Lecture 2: Viral Definition Origins and Classification Flashcards
How was a virus first defined?
It was discovered in 1884-92 by Ivanovski and thought of as a filterable agent (not so much nowadays) and named Virus for “poison” in Latin.
As of now, 5,000 or so distinct viruses are known (many others exist) but these are detectable by their nucleic acid genomes.
What is the physical definition of a virus?
Set of nucleic acid (RNA or DNA) genes packaged within a protein coat (mostly smaller, and fewer genes than, the simplest cellular organism).
Thus, viruses are the smallest and simplest of all biological entities.
What is the functional definition of a virus?
A molecular genetic parasite dependent on its host for replication, transmission, and/ or maintenance (S. Luria 1952).
What is likely the best functional definition?
An obligate intracellular parasite.
Since viruses can only replicate inside living cells and the host cell machinery is required for virus reproduction (mRNA translation and energy metabolism).
Is a virus an living organism based on the 7 characteristics of living things theory?
In terms of the 7 characteristics of living things, NO!
Grow- No
Reproduce (undergo replication)- Yes
Responsiveness/”irritability”: No
Organized into cells: No
Evolve: Yes
Respiration: No, excretion, movement, metabolism.
Free living thing: No
What is the living systems theory?
Living systems can be defined as those systems that are able to process and be maintained by flows of:
Matter: (atoms, molecular “metabolism”).
Energy (respiration)
Information (genetics)
What is Prof Gershon’s definition?
Require water (as the universal solvent).
Are based on carbon-containing molecules
Exhibit a continuum of complexity (from simple viruses to humans).
Is a virus a living organism in terms of the living system theory?
Flow of matter- Yes (encode biosynthetic enzymes).
Flow of energy: No (don’t encode enzymes of energy metabolism)
Flow of information: Yes (pass on their genes)
Is a virus a living organism in terms of Gershon criteria?
Require water: Yes
Based on carbon: Yes
Viruses are declared to be not alive by who and when?
In 2000, the International Committee on Taxonomy of Viruses officially declared that viruses are NOT alive.
Because: we can now synthesize a virus in a test tube and count the atoms).
Viruses are declared to be not alive by who and when?
In 2000, the International Committee on Taxonomy of Viruses officially declared that viruses are NOT alive.
Because: we can now synthesize a virus in a test tube and count the atoms).
Perhaps inside the cell = Alive
Outside the cell = Non-living
What are giant viruses?
Discovered in 2004, giant viruses are non-filterable (Mimivirus, Megavirus). Have genomes larger/more genes than genomes of many bacteria.
Therefore: “Alive”? Well size does not alter any of the other criteria.
What are viruses in their simplest form?
Simple nucleic acid genome in a protein coat.
What are viroids?
a small piece of nucleic acid (no protein encoded).
Viroids are the smallest known infectious pathogens.
Ex. Cause transmissible disease in plants! (transmitted via leaf-leaf contact, aphids, plasmodesmata.
A viroid may hitch a ride with a virus.
In animals (humans) hepatitis D is a viroid.
Hepatitis D: Packaged in the protein coat of Hepatitis B virus: Hep D is a parasite of a virus.
Where is the boundary between life and non-life since the simplest transmissible disease causing entity is a single molecule? Is it at the level of?
Organism (clearly living)
Single Cell? (clearly living: bacteria/ our cells can happily divide indefinitely in a Petri dish).
Virus: not free living perhaps the boundary is here
Single molecule viroid whose only life like property is to reproduce.
Maybe life is a progressively emerging property therefore no hard boundary exists.
What is the RNA world argument?
RNA world is an appealing hypothesis in which life originated as a self-replicating molecule that carried only information required for its own replication. Note: Planet = 4.54 billion years old.
Viroids and Viruses Origin
Perhaps they started as very crude RNA-based self-replicators. Later after the advent of cellular life/proteins/central dogma could only compete with cells by parasitizing them (and hijacking/hacking) the cellular machinery to make virus proteins?
What is the phylogenetic argument?
How organisms change over time/order of events. The simplest order of descent to account for three closely related genomic sequences found today *Blue mutation first and then red added later). (refer to slide in power point).
When we do phylogeny for all known DNA polymerase genes, which both cells and many DNA based viruses have in common ___ virus families appear to have very ___ and __ origins
different, different, ancient
What is the branch for DNA pols?
There is no single branch for DNA pols of all DNA viruses. Viruses don’t have a common origin unless you extrapolate right back to the very root of the tree where everything first diverged.
DNA pol genes orientate at the very deepest roots of the tree of life.
Viruses may be as ancient as life itself.
Since viruses don’t all fit nicely in one branch on the universal tree of life, are viruses a 4th kingdom of life?
Giant DNA viruses might be regarded as the 4th domain of life. In general though all organisms have either ribosomes (eukaryotes, eubacteria, archaea) or a capsid (viruses).
What are caveats to phylogenetic arguments?
Molecular clock not running at the same speed in all organisms.
Horizontal gene transfer (genes jump from species to species).
Did viruses contribute to our evolution?
Definitely: Those ERV genomes embedded in our genomes (prior lecture) are now re-purposed with numerous regulatory functions in today’s higher organisms (us) allowing, for example placental mammals to exist.
Virus classification via human disease
It turns out that similar viruses do not necessarily have similar pathology and vice versa.
What is not important for virus classification?
Nature of host not important (certain viruses of animal plants bacteria may be similar to each other).
Nature of disease not important (hepatitis B related to polio; hepatitis A-G unrelated to each other.
Traditional ___ classification scheme can be applied to viruses from the family level downwards based on common characteristics.
Linnaean
Order ( not definable for most viruses to not very useful).
Family (Families are fundamentally different, but there is a common ancestor for all viruses within a family).
sub- family
genus
species
strain (strains are only subtley different)
What are the common characteristics used for classification?
Nature of the viral genome (DNA/RNA, single/double stranded, linear/circular)
Presence/absence of a viral lipid envelope.
Morphology of the virus particle.
Features of replication cycle.
Is the Linnaean scheme still predominantly used for viruses today?
Yes the ICTV (International Committee on Taxonomy of Viruses) maintains this single universal taxonomic scheme for 5450 viruses of medical or economic importance to humans.
Arranged in: 3 orders
73 families
287 genera
2000 species
5450 strains
However, although this scheme covers all viruses (families are largely unconnected from one another). So in the case of viruses it does not address the concept of common vs independent ancestry of virus families. It simply addresses the degrees of difference within families.
All cellular life exhibits __ __ above the family level.
critical connections
Is there an approach that may better connect virus families?
Evolutionary or Phylogenetic approach: we would need a gene that is common to all viruses.
What is the potential problem with using the evolutionary/phylogenetic approach?
There is no single universal gene that is found in all viruses. Previously we looked at DNA polymerase genes. But these only exist in viruses with DNA genomes.
Certainly ___ virus families there are universally shared genes so we can infer their ancestral relationships and generate their ____ by ____
1) within 2) trees 3) computer
But ____ virus families there are no universally shared genes and genomes are too different!
Between
What is the unifying type of molecule shared by all viruses.
Baltimore class but it does not imply a common ancestor. Ex. Class IV includes multiple virus Families/Orders of (+) ssRNA viruses (like Picornavridae and Calicviridae). Virus families are still considered too divergent for there to be clearly a common ancestor.
What did David Baltimore discover?
Helped understand the gene expression strategies of all virus families. From this understanding, we know there is a universal type of molecule common to all viruses namely mRNA (the central molecule used for expression of all genes including all virus genes). We can classify all virus families according to their route from genome to mRNA and thereby reduce 73 ICTV families to just 7 fundamental classes of viruses.
What are the 7 fundamental classes of mRNA?
I: dsDNA
II: ssDNA
III: dsRNA
IV: (+) ssRNA
V: (-) ssRNA
VI: (+) ssRNA
VII: dsDNA
What does Group IV of the fundamental classes of mRNA do?
Route to mRNA production not (+) strand appearance since group IV genome does not have mRNA cap.
What does Group VII of the fundamental classes of mRNA do?
Hepadnarviridae genomes are partially dsDNA partially ssDNA. Replicated via an RNA intermediate.
Does a single Baltimore class imply a common ancestor?
No, for example, class IV includes multiple virus Families/Orders of (+) ssRNA viruses (such as Picornavirdae and Calicivirdae) Virus families are still considered too divergent for there to be clearly a common ancestor.
What are (+) sense genomes?
Equivalent strand to mRNA
What are (-) sense genomes?
Complementary strand to mRNA.
Why is virus evolution/adaption very rapid?
Viruses always comprise populations and can be very rapid because: a) genome replication is error prone due to simplicity of their polymerases (absence of proof-reading/error repair functions) b) short generation times and c) very large # of virons (# of genomes) in a typical population.
A single infection of just a single host (you) can yield a diverse population of viruses at any time in any one tissue (e.g. in your blood or lungs).
Explain horizontal gene transfer in viruses?
Viruses may evolve by exchanging alleles. They may undergo genetic exchange with each other and hosts (sudden appearance of a very different virus species)
Explain horizontal gene transfer in viruses?
Viruses may evolve by exchanging alleles. They may undergo genetic exchange with each other and hosts (sudden appearance of a very different virus species)
Describe horizontal gene transfer in segmented genomes?
Reassortment (shuffling of segmented genomes/genetic shift)
Describe horiztontal gene transfer in non-segmented genomes?
Spontaneous recombination (shuffling and covalent joining of equivalent segments).
Do viruses only infect humans?
No, viruses have been found to infect organisms all over the tree of cellular life.
What type of biomass do viruses have?
Viruses have an incredible biomass and are the most abundant form of life on earth. Likely to play a role in the planetary carbon cycle.
How many bacterial viruses are there in seawater?
There are 10-50 million bacterial viruses per mL of seawater (even more in soils).
How many viruses are present on this planet?
10^31 (10 billion trillion trillion) bacterial viruses present on this planet (10x greater than # of bacteria).
How many tons of viruses are on the planet?
100 million tons of viruses on the planet. Same weight as 1 million blue whales.
If all viruses in the world were aligned head to tail this would stretch ___ million light years (__ the diameter of our galaxy)
200 million light years
20x
What are the influences of viruses upon biogeochemical cycles? (Carbon cycles)
90% of ocean biomass is microbial. Bacterial viruses kill > 20% of ocean bacterial biomass each day. Bacterial infection by virus leads to cell lysis. The non-recyclable carbon rich bacterial cell wall material is sequestered by sinking to ocean depths. (3 billion tons of carbon sequestered per year).
Recyclable material (cytoplasm) eventually joins the atmosphere of CO2.
What are the main key points of lecture 2?
Viruses can be classified by taxonomic schemes which catalogs similarities and differences.
Don’t appear to have one root in the tree of life.
But Baltimore scheme considers mRNA to be the strategic route of all viruses and classifies the route from genome to mRNA.
Virosphere builds on the seven resulting classes subdividing them according to the host.
Don’t regard viruses evolution only through point mutations arising from errors. Genes may jump between viruses (antigenic shift)
