Molecular and Computational Studies in Epidemiology and Evolution of Pandemic Virus

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: 25 April 2025 | Viewed by 15011

Special Issue Editors


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Guest Editor
Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
Interests: pandemic viruses, vaccines, synthetic biology and biotechnology, motif identification; protein engineering; biocatalysis; bioremediation; neurodevelopment and neurological disorders; biomimetics and regenerative medicine; subcellular trafficking
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
Interests: pandemic viruses; vaccines; structural predictions and simulations; enzyme evolution and engineering; biocatalysis; design of biomimetic molecules
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The continuous emergence of pandemic viruses such as influenza A, coronaviruses, and, more recently, arboviruses poses significant challenges to global public health. Advances in molecular biology and computational methods have restructured our comprehension of viral evolution, epidemiology, and pathogen–host interactions.

This Special Issue is aimed at reporting molecular and computational studies that provide crucial insights into the mechanisms underlying the epidemiology and evolution of pandemic viruses. 

Original research articles, reviews, and method papers are welcomed, addressing topics including, but not limited to, the following:

- Molecular analyses and computational modeling of virus evolution, including clade/subclade dynamics and variant emergence.

- Identifing or suggesting sequence/structural fingerprints in virus–host interactions, underlying host specificity and host jump (zoonosis) phenomena.

- Identify or suggest crucial mutations resulting in epitope variation and hence “immune escape”.

- Identify sequence/structural motifs (and their variation) modulating binding affinity to functional receptors of the host, thus predicting tissue-specific spreading and pathogenicity.

- Guide and/or improve design of antiviral molecules and vaccines.

Dr. Francesco Filippini
Dr. Irene Righetto
Guest Editors

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. Viruses 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

  • pandemic virus
  • avian influenza
  • coronavirus
  • SARS-CoV-2
  • immune escape
  • structural bioinformatics
  • variant
  • mutation
  • antiviral design
  • host jump
  • pathogenicity shift
  • antivirals design
  • epitope identification

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Published Papers (1 paper)

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Research

22 pages, 3968 KiB  
Article
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows
by Ryan Connor, Migun Shakya, David A. Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J. Rodney Brister, Patrick S. G. Chain, Courtney A. Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S. Katz, Andrey Kochergin, Tré LaRosa, Jiani Li, Po-E Li, Chien-Chi Lo, Sujatha Rashid, Evguenia S. Maiorova, Chunlin Xiao, Vadim Zalunin, Lisa Purcell and Kim D. Pruittadd Show full author list remove Hide full author list
Viruses 2024, 16(3), 430; https://doi.org/10.3390/v16030430 - 11 Mar 2024
Viewed by 14451
Abstract
Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for [...] Read more.
Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response. Full article
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