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Life
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Genetic and Antigenic Diversity of Pathogenic Viruses
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Genetic and Antigenic Diversity of Pathogenic Viruses

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 2438

Special Issue Editor

Prof. Dr. Yoshiyuki Suzuki

E-Mail Website
Guest Editor
Graduate School of Science, Nagoya City University, 1 Yamanohata, Mizuho-ku, Nagoya-shi, Aichi-ken 467-8501, Japan
Interests: medicine; evolution; prediction; vaccine; virus

Special Issue Information

Dear Colleague,

Pathogenic viruses represent a serious health hazard to humans worldwide by infecting and replicating within human cells and causing diseases. These viruses are characterized by an important genetic and, consequently, antigenic and pathogenic diversity. Understanding the role of genetic and antigenic diversity provides valuable information on controlling patterns of pathogen emergence, vaccination recommendations, and identification of likely infection sources.

The purpose of this Special Issue is to highlight the newest studies on genetic, antigenic, and biologic diversity among pathogenic viruses. We welcome submissions of original research papers and reviews from different disciplines, including microbiology, molecular biology, genetics, and medical sciences.

Prof. Dr. Yoshiyuki Suzuki
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • virus
  • genome
  • diversity
  • antigenicity
  • evolution
  • pathogenicity

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Published Papers (2 papers)

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11 pages, 3081 KiB  
Brief Report
In Silico Physicochemical Characterization of Fusion Proteins from Emerging Amazonian Arboviruses
by Crislaine S. Leal and Carlos Alberto M. Carvalho
Life 2023, 13(8), 1687; https://doi.org/10.3390/life13081687 - 4 Aug 2023
Cited by 1 | Viewed by 1035
Abstract
Mayaro (MAYV), Saint Louis encephalitis (SLEV), and Oropouche (OROV) viruses are neglected members of the three main families of arboviruses with medical relevance that circulate in the Amazon region as etiological agents of outbreaks of febrile illnesses in humans. As enveloped viruses, MAYV, [...] Read more.
Mayaro (MAYV), Saint Louis encephalitis (SLEV), and Oropouche (OROV) viruses are neglected members of the three main families of arboviruses with medical relevance that circulate in the Amazon region as etiological agents of outbreaks of febrile illnesses in humans. As enveloped viruses, MAYV, SLEV, and OROV largely depend on their class II fusion proteins (E1, E, and Gc, respectively) for entry into the host cell. Since many aspects of the structural biology of such proteins remain unclear, the present study aimed at physicochemically characterizing them by an in silico approach. The complete amino acid sequences of MAYV E1, SLEV E, and OROV Gc proteins derived by conceptual translation from annotated coding regions in the reference sequence genome of the respective viruses were obtained from the NCBI Protein database in the FASTA format and then submitted to the ClustalO, Protcalc, Pepstats, Predator, Proscan, PCprof, Phyre2, and 3Drefine web servers for the determination of sequence identities, the estimation of residual properties, the prediction of secondary structures, the identification of potential post-translational modifications, the recognition of antigenic propensities, and the modeling/refinement of three-dimensional structures. Sequence identities were 20.44%, 18.82%, and 13.70% between MAYV/SLEV, SLEV/OROV, and MAYV/OROV fusion proteins, respectively. As for the residual properties, MAYV E1 and SLEV E proteins showed a predominance of the non-polar profile (56% and 55% of the residues, respectively), whereas the OROV Gc protein showed a predominance of the polar profile (52% of the residues). Regarding predicted secondary structures, MAYV E1 and SLEV E proteins showed fewer alpha-helices (16.51% and 15.17%, respectively) than beta-sheets (21.79% and 25.15%, respectively), while the opposite was observed in the OROV Gc protein (20.39% alpha-helices and 12.14% beta-sheets). Regarding post-translational modifications, MAYV E1, SLEV E, and OROV Gc proteins showed greater relative potential for protein kinase C phosphorylation, N-myristoylation, and casein kinase II phosphorylation, respectively. Finally, antigenic propensities were higher in the N-terminus half than in the C-terminus half of these three proteins, whose three-dimensional structures revealed three distinctive domains. In conclusion, MAYV E1 and SLEV E proteins were found to share more physicochemical characteristics with each other than the OROV Gc protein, although they are all grouped under the same class of viral fusion proteins. Full article
(This article belongs to the Special Issue Genetic and Antigenic Diversity of Pathogenic Viruses)
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9 pages, 267 KiB  
Brief Report
Predicting Dominant Genotypes in Norovirus Seasons in Japan
by Yoshiyuki Suzuki
Life 2023, 13(8), 1634; https://doi.org/10.3390/life13081634 - 27 Jul 2023
Cited by 1 | Viewed by 1086
Abstract
Human noroviruses are an etiological agent of acute gastroenteritis. Since multiple genotypes co-circulate every season changing their proportions, it may be desirable to develop multivalent vaccines by formulating genotype composition of seed strains to match that of dominant strains. Here, performances of the [...] Read more.
Human noroviruses are an etiological agent of acute gastroenteritis. Since multiple genotypes co-circulate every season changing their proportions, it may be desirable to develop multivalent vaccines by formulating genotype composition of seed strains to match that of dominant strains. Here, performances of the models for predicting dominant genotypes, defined as the two most prevalent genotypes, were evaluated using observed genotype frequencies in Japan and genomic sequences for GI and GII strains. In the null model, genotype proportions in the target season were predicted to be the same as those in the immediately preceding season. In the fitness model, genotype proportions were predicted taking into account the acquisition of novel P-types through recombination and genotype-specific proliferation efficiency, as well as herd immunity to VP1 assuming the duration (d) of 0–10 years. The null model performed better in GII than in GI, apparently because dominant genotypes were more stable in the former than in the latter. Performance of the fitness model was similar to that of the null model irrespective of the assumed value of d. However, performance was improved when dominant genotypes were predicted as the union of those predicted with d = 0–10, suggesting that d may vary among individuals. Full article
(This article belongs to the Special Issue Genetic and Antigenic Diversity of Pathogenic Viruses)
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