Special Issue "Viral Genomics and Bioinformatics"

Guest Editor
Dr. Donald Seto
Bioinformatics and Computational Biology, 10900 University Blvd., MSN 5B3, Occoquan Bldg, Rm 325, George Mason University, Manassas, VA 20110, USA
Website: http://binf.gmu.edu/dseto/
E-Mail:
Interests: genomics and bioinformatics of adenovirus; molecular evolution; coinfections; emergent viral pathogens; comparative genomics; bioinformatic tools development; diagnostics and surveillance

Dear Colleagues,

The applications of ‘state-of-the-art’ genomics and bioinformatics to viruses are very important in many regards. Viruses are human pathogens and present a tremendous burden in morbidity and mortality. Modern genomics allowed a rapid identification of a coronavirus as the causal agent of the SARS outbreak. This is but one example of the benefits of the viral genomics revolution.

As model organisms, viruses have served to increase our understanding across many fields of the life sciences, including medicine, biochemistry, genetics, cell biology, molecular biology, applied biology, biotechnology, etc. They have proven useful demonstrations of novel technical and methodological applications. And their relatively small genomes contain fascinating and often paradigm changing biological information. Viral genomics and bioinformatics have grown with high throughput DNA sequencing technology, and these are being applied to larger, multiple and more complex genomes recently.

The first DNA genome to be sequenced, at 5,375 bases, was phi-X 174 by Sanger et al., performed in 1977 as a demonstration of the utility of DNA sequencing. At the other side of the spectrum was the genome determination of Mimivirus at 1.2 Mb by Raoult et al., in 2004. In between, novel pathogens such as the SARS coronavirus have been identified rapidly based in part by their genome sequence. The pathoepidemiology and natural history of viruses can be followed by genomics and bioinformatics – HIV is a prominent example. High-throughput genome sequencing allows massive numbers of viral genomes to be sequenced, and outbreaks to be followed in great detail. The same methodology and technology are being used to understand more completely the bacteriophages, as well as plant viruses.

As improved high throughput technology is available and more bioinformatic tools are developed, application of these methodologies to viruses will solve some of the outstanding biological questions of current times, and will allow new strategies to prevent outbreaks and to alleviate the burden of viral infections on global public health.

Dr. Donald Seto
Guest Editor

Related Journal

• Genes - an Open Access journal of genetics and genomics.

Submission

All manuscripts should be submitted to viruses@mdpi.org with a copy to the Guest Editor. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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.

• genomics
• bioinformatics
• high-throughput sequencing
• infectious disease monitoring
• pathogen evolution and natural history
• animal viruses
• plant viruses
• insect viruses
• bacteriophages

Type of Paper: Article
Title: The Evolution and Diversity of the Iridoviridae
Authors: Heather E. Eaton, Brooke Ring and Craig R. Brunetti
Affiliation: Trent University, Department of Biology, 1600 East Bank Dr., Peterborough, ON, K9J7B8, Canada; E-Mail: craigbrunetti@trentu.ca
Abstract: The Iridoviridae family are large viruses (~120-200 nm) that contain a linear double-stranded DNA genome. The genomic size of Iridoviridae family members range from 105,903 bases encoding 98 open reading frames (ORFs) for frog virus 3 to 212,482 bases encoding 468 ORFs for Chilo iridescent virus. The family Iridoviridae is currently subdivided into five genera: Chloriridovirus, Iridovirus, Lymphocystivirus, Megalocytivirus, and Ranavirus. Iridoviruses have been found to infect invertebrates and poikilothermic vertebrates, including amphibians, reptiles, and fish. With such a diverse array of hosts, there is a great diversity in gene content between different genera. To understand the origin of Iridoviruses, we explore the phylogenetic relationships between individual iridoviruses, define the core-set of genes shared by all members of the family, examine horizontal transfer of host genes, and explore the population genetics of the family.

Type of Paper: Review
Title: Genomics, genetic diversity and evolution of rotaviruses
Authors: Krisztián Bányai ¹, Jelle Matthijnssens ², Max Ciarlet ³, Vito Martella ⁴
Affiliations: ¹ Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary; E-Mail: bkrota@hotmail.com
² Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
³ Vaccine & Biologics Clinical Research, Merck Research Laboratories, North Wales, PA, USA
⁴ Department of Veterinary Public Health, University of Bari, Bari, Italy
Abstract: Rotaviruses are important enteric pathogens of mammals and birds. Currently 5 species (Rotavirus A to E) and 2 tentative species (Rotavirus F and G) are listed by the International Committee on Taxonomy of Viruses. The rotavirus genome consists of 11 segments of double-stranded RNA and measures ~17-19 kbp in length. At least 11 proteins are encoded by the genome with most of the encoded proteins being homologous among members of various species. The evolutionary strategy of rotaviruses is complex: accumulation of point mutations leads to genetic and often antigenic drift, reassortment of cognate genome segments may generate new combinations of the gene segments of parental strains, intragenic recombination may result in altered sizes of individual genome segments and, potentially, may increase the protein coding capacity, intergenic recombination may create mosaic proteins with altered function or antigenicity, while interspecies transmission may increase the rotavirus diversity in a heterologous host species by introducing new alleles of cognate genes. The continuously increasing number of rotavirus gene sequences available in DNA databases serves as the basis to better understand and quantitatively evaluate the importance of various strategies in rotavirus evolution. Advancements in rotavirus genomics and the recognized genetic diversity of these medically and economically important viruses are reviewed by the authors.