Virology Flashcards
describe the key features of virus morphology and viral genetics and how they are used to
classify viruses
Morphology (shape, size): * icosahedral viruses - the capsids of “spherical” viruses usually have
icosahedral symmetry
* filamentous viruses
– the nucleocapsid
proteins (protomers
/capsomeres) wrap
around the nucleic acid in a helical array
* pleomorphic viruses
– variable in
size/shape
- typically have a helical or
icosahedral capsid beneath a
pleomorphic envelope
Chemical composition of genome * DNA or RNA, single stranded (ss) or
double stranded (ds), linear or circular
* genome may comprise one nucleic acid
molecule or several nucleic acid
segments with identical or different
genes on each segment
* different types of genome utilize different
replication strategies
explain rotational symmetry and identify symmetry axes in 2-dimensional objects;
A shape has Rotational Symmetry when it still looks the same after some rotation on its axes a fraction of 360.
Slide 12
describe a simple icosahedral viral capsid structure, including its symmetry and
composition;
adenovirus -
The adenovirus capsid is comprised of two different types of
capsomeres: pentons and hexons.
The pentons of the 12 vertices consist of 5 identical 85 kD protein
subunits and show 5-fold rotational symmetry
discuss why viruses must be “semi-stable” to promote infectivity;
To survive in a harsh extracellular environment, the virus
genome must be contained inside a stable, protective coat (or
capsid). However, to propagate inside a host cell, this
protective capsid must become unstable and release the virus’s
genetic material.
explain why some viruses do not follow Crick’s central dogma of molecular biology
- viruses with (+) RNA genome can make protein directly from their genome, which serves as mRNA
Slide 28
understand and apply the Baltimore Classification scheme
The Baltimore Classification System is a scheme for classifying viruses based on the type of genome and its replication strategy.
Slide 32 or yt video
discuss basic principles of phylogenetics
Phylogenetics refers to the use of genetic information to infer
similarities among members of a group
* Sub-groups are organized into clusters around nodes on a
phylogenetic tree.
* Sequence alignment and tree structure are maximized
using computational methods
* Branch length IS and indication of similarity among
individuals, inferred using computational methods.
Steps required to build a phylogenetic tree:
1. Sequencing
2. Alignment and analysis
Maximum parsimony methods attempt minimize the total number of evolutionary events. Shortest tree that explains data is considered best.
Maximum likelihood methods use statistical techniques to assign
probabilities to possible phylogenetic trees and selects the one with the
highest probability. Tree with fewest mutations at internal nodes is
considered best.
3. Visualization
describe the key steps involved in virus entry;
1.Attachment:
* Binding of viral surface proteins to cellular surface proteins, carbohydrates,
and lipids.
2. Entry (penetration):
* Movement of the viral capsid/genome across the plasma membrane and into
the host cell cytoplasm
3. Capsid uncoating:
* Disassembly of the stable capsid particle, leading to genome replication
4. Intracellular trafficking
* Localization of the viral genome to the correct cellular compartment for
replication (either the nucleus or within the cytoplasm)
explain viral tropism at the level of cells, tissues and hosts
Tropism: The types of cells,
tissues, or organisms that can be
infected by a pathogen
Viral tropism is determined by:
* host cell susceptibility (i.e. the
presence or absence of an entry
receptor); and
* permissiveness (i.e. the
metabolic activity, expression of
essential proteins, and ‘innate’
antiviral properties of the cell)
*CELLULAR TROPISM - HIV NORMALLY INFECTS MACROPHAGES BUT NOT NEURONS
*TISSUE TROPISM- INFLUENZA VIRUS INFECTS LUNG TISSUES BUT NOT BRAIN TISSUES
* HOST TROPISM - MYXOMA VIRUS NORMALLY INFECTS RABBTIS BUT NOT HUMANS
explain how conformational changes in viral surface proteins are initiated and
why they are important during the entry process
Lipid mixing is initiated by a fusion peptide
locate in the viral surface/spike protein
* Conformational changes in the viral
surface protein (hairpin intermediate)
bring the virion membrane into close
proximity to the cellular membrane
discuss virus and cellular factors that determine tropism, including the role of
host dependency factors and host restriction factors;
Distinct surface molecules and entry receptors
* Overlapping as well as distinct cellular proteins or isoforms
involved in viral replication and protein
“Direct” impacts
via interactions
with viral proteins
(i.e. TMPRSS2)
* “Indirect” impacts
via alteration of
normal cellular
functions (i.e.
protein trafficking
and modifications )
Host cell molecules that promote virus replication are called dependency factors
Restriction = opposite
describe how ”functional genomics” methods are used to explore host/virus interactions
We can screen for proviral host factors or restriction factors through loss of function and gain of function mutagenesis.
explain the general strategies used by DNA and RNA
viruses to replicate their genomes;
DNA:
Bi-Directional:
- Most similar to host cell replication
- Basic DNA replication review slide for steps
Example - Papillomavirus (~8000 Nucleotides):
- Use bi-directional replication strategy
- Occurs in nucleus and requires host cell proteins
- Two viral proteins are critical:
- E1 recruits cellular DNA polymerase to viral ori
- E2 recruits a cellular ssDNA binding protein (RPA)
Strand Displacement:
- ssDNA synthesis usually initiated by a “hairpin” loop located at the 3’ end of the DNA
genome (serves as primer for DNA polymerase)
- In adenovirus (dsDNA) replication is primed by a viral protein (pre-terminal
protein pTP)
- Produces a ssDNA which can be copied into a double-strand-DNA
- Concatemers are processed post-replication
Rolling Circle: - Viral endonuclease creates a nick in the origin of replication
- Replication machinery assembles with the DNA polymerase on the 3’ extremity
- The DNA polymerase and associated factors begins to proceed to a strand displacement
synthesis, producing a concatenated linear ssDNA with one genome copy per turn of
replication - On concatemer strand RNA primer are removed and Okazaki fragments are ligated
- Replication forks go on and produces a long linear concatemer which will be processed
into linear genomes and encapsidated
RNA:
Monocistronic: genomic RNAs encode a single mRNA that is translated into a
single viral protein (typical of segmented genomes, where each “chromosome”
will encode a unique protein product).
Polycistronic: genomic RNA forms a single mRNA that is translated into a single
polyprotein, which is subsequently cleaved to form the viral proteins
Complex: various mechanisms used to produce different viral proteins from the
same strand of RNA (including subgenomic mRNAs, ribosomal frameshifting and
proteolytic processing of viral polyproteins)
describe the role of RNA-dependent RNA polymerase
(RdRp)
- RNA-dependent RNA polymerase (RdRp) is responsible for both viral RNA replication and RNA transcription for most RNA viruses.
– Replication: synthesis of an exact replica of the viral RNA genome
– Transcription: synthesis of new mRNAs, most of which are not full-length
copies of the viral RNA genome
explain the general strategies used by viruses to exit
infected cells;
Many viruses exit cells using the “biosynthetic
secretory” pathway
discuss the role of viral replication compartments
- Consolidate viral proteins (and genomes) to enhance virion production
- Protects viral products from recognition by host cell defenses
- Frequently requires reorganization of cellular lipid membranes
Viruses rearrange cellular membranes by co-opting and redirecting normal
cellular machinery
describe general features of the immune response to viral infections,
including some important cellular mechanisms, receptors and cell
types that are involved
Immediate response - preformed effectors
Induced response - soluble effectors
Delayed response - antibodies and effector t cells
discuss the differences between “innate” and “adaptive” immune
responses and know their distinct roles;
Innate immunity is the body’s first line of defence against pathogens. It is general and non-specific, which means it does not differentiate between types of pathogens. Adaptive immunity is a type of immunity that is built up as we are exposed to diseases or get vaccinated
explain the importance of interferon and inflammation;
They are secreted from infected cells and activate innate immune response that promotes not only cytokine production but also natural killer cell functions and antigen presentation
Inflammation enhances the host
response by stimulating and
recruiting new immune cells to
the site of infection
Triggered by macrophages,
which express numerous
“scavenger” receptors
explain the term “antigen” and how antigens contribute to the
adaptive immune response
Antigens bind to antibodies and can trigger adaptive immunity as Lymphocytes express unique receptors that allow them to recognize a pathogen-derived
protein or protein fragment
discuss some strategies used by viruses to evade host immunity,
including “sequence adaptation”
- Glycosylation (and other post-translational modifications)
* alters the structure of viral Surface proteins
* physically blocks antibody binding and immune recognition - Sequence evolution
* “adaptation” to immune selection pressures
* alters the sequence of viral Surface and Internal proteins to evade
B cells/antibodies and T cells - Modulation of critical cellular defense mechanisms, including immune
receptors and signaling proteins
* Herpesviruses (and other large DNA viruses) encode multiple
strategies to impair innate and adaptive immunity
ex hiv 1- the glycan shield
describe active vs. passive immunization
Active immunization
* administration of a vaccine, an agent that can elicit a
protective immune response against a specific pathogen
* prophylactic – prevents disease caused by future infections
* lifelong immunity is achieved for some vaccines – depends on
the pathogen and the vaccine
* protection is mostly antibody-mediated
* typically given to children at a young age, before they contract
infections that are typically acquired early in life
Passive immunization
* administration of antibodies (or lymphocytes) that provide
protection post-exposure
* this provides transient immediate protection but no memory B
are produced so there is no protection against future infections
of the same pathogen - passive immunization is a treatment
* E.g. the immunoglobulin component of the rabies vaccine
discuss the similarities and differences between vaccine strategies
most vaccines target pathogens that have low antigenic variability, pathogens for which protection depends on antibody-mediated (humoral) immunity
* some vaccines offer “sterilizing immunity” meaning
Vaccines are agents that elicit a protective immune response. Vaccines are typically non-toxic or
greatly attenuated whole cells/viruses or components of pathogens, which are injected, ingested
or inhaled.
they prevent infection because the pathogen cannot
replicate; these are the most effective vaccines as
they prevent transmission; e.g. measles vaccine
* other vaccines do not prevent infection but do
prevent severe disease –
explain nucleoside and non-nucleoside analog inhibitors of viral replication for HSV and HIV – how do they work, how are they specific for infected cells, how resistance emerges;
Nucleotide/nucleoside “analogs” mimic
nucleotides/nucleosides, interact with the
polymerase, block activity or get incorporated
into the growing nucleic acid (DNA, RNA)
strand resulting in termination of
polymerization “ viral replication is halted
Non nucleoside are allosteric non-competitive inhibitors
work by binding to a hydrophobic pocket
next to the active site of RT, which
causes a conformational change in RT
that prevents DNA polymerization
explain other anti-HIV and anti-influenza virus therapies, the processes they inhibit and how resistance emerges;
Inhibitors of HIV protease:
Peptide inhibitors
(“peptidomimetics”) mimic the
substrates and compete with
them. They bind to the HIV
protease and inhibit it.
explain how monoclonal antibodies act as antiviral agents
So far, monoclonal
antibodies (mAbs) are
proving to be the most
effective antiviral
treatment for COVID19.
mAbs bind to and
neutralize SARS-CoV2.
Corticosteroids and
mAbs that dampen the
immune response are
effective in treating later
stages of COVID19.
