Viral Genes and the Host: Evolution in Action

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

Deadline for manuscript submissions: closed (31 May 2019) | Viewed by 17211

Special Issue Editors

Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
Interests: virus evolution; HIV-1; hepatitis B virus; endogenous viral elements; patient-related virology
Special Issues, Collections and Topics in MDPI journals
Laboratory of Experimental Virology, Department of Medical Microbiology, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
Interests: HIV-1 gene expression and latency; viral RNA structure and function; virus evolution; antiviral therapy; patient-related virus studies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We would like to invite you to contribute a research paper or review article to a Special Issue of Genes entitled “Viral Genes and the Host: Evolution in Action”.

Viruses are essentially tightly-packaged transmissible RNA or DNA molecules acting as free-roaming genes that amplify in an organism before spreading to other individuals. Viruses rely heavily on host cells for their proliferation and, in the process, frequently derail cellular pathways to optimize virus production. Despite this intense virus–host interaction, the structure of viral genes sets them apart from cellular genes. For instance, most viral genomes have a very different nucleotide composition and codon usage compared to the eukaryotic host genome. Viruses can produce unique mRNA species, e.g. with an internal ribosome entry (IRES) or with the m7G cap at the 5’ end replaced by an RNA-binding viral protein. Moreover, viruses have adopted specialized gene expression strategies to allow the expression of multiple proteins from one or a limited number of mRNA species. Unlike the intron-rich megabase-spanning genes of the host, viruses have condensed their genetic information and frequently use overlapping and antisense reading frames and alternative splicing. Viruses also differ from the host in terms of genome evolution as they copy their genome using error-prone polymerases, which quickly generate a swarm of mutant genomes or quasispecies as the raw material for the subsequent selection process. Evolutionary pressure comes from the host immune system on a daily basis, but may also play a key role during zoonotic transmission events (host switching) and during antiviral therapy in patients. 

Viruses are extremely divergent and employ different replication strategies, ranging from the transient infection of only a small subset of a susceptible host population to persistent infection with a close to 100% prevalence. Members of virus families, such as the Anelloviridae and the herpesviruses, will stay life-long with their hosts, either with or without occasional disease manifestations. Some viruses go even further in their interplay with the host. Retroviruses can integrate their genome in that of the host and if this happens in the germ line, these viral sequences will be passed on as Mendelian genes to the offspring. In fact, our chromosomes are riddled with the remains of retroviral infections of the past. But such endogenized viral elements can occasionally spur host evolution, e.g., by repurposing the viral sequences for a new cellular function, either by encoding a new protein function or as driver of the expression of a host gene. And if one has a closer look in cancer cells, one can often find other viral elements, e.g., papilloma-, polyoma- or hepadna- virus genes - that play a direct or indirect role in the oncogenic process. Adeno-, parvo-, and herpesviruses may have their genes inserted into host chromosomes as well.

This Special Issue aims to provide a wide range of examples on various aspects of viral genes, their expression strategy, but also their evolution and interactions with the host organism. We invite submissions for reviews, research articles, or short-communications reporting evolutionary aspects, molecular genetics and genomics studies of viruses and their hosts.

Dr. Antoinette van der Kuyl
Prof. Ben Berkhout
Guest Editors

Manuscript Submission Information

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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.

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Keywords

  • Viral RNA and DNA genomes
  • Genome organization
  • Viral gene expression
  • Replication strategies
  • Nucleotide composition
  • Virus and host evolution

Published Papers (3 papers)

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Research

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16 pages, 2406 KiB  
Article
Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression
by Tsung-Lin Tsai, Chen-Chang Su, Ching-Chi Hsieh, Chao-Nan Lin, Hui-Wen Chang, Chen-Yu Lo, Ching-Houng Lin and Hung-Yi Wu
Genes 2018, 9(12), 591; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9120591 - 29 Nov 2018
Cited by 2 | Viewed by 2923
Abstract
In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 [...] Read more.
In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis-acting elements in the 5′ and 3′ untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS. Functional analyses using coronavirus defective interfering (DI) RNA revealed that such variations in cis-acting elements for the TW strain compared with the CV777 strain have an influence on the efficiency of gene expression. The current data show for the first time the evolution of PEDV in terms of cis-acting elements and their effects on gene expression, and thus may contribute to our understanding of recent PED outbreaks worldwide. Full article
(This article belongs to the Special Issue Viral Genes and the Host: Evolution in Action)
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15 pages, 3465 KiB  
Article
Functional Evolution of Avian RIG-I-Like Receptors
by Wanjing Zheng and Yoko Satta
Genes 2018, 9(9), 456; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9090456 - 12 Sep 2018
Cited by 13 | Viewed by 4572
Abstract
RIG-I-like receptors (retinoic acid-inducible gene-I-like receptors, or RLRs) are family of pattern-recognition receptors for RNA viruses, consisting of three members: retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2 [...] Read more.
RIG-I-like receptors (retinoic acid-inducible gene-I-like receptors, or RLRs) are family of pattern-recognition receptors for RNA viruses, consisting of three members: retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). To understand the role of RLRs in bird evolution, we performed molecular evolutionary analyses on the coding genes of avian RLRs using filtered predicted coding sequences from 62 bird species. Among the three RLRs, conservation score and dN/dS (ratio of nonsynonymous substitution rate over synonymous substitution rate) analyses indicate that avian MDA5 has the highest conservation level in the helicase domain but a lower level in the caspase recruitment domains (CARDs) region, which differs from mammals; LGP2, as a whole gene, has a lower conservation level than RIG-I or MDA5. We found evidence of positive selection across all bird lineages in RIG-I and MDA5 but only on the stem lineage of Galliformes in LGP2, which could be related to the loss of RIG-I in Galliformes. Analyses also suggest that selection relaxation may have occurred in LGP2 during the middle of bird evolution and the CARDs region of MDA5 contains many positively selected sites, which might explain its conservation level. Spearman’s correlation test indicates that species-to-ancestor dN/dS of RIG-I shows a negative correlation with endogenous retroviral abundance in bird genomes, suggesting the possibility of interaction between immunity and endogenous retroviruses during bird evolution. Full article
(This article belongs to the Special Issue Viral Genes and the Host: Evolution in Action)
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Review

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24 pages, 404 KiB  
Review
RNA Viruses as Tools in Gene Therapy and Vaccine Development
by Kenneth Lundstrom
Genes 2019, 10(3), 189; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10030189 - 01 Mar 2019
Cited by 46 | Viewed by 9051
Abstract
RNA viruses have been subjected to substantial engineering efforts to support gene therapy applications and vaccine development. Typically, retroviruses, lentiviruses, alphaviruses, flaviviruses rhabdoviruses, measles viruses, Newcastle disease viruses, and picornaviruses have been employed as expression vectors for treatment of various diseases including different [...] Read more.
RNA viruses have been subjected to substantial engineering efforts to support gene therapy applications and vaccine development. Typically, retroviruses, lentiviruses, alphaviruses, flaviviruses rhabdoviruses, measles viruses, Newcastle disease viruses, and picornaviruses have been employed as expression vectors for treatment of various diseases including different types of cancers, hemophilia, and infectious diseases. Moreover, vaccination with viral vectors has evaluated immunogenicity against infectious agents and protection against challenges with pathogenic organisms. Several preclinical studies in animal models have confirmed both immune responses and protection against lethal challenges. Similarly, administration of RNA viral vectors in animals implanted with tumor xenografts resulted in tumor regression and prolonged survival, and in some cases complete tumor clearance. Based on preclinical results, clinical trials have been conducted to establish the safety of RNA virus delivery. Moreover, stem cell-based lentiviral therapy provided life-long production of factor VIII potentially generating a cure for hemophilia A. Several clinical trials on cancer patients have generated anti-tumor activity, prolonged survival, and even progression-free survival. Full article
(This article belongs to the Special Issue Viral Genes and the Host: Evolution in Action)
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