RNA Virus Genomes

Abstract

RNA (ribonucleic acid) viruses are the most abundant group of molecular parasites that infect humans, animals and plants. They are associated with important diseases such as human influenza, newly emerging haemorrhagic fevers or several forms of hepatitis. Virus particles are disparate in size, shape and composition, and enclose an RNA genome that can be either single stranded, double stranded, nonsegmented or segmented. Application of deep sequencing methodologies has unveiled their great abundance and ubiquity. The structural diversity of viral RNA is reflected in differences in their replication cycles that are completed through complex interactions between viral and host proteins. RNA viruses share errorā€prone replication that confers on them the capacity to adapt to a wide range of environments. Despite considerable progress in the understanding of virus structure and expression of their genetic programmes, the success of preventive and control strategies has been limited. Application of Darwinian principles to RNA viruses might result in new approaches for viral disease control.

Key Concepts

  • RNA viruses are the most abundant group of cellular parasites.
  • RNA viruses are associated with many established, emerging and reemerging infections.
  • RNA viral genomes are diverse in structure and nucleotide sequences.
  • Application of deep sequencing has confirmed an extreme diversity of individual viral populations.
  • RNA viruses evolve following Darwinian principles.
  • RNA virus adaptability demands new approaches for the control of viral disease.
  • Lethal mutagenesis is a new antiviral strategy based on extinguishing a virus by excess mutations.

Keywords: RNA replication; virus life cycle; host function; viral protein synthesis; antiviral strategy; control of viral disease

Figure 1. Some positive‐strand RNA viral genomes and their replication and expression strategies. A number of families of mammalian RNA viruses are included; additional features are given in Table. Continuous lines represent genomes of positive polarity and mRNAs. Discontinuous lines represent genomic RNAs of negative polarity and negative (antigenomic) strands of RNA viruses of positive polarities. Squares at the 5′ end of genomic and mRNAs indicate a protein or a cap structure, respectively, linked to the RNA. As and Us refer to homopolymeric tracts found in genomic and antigenomic RNAs. A number of features such as relative size of genomic RNA and mRNAs, as well as the location and number of overlapping reading frames, may vary for individual representatives of the same virus family. Proteins are depicted as wavy lines with an indication of the N‐ and C‐termini. The location of a few coding regions is indicated on the genomes (S, structural proteins; NS, nonstructural proteins; 3D, the picornavirus polymerase). Lines are not drawn to scale.
Figure 2. Some negative‐strand and ambisense RNA viral genomes and their replication and expression strategies. A number of families of mammalian RNA viruses are included; additional features are given in Table. For negative‐strand RNA viruses, discontinuous lines represent genomic RNAs of negative polarity and continuous lines represent their complementary strand that acts as replicative intermediate or mRNA. Symbols and limitations are as in Figure. PB1, subunit one of the influenza virus polymerase. In the case of Arenaviridae, the ambisense strategy is illustrated with one of the two genomic segments.
Figure 3. A schematic representation of 10 segments of double‐stranded RNA which is a typical genome structure of Reoviridae, although the number of genomic segments varies among members of the family. Below the genome, synthesis of mRNA and complementary RNA is depicted for one fragment with symbols as described for Figure.
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Further Reading

Domingo E, Parrish CR and Holland JJ (eds) (2008) Origin and Evolution of Viruses, 2nd edn. Oxford, UK: Elsevier.

Domingo E (2016) Virus as Populations. Amsterdam: Academic Press/Elsevier.

Domingo E and Schuster P (2016) Quasispecies: From Theory to Experimental Systems. Switzerland: Springer.

Ehrenfeld E, Domingo E and Ross RP (2010) The Picornaviruses. Washington, DC: ASM Press.

Flint SJ, Racaniello VR, Rall GF, Skalka AM and Enquist LW (2015) Principles of Virology, 4th edn. Washington, DC: ASM Press.

Gesteland RF, Cech CR and Atkins JF (eds) (2006) The RNA World, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Lee KM, Chen CJ and Shih SR (2017) Regulation mechanisms of viral IRES‐driven translation. Trends in Microbiology 25: 546–561.

Paul D, Madan V and Bartenschlager R (2014) Hepatitis C virus RNA replication and assembly: living on the fat of the land. Cell Host & Microbe 16: 569–579.

Weissmann C (1974) The making of a phage. FEBS Letters 40: S10–S18.

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How to Cite close
Domingo, Esteban, and Perales, Celia(May 2018) RNA Virus Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001488.pub3]