Lecture 5&6

conditionally lethal viral mutants

A lethal mutation in a virus, but behaves like the wild-type virus when grown under very defined conditions, including different body temperatures -Cold-adapted influenza viruses ---FluMist vaccine

amantadine

A single amino acid substitution in influenza matrix 2 protein of human influenza H3 viruses has made them almost 100% resistant to ________ antiviral therapy

RNA

Anteginic drift and immunity influenza= ________ virus- mutates easily Each year's flu vaccine contains three/four flu strains -- two A strains and one/two B strain(s) -- that can change from year to year After vaccination, antibodies against the flu strains in the vaccine are produced, providing protection.

RNA

BVDV- viral recombination with host genes - recombination can occur between BVDV ________ genome and host cellular mRNA

Pestivirus

Bovine Diarrhea virus (BVDV) -_____________ (Flaviviridae) ----classical swine fever is also caused by this

Hepatitis B

Complementation -__________ virus provides its surface antigen to hepatitis D (delta) virus, which is defective in its ability to produce its own outer protein. -Both HDV superinfection and co-infection result in more severe disease

fit

Despite all of the H5N1 avian influenza outbreaks, it remains poorly transmissible to humans and from human to human - why? Avian influenza H5N1 seems to be poorly ____ to replicate in human cells Receptors (a-2,3 linked) are only present deep in the human respiratory tract

ebola

Emergent viral diseases (e.g., Hanta and ________ viruses) Disease is caused by urbanization of humans -> come in contact with animals harboring viruses and not likely due to mutations

FECV FIPV FIPV

FIPV and feline enteric coronavirus (FECV) are coronoviruses of felids _______ is ubiquitous, and causes a mild enteric disease _________ is rare, but causes a fatal systemic disease Uncommon for ______ to be transmitted from cat to cat

auto-infection

FIPV is believed to be a mutant of FECV and infection may be due to ___________ from mutated FECV -Insertions, deletions or substitutions (e.g., single nucleotide polymorphisms (SNPs)) have been detected -Mutations may produce an early stop codon with truncated viral proteins or eliminate protease cleavage sites

dogs

Felin panleukopenia virus (FPV) does NOT infect ______, but CPV-2 likely evolved from FPV by infecting intermediate carnivore animal species -5 amino acid mutations affect ability of CPV-2 virus to bind to canine transferrin receptor and infect dogs CPV-2 mutated to form 2a and 2 b, which had greater affinity CPV-2b mutated to form 2c - a single pint mutation created 2c - do we need a new vaccine ??

stable evolving Dead-end Resistant host

General interactions of hosts and viruses -____________- maintains the virus in the ecosystem (AIV and aquatic birds) -__________- passage of a virus from "experienced populations" to naive populations in the same host species (Human flu) -___________- a one-way passage into a different species. Either the host dies or the virus does not transmit efficiently in the new species. (WNVin humans) -______________- the new species completely blocks infection (CPV-2, FeLV, or Shope's papillomavirus )

government

H5N1 transmission studies -avian influenza -asked what will HPAI need to do to transmit within humans -"Gain of function" studies -"Doosday virus" -Fouchier and Kawaoka labs -two research groups created mutant avian H5N1 viruses that could be transmitted from ferret to ferret - research was halted by _______________

Multiple virulence genes are deleted, instead of a single gene deletion

How is the fear of reversion of virulence been overcome for vaccine use in the real world?

Mutations are believed to enhance the ability of FIPV to bind to host receptor(s) on macrophages

How may mutations play a role in FIPV pathogenesis?

p80

In cytopathic BVDV, the viral genome recombines with host mRNA to add a ubiquitin protease cleavage site in the p125 gene to produce p54 and p80 genes ---__________ is expressed in host cells infected with cytopathic BVDV

p125

In non-cytopathic BVDV, the nonstructural protein NS2-3 precursor (________) is expressed as an intact protein and not proteolytically processed ---no p80 expressed in host cell infected with non-cytopathic BVDV

antibody escape

Influenza antigenic drift helps produce __________ mutants After your yearly vaccination, you produce antibodies against the different HA molecules in vaccine If you're exposed to an influenza virus that structurally matches the vaccine strains, you will likely be protected In the event that you're exposed to a H3N2 virus, which is significantly different (mutated) from the H3 strain in the vaccine, H3 antibodies will weakly recognize the virus infecting you --> you will have some protection, but will likely get sick Weak immunity (antibodies) will allow the H3N2 virus to replicate and undergo more mutations from lack of selective pressure --> antibody escape mutant is created

hemagglutinin (HA) cleavage

Insertion of multiples of three nucleotide bases (in frame) to a viral gene will result in a single amino acid insertion to the protein The virulence of avian influenza viruses is affected by the presence of basic amino acids in the viral __________ site

mucosal disease

Later in life, PI infected calf is exposed to cytopathic strain of BVDV and develops ___________ Recombination plays a major role in generating cytopathic BVDV isolate

truncated

Lethal point mutations a mutation that induces a premature stop codon -the resulting viral protein would be _________ - the function of this proteins may be absent (or altered and affect the replication and/or transmissibility of this virus

monobasic multibasic

Low pathogenic avian influenza viruses have a ___________ HA cleavage site, which are susceptible to cleavage by the trypsin family of proteases (found in the respiratory and GI tract) Highly pathogenic avian influenza viruses (e.g., H5N1) have a___________ amino acid insertion at the HA cleavage site (e.g., -RRRKKR-), and can be cleaved by the furin family of proteases (ubiquitous expression in the animal host) Low pathogenic avian influenza isolates can become highly pathogenic after the insertion of multiple basic amino acids (e.g., lysine and arginine) at the cleavage site of the HA gene

revert to virulence

Modified live vaccines replicate to a limited amount in host cells, but dont produce full viral disease - have specific genetic deletion of a key virulence genes ** this vaccine may ________________ by replacing the missing gene(s) and genetically recombining with a wild type virus

Antigenic drift

Nonsegmented viruses like foot-and-mouth or canine distemper virus can evolve through? Antigenic shift Antigenic drift Both A and B None of the above

poliomeyelitis (polio)

Not all disease emergence is caused by virus mutation mutations are important in viral pathogenesis but are not the cause of all viral diseases ___________________- was not a problem when hygiene was poor, because children were exposed to it early on and developed antibodies. when hygiene improved, children werent exposed early on, but were exposed later on and got sever disease- neurological disease Industrialization and urbanization, combined with increased sanitation reduced natural (childhood) exposure

The Spanish influenza

Pandemics do not always require reassortment -____________ pandemic (1918 H1N1) appears to have come directly from birds to humans ----1918 H1N1 virus was resurrected from fixed/frozen tissues of dead humans by Dr. Terry Tumpy at CDC using reverse genetics -------While not pandemic yet, avian H5N1 and H7N9 viruses in SE Asia have infected humans directly

persistently infected (PI)

Pregnant cow is in infected with a non-cytopathic strain of BVDV, which infects fetus < 50 days old -> fetus dies 50 to 125 days old -> fetus is __________- immune system is tolerant to viral antigens and virus replicates uncontrolled Never any antibodies generated to virus > 125 days old -> healthy calf is born (immune system recognizes and kills virus)

polymerase changes from one RNA template to another during replication after breaking and rejoining of two DNA strands

RNA viruses --> recombination usually happens when _______________________________ DNA viruses--> recombination usually happens ___________________

B

Regions within a viral genome may be termed mutational hotspots. Which statement is correct about hotspots? a. The region contains secondary structures that promotes polymerization mistakes, increasing the number of mutations. b. The region encodes for a protein that can be more accepting of changes, enabling mutations build up in the area. c. The region reacts to antivirals, producing more mutations. d. None of the above

viral population

Some viral genomes are very dynamic and are prone to genetic change (mutation) Viral evolution is the constant change of a viral genomes within a population of viruses in the face of selection pressures from the host What kind of selection do viruses experience? Adapting to new species of animals Acquired immune response Antibodies CD8+ cytotoxic T cells Innate immune system Innate response (e.g., interferon alpha/beta) Virus evolution refers to a __________ and NOT the individual virion

pandemic

Swine are an intermediary host to produce reassorted human influenza viruses -Italian swine became infected with different avian or human viruses reassortment eventually occurred during 1985-89 but did not create a pandemic virus - Swine, avian and human influenza A viruses reassorted in pigs to create the swine H1N1 __________ virus which is now the sole H1 virus circulating in humans

1 drug for 1 bug= resistance (selection is super high) give multiple drugs to prevent getting resistant mutants

Tamiflu resistance in H1N1 influenza viruses - selecting for a virus that can grow despite the antibodies Why is HAART (highly active antiretroviral therapy - a drug cocktail) is used for HIV therapy in humans vs. a single antiretroviral drug?

recombination

Turkey coronaviruses (TCoV) an enteric disease virus similar to infectious bronchitis virus (IBV) Genetic analysis suggests ______________ of the spike protein in IBV (respiratory virus of chickens) resulted in cross-species transmission and enteric disease in turkeys

p80

________ is toxic and produces the cytopathic effect

Point Deletions or insertions

________ mutations can be reverted easily to original genotype ____________- are more difficult (almost impossible) to revert back to original genotype Viruses harboring non-lethal mutation(s) may overtake the wild-type virus if: The resulting mutations confer some selective advantage which allows it to swap animal species, change its growth rate, evade the immune response etc.

ssRNA DNA

_________ viruses have approximately 1 nucleotide misincorporation per 10^3 - 10^5 nucleotides polymerized _________ viruses are much more genetically stable with misincorporations of 1 nucleotide per >10^8 nucleotides polymerized

Cpmplementation

__________- can occur when either one or both of two viruses that infect a cell have a mutation that results in a nonfunctional protein. The non-mutated virus helps the mutated one by making a functional protein that serves for both viruses. -an important method by which a helper virus permits replication of a defective virus. - not permanent as the defective genome is maintained

viral fitness

____________ is defined as the replication capacity of a virus -virus with the highest will replicate to the highest number within a viral quasispecies of an animal host, and have a greater change to infect a new animal host -lowest - will replicate to lesser numbers and may have less of a change to infect a new animal host

Recombination

____________ is used to produce cytopathic strains of bovine viral diarrhea virus (BVDV) that can produce mucosal disease

Antigenic drift Antigenic shift

____________ results in point mutations in the two major surface viral glycoproteins; hemagglutinin (H) and neuraminidase (N) - if it has enough point mutations, host may not be protected from the annual influenza vaccine ____________ results in major genetic rearrangement (reassortment) of the H or N genes -the reassorted virus is novel to the immune system and seasonal vaccine will not likely confer protection

Non-synonymous

_____________= Not silent -a nucleotide substitution that alters the amino acid sequence of a proteins

antigenic drift

______________ of influenza A virus: antibody escape mutants -16 different subtypes of hemagglutinin (HA) -9 different subtypes of neuraminidase (NA) -Viruses are named based on their composition HA and NA antigens on the surface of the virion e.g. H1N1, H3N2 or H5N1 -Antibodies generated against influenza the surface glycoprotein HA are protective

selection

______________- does not cause mutations, but instead it selects for particular mutants (the mutants must already exist) - example--- viral quaisispecies or swarm--> receive a vaccine--> only one variety of swarm can replicate--> new swarm will form, but all will include the necessary changes to grow in presence of antibodies

viral reassortment

_______________ may happen when the cell is co-infected by two, of more of the same segmented viruses (e.g. influenza A or rotavirus) ** only in segmented ****does NOT occur when a host cell is co-infected with two unrelated viruses -segments may get shuffled like cards and new progeny viruses may be generated with a mixture of the RNA segments from the viruses that originally infected a cell

synonymous mutation

_______________ mutation =silent - a substitution of one nucleotide for another in an open reading frame, such that the produced amino acid squence is not modified *these mutations can affect transcription, splicing, mRNA transport, and translation, any of which could alter phenotype, rendering the mutation non-silent

hotspots

________________=certain positions in viral genomes that have higher rates of mutations

Reactivation

_________________-- may occur when multiple inactivated (killed) viral particles can recombine genetic material to produce an infectious virion -Unlikely to occur if the viral nucleic acid is inactivated by a chemical that covalently modifies the nucleic acid Probably more theoretical than realistic, but is still possible

intramolecular recombination

______________________- there is exchange of a portion of the genome between multiple genetically related viral genomes of host cell genetic material

mutation

a _________________ is the change in base sequence of a nucleic acid, resulting in an alteration of the resulting protein

antiviral drug resistant mutants

a mutation that confers resistance to antiviral drugs -may arise rapidly

substitution

a point mutation in a codon that leads to a change in a protein (for example TTA to TTC= Leu changing to Phe) - this type of mutation might change some properties of the viral protein and possible change its function

silent mutation

a point mutation in a codon that produces the same viral protein sequence

pandemic influenza virus

antigenic SHIFT has the potential to produce a _________________ virus- infectious disease that spreads throughout mankind/animal species around the world

mutation rate

canine parvovirus-2 -small ssDNA virus - has high ___________ compared to other DNA

frame-shift

deletion of nucleotides result ina _______________ mutation and change the amino acid sequence downstream of the deletion -The neuraminidase protein from highly pathogenic avian influenza virus isolates has a characteristic nucleotide deletion in its stalk region, which results in a protein 20 amino acids shorter

dsDNA ssRNA

high output with high mutation rate -drug-resistant mutants __________ are the most stable viruses __________ are the least stable

-Mutation rate cannot be too high because progeny virus would be defective (defects in viral structure or enzymatic proteins =not infectious) -mutation rate cannot be too low because progeny virus need to be able to adapt to the environnment

how do mutations benefit and harm RNA viruses- explain mutation rate balance

quasispecies

many mutant viruses can be produced in an infected animal host and exist together in a non-homogenous population known as a __________________--> the fittest prevail

refractory

mechanisms for hotspots are unclear, but there is evidence that some regions of viral genomes are "_____________ to mutation"= the structural requirements do not allows for mutation - doesnt mean that the genome does not get mutated in these regions, it means the selective pressure prevents these viruses from amplifying

class V

need to remember which viruses are prone to mutations when deciding whether to use a vaccine to control viral disease Which of the following Baltimore classes of viruses is most likely to require developing a new vaccine each year, and why? Class I Class II Class V

myxomatosis (Myxovirus) Rabbit calicivirus

rabbits in australia poxvirus causes __________ in rabbits -reduced rabbit population - both rabbits and the virus evolved -________________- (rabbit hemorrhagic disease), was similarly released later on, but resistance is once again developing

antigenic shift

reassortment is the major driving force of _________________ of influenza A virus

non-infectious virus

some viral proteins are more accepting of mutations (capsid or non-structural genes) whereas others cant tolerate much change (RNA/DNA polymerases)- mutating these results in _____________

Plaque Antibody escape Conditionally lethal Drug resistant

viral mutations can also be classified by their phenotype _______ mutants - Cytopathic plaques from mutants may be larger or smaller than in the wild type virus __________ mutants - These mutants do not react to existing antibody and avoid pre-existing immunity --> Antigenic drift in seasonal influenza ___________ mutants - These mutants do not survive under a certain condition in the body (temperature sensitive) ____________ mutants - This is important in the development of antiviral agents - the possibility of resistant mutants arising must always be considered

Drift (point mutations) Deletions Insertions Reassortment (only in segmented viruses) Recombination

what are the 5 mechanisms of mutation (evolution

-intramolecular recombination -reassortment (only in segmented) -reactivation

what are the three types of viral genetic recombination

during replication of nucleic acid

when in the replication cycle do viruses mutate?

Foot and Mouth

which produces more mutations African swine fever virus Equine papillomavirus Foot and mouth disease virus Monkeypox virus Infectious canine hepatitis virus

viral polymerases from RNA viruses lack a proofreading mechanism

why are RNA viruses so sloppy