Bioinformatics-Driven Analysis of Mechanisms Underlying the Function and Evolution of Pandemic Viruses

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 14795

Special Issue Editors


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Guest Editor
Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, 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, Padova, 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,

In recent decades, progress in molecular sciences and bioinformatics has strongly enhanced discoveries in every field of life sciences, including virology. At the same time, the power of computational biology has improved the rational design of antivirals through high-confidence simulations.

This Special Issue aims to report bioinformatics-driven analyses of pandemic viruses, such as influenza A virus and coronaviruses, that are able to:

  • Shed light on trends in virus clade/subclade/variant evolution;
  • Identify or suggest sequence/structural fingerprints in virus–host interactions, and eventually identify 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 the binding affinity to functional receptors of the host, thus predicting tissue-specific spreading and pathogenicity;
  • Guide and/or improve the design of antiviral molecules and vaccines.

Dr. Francesco Filippini
Dr. Irene Righetto
Guest Editors

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Keywords

  • pandemic virus
  • avian influenza
  • coronavirus
  • SARS-CoV-2
  • immune escape
  • structural bioinformatics
  • variant
  • mutation
  • antiviral design
  • host jump
  • pathogenicity shift
  • antiviral 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 14274
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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