Viruses Flashcards
What’s a virus?
obligate cellular parasites
• smaller than a bacterium
– broadly distributed and the most effective replicators on earth;
– affect all forms of life – including other viruses!
• able to function only within the living cells of a host animal, plant, or microorganism,
• consists of a nucleic acid molecule (either DNA or RNA) surrounded by a protein coat, often with an outer lipid membrane.
Have only been known about for ~100yrs (original definition was simply if it passed through a filter – defo no longer valid!!)
Methods of studying viruses
- Pathology and transmission studies
- Electron microscopy
- Culture
- Detection of virions and immune responses
- X-ray crystallography
- Nucleic acid detection, sequencing, and analysis
The evolution and taxonomy of viruses remain dynamic sciences,
revolutionised by high-throughput nucleotide sequencing
diff bits of virus structure
capsid head w nucleic acid collar sheath baseplate spikes tail fiber
name 4 properties viruses can differ in
STRUCTURE
GENOME COMPOSITION
Nucleic acid
- DNA, RNA, both at diff stages in life cycle
Genome shape
- linear, circular, segmented
Strandedness
- Single-stranded, Double-stranded, DS with regions of SS
Sense
- + sense, - sense, ambisense (+/-)
GENOME MUTATION RATE (RNA has higher mut rate than DNA)
LIFECYCLES
what’s the baltimore system of classification and why is it needed?
o Groups viruses into families depending on type of genome and method of replication
o This system is needed as there is no presumed common ancestor for viruses
Group 1: dsDNA
Group 2: ssDNA (+)
Group 3: dsRNA
Group 4: ssRNA (+)
Group 5: ssRNA (-)
Group 6: ssRNA-RT (+) RNA with intermediate DNA in life-cycle
Group 7: dsDNA-RT DNA with RNA intermediate in life cycle
Group 6&7 are retroviruses, uses its own reverse transcriptase to convert its own RNA to DNA, which it then incorporates into the host genome
difference between RNA and DNA
The properties of DNA mean it’s more stable for our genomes
DNA
- Deoxyribose less reactive due to C-H bonds
- Stable in alkaline conditions
- Smaller grooves, more resistant to enzymatic attack
- Mostly double stranded
- > Lower mutation rate
RNA
- Ribose more reactive due to C-OH
- Not stable in alkaline conditions
- Larger grooves, more sensitive to enzymatic attack
- Mostly single stranded
- > Higher mutation rate
As mutation rate increases, genome size …..
- what does this mean for the high mutation rate of RNA?
- In general, as mutation rate increases, genome size decreases
- High mutation rate of RNA means it’s much harder to track viral phylogeny
- Higher eukaryotes (us!!) have v low mutation rates and big! genomes!
Is viral genome size related to host that they infect?
• Huge range in genome size and type of viruses, regardless of the host that they infect
eg. Similar range for invertebrates and protists – for no reason whatsoever!
Some viral genomes are segmented
- why?
- what does it enable?
- example of why it’s important
• For RNA viruses, each segment often codes for only one protein, usually found together on one capsid
WHY?
• RNA viruses often segmented because they need to have genomes in smaller bits so that an error in a single component won’t affect the whole genome (due to high error-rate when replicating)
Eg. Influenza A virus
WHAT DOES IT ENABLE?
• Enables re-assortment and recombination of their genomes – can have important consequences for viral evolution and immune escape by creating progeny with unique characteristics by shuffling genes
Eg. RNA exchange between mammalian and avian influenza viruses gave rise to influenza pandemic
What does lysogeny mean?
One of two cycles of viral reproduction
- Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host genome
- In this condition the bacterium continues to live and reproduce normally.
Latency and lysogeny (only applies to phages!!)
o rather than lysing the infected host cells immediately, phages can insert their DNA into host bacterial DNA
o bacteria divide many times, phage is latent within!!
o This enables long-term survival and introduces complex interactions of host and phage genomes
o phage induction happens, controlled by a genetic switch, where host DNA is destroyed and cell is lysed (baso standard lytic cycle)
o means lots more phages may be produced in the long term
Pseudolysogeny
- what?
Pseudolysogeny normally occurs under nutrient-deprivation, when bacterial host can’t support replication of its own DNA, the virus can’t replicate either until favourable nutrient-rich conditions ensue
Eukaryotic virus life cycle
Attachment
– specific binding between viral capsid proteins and receptors on host cell surface. This specificity determines the range of hosts that a virus can infect
Penetration
– virions enter host cell through endocytosis/membrane fusion
Uncoating
– viral capsid removed (degradation by viral/ host enzymes, releasing viral genomic nucleic acid
Replication of viruses
– synthesis of viral mRNA, assembly of viral proteins
Assembly
– self assembly of virus particles
Release
– cell bursts (lysis) or budding
Viral strategies to enter the cell
- barriers
- how to get over them
- The cell imposes intrinsic barriers to virus entry eg. Plasma membrane, actin cortex
- Viruses have evolved various strategies to overcome these barriers
Receptor-mediated endocytosis
o Eg. Bacteriophages have long tails used to attach to receptors on bacterial surface
o Eg. HIV can only infect a limited range of human leucocytes as the viral surface protein gp120 specifically interacts with the CD4 molecule found on the surface of CD4+ T cells
pH dependent fusion
o Acidic conditions of the endosome can induce fusion, releasing virus from vesicle into cytosol
Which 3 classes of virus all use +RNA strands as intermediates, as the templates for both translation and genome replication
dsRNA, ssRNA (+), retroviruses ssRNA-RT (+) &: dsDNA-RT
•dsRNA
+mRNA is synthesised (so there are 3 strands total), translated to form protein (which forms new virion cores). The cores mature, synthesising -RNA and adding exterior proteins. Result is spanking new virion!
•ssRNA (+)
can be directly translated by host ribosomes to form virion proteins. Small amounts of -RNA are produced and used as templates to greatly amplify viral +RNA, which is encapsidated into new virions.
•Retroviruses
use reverse transcriptase to convert RNA into cDNA, which are spliced into the host genome before they are transcribed to make +RNA, that is then translated into virion proteins using host polymerases
Using a diagram, describe the life cycle of a positive sense RNA virus
can be directly translated by host ribosomes to form virion proteins.
Small amounts of -RNA are produced and used as templates to greatly amplify viral +RNA, which is encapsidated into new virions.
difference between positive and negative sense RNA
Negative-sense RNA
- nucleotide sequence complementary to the mRNA that it encodes.
- cannot be translated into protein directly
- Instead, it must first be transcribed into a positive-sense RNA that acts as an mRNA
Positive-sense RNA
- can act as mRNA and be directly translated into protein!
Impacts of viruses on evolution
Large proportion of animal genomes are of viral origin
What are viral factories?
- Intracellular compartments which increase the efficiency of viral replication assembly and shield it from host defences.
- Can be cytoplasmic or nuclear
Spherules
– membrane invagination, can appear on many cellular compartments eg. Mitochondria or chloroplasts
Viroplasm – cytoplasmic inclusions
Double membrane vesicles – derived from ER or golgi
Nuclear viral factories – eg. Replication compartments
Retrovirus life cycle
•They have their own reverse transcriptase which they bring along with them
- Attachment - specific binding between viral capsid proteins and receptors on host cell surface.
- Adsorption and entry into cell of virions (endocytosis/membrane fusion)
- Uncoating – viral capsid removed (degradation by viral/ host enzymes, releasing viral genomic nucleic acid
- REVERSE TRANSCRIPTION - synthesis of cDNA using reverse transcriptase
- Nuclear import and integration of cDNA into host genome
- Transcription to make +RNA and nuclear export
- Translation into virion proteins, self assembly of virus particles and encapsidation
- Viral assembly and budding
Example of virus transforming a cell
Eg. Epstein-Barr Virus (EBV) transforms B cells
• V. common herpes virus, infects almost 90% of humans worldwide (normally harmless)
• Best known as cause of ‘mono’ or ‘glandular fever’
• The intrahost reservoir is B cells, almost always remains latent in these cells
EBVs can transform B cells, producing viral proteins that result in the development of malignant B-cell lymphomas (cancer!!) by causing uncontrolled proliferation, preventing apoptosis, and mimicking cell signalling pathways
What’s a retrotransposon?
A class of interspersed repeats that make up huge amounts of genomes
• mobile DNA sequences which can migrate to different regions of the genome
Class 1: Retrotransposons
o Require an RNA intermediate to transpose (unlike DNA transposons)
o Viral elements found in the genome that closely resemble retroviruses
o Thought to result from retrovirus invasion of host genome
o Include LINES, SINES, and LTR transposons
Impact of interspersed repeats on genome evolution
Interspaced repeats have a profound impact on genome evolution because they catalyse gene duplication
LINES
LINES (Long Interspersed Elements)
• Autonomous
• Ie. Encode their own reverse transcriptase
• retrotransposons derived from selfish DNA sequence
• Very ancient
• LINE1, LINE2, and LINE3 families make up ~21% of the human genome, but only a few of them are still able to transpose (move!)
• Dispersal via an RNA intermediate
SINES
SINES (Short Interspersed Elements)
• Do not encode their own reverse transcriptase
• NON-autonomous elements - relies on the reverse transcriptase to be produced elsewhere (eg. from LINE elements)
• Disperse via an RNA intermediate that goes under reverse transcription
• Evolved from small cellular RNAs eg. tRNAs – they are NOT old retroviruses!
• Those present indifferent organisms appear to have independent origins
Eg. Alu family
▪ repetitive elements found in primate genomes
▪ 300bp long
▪ There are more than 1million in the human genome (13% of human genome!)
LTR transposons
LTR (long terminal repeat) retrotransposons
• Really long repetitive regions on either end of a coding region/retrovirus
• Can help a TE/ retrovirus insert itself into the genome
• Integrated retroviral genomes!
• Most of them are decayed relics
• Usually not capable of transposing
• In cereal grasses, differences in genome size has been shown to correlate with the no. LTR retrotransposons
• No env gene means they can’t leave the cell
Viral evolution and origins
• Difficult to determine origin of viruses
- Debate as to whether they represent a 4th domain with a separate origin
- OR RNA viruses are a relic of the RNA world
- Or are they escaped genes?
• The sequence diversity is so wild because of the massively high mutation rate
• Recent improvements in nucleotide sequencing and analysis techniques are illuminating this area
• One suggestion that evolution of all classes of eukaryotic viruses involved fusion between structural and replicative gene modules from diff sources
Name a dsDNA virus
Varicella zoster virus
Name a ssRNA virus
+) and (-
(+) Dengue & Zika Flavivirus
(-) Rhabdovirus (rabies!!), Influenza A virus, measles morbillivirus
Name a ssRNA RETROvirus
+) and (-
(+) HIV
-) HTLV (Adult T-cell lymphoma
Name diff methods viruses use to transmit
and an example of each
Use pretty much every transmission method
• Direct transmission,
– Rabies (enveloped -ve ssRNA Rhabdo virus)
– Measles (-ve ssRNA morbillivirus)
– Varicella zoster virus (dsDNA)
• Respiratory tract, airborne,
– Influenza (enveloped, segmented -ve ssRNA)
• Gastrointestinal,
– Polio (naked +ve ssRNA Picornavirus, Enterovirus).
• Sexually transmitted,
– HIV (enveloped +ve ssRNA Retrovirus).
• Vertical transmission,
– HTLV (+ve ssRNA Retrovirus, also sexually transmitted and through
blood contamination).
• Arthropod borne,
– Dengue (+ve ssRNA Flavivirus),
– Zika (+ve ssRNA Flavivirus, also vertically transmitted)
Give an example of a segmented virus
Influenza (-) ssRNA
Factors affecting severity of disease caused by viruses
- Tissue tropism (some viruses virulence depends drastically on the tissue type infected)
- Acute or chronic phases of infection
- Host immune responses
- Immune status and age of host
- Interaction with microbiome
- Role of pathology in transmission
Eg. Rabies aggressive behaviour - Viral replication method
- Host factors
depending on these factors, infection with the same virus can have very different outcomes indifferent individuals or host species
Rhabdovirus
- causes what
- affects who
- type of nucleic acid
- how many proteins does it encode
- how transmitted
- how spread through host
Rhabdovirus
• Causes RABIES in a wide range of hosts (mammals, birds, reptiles, insects)
• Zoonotic infection of humans
- Enveloped (-) ssRNA genome
- Encodes 5 proteins
- Globally distributed, transmission directly from host-host through biting (saliva)
- Aggressive behaviour in the host is an essential component of disease – pathology vital to promoting transmission
• Spreads through host in NEURAL tissue ‘neurotropic virus’
- Referred to as an ‘immune privileged site’ because we don’t have lots of defences there
Replication cycle of rhabdo virus
- Binding and entry into host cell by endocytosis
- Fusion of viral membrane and endosome membrane to release viral genome
- Encapsidated -ve ssRNA serves as template for transcription, producing viral +mRNA by viral polymerase
- Translation and assembly of the 5 viral proteins into nucleocapsids
- Budding and release of rabies virus virions
Rabies virus entry into neurons and intraneuronal transport
o Rabies (rhabdo) virions introduced by animal bite
o ACh receptor at postsynaptic muscle membrane either enriches virus at NMJ/synaptic cleft, enabling more efficient infection of connected motor neurone, OR ACh receptor helps virus infect muscle cells
o Virus enters neurone
o Rapid transport through neuron as whole virions
o Once in brain virus multiplies, changing behaviour of host and killing it
o Salivary glands are important propagation site and exit route for virions
o Enriched at neuromusclular junction (enables more efficient infection of connected motor neurone) or initial amplification in muscle
Orthomyxovirus (Influenza A virus)
- Causes influenza in humans, birds, horses, pigs. Causes all flu pandemics
- Enveloped segmented -ve ssRNA
• Nucleocapsid contains
- Viral (-) ssRNA
- Viral RNA polymerase
- Endonuclease
• Encodes two proteins on surface of viral envelope (glycoproteins receptors!!)
- Haemagglutinin (HA)
- Neuraminidase (NA)
• Genome replication and transcription occur in host nucleus. Then exported for translation
Host specificity in Influenza
Trophic transmission is restricted by… Difference in expression patterns of viral receptors (Haemagglutinin/Neuraminidase) in diff hosts
o In PIG, swine trachea contains receptors for both avian and human virus so serve as a ‘mixing vessel’ in which reassortment can occur
o Highly virulent avian flu COULD evolve to use humans as a host – would be extremely problematic
Influenza pathogenesis
- what contributes towards it?
Combination of viral and host factors contribute to pathogenicity
VIRAL FACTORS: variation in viral proteins
▪ NA promotes efficient release of viral progeny from infected cells
▪ HA determines receptor binding
▪ PB1-F2 induces apoptosis
HOST FACTORS: certain risk factors determine virulence
▪ Elderly, children, pregnant women, immunocompromised
▪ Obesity, asthma etc.
Influenza outbreaks
- the two types
- what causes them
Seasonal influenza
o Causes annual epidemics
o Caused by POINT MUTATIONS in RNA that lead to ANTIGENIC VARIATION on viral surface
→ New flu vaccines required every year
Pandemic influenza
o Caused by simultaneous infection of a single cell by two pre-existing influenza A virus strains – RE-ASSORTMENT (gene mixing) results in generation of NOVEL influenza virus strain. This is called ‘ANTIGENIC SHIFT’
→ Virus able to get past the first line of defence (host immunity) increasing the number of hosts susceptible to the disease, therefore improving transmission.
Eg. RNA exchange between mammalian and avian influenza viruses gave rise to influenza pandemic
Influenza has achieved spread worldwide on more than one occasion, most notably 1918 pandemic that killed up to 100 million people
Human immunodeficiency virus (HIV)
- causes what
- affects who
- type of nucleic acid
- how transmitted
- how spread through host
- strategy
- Causes AIDS in humans
- Enveloped (+) ssRNA retrovirus
- Mostly sexually transmitted by contact of blood, semen etc., can occur vertically from mother to child through bodily fluids such as blood, breast milk
- Infects immune cells
- CD4+ T helper cells
- Macrophages
- Dendritic cells
- Progressive failure of immune system allows life-threatening opportunistic infections and cancers to thrive
Strategy - COLONISER - keep host alive as long as possible to keep transmitting, eventual breakdown into (AIDS).
Progression of HIV to aids
- Acute HIV infection
▪ acute spike in viremia
▪ Large no.s of viruses produced, attack CD4+ cells
▪ Rapid drop in no. CD4 T cells
▪ Flu-like symptoms eg. Fever, headache, rash
▪ Viral set point maintained by combination of cellular and humoral response - Chronic HIV infection
▪ May be asymptomatic
▪ HIV continues to multiply but at v low levels
▪ extended ‘clinical latency’ phase at ‘set point’
▪ Gradual depletion of CD4 count over time
▪ Can last 10 yrs or longer - AIDS
▪ Occurs following opportunistic infection
▪ If virus wins battle against CD4 T cells , drop of T cells (count below 200cells/mm3) causes lack of control of viremia, leading to full blown aids.
▪ Ends in death
Population dynamics of HIV
Colonisers (eg. HIV) are modelled as SI systems
• SI systems exhibit logistic growth with carrying capacity at 1-1/Ro
• SI systems do not have a tendency to oscillate
HIV Replication cycle
- Attachment to T cells via CD4+ receptors
- Fusion and uncoating
- +ssRNA reverse transcribed to dsDNA
- Imported into nucleus and integrated into cellular DNA by integrase enzyme
- Has both acute and chronic phases ie. may become latent once integrated
- OR Trancription to make mRNA, nuclear export, translation of viral proteins, assembly
How does HIV persist and evade the immune system & maintain chronicity?
- Escape from CD8+ T cell responses – peptides can acquire mutations so no longer recognised by CD8 T cells (??)
- Escape from antibody responses - HIV capable of varying its envelope proteins
- Switch in tropism - HIV able to switch receptor. Allows it to exploit different resource
Dengue flavivirus virus
- causes what
- type of nucleic acid
- how transmitted
- encodes
- Family Flavivirus (v closely related to zika virus)
- Causes dengue fever
- Enveloped (+) ssRNA
- Mosquito bourne
• Emerging disease in tropical regions
- Most infections have minimal/no symptoms
Encodes
- 3 structural proteins in capsid
- 7 non-structural proteins
4 SEROTYPES (genetically and antigenically related viruses that cause same diseases)
Dengue flavivirus life cycle
Life cycle
- Dengue virions bind to cell surface receptors and are endocytosed
- Acidification of endocytic vesicle causes fusion of viral and vesicle membrane, and release of viral ssRNA
- Etc. etc.
Dengue ‘antigenic sin’
- what
- can lead to
There is long-lasting HOMOTYPIC protective immunity against the serotype/strain of dengue infected with on primary infection
• Secondary infection with a diff serotype much more dangerous
‘Original antigenic sin’
Immunological memory is ‘skewed’ towards serotype of previous infection, memory B and T cells are not as optimal as would be when responding to new virus
Can lead to severe and life threatening haemorrhagic fever
