Lecture 8- viral diversity Flashcards
what was the first virus?
Dmitri Ivanovski, Russian botanist: 1864-1920. Tobacco mosaic disease
In 1892 reported that extracts from infected leaves were still infectious after filtration through a Chamberland filter - pores are too small for bacteria to pass through
Suggested the disease was caused by a novel “micro-bacteria” or toxin
Martinus Beijerinck, Dutch botanist: 1851-1931
In 1898, further showed that the infectious agent was able to migrate in an agar gel
Infectious soluble agent: contgium vivum fluidum
He used the word ‘virus’ to describe it from the Latin for liquid poison
what are filterable agents?
Filterable agent: disease producing agent that can pass through filters having a pore diameter smaller than the smallest known bacteria
1892: foot-and-mouth disease – first filterable agent in cattle
1901: yellow fever - first filterable agent in humans
1935: American chemist Wendell M. Stanleycreated a crystallized sample of the tobacco mosaic disease agent that could be visualized with X-rays [1946 Nobel Prize].
1941: the first clear, directphotographs [electron transmission microscope] of tobacco mosaic virus
what are viruses?
Viruses are the smallest of all microbes
They are only ‘alive’ and able to multiply inside the cells of other living things
The cell they multiply in is called the host cell
Virus particles are not cells, and by themselves they do very little.
They are simply containers for instructions which, once infected, host cells can be forced to follow.
what is the virus makeup?
A virus is made up of a core of genetic material – either DNA or RNA
Surrounded by a protective coat called a capsid which is made of viral proteins
Sometimes the capsid is surrounded by an additional coat called an envelope
what is the virus makeup (envelopes) ?
Envelopes are typically derived from portions of the hostcell membranes, but include some viralglycoproteins.
Glycoproteins on the surface of the envelope serve to identify and bind toreceptor sites on the host’s membrane
Capsid proteins do this function for non-enveloped viruses
The viral envelope then fuses with the host’s membrane, allowing the capsid and viral genome to enter and infect the host.
In general, non-enveloped viruses are more stable
what is the Baltimore classification?
1971: the Baltimore classification groups viruses into one of seven classes depending on a combination of their:
nucleic acid (DNA or RNA)
stranded-ness (single-stranded or double-stranded)
sense
method of replication
what is positive sense RNA?
Positive-sense single stranded RNA viruses have genomes that are functional mRNAs.
The genome itself is infectious if enters a cell
Their genomes are translated shortly after entry into the host cell to produce the RNA dependent RNA polymerase (RdRp), as well as the other viral proteins.
The RdRp (orRNA replicase)is anenzyme that catalyses thereplication of RNA from an RNA template. Specifically, it catalyses the synthesis of the RNA strandcomplementary to a given RNA template.
Error prone
Copies of the genome are needed for proliferation and to populate new virions to infect more host cells
What is negative sense RNA?
Negative-sense single stranded RNA viruses are not functional mRNAs – the host ribosomes can not translate the genome to create the RdRp
Therefore the virion contains an RdRp already – first step after cell entry is for the RdRp to transcribe mRNAs from the viral genome
Followed by replication where the RdRp replicates the genome
What are taxonomically classifying viruses?
Baltimore classification is not strictly taxonomy - the discipline of classifying and naming things
Viruses lack universal genes that can be used to construct a unified phylogeny into which all viruses can be placed.
There is no viral equivalent to the cellular tree of life that has been established through comparisons of ribosomal RNA and universal protein-coding genes in bacteria, archaea and eukaryotes
Virus classification was traditionally a descriptive system based mainly on phenotypic characters – the size and shape of a virus particle, the range of infected hosts and the diseases associated with infection.
This changed in recent years because of the high-throughput sequencing of environmental samples (metagenomics), which has led to the detection of an astonishing range of viruses.
Classifying viruses based on the relationships between their protein and nucleic acid sequences (phylogenetics) has become a key means of defining taxa.
what is a virion?
Virion - a complete virus particle that consists of an RNA or DNA core with a protein coat sometimes with external envelopes
Virion - the extracellular infectious form of a virus
what are viral hosts and metagenomics?
Where there is life, there are viruses.
Algae, Archaea, Fungi, Bacteria, Plants, Protozoa, Invertebrates, Vertebrates
It is clear from ecological studies, and more recently from metagenomic studies, that viruses represent a major part of the modern biosphere.
At least 1031virus particles exist globally at any given time
Their current biomass has been estimated to equal that of 75 million blue whales (approximately 200 million tonnes)
If placed end to end, the collective length of their virions would span 65 galaxies
Metagenomic studies in particular are discovering large numbers of new viruses
what are types of virus hosts for different organisms?
Plants
Maize streak virus – single stranded, circular DNA genome ~2.7K bases, family Geminiviridae
Tobacco mosaic virus- positive-sense single-stranded RNA virus, genome ~6.4k bases, family Virgaviridae
Insects
Deformed wing virus - positive-sense single-stranded RNA virus, genome ~10k bases, family Iflaviridae
Linked to honey bee colony collapse disorder
Fish
Cyprinid herpesvirus 3 - double-stranded DNAvirus, genome ~ 295kbp, family Alloherpesviridae
Australian government were considering using as a biological agent to reduce the carp population
Archaea
Bottigliavirus ABV – double-stranded DNA virus, genome ~24k bases, family Ampullaviridae
Champagne bottle virion
Algae
Coccolithoviruses – double stranded DNA virus, genome ~419kbp, family Phycodnaviridae
Coccolithoviruses play an important role in the decline of algal blooms and carbon cycling
Bacteria - bacteriophages
What is viral species diversity and demarcation?
As there is no universal classification system for viruses, the species demarcation criteria varies between viral families.
Demarcation = the action of fixing the boundary or limits of something
e.g. how different do 2 nucleotide sequences need to be to be from viruses belonging to different species
Hepatitis C virus (species Hepacivirus hominis, family Flaviviridae) exists as 7 divergent genotypes differing from each other by about 15-25% at the nucleotide level
The Hepacivirus demarcation criteria is > 25% divergence in a conserved region of the NS3 protein
Viral members of species Enterovirus C (family Picornaviridae) include Poliovirus (which causes the disease polio) and numerous other Enterovirus C subtypes (some of which cause polio-like conditions).
The Enterovirus species demarcation criteria is > 30% divergence at the amino acid across the polyprotein
Caudoviricetes (phages) has a demarcation criteria of > 5% diversity at the nucleotide level
what are virus examples?
Rhinoviruses - causes common cold (rhino is Latin for of the nose)
Family Picornaviridae: linear single-stranded positive-sense RNA genome ~7-8.5 kb in length, single ORF
Herpes simplex virus - causes cold sores
Family Herpesviridae: enveloped, linear double-stranded DNA genome ~152 kbp in length, > 70 ORFs
Influenza virus - causes flu
Family Orthomyxoviridae: 6-8 linear single-stranded negative sense RNA segments (~10-14 kb in total length), at least one ORF on each segment
Human immunodeficiency virus - causes AIDS (acquired immunodeficiency syndrome)
Family Retroviridae: linear single-stranded positive-sense RNA genome ~9.75 kb in length [dimeric – two copies within the capsid], 9 ORFs
A retrovirusinserts a DNA copy of itsRNA genome into theDNA of the host cell (retro Latin for backwards)
Rabies virus – causes inflammation of the brain (rabies Latin for madness)
Family Rhabdoviridae: linear single-stranded negative-sense RNA genome ~12 kb in length, 5 ORFs
Most viruses do not infect humans!
Viruses have been invaluable model systems in the development of molecular biology and genomics.
what are bacteriophages?
Bacteriophages are viruses that infect bacteria
From the Greek ‘phagein’ meaning “to devour”
Phages are veryspecies-specific with regard to their hosts and usually only infect a single bacterial species or even specific strains within a species.
Phage genomes are composed of either DNA or RNA, which may be double-stranded or single-stranded.
This genetic material is packaged into a capsid that can be polyhedral (Microviridae, Corticoviridae, …), filamentous (Inoviridae),pleomorphic(Plasmaviridae) or connected to a tail.
Most isolated phages come from the class Caudoviricetes – currently about 1/3 of the total ICTV species
what is the lytic cycle?
Thelytic cycleresults in the destruction of the infectedhost cell and its membrane – the virus replicates to the point of cell bursting
Bacteriophages that only use the lytic cycle are calledvirulent phages
In the lytic cycle, the viral DNA exists as a separate free floating molecule within the bacterial cell, and replicates separately from the host bacterial DNA.
what is the lysogenic stage of viral production?
In Lysogeny, or thelysogenic cycle, a phage accesses a host cell but instead of immediately beginning the replication process leading to lysis, enters into a stable state of existence with the host.
Characterized by integration of thebacteriophagenucleic acid into the host bacterium’s genome – called a prophage - can be transmitted to daughter bacterial cells at each subsequent cell division
Later events (such asstress, UV radiationor the presence of certain chemicals) can release the prophage, causing proliferation of new phages via the lytic cycle.
Phages capable oflysogenyare known as temperate phages.
what is phage therapy?
Virulent bacteriophages can be used to treat pathogenic bacterial infections – phage therapy
First pioneered in 1919 by Felix d’Herelle, a French microbiologist who used ”an invisible, antagonistic microbe of the dysentery bacillus” i.e. phages, to cure a boy suffering from severe dysentery
However, the discovery of penicillin in 1928 and itssubsequent commercial production by the 1940s unleashed the antibiotic era
Antibiotic resistance is leading to a resurgence in phage therapy
Used therapeutically to treat bacterial infections in Russia and Georgia
High bacterial strain specificity of phage therapy – needs to be tailored for individual patients
what are RNA viruses?
Many notable human diseases are caused by RNA viruses
Common cold (Rhinovirsues, Picornaviridae) and Influenza (Orthomyxoviridae)
Measles (Measles morbillivirus, Paramyxoviridae), Mumps (Mumps orthorubulavirus, Paramyxoviridae), Rubella (Rubivirus rubellae, Matonaviridae), Chicken pox (Human alphaherpesvirus 3, Herpesviridae)
Norovirus (Norwalk virus, Calicivirdae)
Polio (Enterovirus C, Picornaviridae), Smallpox (Variola virus, Poxviridae)
Ebola (Zaire ebolavirus, Filoviridae), Zika (Zika virus, Flaviviridae), COVID-19 (SARS-CoV-2)
Yellow fever, West Nile fever, rabies, Hepatitis C, AIDS, Chikungunya, …
Many notable diseases of animals are also caused by RNA viruses:
Foot-and-mouth disease, Bluetongue, Schmallenburg, African swine fever, Classical swine fever, Canine distemper, avian influenza
do RNA viruses evolve?
RNA viruses evolve rapidly due to their error-prone RNA-dependent RNA polymerase [no proof reading]
Mutation rates of RNA viruses are cited to be between 10−4(1 in 10,000) and 10−5(1 in 100,000) substitutions per nucleotide per infection cycle (s/n/c)
Trade off between genome size and mutation rate – mutations are not necessarily good for a virus
do RNA viruses have large populations?
RNA viruses often have very large population sizes due to explosive replication
The number of viral particles in a given organism might be as high as 1012 [one trillion]
A single infectious particle can produce an average of 100,000 viral copies in 10 hours.
Holmes et al 2004 Nat Rev Microbiol. 2(4): 279-288
Combined with a high mutation rate this means RNA viruses often exist within host as a viral swarm – a large population of viruses with related genomes (containing a diverse spectrum of mutations)
what is foot and mouth disease virus?
Single-stranded positive-sense RNA genome ofapproximately 8.3 kb, family Picornaviridae
The virus causes a high fever followed byblisters [lesions] inside the mouth and on the feet that may rupture and cause lameness, sometimes fatal
An error rate of 10-4 substitutions per nucleotide per infection cycle
Equates 0.83 substitution on the viral genome per infection cycle
Mutations are random, but mutations that are beneficial to viral fitness will be rapidly selected for via selective pressures; and those detrimental selected against
Transmission bottlenecks between cells and hosts (the number of virions passing from parent to child) play an important role in transmission
Transmission chain experiment
Cow B1 infected with FMDV followed by controlled infectious contacts between cows
Full genome sequencing from the lesions of infected cows showed the virus mutates between 1-4 times per host
what are segmented viruses?
A viral genome fragmented into two or more nucleic acid molecules.
The entire Influenza A virus genome is 13,588 bases long and is contained on eight RNA segments (-ve ssRNA)
PB1 - polymerase complex
PB2 - polymerase complex
PA - polymerase complex
HA - hemagglutinin - protein the virus uses to attach to host cells
NP
NA - neuraminidase - enables the virus to be release from host cells
M
NS
Currently, there are 18 (H1 to H18) known types of hemagglutinin and 11 (N1 to N11) known types of neuraminidase, which gives 18x11 = 198 different possible combinations of these proteins.
what is antigenic shift?
Antigenic shift: an abrupt, major change in the influenza virus
Results in a new HA and/or NA proteins in flu viruses that infect humans, or new combination of existing HA and NAs
Shift can happen if a flu virus from an animal population gains the ability to infect humans.
This can be the result of co-infection of mutliple influenza viruses into a single host and reassortment of segments
When shift happens (not frequent), most people have little or no immunity against the new virus
what is antigenic drift?
Antigenic drift: small changes (via mutations) in the influenza virus genes particularly HA and NA
Driven by the high error rate of RdRp – drift is frequent/constant
What are antigenic shifts in influenza A virus?
Antigenic shift is the result of re-assorting between segments of different influenza A (different human viruses or between human and animal viruses)
New H or H&N in human population to which little or no immunity exists
Aquatic birds are natural reservoir for influenza A viruses
what are more types of viruses?
“Parasitic” satellite viruses or subviral agents
Hepatitis delta virus requires the envelope proteins of the helper virus, human hepatitis B virus (HBV) (familyHepadnaviridae) for assembly and release of infectious particles.
Recent discoveries of “giant viruses” with functions traditionally associated only with cellular organisms such as translation machinery, DNA maintenance, and metabolic enzymes.
For years Acanthamoeba polyphagamimivirus (APMV) was considered to be an intracellular bacterium of amoebae until sequencing
Mimiviruses can be infected by parasitic viruses (termed virophages)
Vector-borne viruses such as Zika infect and replicate in both the host (humans) and the vectors (mosquitoes)
Viroids - small single-stranded, circular RNAs that are infectious pathogens, lack a protein coat
Endogenous viral elements, or “EVEs,”arise when whole or fragmented viral genomes are incorporated into host cell germlines. - paleovirology
Not all viruses are bad!
Some viruses have beneficial properties for their hosts in a symbiotic relationship – “The good viruses: viral mutualistic symbioses” Roossinck, Nature review microbiology 99–108 (2011)
Viruses have been invaluable model systems in the development of molecular biology and genomics, phage therapy, viruses being used as vaccine delivery agents
what is phage T4?
Escherichia virus T4(family Myoviridae) has a 169 kb double stranded DNA genome - it encodes over 250 proteins
It is a virulent bacteriophage - kills the host bacterium by lysis.
Virulent phages always undergo a lytic life cycle, causing the death of host bacterium after each infection cycle
what is a virulent phage?
Bacteriophages that replicate only through the lytic cycle
No
Lytic cycle
Kills the bacterium after the infection cycle
what is a temperate phage?
Bacteriophages that replicate using both the lytic and lysogenic cycles
Yes [lysogenic cycle]
Both lytic and lysogenic cycles
Does not kill the bacterium immediately after infection
what is a lambda?
Enterobacteria phage λ(lambda phage,coliphage λ, officiallyEscherichia virus Lambda) is a bacterial virus, orbacteriophage, that infects the bacterial speciesEscherichia coli(E. coli)
Family Siphoviridae, linear dsDNA genome 48.5 kb in length
The Lamda cII gene plays a key role in determining whether the bacteriophage will incorporate its genome into its host and lie dormant (lysogeny) or replicate and kill the host (lysis).
cII is a transcriptional activator, and also unstable with a very short half life, enables environmental and cellular conditions to factor into the decision to lysogenize or to lyse its host
what is viral taxonomy?
Viruses are classified into groups called taxa according to their similarities and dissimilarities.
The lowest rank is the species
Species grouped into a Genus
Genera grouped into a Family
Families grouped into an Order
ICTV annually release a new viral taxonomy - metagenomics is expanding the taxonomy rapidly
Riboviria – all viruses with an RdRp
what is taxonomy?
Taxonomy - the discipline of classifying and naming things
Species are collected into genera, and so on up into families, orders, classes, phyla, kingdoms
