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How are Viruses Named

AFter geographic locales


Viruses Can infect bacteria: Bacteriophages

Gut virome is largely unexplored
Bacteriophage outnumber bacteria in the gut
- could be indicators of microbiome health
- could be used to alter microbiome therapeutically
- phases for food safety
- phases as biomarkers of health/disease
- phases as reporters of microbiome diversity
- phases for disease therapy
- phases as drivers of microbiota
- phases as delivery vectors


Plant Viruses

Viruses can also infect plants
Fungi are most important plant pathogens with viruses coming in second


Virus Eradication through Vaccination

Polio (soon)

If a virus only infects humans (like measles) and there is a good vaccine (Eg measles) then the virus can theoretically be eradicated through mass vaccination


History and important

Viruses in the 1860s Pasteur speculated about a pathogen too small to be detected with a microscope
1931 first images of viruses with electron microscopy

SARS, west Nile, influenza, Influenza, Ebola, enterovirus, Zika

- viruses are most abundant biological entity on early (10x higher than bacteria)
- major cause of human disease
- can cause cancer
- new viruses emerge all the time
- bacterial viruses help to move genetic information between bacteria increasing spread of drug resistance and affecting pathogenesis
- now we have antivirals


Virus size

100-1000x smaller than cells

<100nM in diameter or less
Smaller than RBC!!

Filamentous viruses like Ebola can be long and threadlike with lengths up to 1000 mm

Largest known infects algae and is 1/4 size of ecoli


Properties of Viruses

Contain DNA or RNA genome (never both)

No protein synthesis machinery (no ribosomes)

No energy generating machine

Nucleic acid enclosed in a protective coat (capsid)

Viral replication has two phases
- outside host: inert collection of macromolecules called a virion
- inside host: utilize host cell machinery to copy self and produce more virus

Do not grow or undergo division, assembled from pre-formed components

Obligate intracellular pathogens *NO EXCEPTIONS*


Basic Virus Structure

Protein shell (capsid) surrounding nucleic acid genome --> full assembly is called a nucleocapsid

Enveloped viruses have lipid membrane surrounding nucleocapsid

Naked or non-enveloped viruses have no membrane

Projections from surface of virion (spikes or envelop proteins) serve as sites of attachment to receptors on host cells


Virus Classification

DNA vs RNA **
Presence or absence of envelope **
Ds or ss genome, genome segmented or not


Practical implications of RNA vs DNA genomes

RNA dont have proof reading functions so they mutate more than DNA viruses

RNA viruses replicate quickly, particularly + RNA viruses, since their genome is in effect mRNA
--> do not cause chronic infections


Genome Size

Ranges from 2000 bp to 800,000 basepairs, super small! Depend on host cell p athways

- dont have to make ribosomes
- when viruses have larger genomes they encode proteins that modulate host in some way


How do viruses conserve genetic space?

1. Polyprotein production
- make polyprotein that is cleaved by a viral or cellular protease eg least efficient way for a virus to code for proteins is to have a separate gene for each with each gene having its own promoter so the polyprotein is cleaved by a viral protease resulting in production of final p rotein products
- clinically protease inhibitors used to treat HIV and hepC --> block viral polyprotein cleavage

2. RNA splicing
- same promoter, just splice things together

3. Overlapping Reading frames (and splicing)
- single promoter with overlapping reading frames
- when coupled with mRNA splicing, you again get different proteins produced via a common promoter
- given nucleotide may play a role in encoding two or even three different viral proteins

4. Ribosomal frame-shifting
- while scanning along mRNA ribosome will slip back one base and then continue again--> frameshift and production of a different protein


Capsid Functions

Capsid can have an icosahedral or helical shape

Packing or condensation

Protection of nucleic acid

Transport nucleic acid from cell to cell

Provides specificity for attachment

Metastable:capsid undergo changes that result in delivery of the genetic material into a cell (for a virus to infect a cell, it has to deliver its genome into the cytoplasm of the cell)


Virus Membranes

Some viruses consist of only a capsid (polio, hepatitis A, rhinoviruses)

Some viruses surround their capsids with a lipid membrane:
- all helical capsids are membrane enveloped (rabies, Ebola, flu)
- some icosahedral capsids are membrane enveloped (west Nile virus, yellow fever)
- since viruses cant make their own membranes they steal membrane from the cell through a process called budding



The process in which a viral matrix protein steal membrane from the cell to go from virion in the cell to free infection virion with a membrane around it

These have spike proteins which mediate attachment of virion to the host cell


Maturation and Budding of enveloped virion

- viral capsid assembles in the cytoplasm
- virus also makes one or more integral membrane proteins (the spike or envelope protein)
- capsid interacts with cytoplasmic domain of viral glycoproteins and zippers up
- virus buds from cell surface, pinching off and forming a new virus particle
- host cell proteins are excluded from the budding virus particle

**budding normally occurs at cell surface, but some viruses bud from ER (west Nile, hep B) and others from the golgi (Rift Valley river)


Spike Proteins

Enveloped proteins have one or more, they attach a virus to cell surface, get virus into cell, and are targets for antibodies


How does the envelope affect transmission?

Presence or absence of an envelope affects transmission
- enveloped viruses = HIV, hepB, influenza, herpes simplex, Ebola and are spread by body fluid and are stable outside the body
- enveloped viruses have lipid membranes that are stable making them very sensitive to osmotic stress, desiccation, and extremes of pH and salt so viruses surrounded by lipid membranes are transmitted by transfer of body fluids eg sexual transmission

non enveloped
- way more stable outside human body, can be transmitted by other mechanisms eg fecal-oral route (how polio and many other GI viruses are transmitted) eg rhinovirus, hepatitis A, polio
Not inactivated by ether (70% ethanol), simple soaps or Lysol but enveloped viruses are


Does Purell work?

Only against enveloped viruses like influenza, hepB, herpes simples 1 and 2 but less effective in controlling transmission of human enteric viruses


What should we know about viruses


Genome segmented? Eg influenza


Plaque Forming Units PFU

Way to measure virus in solution

Virus solution is serially diluted and placed on a monoolayer of cells growing in a dish, if virus lands on and infects a cell, new viruses will be made and these will infect adjoining cells

In 2 - 3 days monolayer will develop holes in it or plaques which you can see and count

Number of plaques correlates to number of infectious viruses--> can determine how much infectious virus you have


Viral Titer During a Single Cycle of Viral replication

PFU vs time,
Eclipse phase: attachment, disassembly (at first PFU goes down as the virus you add binds to and infects the cells), replication all intracellular, between start of infection and when the first progeny virus emerge

Post eclipse phase, PFU ^^ viruses are being made and released from infected cells


Virus Lifecycle

Translation, Transcription, Replicatin



Virus binds to a specific receptor, and the presence or absence of these receptors dictates virus tropism (ability of virus to infect some cell types not others)

Viral receptors are host cells that
- bind virus to cell (nonenveloped - bind capsid; enveloped - bind glycoprotein, receptor binding protein)

Act to tether virus

Trigger conformational changes in capsid or glycoprotein needed for entry

Send signals to cell that in some way prepare it for infection - i e the virus induces the cell to become a more permissive host

Receptors usually host surface proteins, sometimes carbs



Virus has to get inside cell - OBLIGATE INTRACELLULAR PARASITES - must find a way to get their genetic material into the cytoplasm because they cannot replicate in a vacuole like some bacteria and parasites
- some endocytosed
- enveloped viruses cause fusion between their membrane and that of the cell
- nonenveloped viruses either make a pore or actually disrupt the membrane

Three main ways to penetrate
- membrane fusion (enveloped) (attachment, receptor engagement, trigger event pH dependent or independent, conformational change, membrane fusion)
- pore formation (non enveloped) low pH in endoscopes induces conformation change in capsid proteins such that hydrophobic domains are exposed and insert into endosomal membrane forming a pore, viral DNA or RNA enters via the pore eg poliovirus
- membrane lysis (nonenveloped--> enter cells by endocytosis then lyse vacuole and escape to cytoplasm)



Viral genome is tightly compacted within capsid, so capsid has to uncoat for replication to proceed


Translation, transcription, replication

Make viral proteins, make viral RNA, replicate viral genome to make new viruses


Assembly and RElease

Put viral proteins, RNA and genome together to make new virus particles


Viral Tropism

Tropism: spectrum of tissues and cell types infected by a given virus

Some viruses have very restricted tropism, others broad

Explained by presence or abscence of viral receptor

Each type of virus binds to one receptor to attach to cell surface, initiating entry process


How do different viruses replicate their genomes

DNA genomes - large viruses (pox-, herpes-) encode enzymes required (eg DNA polymerase) and are more autonomous
- small viruses use host cell polymerase and other enzymes and DNA synthesis is inside the nucleus

RNA genomes - encode their own RNA dependent RNA polymerase, which uses complementary RNA as a template

Retroviruses (and HBV) copy a ss+ RNA genome into dsDNA which is the template for new genome synthesis

Key point: RNA dependent polymerase lacks proofreading and so RNA viruses mutate quickly and replicate faster