Structure and Taxonomy of viruses

What is a virus?

An infectious, obligate intracellular parasite comprising of genetic material (DNA/RNA), surrounded by a protein coat

T/F Viruses are everywhere

True

Where do viruses come from?

1. Originate from primitive, pre-cellular RNA replicons (virus first hypothesis)

2. From segments of cellular nucleic acid (progressive hypothesis)

3. From free-living organisms which gradullay lost genetic info (regressive hypothesis)

4. Originated at the same time as host cells and have co-evolved from them

Are viruses alive?

Outside of cell = no

Inside host cell = yes

T/F Viruses are active agents

False

They are passive

T/F Viruses are extremely small

True

T/F Viruses cannot be filtered due to their size

False

They can still somehow be filtered

When and who created the first vaccine?

1796 Edward Jenner

What is the filter used to filter viruses?

Pasteur-chamberland filter

What virus can still pass through the filter?

Rabies

How are viruses classified?

Nature and sequence of viral genome

What is the structure of a virus?

Nucleid acid

Capsid and nucleocapsid

Envelope

Envelope glycoproteins or peplomers (spike proteins)

Matrix proteins (tegument)

What are the 2 types of capsid/nucleocapsid symmetry in viruses?

Icosahedral

Helical

What is the function of structural proteins?

Protection of the genome

Delivery of the genome

Poliovirus: virus structure

Nonenveloped

single-stranded, positive-sense RNA genome (+ssRNA)

Adenovirus: virus structure

Nonenveloped

dsDNA genome

Rabies virus: virus structure

Enveloped: bullet-shaped

-ssRNA genome

Influenza virus: virus structure

Enveloped

-ssRNA that is segmented

SARS-CoV-2: virus structure

Enveloped

+ssRNA genome

Marburg virus: virus structure

Enveloped, filamentous particle

Shape of a U or a 6

-ssRNA genome

Retrovirus/HIV: Virus structure

Enveloped

2 copies of +ssRNA genome

How do we grow viruses?

Animals

Embryonated chicken eggs

Cell culture

What are the 6 steps of viral infectious cycle?

1. attachment

2. entry

3. uncoating

4. replication

5. assembly

6. release

What is required for the synthesis of viral proteins by host cells?

Production of viral mRNA

How can DNA viruses synthesize viral mRNA?

subvert host cell transcriptases

Which enzyme is not present in host cells, therefore viruses must encode and package it themselves?

RNA-dependent RNA polymerase

What is another method RNA viruses can get mRNA?

Use the viral genome as mRNA

How do we classify viruses?

Nature and sequence of viral genome

Symmetry of protein shell (capsid)

Presence or absence of lipid membrane (envelope)

Size of virus particle

Replication characteristics and disease

What types of viral genomes do we have?

ssDNA

dsDNA

ssRNA +/-

dsRNA

Linear or circular

Segmented vs non-segmented

What at the steps of viral replication?

Attach

Entry

Uncoating

Replication

Assembly

Release

What are the pathways of viral mRNA synthesis and translation?

IDK

Viral evolution

The constant change in the viral population in the face of selection pressures

What are the 4 drivers of virus evolution?

1. large # of progeny

2. Extremely frequent mutations

3. Viral quasispecies or mutant cloud

4. selection = survival of the fittest

What is a mutation?

An alteration the nucleotide sequence of a virus as a result of mistake(s) during the copy of viral DNA or RNA

What is a quasispecies?

non-identical but related replicons

T/F Viral infections are initiated by a population of particles, not a single virus particle.

True

Mutations -> (drift/shift)

Recombination -> (drift/shift)

Reassortment -> (drift/shift)

Drift

Shift

Shift

What is recombination?

Exchange or transfer of genetic material b/w different but closely related virusus inflicting the same cell

What is template switching?

during genetic recombination, the template used for transcription/replication will contain a mixture of the different genomes in the cell

Template switching commonly occurs b/w what type of genome?

+ssRNA viruses

RNA polymerase switches b/w template strands during synthesis of what?

The complimentary negative-sense strand

What viruses have observed exceptionally high frequency of genetic recombination?

Coronaviruses

The epidemiology of the influenza virus resulted from ___________ where a cell is infected with multiple viruses and the genome is made of the variation of the viruses.

rapid antigenic shift

What 6 things does phenotypic expression result in?

1. host-range mutants

2. changes in pathogenicity

3. antibody-escape mutants

4. conditional-lethal mutants

5. defective-interfering mutants

6. genetic reactivation

_____ mutants can infect host species different from those of parent viruses

host-range

In host-range mutants, how does it act differently in nature vs a lab?

Nature = a virus will cross from one host species to another and will adapt to become highly transmissible in the new host species

Lab = multiple serial passages of parent virus on permissive cells from another mammalian host species can attenuate the virus for the original host species.

3 Consequences of adaption:

1. improved binding to receptor -> increased transmissibility

2. change on receptor preference -> ability to infect other tissues

3. Changes in replication kinetics -> increased infectivity

T/F Antibody-escape mutants can be selective

True

When can conditional-lethal mutants replicate?

Under defined permissive conditions such as temperature -sensitive mutants

What are defective-interfering viral particles?

Incomplete viral particle lacking some of its components or having alterations

Most defective-interfering viral particles are what kind of mutants?

Deletion

Most defecting-interfering viral particles display an advantage in replicating their genome and packaging this defective (shortened/lengthened) genome into capsids encoded by the wild-type helper virus.

Shortened

What do defective-interfering viral particles require in order to replicate?

The presence of a complementing helper virus

After a mixed infection of a cell, infectious progeny are produced from parental viruses, of which one or both are non-infectious. This is an example of what phenotype expression.

Genetic reactivation

In virus taxonomy, what are the suffixes used for Order, Family, and Genus?

Order = -virales

Family = -viridae

Genus = -virus

What are the 4 parts of the infectious cycle?

1. inoculation: inoculum of virus bind to cell

2. Eclipse: virions penetrate the cells

3. Burst: host cells release many viral particles

4. Burst size: number of virions released per bacterium