http://www.mdpi.com/journal/viruses/special_issues/vi-genom-bioinf/ 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.com 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. Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues, to be published in 2009 and 2010, the Article Processing Charges (APC) in this Open Access journal will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections. http://www.mdpi.com/1999-4915/2/12/2587/ From the recognition by Ivanovski in 1892 that tobacco mosaic disease is caused and transmitted by fine pore filtrates [1], viruses have been isolated, characterized, identified and studied from animals, plants, protists, bacteria and even other viruses [2,3]. As human and global public health pathogens that can be highly contagious and have devastating morbidity and mortality consequences, viruses are the focus of much research. The difficult challenge has been to define and study a miniscule “being” with the appropriate tools. In the past, these tools often provided only low-resolution views. A first approach to studying an unknown virus is to know exactly its identity, and to place it into context of other related and non-related viruses. For human and public health, this is important as the identity may provide a course of action to limit the effects of the pathogen. [...] http://www.mdpi.com/1999-4915/2/12/2587/ Tue, 30 Nov 2010 00:00:00 CET Viruses 2010-11-30 2 12 Editorial 2587 2593 1999-4915 Viral Genomics and Bioinformatics 2010-11-30 doi: 10.3390/v2122587 Donald Seto http://www.mdpi.com/1999-4915/2/10/2258/ Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop. http://www.mdpi.com/1999-4915/2/10/2258/ Wed, 13 Oct 2010 00:00:00 CEST Viruses 2010-10-13 2 10 Editorial 2258 2268 1999-4915 Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop 2010-10-13 doi: 10.3390/v2102258 James Rodney Brister Yiming Bao Carla Kuiken Elliot J. Lefkowitz Philippe Le Mercier Raphael Leplae Ramana Madupu Richard H. Scheuermann Seth Schobel Donald Seto Susmita Shrivastava Peter Sterk Qiandong Zeng William Klimke Tatiana Tatusova http://www.mdpi.com/1999-4915/2/9/1933/ Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses. Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family. It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats. Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus. Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets. These techniques allowed us to unambiguously identify the gene loss/gain events that have occurred over the course of orthopoxvirus evolution. It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species. All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain. These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche. http://www.mdpi.com/1999-4915/2/9/1933/ Wed, 15 Sep 2010 00:00:00 CEST Viruses 2010-09-15 2 9 Article 1933 1967 1999-4915 Orthopoxvirus Genome Evolution: The Role of Gene Loss 2010-09-15 doi: 10.3390/v2091933 Robert Curtis Hendrickson Chunlin Wang Eneida L. Hatcher Elliot J. Lefkowitz http://www.mdpi.com/1999-4915/2/9/1867/ We describe the use of Java Pattern Finder (JaPaFi) to identify short ( http://www.mdpi.com/1999-4915/2/9/1867/ Tue, 31 Aug 2010 00:00:00 CEST Viruses 2010-08-31 2 9 Article 1867 1885 1999-4915 JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences 2010-08-31 doi: 10.3390/v2091867 Aliya Sadeque Marina Barsky Francesco Marass Peter Kruczkiewicz Chris Upton http://www.mdpi.com/1999-4915/2/8/1804/ The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses. http://www.mdpi.com/1999-4915/2/8/1804/ Tue, 24 Aug 2010 00:00:00 CEST Viruses 2010-08-24 2 8 Review 1804 1820 1999-4915 Coronavirus Genomics and Bioinformatics Analysis 2010-08-24 doi: 10.3390/v2081803 Patrick C. Y. Woo Yi Huang Susanna K. P. Lau Kwok-Yung Yuen http://www.mdpi.com/1999-4915/2/7/1458/ 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 97 open reading frames (ORFs) for frog virus 3 to 212,482 bases encoding 211 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 great diversity in gene content between different genera. To understand the origin of iridoviruses, we explored the phylogenetic relationship between individual iridoviruses and defined the core-set of genes shared by all members of the family. In order to further explore the evolutionary relationship between the Iridoviridae family repetitive sequences were identified and compared. Each genome was found to contain a set of unique repetitive sequences that could be used in future virus identification. Repeats common to more than one virus were also identified and changes in copy number between these repeats may provide a simple method to differentiate between very closely related virus strains. The results of this paper will be useful in identifying new iridoviruses and determining their relationship to other members of the family. http://www.mdpi.com/1999-4915/2/7/1458/ Thu, 15 Jul 2010 00:00:00 CEST Viruses 2010-07-15 2 7 Article 1458 1475 1999-4915 The Genomic Diversity and Phylogenetic Relationship in the Family Iridoviridae 2010-07-15 doi: 10.3390/v2071458 Eaton Ring Brunetti http://www.mdpi.com/1999-4915/2/7/1367/ Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV), HAdV–C2 and HAdV–C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910) within the hexon gene, of which HAdV–C2 and HAdV–C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics. http://www.mdpi.com/1999-4915/2/7/1367/ Mon, 28 Jun 2010 00:00:00 CEST Viruses 2010-06-28 2 7 Review 1367 1381 1999-4915 The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses 2010-06-28 doi: 10.3390/v2071367 Torres Chodosh Seto Jones