Structure and Classification of viruses

• Viruses contain DNA or RNA, surrounded by a protein coat (capsid), and possess a nucleic acid core.
• Viruses may be enclosed in a protective envelope.
• Viruses lack organelles and can't grow, respire, or metabolize on their own.
• Viruses are obligate intracellular parasites, inactive outside host cells and active within.
• During reproduction the protein coat dissembles allowing for viral replication, assembly, and release within host cells.
• Two Classification Systems: ICTV and Baltimore.
• ICTV Nomenclature: Order (virales), family (viridae), subfamily (virinae).
• Baltimore Classification: includes 7 groups.

History of Taxonomy

• There initially was no systemic approach to virus naming, which led to haphazardness.
• Examples of unsystematic naming conventions: disease (rabies, hepatitis), cause (influenza), body site (rhinovirus), area of discovery (Rift Valley fever), or person who discovered it (Epstein-Barr virus).
• In the 1960s, electron microscopy led to more info regarding viral structure, shape, and composition.
• Researchers realized viruses didn't fit existing cellular organism classification systems.
• A hierarchical system was developed based on nucleic acid in the virion, protein shell symmetry, presence/absence of lipid membrane &dimensions of the virion/capsid.
• In the 1970s, sequencing technologies and genomics had an impact on virus taxonomy.
• There was a need to adjust classification, and the International Committee on Taxonomy of Viruses (ICTV) was developed.
• David Baltimore simultaneously developed an alternative classification system based on genome type and replication method.

Taxonomy Concepts

• Monothetic systems are based on a single characteristic or a series, and suitable for plants and animals.
• Polythetic systems are akin to family resemblance and use a set of criteria.
• A minimum number of criteria must be met but no single criterion is essential.
• Polythetic systems suit viruses well, accounting for several properties simultaneously.
• The ICTV uses a polythetic approach in dealing with viral species.
• Viral species must be represented by at least one virus isolate.
• Distinguishing properties for genera, families, and orders are virus morphology, method of replication, genome organization and size of proteins.
• Hierarchy levels are: (Order), Family, (Subfamily), Genus, Species.

Nomenclature

• Suffixes are assigned by taxonomic level:
  • Order: -virales
  • Family: -viridae
  • Subfamily: -virinae
  • Genus: -virus
  • Species: No specific suffix.
• In virus taxonomy, taxa names are capitalized; species' first word is not, unless proper nouns. Taxa names are written in italics and Preceded by the name of the taxon

Classification Systems

• Formal description of human respiratory syncytial virus: Order Mononegavirales, family Paramyxoviridae, subfamily Pneumovirinae, genus Pneumovirus, species Human respiratory syncytial virus.
• Viral species can be described using informal names, such as herpesvirus = any member of the family Herpesviridae.

Baltimore Classification

• Based on nature of genome (DNA vs RNA), genome polarity (positive vs negative sense), and reverse transcription (yes/no).
• Classification is based on the pathway nature from nucleic acid to mRNA synthesis.
• The 7 categories include:
  • Groups 1&2: DNA, replicates via DdDp
  • Group 3: dsRNA, replicates in cytoplasm
  • Groups 4&5: +ssRNA, polarity of the genome
  • Group 6: +sense RNA viruses that replicate via a DNA intermediate
  • Group 7: dsDNA viruses that replicate via a ssRNA intermediate

Virus Taxonomy

• Advances in nucleotide sequencing have revolutionized biology and taxonomy.
• Universal virus taxonomy provides a classification scheme based on data and expert consensus.
• This framework is essential for studying current and identifying new viruses.

Viral Structures

• Enveloped virus structures: envelope protein, envelope, viral tegument, viral genome and nucleocapsid
• Definition of Terminology Utilized in Viral Structure:
  • Subunit- Single, folded polypeptide chain
  • Structural unit- Unit from which capsid or nucleocapsid are built (maybe made up of one or more protein subunits
  • Capsid- Coat – Protein shell surrounding the viral nucleic acid
  • Nucleocapsid- Core -Nucleic acid-protein assembly packaged within the virion
  • Envelope-Viral Membrane- Host cell-derived lipid bilayer with viral glycoproteins
  • Virion -Viral particle- Infectious viral particle

Viral Structure Principles

• Virions contain structural proteins and nonstructural components like enzymes, small RNAs, and cellular macromolecules.
• Primary virion functions: protect viral genome and ensure genome transmission between hosts.
• Virions are designed to protect the viral genome via capsids, capsids are constructed using primarily small subunits
• Virus particles are metastable structures

Viroid Protein Functions

• Protection of the Genome- assembly of stable protective protein shell, specific recognition and packaging of nucleic acid with the interaction of host cell membranes to form the envelope
• Delivering of the genome- binding to external receptors of the cell that transmit signals that induce uncoating of the fusion with host cell membranes so that there is transport of genome to the appropriate site
• Additional functions - interaction that ensures efficient infectious cycle

Methods of Studying Structure

• Electron microscopy is used
• Physical and chemical methods

Electron Microscopy (EM)

• Used to examine virus particle structure and morphology.
• Overcomes light microscopy limitations.
• Includes transmission electron microscope (TEM) and scanning electron microscope (SEM).
• Provides information on number of virus particles present and virion structure.

Physical Methods for Studying Viruses

• Filtration was historically used to estimate virus particle size.
• Differential centrifugation is used to obtain purified/concentrated virus preparations, free of host cell contamination based on Sedimentation properties in utracentrifuge
• Relative particle density is measured in sucrose solutions, which reveals nucleic acid and protein proportions.
• Spectroscopy analyzes nucleic acid content using ultraviolet light.
• Electrophoretic analysis is studying the DNA by way of their Proteins or their proteins that make of the viral DNA structure. (Studding by way of the gel electrophoresis
• X-ray Diffraction is used to find the structures within a virus that is images can measured in Angstoms
• Nuclear Magnetic Resonance Imaging: Radiation of radio frequency by nuclei in the presence of magnetic fields to study the atoms

Chemical Methods

• Classical method: disrupting particles by slowly altering pH or by detergents.
• Reveals basis of stable interactions or changes in surface antigenic sites.

Viral Capsids

• All viruses have a capsid or nucleocapsid "core"
• Most viral particles appear rod-shaped or spherical under electron microscopy (EM).
• Caspids are constructed from small number of proteins that are regularly and actively arranged to create a maximal contract with non- Covalent Bonds that result in symmetrical shapes.
• Helical symmetry
• Icosahedral Symmetry
• The virus particles can form spontaneously

Helical Symmetry

• Examples: Influenza, Measles, Rabies
• All Helical animal viruses have similar ss RNA genoms and an envelope
• Filamentous or rod like Open structure
• The longer helical particles can curve or bend
• E.G. Tobacco mosaic virus

Icosahedral Symmetry

• Examples are : Herpesviruses, adenovirus, picornaviruses
• First noticed by electron microscopy, the Structure us volume is closed with limited access
• Most Icosahedral viruses have a large amount of proteins with subunits(3 subunits (i.e. a trimer) per face. This is the simplest confirmation with each subunit by there are 60
• Simple icosahedrons display 2-3-5 rotational symmetry

Other Capsid Architectures

• Most viruses are helical or icosahedral
• Examples of Exceptions by the use of : Retroviridae- two single strands of RNA that are enveloped spherical cylindrical or conical capsids Poxviridae- Large brick shaped particles that are over 200-400 nm , made up of more than 100 proteins that have T=7 symmetry.
• The Packaging of nucleic acid is an enclosed process that is meditated by non-Structural proteins or Packaging that is meaditaed by: direct contacting or by cellular proteins.

Envelopes

• As viruses escape cell without harm they bud off the surface of cells that acquire a lipid envelope through
• Envelopes consist of: Transmembrane proteins- Contain hydrophobic domais, channels, enabales virus to control the membranes External proteins- Sits osisde and anchored by glycoproteins that can be visual on the EM
• Importance of enveoples in membrane fusion, major antigens, receptor binding and Haemmaglutination