Special Issue "Paleovirology"

Guest Editor
Dr. Anna Marie Skalka
Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
Website: http://www.fccc.edu/
E-Mail: am_skalka@fccc.edu
Phone: +1 215 728 2490
Fax: +1 215 728 2778
Interests: retroviral DNA integration and gene expression; impact on host cell biology

Dear Colleagues,

With the exception of retroviruses, until very recently it was not possible to trace the evolution of currently circulating viruses further back than a few thousand years. All of this changed in the past decade with increasing availability of the genomic sequences of a variety of organisms, and new computational methods for their annotation and investigation. In the last two years, application of these methods anaalyses have uncovered genomic fossils from ancient relatives of a number of virus families with both DNA and RNA genomes, revealing some to have existed for longer than ~90 million years, the current theoretical limit of such calculations. Such revelations have raised important and fascinating new topics for inquiry: By what mechanism(s) were these viral sequences integrated into their host species genomes? What selective pressures, if any, have led to their maintenance in the host populations? What new information may be gained concerning the organization and evolution of our own genomes and those of other species in our environment?

This special issue of viruses focuses on the emerging field of Paleovirology, and will include articles that summarize the new findings and methods cited above, and well as issues related to some fundamental questions now open for consideration. The search for answers and new knowledge obtained is sure to increase our understanding of both virus and host biology and evolution in the future.

Prof. Dr. Anna Marie Skalka
Guest Editor

• virus fossils
• LINE-facilitated integration
• intrinsic resistance
• virus reservoir species
• selective pressures
• genomic analyses

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	p. 1933-1958 Open Access Review Review: Viral Ancestors of Antiviral Systems by Luis P. Villarreal Viruses 2011, 3(10), 1933-1958; doi:10.3390/v3101933 Received: 7 September 2011 / Revised: 1 October 2011 / Accepted: 10 October 2011 / Published: 20 October 2011 Show/Hide Abstract | Cited by 4 | PDF Full-text (231 KB) Abstract: All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features. (This article belongs to the Special Issue Paleovirology)
	p. 1836-1848 Open Access Review Review: Non-Retroviral Fossils in Vertebrate Genomes by Masayuki Horie and Keizo Tomonaga Viruses 2011, 3(10), 1836-1848; doi:10.3390/v3101836 Received: 3 August 2011 / Revised: 22 September 2011 / Accepted: 27 September 2011 / Published: 10 October 2011 Show/Hide Abstract | Cited by 7 | PDF Full-text (317 KB) Abstract: Although no physical fossils of viruses have been found, retroviruses are known to leave their molecular fossils in the genomes of their hosts, the so-called endogenous retroviral elements. These have provided us with important information about retroviruses in the past and their co-evolution with their hosts. On the other hand, because non‑retroviral viruses were considered not to leave such fossils, even the existence of prehistoric non-retroviral viruses has been enigmatic. Recently, we discovered that elements derived from ancient bornaviruses, non-segmented, negative strand RNA viruses, are found in the genomes of several mammalian species, including humans. In addition, at approximately the same time, several endogenous elements of RNA viruses, DNA viruses and reverse-transcribing DNA viruses have been independently reported, which revealed that non-retroviral viruses have played significant roles in the evolution of their hosts and provided novel insights into virology and cell biology. Here we review non-retroviral virus-like elements in vertebrate genomes, non-retroviral integration and the knowledge obtained from these endogenous non-retroviral virus-like elements. (This article belongs to the Special Issue Paleovirology)
	p. 620-628 Open Access Article: Characterization of a Full-Length Endogenous Beta-Retrovirus, EqERV-Beta1, in the Genome of the Horse (Equus caballus) by Antoinette C. Van der Kuyl Viruses 2011, 3(6), 620-628; doi:10.3390/v3060620 Received: 18 April 2011 / Revised: 9 May 2011 / Accepted: 11 May 2011 / Published: 1 June 2011 Show/Hide Abstract | Cited by 5 | PDF Full-text (200 KB) Abstract: Information on endogenous retroviruses fixed in the horse (Equus caballus) genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus), was 10434 nucleotide (nt) in length with the usual retroviral genome structure of 5’LTR-gag-pro-pol-env-3’LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV). A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus), and the murine beta-retrovirus MMTV. (This article belongs to the Special Issue Paleovirology)
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Last update: 5 March 2014