Special Issue "Virus Ecology and Evolution: Current Research and Future Directions"

A special issue of Viruses (ISSN 1999-4915).

Deadline for manuscript submissions: closed (30 April 2020).

Special Issue Editor

Prof. Dr. John J. Dennehy
E-Mail Website
Guest Editor
Department of Biology, Queens College of the City University of New York, NY 10016, USA
Interests: virus ecology and evolution; single cell studies of gene expression; urban metagenomics

Special Issue Information

Dear colleagues,

Understanding virus ecology and evolution is essential to vaccine and antiviral drug development, virus epidemiological surveillance and emergence prediction, virulence progression, and other phenomena relevant to public health, conservation, and agriculture. Topics in virus ecology and evolution may include virus–host coevolution, immune and vaccine evasion, virulence evolution, virus host-range evolution and emergence, virus life history evolution, coinfection and viral ‘sex’, evolution of virus genome structure and origins of virus genes, virus population genetics and phylodynamics, virus quasispecies, virus adaptive landscape structure, virus robustness and evolvability, and virus experimental evolution. The aim of this Special Issue is to communicate the latest research results and reviews on these topics and others relating to virus ecology and evolution.

Prof. Dr. John J. Dennehy
Guest Editor

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 papers will be 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. Viruses 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 2200 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

  • adaptive landscape 
  • coevolution 
  • coinfection 
  • collective infection 
  • emergence
  • epistasis 
  • evolvability
  • host-range
  • lethal mutagenesis
  • life history evolution 
  • metapopulation 
  • phylodynamics 
  • recombination and reassortment 
  • robustness 
  • tradeoffs 
  • virulence

Published Papers (5 papers)

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Research

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Open AccessArticle
The Epidemiological Signature of Pathogen Populations That Vary in the Relationship between Free-Living Parasite Survival and Virulence
Viruses 2020, 12(9), 1055; https://doi.org/10.3390/v12091055 - 22 Sep 2020
Cited by 2 | Viewed by 890
Abstract
The relationship between parasite virulence and transmission is a pillar of evolutionary theory that has implications for public health. Part of this canon involves the idea that virulence and free-living survival (a key component of transmission) may have different relationships in different host–parasite [...] Read more.
The relationship between parasite virulence and transmission is a pillar of evolutionary theory that has implications for public health. Part of this canon involves the idea that virulence and free-living survival (a key component of transmission) may have different relationships in different host–parasite systems. Most examinations of the evolution of virulence-transmission relationships—Theoretical or empirical in nature—Tend to focus on the evolution of virulence, with transmission being a secondary consideration. Even within transmission studies, the focus on free-living survival is a smaller subset, though recent studies have examined its importance in the ecology of infectious diseases. Few studies have examined the epidemic-scale consequences of variation in survival across different virulence–survival relationships. In this study, we utilize a mathematical model motivated by aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) natural history to investigate how evolutionary changes in survival may influence several aspects of disease dynamics at the epidemiological scale. Across virulence–survival relationships (where these traits are either positively or negatively correlated), we found that small changes (5% above and below the nominal value) in survival can have a meaningful effect on certain outbreak features, including R0, and on the size of the infectious peak in the population. These results highlight the importance of properly understanding the mechanistic relationship between virulence and parasite survival, as the evolution of increased survival across different relationships with virulence may have considerably different epidemiological signatures. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions)
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Open AccessArticle
Orthohantavirus Isolated in Reservoir Host Cells Displays Minimal Genetic Changes and Retains Wild-Type Infection Properties
Viruses 2020, 12(4), 457; https://doi.org/10.3390/v12040457 - 17 Apr 2020
Cited by 1 | Viewed by 987
Abstract
Orthohantaviruses are globally emerging zoonotic pathogens. While the reservoir host role of several rodent species is well-established, detailed research on the mechanisms of host-othohantavirus interactions has been constrained by the lack of an experimental system that is able to effectively replicate natural infections [...] Read more.
Orthohantaviruses are globally emerging zoonotic pathogens. While the reservoir host role of several rodent species is well-established, detailed research on the mechanisms of host-othohantavirus interactions has been constrained by the lack of an experimental system that is able to effectively replicate natural infections in controlled settings. Here we report the isolation, and genetic and phenotypic characterization of a novel Puumala orthohantavirus (PUUV) in cells derived from its reservoir host, the bank vole. The isolation process resulted in cell culture infection that evaded antiviral responses, persisted cell passaging, and had minor viral genome alterations. Critically, experimental infections of bank voles with the new isolate resembled natural infections in terms of viral load and host cell distribution. When compared to an attenuated Vero E6 cell-adapted PUUV Kazan strain, the novel isolate demonstrated delayed virus-specific humoral responses. A lack of virus-specific antibodies was also observed during experimental infections with wild-type PUUV, suggesting that delayed seroconversion could be a general phenomenon during orthohantavirus infection in reservoir hosts. Our results demonstrate that orthohantavirus isolation on cells derived from a vole reservoir host retains wild-type infection properties and should be considered the method of choice for experimental infection models to replicate natural processes. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions)
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Open AccessArticle
Infection Load and Prevalence of Novel Viruses Identified from the Bank Vole Do Not Associate with Exposure to Environmental Radioactivity
Viruses 2020, 12(1), 44; https://doi.org/10.3390/v12010044 - 30 Dec 2019
Cited by 1 | Viewed by 1119
Abstract
Bank voles (Myodes glareolus) are host to many zoonotic viruses. As bank voles inhabiting areas contaminated by radionuclides show signs of immunosuppression, resistance to apoptosis, and elevated DNA repair activity, we predicted an association between virome composition and exposure to radionuclides. [...] Read more.
Bank voles (Myodes glareolus) are host to many zoonotic viruses. As bank voles inhabiting areas contaminated by radionuclides show signs of immunosuppression, resistance to apoptosis, and elevated DNA repair activity, we predicted an association between virome composition and exposure to radionuclides. To test this hypothesis, we studied the bank vole virome in samples of plasma derived from animals inhabiting areas of Ukraine (contaminated areas surrounding the former nuclear power plant at Chernobyl, and uncontaminated areas close to Kyiv) that differed in level of environmental radiation contamination. We discovered four strains of hepacivirus and four new virus sequences: two adeno-associated viruses, an arterivirus, and a mosavirus. However, viral prevalence and viral load, and the ability to cause a systemic infection, was not dependent on the level of environmental radiation. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions)
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Review

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Open AccessReview
Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer
Viruses 2020, 12(6), 612; https://doi.org/10.3390/v12060612 - 04 Jun 2020
Cited by 3 | Viewed by 1138
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5′-untranslated region (5′UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5′-end-independent initiation of [...] Read more.
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5′-untranslated region (5′UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5′-end-independent initiation of translation by a different mechanism. Picornavirus 5′UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions)
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Open AccessReview
Systematics, Ecology, and Host Switching: Attributes Affecting Emergence of the Lassa Virus in Rodents across Western Africa
Viruses 2020, 12(3), 312; https://doi.org/10.3390/v12030312 - 14 Mar 2020
Cited by 5 | Viewed by 969
Abstract
Ever since it was established that rodents serve as reservoirs of the zoonotic Lassa virus (LASV), scientists have sought to answer the questions: which populations of rodents carry the virus? How do fluctuations in LASV prevalence and rodent abundance influence Lassa fever outbreaks [...] Read more.
Ever since it was established that rodents serve as reservoirs of the zoonotic Lassa virus (LASV), scientists have sought to answer the questions: which populations of rodents carry the virus? How do fluctuations in LASV prevalence and rodent abundance influence Lassa fever outbreaks in humans? What does it take for the virus to adopt additional rodent hosts, proliferating what already are devastating cycles of rodent-to-human transmission? In this review, we examine key aspects of research involving the biology of rodents that affect their role as LASV reservoirs, including phylogeography, demography, virus evolution, and host switching. We discuss how this knowledge can help control Lassa fever and suggest further areas for investigation. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions)
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