Intro to viruses Flashcards
Description of viruses
1. Small, obligate intracellular pathogens
- Filterable agent
- not visible by light microscopy
2. no subcellular organelles
3. replicate only in living cells
- can not be cultured like bacteria
- rely on host cell protein synthesis machinery
4. New viral particles (virions) are assembled, the virus does not divide
Components of a virus
Composition of viruses (naked vs.. enveloped viruses)
1. Naked Viruses
DNA/RNA + Structural Proteins (Capsid proteins) +/- Enzymes and Nucleic acid-associated proteins = Nucleocapsid
2. Enveloped Viruses:
Nucleocapsid + glycoproteins & membrane = Enveloped virus
Naming Viruses:
- After clinical conditions
Naming Viruses:
- After their location of discovery
Naming Viruses:
- After their properties
&
- After people
Basis of “Baltimore classificaton system” and what are the classes
Baltimore classification system
- Based on the type of nucleic acid genome & replication strategy of the virus
- Type of nucleic acid dictates replication strategy
Classes:
- I: dsDNA viruses
- II: ssDNA viruses
- III: dsRNA viruses
- IV: positive-sense ssRNA viruses (+ssRNA)
- V: negative-sense ssRNA viruses (-ssRNA)
- VI: RNA viruses that reverse transcribe
- VII: DNA viruses that reverse transcribe
Classification of medically important DNA viruses
Classification of medically important RNA viruses
How do viruses infect cells?
- Attachment
* Can’t infect a cell if it can’t bind to that cell
2. Entry/uncoating
- Genome needs to be released into the host cell
3. Macromolecular synthesis
- Viral proteins get transcribed/translated
- Genome gets copied (replicated)
4. Assembly & release
- New viral particles self assemble
- Released from the host cell & spread to infect new cells
DNA vs. RNA Viruses
What are the clinical consequences of different types of genomes in viruses?
- DNA viruses and retroviruses
- Transformation
- Latent infections
- RNA viruses:
* Variability ==> “quasi-species” ==> Immune escape variants
Different capsid in viruses
- Helical
- Icosahedron
- Complex
- Poxviruses
- Oval shaped virus with dumbell shaped capsid
What are the functions of the viral capsid?
- Protect the genome
2. In naked viruses – involved in attachment
- Involved in entry & uncoating
4. Involved in assembly
- package viral enzymes if necessary
Properties of Naked, Icosahedral viruses
They are tough!!!
- Can dry out and RETAIN infectivity
- Can survive the acidic consitions of GI tract
- Resistant to extreme temperatures, detergents and poor sewage treatment
- Typically* released via cell lyses
- Survival in environment enables transmission via fomites
* difficult to disinfect contaminated surfaces - Survival in GI tract enables transmission via fecal-oral route
- shed in stool
- present in sewage/contaminated water
- responsible for most cases of viral gastroenteritis
- Cytopathic
* cell undergoes morpholical changes after addition of virus
Describe the viral envelop
- Host derived lipid membrane
- Viral encoded proteins
- Matrix proteins = for assembly
- Surface (envelope) glycoproteins
- viral assembly
- virus-cell fusion
- induce neutralizing (protective) antibody
Properties of enveloped viruses
- must stay wet to retain infectivity
- Acid and heat labile
* acid and heat causes destruction of virus - Infectivity is destroyed by organic solvents and detergents
- Released by budding (may cause cell lysis over time)
clinical properties of enveloped viruses
Remeber they must be wet to be infective
- Transmitted via respiratory droplets and secretions
- respiratory route
- blood
- organ transplant
- Cannot survive in the GI tract (Usually*)
* Not transmitted fecally or orally - Does not need to kill infected cell in order to spread
* Potential for persistance
Viral Replication
Steps in viral replication
- Attachment
- Entry and uncoating
- Macromolecule synthesis
- Transcription of viral genes
- Translation of viral proteins
- Replication of viral genome
- Assembly and release of new viral particles
5.
Attachment phase (in viral replication)
- Mediated by surface glycoproteins of enveloped viruses
- Mediated by capsid proteins of naked virions
- Important determinant of viral tropism
Viral Receptors
- Proteins or carbohydrates on cellular glycoproteins or glycolipids
- Physiological role in host cell
- Type of receptors:
- molecules involved in cell-cell interactions
- hormone, cytokine, or complement receptors
- enzymes
Viral Entry through PM
Naked vs Enveloped viruses
- Naked Viruses:
* Hydrophobic interactions create a channel through the membrane
- Enveloped viruses
* Hydrophobic domain (fusion peptide) in the attachment protein is exposed, following binding to a receptor or proteolytic cleavage at the plasma membrane
What are the 3 endocytotic pathways utilized by viruses?
- Phagocytosis
- Macropinocystosis
- Various endocytotic pathways:
- Clathrin-dependent endocytosis
- Caveolin-dependent endocystosis
- clarthrin and caveolin independent endocytosis
Clathrin-mediated vs Caveolin-mediated ENDOcytosis
Clathrin-mediated:
- pH-dependent entry into an endosome
- virus gets internalized from a region of the plasma membrane that contains a protein called clathrin, forming a “clathrin-coated pit”. The virus becomes enclosed within a vesicle called an endosome, which subsequently fuses with a lysosome. During this process, the pH of the endosome becomes more acidic. Some viral fusion proteins require exposure to either an acidic pH or lysosomal proteases to become activated so that they can mediate fusion between the viral envelop & the membrane of the endosome.
Caveolin-mediated:
- pH independent entry
- In caveolin-mediated endocytosis, virus becomes internalized at membrane invaginations that contain a protein called caveolin. These invaginations occur at a region in the plasma membrane that has a high density of relatively detergent-resistant lipids called lipid rafts. The vesicles containing virus fuse with other caveolin-containing vesicles forming a caveosome – these vesicles do not become acidified. Virus can be transported to other regions of the cell (such as the ER) before the genome is released into the cytosol.
Receptor mediated endocytosis of Naked, Icosahedral viruses
1. Viral capsid proteins form a pore through the endosomal membrane
- Viral capsid proteins lyse the endosomal membrane
- Conformational change in capsid proteins
- Expose a hydrophobic region (make a pore)
- Dissociate to release the genome (uncoating)
- Potential triggers for conformational change
- Acidic pH
- Proteolytic activity
- Receptor binding
Example of viral entry
Viral uncoating == release of genome
Objectives:
- get rid of the capsid
- RNA ==> cytoplasm
- uncoating coincides with entr
- DNA ==> nucleus
Triggers for uncoating include:
- binding to a receptor
- change in pH
- proteolytic degradation
On image:
- Step 1 involves attachment of the fiber to the primary receptor, which is on most cell types and for most HAdV types is either CAR or CD46.
- This is followed by clathrin-mediated endocytosis in step 2, which is facilitated by the penton base interaction with αv integrins.
- The virion begins to dissociate in the low pH environment of the early endosome (step 3),
- and releases the vertex proteins including pVI in the early or late endosome (step 4). Protein pVI has been implicated in disruption of the endosomal membrane, allowing the virion to escape from the endosome.
- The partially disassembled virion is transported by the microtubule motor dynein along microtubules to the nuclear pore complex (step 5).
- At the nuclear pore the viral DNA is imported into the nucleus (step 6).
Reasons for taking over host cell
- Control transcription
* make viral mRNA - Replicate genome
3. Control protein synthesis
- make viral proteins
- shut down synthesis of host proteins
Viral Transcription: general properties
1. Early transcripts:
- encode regulatory enzymes & proteins
- control transcription of viral mRNAs
- initiate replication of the viral genome
- shut down host protein synthesis
- Late transcripts:
* encode viral structural proteins
Properties of DNA viruses
- Transcription & replication occurs in the nucleus
* exception = pox viruses - Genome = template for mRNA
3. DNA viruses can be single or double stranded
4. Some DNA viruses use cellular polymerases to replicate the genome & transcribe viral mRNA
Replication of DNA viruses (image)
See image
+strant vs -strand RNA viruses
1. Genome can function as mRNA
- ¡Comparable to the DNA coding strand
- ¡translated as a polyprotein, then cleaved
2. Virus encodes an RNA-dependent RNA polymerase
- Transcription produces (–) strand RNA
- ¡template for mRNA
- ¡template for genomic RNA
+strand RNA viruses
- Genome can function as mRNA
- Comparable to the DNA coding strand
- translated as a polyprotein, then cleaved
(Coding DNA strand is the one thats identical to transcribed mRNA, sans U residues : U–>T)
2. Virus encodes an RNA-dependent RNA polymerase
3. Transcription produces (–) strand RNA
- template for mRNA
- template for genomic RNA
(-) strand RNA viruses
1. Virus encodes an RNA-dependent RNA polymerase
- core protein
2. The genome is a template for mRNA
- Comparable to the DNA template strand
3. A (+) strand copy of the genome is the template for genomic RNA
Double stranded RNA viruses
- Genome is segmented
* Each segment encodes a protein
2. Virus encodes an RNA-dependent RNA polymerase
- Core protein
Retroviruses
- (+) strand RNA is transcribed into DNA
* reverse transcriptase (RNA-dependent DNA polymerase) is a core enzyme - DNA travels to the nucleus where it integrates into host chromosomes
3. Transcription of DNA produces mRNA and genomic RNA
Assembly and release (of virions)
- Capsids self assemble
* Package genome & core enzymes - Naked virions are typically released upon cell lysis
3. Enveloped viruses bud
- Matrix proteins determine site of budding
- plasma membrane, ER, golgi, nuclear membranes; released via exocytosis
- act as a bridge between nucleocapsid & surface glycoproteins
NOTE – There is evidence that some naked viruses can be released without lysis of the host cell. These viruses appear to induce formation of vesicles that resemble autophagosomes & viral particles are released from these vesicles.
Viral Budding (images)
- Budding from the cell membrane
- Budding into the ER
Role of antiviral therapies
- Disrupt viral structure
* ¡Detergent inactivates enveloped viruses
2. Block a virus-specific activity…
- ¡Targets include enzymes (polymerases, proteases), attachment proteins (virus specific)
- ¡Steps in the replication cycle that are unique to viruses
3. Without interfering with a host cell function
- ¡Disrupt host functions ==> toxicity
Types of viral infections (at the Cellular levl)
1. Productive infection
- Progeny virus is produced
- Infected cells are permissive for the virus
2. Nonproductive infection
- No progeny are produced
- Cells are nonpermissive
Types Productive Infections
recall:
1. Productive infection
- Progeny virus is produced
- Infected cells are permissive for the virus
- Lytic infection
- ¡Destruction (lysis) of the host cell
- ¡Produces a cytopathic effect (CPE)
- Persistent (chronic) infection
- ¡Virus buds from host cell without lysing cell
- ¡Continual shedding of virus
3. Persistent infections with lytic viruses
- ¡Occurs at the tissue or organ level
- ¡Some cells in an organ are lysed but not all
Types of Cytopathic Effects (CPE)
1. Syncytia formation
- Multinucleated giant cells
2. Cell rounding or vacuolization
3. Inclusion bodies
- New material within host cells detected by histological stains
- Sites of viral replication
NB: Type of CPE in a specific host cell helps clinical virologists identify the virus
Types of Non-productive infections
Recall:
Nonproductive infection
- No progeny are produced
- Cells are nonpermissive
1. Abortive
- Host cell cannot support viral replication
- Viral genome is lost
2. Latent infection
- The virus is dormant within the host cell
- The viral genome is maintained
- Viral transcripts may be detected; few or no viral proteins are expressed
- Immune response does not recognize that the cell is infected
- Occurs in DNA or retroviruses
- Reactivation of a productive infection is possible
Examples:
Describe immortalizing or transforming infections
1. One or a few viral genes are expressed
2. Immortalized cells may or may not become tumor cells
- Transformed cells are immortalized
- Immortalized cells over time may pick up mutations that lead to oncogenesis
3. Viral genomes usually integrate into the chromosome in transforming infections
- Cells are semi-permissive for the virus
Mechanisms of transformation
1. Inactivate growth-regulatory proteins
- p53
- Retinoblastoma gene product (RB)
2. Provide or up-regulate genes involved in cell progression through the cell cycle
Possible consequences of transformation
1. Uncontrolled cell growth
2. Increased growth rate
- Alteration of morphology & metabolism
- Decreased requirement for serum growth factors
- Alterations in cell surface components
- Increased metabolic rate
- Loss of contact inhibition of growth
What some examples of transforming viruses
See image
Consequences of viral replication
Types of clinical infection in the host
1. Acute infection
- Localized or disseminated
2. Chronic infection
- Acute infection, then carrier state with persistent shedding of low levels of virus
- Latent infection/reactivation of productive infection
- Transformation – cancer induced by viruses
Acute infection – remains localized
- Localized infection
- Productive infection at the site of entry
- Virus is cleared by the immune response
2. Acute disease
- Symptomatic illness
3. Asymptomatic or subclinical infection
- Infected individual can shed virus
Characteristics of localized infections
1. Self limiting
- Site of entry is often mucosal surfaces
- Respiratory or gastrointestinal tracts
- IgA provides protection
- Immunity often short-lived
- Some cold viruses or viruses causing gastroenteritis
Dissemination of Localized infection
1. Productive infection at the site of entry
- May be asymptomatic
2. Spread via lymphatics, blood or neurons
3. Replication at secondary site
- Characteristic symptoms
4. Secondary viremia is possible
5. Measles, mumps, rubella, varicella (chicken pox)
Characteristics of disseminated infections
1. Virus shedding typically occurs following initial replication
- Patient is infectious before illness is recognized
2. Incubation period occurs as virus disseminates
3. Nonspecific or flu-like symptoms during dissemination = prodrome
4. Symptoms correlate with replication at a secondary site
- Illness is recognized
5. IgG is important for immunity (usually lifelong)
Describe Chronic viral infections
1. Virus persists over time
- Could be productive or nonproductive at the cellular level
2. Productive – viral shedding over time
- Cellular level – host cell is not destroyed by the infection
- Tissue level – only a few cells in the population are infected at any one time
3. Nonproductive – latency or transformation
- Reactivation of a latent virus results in a productive infection
- Individual is infectious during reactivation but not during latency
- Transformation – cells are altered
- Contain viral sequences but do not produce virus, thus individual is not infectious
Productive, persistent (chronic) infection
1. Continual shedding of low levels of virus
- patient becomes a carrier
- patient is infectious even if asymptomatic
- patient may develop clinical disease over time
- Chronic Hepatitis B or C virus; HIV
Describe the process that takes place:
Latency ==> Reactivtion (of virus-causing infection)
- Initial productive infection occurs upon acquisition of the virus (primary infection)
- virus may remain localized or disseminate
- may be symptomatic or asymptomatic
2. Latent infection
- virus is not replicating (nonproductive infection)
- patient is asymptomatic
3. Reactivation of productive infection
- may be symptomatic or asymptomatic
- secondary infections are cleared more rapidly than primary infections
- Herpesviruses
Course of infection (chart)
Disease (caused by virus)
- Depends on whether or not the pathogen can overwhelm the immune response
- Symptoms of disease
- Direct result of a virus infecting & killing a cell
- Result of the immune response to the virus-infected cells (immune-mediated)
- Infection can be subclinical or asymptomatic
* Virus can still be shed and transmitted to a new host
Consequences of viral replication (chart)
What are some Viral factors influencing disease?
- Transmission determines site of entry
- Inoculum size influences severity
3. Tissue tropism determines site of pathology
4. Viral virulence factors
- Mechanisms to control host cell protein synthesis
- Mechanisms to evade the immune response
- Mechanisms to directly damage cells
Host factors influencing disease
- Immune status
- Compromised versus non-compromised immunity
- Prior immunity
- General health of the patient
* Nutrition
3. Age
4. Genetic background
Antiviral therapy - considerations (chronic infections)
1. Acute viral infections – treat symptoms
- Immune system will eliminate the virus
2. Early initiation of therapy
- Viral replication may precede symptoms
3. Chemoprophylaxis
- Outbreaks in a confined setting
- example – flu outbreak in a nursing home
4. Useful for more chronic infections
- HIV, viral hepatitis
5. Current antivirals inhibit actively replicating virus, not latent infections
What type of virus is norovirus, a common cause of viral gastroenteritis?
Information from CDC:
1. Norovirus outbreaks from contaminated food are common in food service settings.
- People infected with norovirus are very contagious.
* … they shed billions of tiny viral particles in their stool and vomit…
3. Norovirus is hard to kill and stays on food, kitchen surfaces, and utensils. It can:
- Remain infectious on foods even at freezing temperatures & until heated above 140°F.
- Stay on countertops and serving utensils for up to 2 weeks.
- Resist many common disinfectants and hand sanitizers.
4. Illness resolves after ~48 hours with no long term consequences
What type of virus is HIV?
- HIV can cause a productive, persistent infection in macrophages; macrophages can shed virus for an extended period of time (days to a couple weeks)
- HIV can cause productive infection in activated T cells but l_atent infection in memory T cells_
- The host immune response & anti-retroviral therapy both provide selection pressure for the generation of quaisispecies
Each bulleted statement implies what viral property? Virulence/virulent factors, tropism
What type of polymerase does HIV encode? Reverse transcriptase (RNA-dependent, DNA polymerase)
What type of virus is Varicella-Zoster virus (VZV), the etiologic agent of chicken pox & zoster?
- Zoster, but not chickenpox, is an endogenous infection
- VZV is transmitted primarily via respiratory droplets, though manifestation of disease involves vesicle formation in the skin
3. Viral entry and uncoating occur at different sites within a cell
Each bulleted statement implies what viral property?
What type(s) of viruses have genomes that are “infectious nucleic acids”?
Viruses with “infectious nucleic acids” have genomes that are capable of initiating viral replication when introduced into a permissive host cell
