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Ancient Viruses and Their Impact on Host Species - Emerging...
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Ancient Viruses and Their Impact on Host Species - Emerging Themes in Paleovirology

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (15 November 2021) | Viewed by 3575

Special Issue Editors

Dr. Daniel Elleder

E-Mail Website
Guest Editor
Institute of Molecular Genetics, The Czech Academy of Sciences, Prague, Czech Republic
Interests: retroviruses; genomics; innate immunity
Dr. Robert J. Gifford

E-Mail Website
Guest Editor
Centre for Virus Research, MRC-University of Glasgow (UK), Glasgow, UK
Interests: ecology and evolution of viruses; viral genomics; paleovirology; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Interactions with viruses have been instrumental in shaping the evolution of species. The sequences of ancient viruses, or at least sequence fragments, have sometimes been fortuitously preserved in host genomes as a result of integration into the host germline. These endogenous viral elements (EVEs) provide a rare source of insight into the biology of extinct viruses (‘paleoviruses’) and allow for the calibration of the evolutionary timeline of virus–host interaction. Furthermore, intriguing roles in host biology have been reported for some EVEs, including the regulation of host gene expression, placental development, and antiviral immunity.

This Special Issue is designed to provide an overview of the emerging themes and currently unanswered questions in paleovirology. We encourage the submission of studies from all areas of paleovirology, and are particularly in interested in the following:

  • Primary research and review articles that examine the putative functional roles of EVEs. 
  • New perspectives on ancient virus diversity and the evolutionary relationships between ancient and modern groups.
  • Experimental studies reporting interesting yet unexplained paleovirus-related phenomena.
Dr. Daniel Elleder
Dr. Robert J. Gifford
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. Genes 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

  • paleovirology
  • endogenous viral element
  • endogenous retrovirus
  • horizontal transfer
  • host–virus interactions
  • cross-species transmission
  • virus diversity
  • virus metagenomics
  • virus taxonomy
  • viral restriction factor

Published Papers (1 paper)

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Research

19 pages, 1309 KiB  
Article
Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes
by Antoinette C. van der Kuyl
Genes 2022, 13(1), 119; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010119 - 10 Jan 2022
Cited by 2 | Viewed by 1861
Abstract
Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high-quality primate genomes warrants a study of the characteristics, evolution, and distribution of SERV proviruses. (2) Methods: Cercopithecinae OWM genomes from [...] Read more.
Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high-quality primate genomes warrants a study of the characteristics, evolution, and distribution of SERV proviruses. (2) Methods: Cercopithecinae OWM genomes from public databases were queried for the presence of full-length SERV proviruses. A dataset of 81 Cer-SERV genomes was generated and analyzed. (3) Results: Full-length Cer-SERV proviruses were mainly found in terrestrial OWM, and less so in arboreal, forest- dwelling monkeys. Phylogenetic analysis confirmed the existence of two genotypes, Cer-SERV-1 and Cer-SERV-2, with Cer-SERV-1 showing evidence of recent germ-line expansions. Long Terminal Repeat (LTR) variation indicated that most proviruses were of a similar age and were estimated to be between <0.3 and 10 million years old. Integrations shared between species were relatively rare. Sequence analysis further showed extensive CpG methylation-associated mutations, variable Primer Binding Site (PBS) use with Cer-SERV-1 using PBSlys3 and Cer-SERV-2 using PBSlys1,2, and the recent gain of LTR motifs for transcription factors active during embryogenesis in Cer-SERV-1. (4) Conclusions: sequence analysis of 81 SERV proviruses from Cercopithecinae OWM genomes provides evidence for the adaptation of this retrovirus to germ line reproduction. Full article
(This article belongs to the Special Issue Ancient Viruses and Their Impact on Host Species - Emerging Themes in Paleovirology)
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