene Expression Regulation, Viral , Humans , Models, Molecular , One Health , Pandemics , Phylogeny , Protein Conformation , Sequence Alignment , Sequence Analysis, Protein
5.
Microbes Infect ; 22(4-5): 188-194, 2020.
Article in English | MEDLINE | ID: covidwho-52542

ABSTRACT

Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide an in-silico survey of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, structural epitope mapping by homology modelling revealed a potential immunogenic value also for specific sequences scoring a lower identity with SARS-CoV-2 nucleocapsid proteins. These evidence provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies.


Subject(s)
Betacoronavirus/metabolism , Coronavirus/classification , Coronavirus/genetics , Epitopes , Nucleocapsid Proteins/metabolism , Amino Acid Sequence , Animals , Betacoronavirus/genetics , Computational Biology , Computer Simulation , Gene Expression Regulation, Viral/immunology , Humans , Models, Molecular , Nucleocapsid Proteins/genetics , Phylogeny , Protein Conformation , Protein Domains , Species Specificity
6.
Microbes Infect ; 22(4-5): 218-220, 2020.
Article in English | MEDLINE | ID: covidwho-11184

ABSTRACT

Outside the Hubei province, China, the mild form of infection and the progressive recover of the COVID-19 patients suggest the intervention of "unconventional" biological mechanisms worthy of attention. Based on the high-homology between the Spike protein epitopes of taxonomically-related coronaviruses, we hypothesized that past contact with infected dogs shield humans against the circulating SARS-CoV-2. Elseways, the recurrent virus exposure over a short time-lapse might result in the Antibody Dependent Enhancement, triggering the violent immune reaction responsible for the severe clinical outcomes observed in the Hubei province. Nevertheless, further experimental studies are desired for a confidential evaluation of the postulated hypotheses.


Subject(s)
Betacoronavirus/chemistry , Coronavirus Infections/immunology , Coronavirus Infections/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Amino Acid Sequence , Animals , Antibody-Dependent Enhancement , Antigens, Viral/chemistry , Antigens, Viral/immunology , Betacoronavirus/classification , Betacoronavirus/immunology , Betacoronavirus/physiology , Coronavirus Infections/veterinary , Dog Diseases/virology , Dogs , Epitopes/chemistry , Epitopes/immunology , Humans , Immunity , One Health , Pandemics , Sequence Alignment , Sequence Homology, Amino Acid , Viral Tropism
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