Viruses and vaccines Flashcards
How many deaths worldwide are associated with communicable/infectious diseases?
Approximately 25% of deaths worldwide are associated with communicable diseases - Kill up to an estimated 12 million people annually.
Communicable diseases and their sometimes chronic aftereffects are the underlying issue for most of the top 10 causes of death in children under age 5 worldwide.
Vaccines help to cut these numbers but many challenges remain, such as uneven distribution, malnutrition and access to sanitation, antibiotics and vaccines.
Sometimes pathogens and infectious agents use other organisms to circumvent host barriers, what are these organisms called?
Vectors.
Which are the most common group of organisms that act as vectors for infectious diseases?
Infectious disease vectors are most often blood-sucking arthropods (e.g., ticks, fleas, flies, or mosquitoes), which breach natural barriers like the skin with their bite and introduce the pathogens they carry directly into a
susceptible host.
These vector-borne infections account for approximately one out of every six instances of human infectious disease and are typically restricted to areas in which the intermediate host is found. Examples include malaria and Zika fever.
Which is the most common entry route for infectious agents?
The majority of, but not all, infectious agents enter through mucosal routes: the mouth, nose, eyes, or urogenital tract. Since these are also the sites for commensal microbes and regularly encounter foreign substances like food, it’s important to handle any infectious agents and still maintain tolerance to the commensals.
What is the standard response to extracellular and intracellular cytosolic/membrane bound pathogens?
- Extracellular infections within the body are controlled by a combination of innate and adaptive effector mechanisms present in extracellular fluid: phagocytosis and pAPC activation (via PRR binding and cytokines), complement activation, and antibody binding.
Intracellular infections are the most difficult for the immune system to detect and eradicate; these can be divided into membrane-bound and cytosolic, with differing key immune response mediators.
- Intracellular vesicular infections are most effectively eradicated via macrophages activated by the cytokines secreted by Th1 cells.
- Intracellular cytosolic infection requires host cell lysis by CTLs (generated with DC-licensing help from Th1 cells), cytotoxic Th1 cells, or NK cells.
What are viruses?
Viruses constitute small segments of nucleic acid with a protein or lipoprotein coat, and require host resources for their replication. They are obligate intracellular pathogens.
Briefly explain two common virus entry strategies.
Viral entry is mediated through binding to cell-surface receptors:
- Receptor mediated endocytosis: often proteins/glycoproteins in the viral envelope bind to receptors on target cells, which induces endocytosis. In the endosomes,, their coat fuses to the endosomal wall (either early or late endosome depending on the pH needed for fusion) which releases it’s genome into the cytoplasm.
- Receptor mediated signalling: binding to the surface receptor allows for fusion of the envelope directly with the plasma membrane, allowing for the viral genome entry to the cytoplasm.
Different viruses bind different surface receptors.
What immune strategies are employed against viral infections?
- Innate response elements commonly engaged by encounter with viral PAMPs, such as secretion of type I interferons, inflammasome complex assembly and NK-cell activation, as well as IL-12 production, can help eliminate the virus but also keeps the virus at bay and provide crucial instructions for the adaptive response that will follow.
- Humoral responses: Many viruses are neutralized by antibodies at the site of infection directly, which blocks them from binding to their target cells. Also circulating antibodies that foster opsonization, complement activation, and phagocytosis, protect the host by blocking or eliminating virus in the extracellular spaces, although they cannot eliminate virally infected cells.
- Cell mediated responses: In order to eliminate an established infection, where host cells harbor intracellular virus, virus-specific CD8+ T cells must be activated to kill infected cells, which requires the assistance of helper T cells (often Th1 type) that recognize the same pathogen, providing cytokines and pAPC licensing for cross-presentation. Th and Tc cells also secrete the type II interferon IFN-γ, which have direct antiviral activity.
Viruses evolve very quickly, why?
Once inside a host cell, replication can occur, genome replication is often error prone, leading to mutations that can make the virus more virulent.
What is the common way for viruses to evolve?
Viruses are more likely to thrive if they don’t kill the host, as it gives more time for replication and spread. Its common for viruses to start out as dangerous and fast killing, to then become less and less dangerous/fatal/pathogenic for the host.
But, many viruses don’t evolve in this manner, e.g. Ebola kills fast, but it’s a bit unusual.
Compare Ebola, Coronavirus and HIV-1 in how pathogenic they are.
Ebola is highly pathogenic and kills the host quickly, hard to see how that is beneficial to the virus as the host may die before it has time to replicate and spread.
Coronavirus was highly pathogenic from the start and have decreased in how dangerous it is, the common way for viruses to evolve as that gives it more time to spread.
HIV is a virus that one can cause no symptoms for a long while, which maximizes spread. Then it kills the host very slowly and have tons of evasion mechanisms - a very “successful” virus.
Briefly describe the life cycle of Coronavirus.
- Coronavirus bind to surface receptors of their target cells and enter through membrane fusion or endocytosis (complex interactions)
- Release of viral genome in the cytoplasm
- The viral polymerase is translated by the host cell ribosomes.
- The viral RNA is replicated
- The viral components are transcribed
- translation of viral structural proteins that bud off ER
- The viral genome gets endocytosed into the bud
- Formation of a membrane bound mature virion (virus inside Golgi vesicle)
- Exocytosis and mature virion is released.
Describe two cells that can recognize influenza virus, how they recognize it and what happens after recognition.
- A macrophage that engulfs a dying, influenza infected cell through phagocytosis will recognize the virus through TLR3 that recognizes viral dsRNA (the virus have replicated its genome). When TLR3 binds the dsRNA it dimerizes which initiates signaling that leads to the transcription factors IRF3 and NF-kB being generated, which induces transcription of genes for type 1 interferons and pro-inflammatory cytokines that help battle the viral infection.
- If a dendritic cell internalize the virus through endocytosis, they will break down the virus in the endosome/lysosome and TLR7 will recognize ssRNA and dimerize with TLR8. TLR7/8 signalling through the MyD88 adaptor protein will also lead to type I interferon expression and pro-inflammatory cytokines.
Interferons are very important response to viral infection. Also inflammasome complex assembly, and NK cell activation.
Interferons (mostly type I) are an important response to viruses, what do they do?
Type I interferon binding to IFN receptors acting through JAK-STAT pathway leads to antiviral activity and resistance to viral replication by induction of viral restriction factors such as APOBECs, SAMHD1, TRIM, RNAses.
Also the humoral response is very important in blocking virus from infecting more cells.
Give an example of a viral evasion mechanism used by HIV.
A common viral evasion mechanism used very elegantly by HIV is to change its surface (spike) proteins. They have an enormous amount of spike protein genes (antigenic variation) that they can switch when antibodies are produced against the one they express. Switching this keeps the neutralization minimal and the virus can continue infecting cells.
Influenza viruses also use this strategy, which is why new vaccines are needed each season, but HIV is the master - extremely high diversity!
Give two examples other examples of evasion mechanisms used by viruses.
- Inhibition of antigen presentation:
- Measles virus/HIV inhibit MHC class II expression and presentation to helper T cells, this leads to minimal T cell activation and thus less B and CTL responses. Very effective but can still be killed by NK cells for example. HIV selectively only downregulates some of the HLA types, not the ones recognized by NK cells, and thus efficiently reduces CTL activity without being susceptible to NK cell lysis.
- HSV inhibits TAP activity, effectively shutting down MHC class I presentation to CD8+ T cells.
- Adenoviruses and cytomegalovirus reduce the surface expression of MHC class I molecules, again inhibiting antigen presentation to CD8 T cells.
- Upregulate immunosuppression/misdirect the immune response.
- HIV-1 causes immunosuppression by depleting CD4+ T cells
- EBV produces a protein that is homologous to IL-10, which suppresses cytokine production by the Th1 subset, resulting in inhibition of the antiviral inflammatory response.
Influenza viruses have been responsible for some of the worst pandemics in history, name three key properties of influenza virus.
- Three basic types: A (most common for pandemics), B and C
- Two key viral glycoproteins:
- Hemagglutinin (HA)―allows attachment of virus to cells
- Neuraminidase (NA)―helps new virus escape from host cells
- Genome has eight segments of ssRNA, each associated with proteins and RNA polymerase.
Strains of influenza virus are tracked yearly by WHO, how do they define each strain?
Each strain defined by its host of origin, geographical origin, strain number, year of isolation, and HA/NA type.
Why does the influenza virus change so much from year to year?
There is a high variation in epidemic influenza strains mainly because its RNA polymerase lacks proof-reading capability, leading to a high mutation potential of RNA genome, which over time leads to antigenic drift (a series of spontaneous point mutations that
occur gradually, resulting in minor changes in HA and NA over time) and antigenic shift, the sudden emergence of a new subtype of influenza, where the structures of HA and/or NA are considerably different from that of the virus present in a preceding year, for example due to rearrangement of virion genome between animal strain and human strain.
This is the reason for changing flu vaccine formulation every year.
What is the difference between emerging and reemerging infectious diseases?
Emerging = something new, not previously observed (e.g., Zika)
Reemerging = something old, coming back again (e.g., TB in the U.S.)
Provide three reasons to why a disease might be reemerging.
Reemerging infectious diseases may be the result of:
- drug resistance/improper antibiotic use
- new virulence factors/combinations of diseases
- antivaxxers or laxity in vaccination program adherence (prioritizing other vaccines), e.g. Diphtheria reemergence in the former Soviet Union, whooping cough and measles outbreaks in the United States.
- Zoonotic pathogens
- environmental and geographic changes
Some noteworthy new infectious diseases
have appeared recently, name three.
- Ebola (1976)
- Legionnaires’ disease (1976)
- Severe acute respiratory syndrome (SARS- CoV, 2002)
- West Nile virus (1999 in U.S.)
- Zika (nationally notifiable in US in 2016)
- SARS-CoV-2 Covid-19 (Wuhan 2019)
In general, how do we go about developing vaccines today?
- Vaccine development begins with basic research to discover immunogens (substances that elicits a B and/or T cell response), where useful immunogens are those from the pathogen that can be recognized by B AND T cells. This step can be hard as there are many different strains of viruses. The key is to find conserved epitopes across different strains which can be targeted by B/T cells which would make the vaccine target many/all strains.
- Then the specific research, defining the specific immune targets/choosing what platform to use to be effective against the virus. For example if we want IgA or IgG depending on the route and capacity to enter circulation, and making sure the virus can be recognized by both B and T cells for an effective response. We also need to make sure that the vaccine elicits the desirable memory response. A lot goes into this part of the reasearch too, it’s hard to make effective vaccines to many viruses!
Passive immunization is still used today, what is it and to what pathogens/agents is it used?
Passive immunization is the delivery of preformed antibodies (produced in another host). This is most often used when there is an immediate threat to life after exposure, so there is no time to wait for the immune system to respond. For example toxins, venoms or rabies. This can also be used in immunodeficient patients that can’t produce abs on their own.
Note, if the antibodies are generated in another species, like horses which is common for venoms, they can lead to Type I (allergy) or III hypersensitivities (immune complexes).
What is active immunization then?
Active immunization is vaccination, which induces immunity and memory. May need booster vaccinations to achieve full and long lived protection.
Vaccine campaigns in children vastly reduces risk of death from infectious disease, campaigns have been shown to be very effective!
What are the three basic requirements for a developed vaccine?
The basic requirements for a developed vaccine are:
- Should be safe
- Should be effective at preventing infection
- Delivery strategy should be achievable in desired population (storage conditions; frozen, fridge, room temp and best before date)
There are nine different approaches to viral vaccine development (differing in the virus/virus part being delivered to induce immunity and memory). Which?
- Live attenuated: capable of replication but not disease causing.
- Whole inactivated: virus inactivated by heat/chemicals (but this treatment can destroy target epitopes)
- Split inactivated: (breaking the virus apart and delivering pieces)
- Synthetic peptides: activates T cells, mainly used in cancer treatment.
- Virus like particles: virus envelope only, no genome (broken down to peptides in the body)
- DNA or RNA vaccines: part of the viral genome, recognized by PRRs and activates the adaptive. often administered in a plasmid and expressed by host cells.
- recombinant viral vectors: Inserting a viral gene into another virus (not disease causing) as a way of delivery.
- recombinant bacterial vector: same idea as previous but into a bacteria instead
- recombinant subunits: yeast produced subunits of virus to be injected. often need adjuvants.
What are adjuvants?
An adjuvant is a substance that enhances the body’s immune response to an antigen. For example alum (Th2), virus like particles.
Adjuvants can both promote inflammation (recruits more immune cells to the area, enhance effectiveness) and slow down Ag release (which can promote longer interactions, enhancing effectiveness)
It can also be a substance that increases effectiveness of a drug.
What are the pros and cons of subunit/conjugate vaccines, DNA/mRNA vaccines and attenuated/inactivated vaccines.
subunit/conjugate vaccines: Use purified macromolecules derived from pathogen
- Pros: primes immune system to recognize for example bacterial toxins (e.g. inactivated exotoxins/toxoids), bacteria (e.g. inactivated capsular polysaccharides) or viruses (E.g. Hep B vaccine, containing viral envelope protein + surface antigen)
- cons: often expensive, time consuming and hard to develop.
DNA/mRNA vaccines: Host cells take up DNA/RNA as plasmids and express it internally - Provides Ag presentation via MHC class I, stimulating CTL production.
- pros: Strong humoral and cellular immune response, relatively inexpensive to manufacture, prolonged expression - enhanced memory, customizable, DNA vaccines are very stable.
- cons: DNA vaccines not super efficient in humans, mRNA vaccines very unstable.
attenuated/inactivated vaccines.
- Pros: strong response and safe as long as it’s certain that the pathogen is fully inactive, we would not use very dangerous viruses/bacteria as vectors because we can’t be 100% sure that its fully inactivated).
- Cons: stability issues and inactivation can destroy epitopes needed to elicit an immune response.
The vector and strategy needs to be tailored to the pathogen and target group.
How have we solved the stability issues with mRNA vaccines?
The solution to the stability issues with mRNA vaccines was solved partly by delivering the vaccine in a lipid nanoparticle (LNP) which protect it until it has fused to the cells, but then the next problem comes, rapid destruction in the cells. What they did to solve this, and they got nobel prize for, was that they modified the RNA bases as they usually are post transcriptionally modified in cells (like uridine –> pseudouridine), which lead to a diminished inflammatory response. This allowed the proteins to be translated and presented on MHC class I which triggered a CTL response (and memory) which provided protection against the real virus (covid-19).
