Structure of viruses

• This chapter provides an in depth study on the structure, composition, and organization of viral genomes, their classification into double stranded and single stranded DNA viruses, positive and negative stranded RNA viruses with and their genome diversity
• Segmentation and re-assortment of viral genomes have been discussed along with the multipartite virus genomes
• Genome details of 13 different viruses have been provided as type studies for better understanding of these topics
• Capsid


  Protective protein shell formed by multiple copies of one or more protein subunits

  
• Concepts of viral genome evolution have also been discussed
• Virus


  A small electron microscopic parasite, incapable of reproducing by its own, survives by directing the host cell machinery for the production of more viruses, which emerges from their respective host cell through lysis
• Most of these viral organisms contain either double stranded or single stranded DNA as well as RNA in their genomes, which may be either single stranded or double stranded
• After the purification and partial crystallization of Tobacco Mosiac Virus in 1935 by Wendell Stanley, the study of viruses has inspired many scientists, which lead to identification and characterization of plant, bacteria, archaea, and animal viruses
• Viruses are capable of infecting a large number of various cell types, genetically modified viruses are being considered for the gene therapy
• Virions


  The complete virus particles that are produced by the assembly of the pre-formed viral components, whose main function is to deliver its genome into the host cell for its expression (transcription and translation)
• Icosahedral virion


  Belonging to the icosahedral or quasi-spherical structural class of viruses, made of 20 identical triangular faces, each face is constructed with three identical capsid protein units making 60 subunits per capsid, with five subunits symmetrically contacting each of the 12 vertices, thus making all proteins in equivalent interaction with each other
• Nucleocapsid


  The viral genome packed inside a symmetric protein capsid, composed of either a single or multiple proteins, each of them is encoding a single viral gene
• Enveloped viruses


  The nucleocapsid is surrounded by a lipid bilayer and is studded with a layer of glycoproteins
• Structural proteins


  • Protection of the genome
  • Allow attachment of virion to host cell
  • Facilitate fusion of virion envelope to host cell membrane (enveloped viruses only)

  
• Viruses possess a great diversity with respect to their size, with Mimivirus being the largest virus reported with 400 nm in diameter, bigger than the Mycoplasma bacteria, which is ~200 to 300 nm long
• Viroids


  Short stretch of highly complementary, single stranded (200–400 nucleotides), circular RNA molecules possessing a rod-like secondary structure without any capsid or envelope, associated with plant and human diseases such as hepatitis D
• Virusoids


  Satellite, circular single-stranded RNAs (1000 nucleotides) dependent on plant viruses for replication and encapsidation, packed into virus capsids as passengers, their genome encodes only structural proteins
• Prions


  Anomalous infectious agents that cause fatal neurodegenerative diseases mediated by contemporary mechanisms, consisting of a single type of protein molecule without any nucleic acid component
• Metastability of virus capsids

  Viral capsids are metastable - they must protect the genome (stable) but also disassemble during infection to release genome (unstable)

  
• It has been estimated that there are 1031–1032 viruses in the earth's atmosphere, which exceeds the number of host cells fairly by an order of magnitude
• Viruses play an important role as obligate intracellular parasites, modulating their host cells for energy and reproduction leading to adverse effects
• Comparative genomics has allowed closely related viruses to be compared and classified
• Sequencing of eukaryotic genomes has revealed that 5–10% of their DNA encodes information for these organisms, with a large fraction of the remainder thought to be composed of mobile retrovirus-like elements (retrotransposons)
• Bacterial genomes do not have such extra genetic material, but the genomes of certain bacteriophages have a close resemblance with bacterial plasmids in their structure and in the way of their replication
• Viruses are broadly divided into

  • DNA viruses
  • RNA viruses
• DNA and RNA viruses

  Can be either single stranded or double stranded, with a circular, linear or segmented arrangement
• DNA viruses are called large viruses and RNA viruses are small
• Capsid composition


  • The capsid is composed of numerous subunits, not one large protein/polypeptide
• Single stranded DNA and RNA viruses are fragile than double stranded viruses
• Genomes of the largest double-stranded DNA viruses such as herpesviruses and poxviruses are quite complex, resembling their host cells
• Genomes of Polyomavirus are complexed with cellular histone proteins, which form a chromatin-like structure inside the virus particle
• mRNAs of Vaccinia virus were polyadenylated at their 3'
• The genome of Adenovirus consists of split genes with non-coding introns, protein-coding exons, and spliced mRNAs
• Introns in prokaryotes were first discovered in the genome of T4 phage in 1984
• The genome of T4 phage is 160 kbp double-stranded DNA, highly compressed with promoters and sequences that control translation are nested within the coding regions of overlapping upstream genes
• Ways the capsid protein subunits and viral genome are arranged

  • Icosahedral
  • Helical
  • Complex

  
• The presence of introns in T4 phage may confer a selective advantage to the phage by offering the possibility of regulating the expression of the intron-containing genes by the regulation of splicing
• Horizontal transfer of the introns between phages through homing has played a significant role in the evolution of group I introns in T-like phages
• The size of viral genomes also depends on the type of host cell, with viruses with prokaryotic host cells tending to replicate quickly to keep up with their host cells, reflected in the compact nature with overlapping genes of many bacteriophages, leading to the minimum genome size
• Viruses with eukaryotic cells as hosts show tremendous compression while the core is getting packed into the capsid so that only optimum amount of genome can be packed