What is a Virus?

 

DEFINITIONS

VIRIONS
OTHER VIRUS-LIKE AGENTS

 


Viruses

Viruses may be defined as acellular organisms whose genomes consist of nucleic acid, and which obligately replicate inside host cells using host metabolic machinery and ribosomes to form a pool of components which assemble into particles called VIRIONS, which serve to protect the genome and to transfer it to other cells.

They are distinct from other so-called VIRUS-LIKE AGENTS such as VIROIDS and PLASMIDS and PRIONS

 


Alternative definitions:

S Luria et al.     AJ Cann

And EP Rybicki, ©2008:

A virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements.


The concept of a virus as an organism challenges the way we define life:

By older, more zoologically and botanically biased criteria, then, viruses are not living. However, this sort of argument results from a "top down" sort of definition, which has been modified over years to take account of smaller and smaller things (with fewer and fewer legs, or leaves), until it has met the ultimate "molechisms" or "organules" - that is to say, viruses - and has proved inadequate.

If one defines life from the bottom up - that is, from the simplest forms capable of displaying the most essential attributes of a living thing - one very quickly realises that the only real criterion for life is:


The ability to replicate


and that only systems that contain nucleic acids - in the natural world, at least - are capable of this phenomenon. This sort of reasoning has led to a new definition of organisms:


"An organism is the unit element of a continuous lineage with an individual evolutionary history."


The key words here are UNIT ELEMENT, and INDIVIDUAL: the thing that you see, now, as an organism is merely the current slice in a continuous lineage; the individual evolutionary history denotes the independence of the organism over time. Thus, mitochondria and chloroplasts and nuclei and chromosomes are not organisms, in that together they constitute a continuous lineage, but separately have no possibility of survival, despite their independence before they entered initially symbiotic, and then dependent associations.

The concept of replication is contained within the concepts of individual viruses constituting continuous lineages, and having an evolutionary history.

Thus, given this sort of lateral thinking, viruses become quite respectable as organisms:


More views on viruses and their definition:

 

http://microbiologybytes.wordpress.com/2007/07/24/its-life-jim-but-not-as-we-know-it/

It’s Life, Jim, but not as we know it… « MicrobiologyBytes via kwout

 

http://microbiologybytes.wordpress.com/2007/06/26/a-feeling-for-the-molechism/

A feeling for the molechism* « MicrobiologyBytes via kwout

Definitions

by EP Rybicki (1999).  An Electronic Introduction to Molecular Virology.  Buglet Electronic Press, Cape Town.

 


Acellular Organisms:
acellular: not composed of cells ( = "bodies of protoplasm made discrete by an enveloping plasma membrane");
Penguin Dictionary of Biology, 9th Edition, 1994

 

 


Genome:
The total genetic complement of a virus. This may be composed of RNA or DNA, and be single- or double-stranded. It may also be fragmented.

 

 


 

Viruses 1:

"Viruses are entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic machinery, and cause the synthesis of specialised elements [virions] that can transfer the genome to other cells".

SE Luria, JE Darnell, D Baltimore and A Campbell (1978). General Virology, 3rd Edn. John Wiley & Sons, New York, p2 of 578.

 


Viruses 2:
"Virus are submicroscopic, obligate intracellular parasites...[and]

AJ Cann (1997). Principles of molecular virology, 2nd Edition. Academic Press, San Diego.

 


Organism:
"An organism is the unit element of a continuous lineage with an individual evolutionary history."

SE Luria, JE Darnell, D Baltimore and A Campbell (1978). General Virology, 3rd Edn. John Wiley & Sons, New York, p4 of 578.

 


Definitions of Life:
Classical
               Newer Versions

 


Classical Properties of Living Organisms:

More modern definitions include the storage and replication of genetic information as nucleic acid, and the presence of or potential for, enzyme catalysis

(Penguin Dictionary of Biology, 9th Edition, 1994)

Newer Definitions of Life


Life may (somewhat irreverently) be defined in general terms as:

"The phenomenon associated with the replication of self-coding informational systems",

 

or more specifically as:

"The phenomenon associated with the replication of nucleic acids".

- Rybicki EP, 1996.

 


Another more serious view:

"Life can be viewed as a complex set of processes resulting from the actuation of the instructions encoded in nucleic acids. In the nucleic acid of living cells these are actuated all the time; in contrast, in a virus they are actuated only when the viral nucleic acid, upon entering a host cell, causes the synthesis of virus-specific proteins. Viruses are thus "alive when they replicate in cells, while outside cells viral particles are metabolically inert and are no more alive than fragments of DNA."

- Dulbecco R and Ginsberg HS, 1980. Virology, p.854-855 (originally published as a section in Microbiology, 3rd Edn., Davis et al., Harper and Row, Hagerstown).

 


Other Autonomous or Semi-Autonomously Replicating Genomes

There are a number of types of genomes which have some sort of independence from cellular genomes: these include "retrons" or retrotransposable elements, bacterial and fungal (and eukaryotic organelle) plasmids, satellite nucleic acids and satellite viruses which depend on helper viruses for replication, and viroids.   A new class of agents - PRIONS - appear to be "proteinaceous infectious agents" (see also here for an ICTV description, here for some local information and more links).
 

Retrons Plasmids Satellite Nucleic Acids
Satellite Viruses Viroids Prions

  
Depiction of Prions infecting Neurons: from Russell Kightley Media

Plasmids
Plasmids may share a number of properties with viral genomes - including modes of replication, as in ss circular DNA plasmids and viruses - but are not pathogenic to their host organisms, and are transferred by conjugation between cells rather than by free extracellular particles.

Satellite Nucleic Acids
Certain viruses have associated with them nucleic acids that  are dispensable in that they are not part of the genome, which have no (or very little) sequence similarity with the viral genome, yet depend on the virus for replication, and are encapsidated by the virus.   These are mainly associated with plant viruses and are generally ssRNA, both linear and circular - however, a circular ssDNA satellite of a plant geminivirus has recently been found.

Satellite Viruses
There are also viruses which depend for their replication on HELPER VIRUSES: a good example is tobacco necrosis satellite virus (sTNV), which has a small piece of ssRNA which codes only for a capsid protein, and depends for its replication on the presence of TNV.  Another good example is the hepatitis delta agent with its circular ssRNA genome.  The adeno-associated viruses (AAVs) are also satellite viruses dependent on the linear dsDNA adenoviruses for replication, but which have linear ssDNA genomes and appear to be degenerate or defective parvoviruses.

Viroids
Viroids are small naked circular ssRNA genomes which appear rodlike under the EM, which are capable of causing diseases in plants. They code for nothing but their own structure, and are presumed to replicate by somehow interacting with host RNA polymerase, and to cause pathogenic effects by interfering with host DNA/RNA metabolism and/or transcription. A structurally similar disease agent in humans is the hepatitis B virus-dependent hepatitis delta agent, which additionally codes for a structural protein.


Retroid Elements and Retroviruses

Retroviridae [ssRNA(+) viruses replicating via a longer-than-genome-length dsDNA intermediate], Hepadnaviridae, caulimoviruses and badnaviruses [family Caulimoviridae, gapped circular dsDNA viruses replicating via longer-than-genome-length RNA intermediates] all share the unlikely attribute of the use of an enzyme complex consisting of a RNA-dependent DNA polymerase/RNAse H in order to replicate. They share this attribute with several retrotransposons, which are eukaryotic transposable cellular elements with striking similarities with retroviruses [such as the yeast Ty element, the mammalian LINE-1 elements, and the Drosophila copia element]; and with retroposons, which are eukaryotic elements which transpose via RNA intermediates, but share no obvious genomic similarity with any viruses other than the reverse transcriptase.

Bacteria such as E coli also have reverse- transcribing transposons -known as retrons - but these are very different to any of the eukaryotic types while preserving similarities in certain of the essential reverse transcriptase sequence motifs.

All of these elements are collectively known as RETROELEMENTS; the fact that the reverse transcriptases of all of them have some amino acid identity suggests a common evolutionary origin.

Several reviewers have pointed out that just such an enzyme as reverse transcriptase would have been necessary for the transition from what is widely believed to have been an RNA world - that is, where all the extant organsisms had RNA genomes - to the present world in which all cellular organisms have DNA genomes.

Viruses with RNA genomes which use RNA-dependent RNA polymerases for their replication may be the only remnants of that pre-DNA era; however, cellular elements and viruses which use reverse transcriptase may share a common origin as cell-derived "modules" coding for a reverse transcriptase, which evolved to become retrons and retroposons and retrotransposons. Addition of structural proteins may have allowed evolution of retroviruses.

The evolution of the DNA retroviruses - Hepadnaviridae, caulimo- and badnaviruses - is more obscure; it appears as though these arose from retrotransposon-like sequences, but this probably occurred near the origin of of these types of element as they are so diverse in sequence and genome organisation.

It is believed that retrotransposons may contribute substantially to the evolution of their hosts. Evidence for this has been obtained by studying human LINE-1s (Long Interspersed Nuclear Elements) - a group of retrotransposable elements which make up approximately 15 % of the human genome. The vast majority of LINE-1s are no longer retrotransposition competent and it is believed that in humans only between 30 and 60 full length LINE-1s are currently active. There is strong evidence from sequences in the sequence databases to suggest that active LINE-1s play an important role in "exon shuffling" (belived to be the major mechanism of macro-evolution whereby entirely new genes are created by reshuffling the components of older genes). The most compelling evidence that LINE-1s do facilitate exon shuffling, however, is the experimental demonstration that they are not only able to move large amounts of non-LINE-1 exonic DNA but also insert this DNA into unrelated expressed genes to obtain chimeras which encode active hybrid gene products.

References:

Chapter 7: "Evolution by transposition" (pp. 172-203) in "Fundamental of Molecular Evolution" by Wen-Hsiung Li and Dan Graur; Sinauer Associates, Inc., Sunderland, Mass., 1991

Moran, J. V., R. J. DeBerardinis, and H. H. Kazazian. 1999. Exon shuffling by L1 Retrotransposition. Science 283:1530-1534.


WHAT ARE VIRIONS?

 

VIRIONS are virus particles: they are the INERT CARRIERS of the genome, and are ASSEMBLED inside cells,  from virus-specified components: they do not GROW, and do not form by DIVISION

HIV Phage Φ29 Phage P22 Influenza Smallpox
Tobacco mosaic Filamentous phage T4 phage Adenovirus Coronavirus
All pictures copyright Russell Kightley www.rkm.com.au

They may be regarded as the EXTRACELLULAR PHASE of the virus: they are exactly analogous to "spacecraft" in that they take viral genomes from cell to cell, and they protect the genome in inhospitable environments in which the virus cannot replicate.

Note the strong resemblance between a bacterial virus - T2, T4 or T6 phage of E coli, which evolved possibly billions of years ago - and the only human-crewed spacecraft to have landed on another planet.

T-Even phage structure - copied from Wikipedia

Lunar excursion module (LEM) of Apollo 16: courtesy NASA

Basically, all virions have:

If the virions are simple NUCLEOPROTEINS - that is, contain only nucleic acid and protein - then they are usually  composed ONLY of virus-specified components.  However, certain host components may be "trapped" within virions, such as POLYAMINES: these are polycationic compounds which serve to neutralise charge on the viral nucleic acid as it is packed into the CAPSID, or protein coat.  PAPOVAVIRUSES may in addition encapsidate host histones associated in NUCLEOSOME complexes with virus genomic DNA.

The essentials of virion structure may be seen by clicking on the images below.

 

smalltmv.gif (14615 bytes) smallccmv.gif (18324 bytes) smallvirion.gif (6595 bytes)
Simple helical structures Simple isometric structures Compound structures Enveloped and complex virions

 

Excellent electron micrographs of virions - and an explanation of their basic structure - may be seen at the University of Cape Town's Medical Microbiology Division teaching pages.

For other excellent representations of virus structure, go to the University of Wisconsin's Institute for Molecular Virology, where Jean-Yves Sgro has assembled a gallery of 3-D image reconstructions of different viruses, together with explanations of structure.


Helical Nucleocapsids

This is one of the SIMPLEST FORMS of viral capsid: the protein is "wound on" to the viral nucleic acid (generally ssRNA, though M13 and other filamentous phage virions contain circular ssDNA) in a simple HELIX, like a screw (see the diagram for tobacco mosaic virus, below).

 

virovirion.jpg (20665 bytes)
Diagram of TMV structure: protein subunits are all in equivalent crystallographic positions, related by a right-hand "screw translation" Image reconstruction of TMV
courtesy L Stannard 8th Report ICTV

 

In the case of TMV this is the entire virion: this is also the case for all RODLIKE and FILAMENTOUS virions where no membranes are involved.  This includes all Tobamoviridae, Potyviridae, and Closteroviridae, but NOT Filoviridae, like Ebola virus (see here).

In other cases, filamentous helical nucleocapsids may be enclosed within matrix protein and a membrane studded with spike proteins:   excellent examples of this are PARAMYXOVIRIDAE, detailed images of which can be found here, at Linda Stannard's site, and for ORTHOMYXOVIRIDAE here in this tutorial.

 


 

Isometric Nucleocapsids

These are built up according to simple structural principles, as amply outlined here, and in more detail here.  Put simply, nearly all isometric virions are constructed around a BASIC ICOSAHEDRON, or solid with 20 equilateral trinagles for faces.  It suffices to say that the "quasi-icosahedral" capsid is possibly Nature's most popular means of enclosing viral nucleic acids; they come in many sizes, from tiny T=1 structures (Nanoviruses, eg: banana bunchy top virus; 18 nm diameter) to huge structures such as those of Iridoviridae or Phycodnaviridae (over 200 nm diameter). 

The simplest virions are those of the viruses with the smallest genomes: these are virions such as those of the ssRNA satellite tobacco necrosis virus (sTMV), the ssDNA canine parvovirus (CPV) and porcine circovirus (PCV), and microviruses infecting E coli and other bacteria (eg: φX174 phage): these all have a simple icosahedral T=1 surface lattice structure.  Some examples are shown below.  All structural subunits of these capsids are in the same positional state, or have the same interactions with their neighbours.

A unique derivative structure is that of geminivirus virions, which have two incomplete T=1 icosahedra joined at the missing vertex.

Satellite tobacco necrosis virus Canine parvovirus Geminivirus: Cover of the ICTV 8th Report
Images from the ICTV 8th report; derived from the Virus World site, for non-profit educational use

An example of a more complex structures are illustrated below.  The animated GIF to the left shows Cowpea chlorotic mottle (CCMV) virion surface structure (courtesy J-Y Sgro), which is composed of 180 copies of a single coat protein molecule, in a T=3 surface lattice.  The different colours in the CCMV picture represent different "positional states" of the capsid protein: subunits around 5-fold rotational axes of symmetry are BLUE, and cluster as PENTAMERS; subunits around 3-fold axes are RED and GREEN to reflect their different 2-fold symmetries; they cluster as HEXAMERS around "local 6-fold axes".

Another example is that of turnip yellow mosaic virus (TYMV): this has exactly the same basic structure, with a 180 copies of a single type of coat protein subunit, with the pentamer-hexamer clustering appearing more pronounced

CCMV capsid TYMV capsid
courtesy J-Y Sgro ICTV 8th report
R16movie.GIF (70838 bytes)
Rhinovirus R16 Rhinovirus R16
courtesy J-Y Sgro

A more complex capsid - that of the common-cold-causing Rhinovirus R16 (family: Picornaviridae), with 60 copies of 4 proteins in a T=3 structure - is shown on the bottom left and right (animation modified from one by J-Y Sgro) and right.  The right image shows a capsid with a cutaway, to reveal internal structure.   BLUE subunits around 5-fold axes are VP1; RED and GREEN are VP3 and VP2 respectively; YELLOW subunits (seen only internally) are VP4.   The VP4 subunits are formed by autocatalytic cleavage of VP0 (into VP2 and VP4) upon binding of a "procapsid" with viral genomic ssRNA. 

Note the similarity between the CCMV and R16 structures - despite one having a single CP, and the other having 3 structural CP subunits.

See here for further details of picornaviruses, here for a scheme showing picornavirus assembly, here for a scheme outlining polyprotein processing of picornaviruses, and here for material on picornaviruses from the University of Leicester course.


More complex capsids are generally found for viruses with larger genomes, whether composed of RNA or DNA.  These include virions such as those of reoviruses and adenoviruses, both of which have complex or multilayered naked isometric capsids.

 

   
Bluetongue orbivirus (Reoviridae) Mammalian reovirus core with spikes Electron micrograph of an adenovirus Link to diagram of an adenovirus structure
courtesy AJ Cann ICTV 8th Report courtesy L Stannard courtesy AJ Cann

 


You may like to look here for structures from the University of Calgary material.

More complex structures may be seen in electron micrographs, and diagrams explaining icosahedral and quasi-icosahedral structure at Linda Stannard's Web site.

 

http://web.uct.ac.za/depts/mmi/stannard/virarch.html

Principles of Virus Architecture via kwout

The "Virus World" site has an excellent set of high-resolution image reconstructions from physical data of non-enveloped simpler isometric viruses.

 

http://www.virology.wisc.edu/virusworld/

Virus World via kwout

 


 

Complex or Compound Virions

Mimivirus.  The huge regular icosahedral capsid contains lipid membranes and other structures

T-even phage particle: note elongated isometric head (icosahedron with hexamer expansion net), helical tail, and base plate and neck structures

Depiction of a orthopoxvirus virion.  Note presence of two lipid bilayers and amorphous structure

Link to Wikipedia

Link to Wikipedia

copyright Russell Kightley

Most bacteriophages - or more properly, archaeal and bacterial viruses - have a more complex structure than the simple isometric and helical nucleocapsids typical of many plant and animal viruses.  Even viruses with relatively small genomes may have more than one type of architecture associated with their virions, normally in the shape of some kind of TAIL structure attached to an isometric HEAD.  The T-even viruses - part of the "T4-like virus" genus, family Myoviridae - have the general structure shown centre, above: this is an isometric head attached via a connector assembly to a contractile helically-constructed tail with a rigid core, with tail fibres and baseplate.  See here for explanation of how the virus gains entry to enterobacterial cells.

λ-like viruses - family Siphoviridae - have thinner non-contractile tails and isometric heads, with tail fibres.   The P22-like and Φ29-like viruses in family Podoviridae and Salmonella phage Epsilon 15 have isometric heads and short, thick tails

 

Enterobacteria phage λ Enterobacteria phage P22 Bacillus phage Φ29 Salmonella phage Epsilon 15
copyright Russell Kightley

Reprinted by permission from Macmillan Publishers Ltd: Jiang W, et al.  Nature. 2006 Feb 2;439(7076):612-6 copyright 2006

 


 

Enveloped Virions

SOME virions additionally have:

Cutaway depiction of West Nile flavivirus: note regular arrangement of envelope protein, underlying membrane and isometric capsid Cutaway depiction of influenza virion: note helical nucleoprotein, matrix and envelope layers and spikes Cutaway depiction of HIV virion: note conical nucleoprotein, isometric matrix and envelope layers and spikes
SARSCoV (SARS coronavirus).  Note elongated membrane spikes and underlying isometric capsid Hepatitis C flavivirus (HCV): note elongated, regularly-spaced spikes and isometric structure Herpesvirus: note many envelope glycoproteins, "tegument" inside membrane, and isometric capsid
copyright Russell Kightley (www.rkm.com.au)

 

Enveloped virions may additionally incorporate host membrane proteins in their envelopes: while this may be a side effect of the "budding" process by which viral nucleoprotein complexes acquire envelopes, it may also in some cases be a mechanism for avoidance of host immune systems (eg: hepatitis B virus incorporates host serum albumin into its capsid; HIV virions may incorporate host MHC proteins).


  ccmvicon.gif (3910 bytes)
Tutorial Contents
 
"What is a Virus?" Isometric Virions Helical Nucleocapsids Compound structures

 

Virus Classification

Introduction

Taxonomic Criteria 

Hosts of Viruses 

Cross-Kingdom Viruses Cross-Phylum Viruses Other Resources 

  Introduction

A universal system for classifying viruses, and a unified taxonomy, has been established by the International Committee on Taxonomy of Viruses (ICTV) since 1966. The system makes use of a series of ranked taxons, with the:

For example, the Ebola virus from Kikwit is classified as:

- Order Mononegavirales

- Family Filoviridae

- Genus Filovirus

- Species: Ebola virus Zaire


The current (2005) Eighth Report of the ICTV lists more than 5,400 viruses in 1938 species, 287 genera, 73 families and 3 orders.

Orders include:

These are presumed to constitute the highest level of "monophyletic" groups of viruses, with a common ancestry, so far recognised.

A comprehensive alphabetical list of viruses appears at the ICTVdb site here.  This includes virus-like agents.


Virus Orthography, or spelling and usage conventions

This format refers only to official taxonomic entities: these are concepts, while viruses are real.

Vernacular or common-use forms of names are neither capitalised nor written in italics.  Thus, while Tobacco mosaic virus refers to the species and Tobamovirus to the taxonomic genus, tobacco mosaic viruses or tobamoviruses are the entities that you work with.


 Taxonomic Criteria

The most important criteria are:

Host Organism(s): eukaryote; prokaryote; vertebrate, etc.

Particle Morphology: filamentous; isometric; naked; enveloped

Genome Type: RNA; DNA; ss- or ds-; circular; linear

- although a number of other criteria - such as

- are important in precise identification, consideration of the above three criteria - and in many cases, just morphology - are sufficient in most cases to allow identification of a virus down to familial if not generic level.

An interactive virus identification key was developed at this site: test it and see how the criteria rapidly allow identification.


Hosts of viruses

These include all classes of cellular organisms described to date:

Prokaryotes:

Archaea

Bacteria

Mycoplasma

Spiroplasma

Eukaryotes: Algae Plants Protozoa Fungi
Invertebrates Vertebrates

This page links to a comprehensive listing of viruses by host infected.


  Cross-Kingdom Viruses

Certain virus families / groupings cross "kingdom" or phylum boundaries.

For example, virus families infecting two kingdoms of organisms are:

The reasons for this are probably caught up in their evolution and cospeciation with their hosts (see also here). 

For example, bunyaviruses and rhabdoviruses probably originated in their present form in insects, and were spread to plants and other animals after insects emerged from the seas and preyed on other terrestrial hosts.

The dsDNA cryptoviruses most probably originated in fungi, and were spread to land plants after these emerged into the terrestrial environment, as fungi began to parasitise them.

The phycodnaviruses - all of which are found in aquatic environments - could well have started out in the progenitors of protozoa and aquatic / marine plants.



 

Cross-Phylum Viruses

Virus families infecting across different phyla (all infecting insects and vertebrates) are:

These viruses almost certainly spread from insects to vertebrates, after vertebrates joined insects on dry land and insects began to feed on them.  An example here is West Nile flavivirus, which infects mosquitoes and birds, and can be transmitted to humans and other animals as well.

 

http://www.cdc.gov/ncidod/dvbid/westnile/cycle.htm

CDC: West Nile Virus - Flowchart: West Nile Virus Transmission Cycle via kwout


Other Resources:

An excellent resource for virus taxonomy is the International Committee on Virus Taxonomy (ICTV) Database, the ICTVdB, maintained by Cornelia Büchen-Osmond and others.

A very good set of pages can be found at the MicrobiologyBytes.com site.

The ICTV virus database (ICTVdb) has a mirror Web site: visit it at the National Center for Biotechnology Information server.

 



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Copyright Ed Rybicki unless otherwise stated, October 1996; November 1997; August 1998; May 2008