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Viruses
Special Issues
Virus Ecology and Evolution: Current Research and Future Directions 2.0
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Virus Ecology and Evolution: Current Research and Future Directions 2.0

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 6107

Special Issue Editors

Prof. Dr. John J. Dennehy

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Guest Editor
Department of Biology, Queens College of the City University of New York, New York, NY 10016, USA
Interests: virus ecology and evolution; single cell studies of gene expression; urban metagenomics
Special Issues, Collections and Topics in MDPI journals
Dr. Irene Hoxie

E-Mail
Guest Editor
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Interests: virus evolution; RNA; bioinformatics; viral coinfection/co-transmission

Special Issue Information

Dear colleagues,

The COVID-19 pandemic highlights the importance of understanding virus ecology and evolution in combatting virus emergence and spread. The ancestral, bat-infecting coronaviruses are not able to productively infect humans, but coronaviruses later designated as SARS-CoV-2 gained mutations, presumably through passage in an intermediate host, allowing human infection and transmission. Once SARS-CoV-2 emerged in humans, it spread globally in months. Since the initial emergence event, SARS-CoV-2 has evolved and diversified, giving rise to numerous competing variants. 

With the rise in urbanization and deforestation, opportunities exist for other emerging viruses to spread between populations or human, wild animal, and domestic animal hosts. Ever-changing epidemiological variables and rapid advances in vaccine and antiviral development make virus ecology and evolution research especially relevant to the current and inevitable future pandemics. 

These topics and others, including virus–host coevolution and zoonoses, immune evasion, virulence evolution, virus life history evolution, coinfection and genetic outcrossing, evolution of virus genome structure and origins of virus genes, population genetics and phylodynamics, virus quasispecies, virus adaptive landscape structure, virus robustness and evolvability, and virus experimental evolution, are the focus of this Special Issue. We encourage all types of manuscripts (e.g., reviews, research articles, and short communications) that further the discussion of virus ecology and evolution.  

Prof. Dr. John J. Dennehy
Dr. Irene Hoxie
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. 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 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

  • 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 (2 papers)

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Research

11 pages, 3742 KiB  
Article
An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology
by Colin Young, Sarah Meng and Niema Moshiri
Viruses 2022, 14(4), 774; https://0-doi-org.brum.beds.ac.uk/10.3390/v14040774 - 08 Apr 2022
Cited by 2 | Viewed by 2408
Abstract
The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data. Like all estimation techniques, they are error prone, yet [...] Read more.
The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data. Like all estimation techniques, they are error prone, yet the impacts of such imperfections on downstream epidemiological inferences are poorly understood. To address this, we executed multiple commonly used viral phylogenetic analysis workflows on simulated viral sequence data, modeling Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV), and Ebolavirus, and we computed multiple methods of accuracy, motivated by transmission-clustering techniques. For multiple sequence alignment, MAFFT consistently outperformed MUSCLE and Clustal Omega, in both accuracy and runtime. For phylogenetic inference, FastTree 2, IQ-TREE, RAxML-NG, and PhyML had similar topological accuracies, but branch lengths and pairwise distances were consistently most accurate in phylogenies inferred by RAxML-NG. However, FastTree 2 was the fastest, by orders of magnitude, and when the other tools were used to optimize branch lengths along a fixed FastTree 2 topology, the resulting phylogenies had accuracies that were indistinguishable from their original counterparts, but with a fraction of the runtime. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions 2.0)
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19 pages, 3909 KiB  
Article
Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species
by Han Du, Lijuan Zhang, Xinqiang Zhang, Fengze Yun, Yuhao Chang, Awaguli Tuersun, Kamila Aisaiti and Zhenghai Ma
Viruses 2022, 14(2), 356; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020356 - 09 Feb 2022
Cited by 6 | Viewed by 2665
Abstract
Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used [...] Read more.
Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42–82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general. Full article
(This article belongs to the Special Issue Virus Ecology and Evolution: Current Research and Future Directions 2.0)
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