Module 9: Viruses (Classification + Exceptions)

Question 1

What are the 2 main issues with classifying viruses?

Answer 1

1) Poor evolutionary information
== We still really do not understand evolutionary connections between viruses

2) No single “genetic yardstick” for comparisons between viruses

== There is no single gene shared between ALL viruses! –> Nothing to determine evolutionary relationships between all viruses!

Question 2

How were bacteriophages mainly named initially?

Answer 2

Mainly named using numbers and greek letters

EX: T2 + Lambda

Question 3

How were plant viruses mainly named initially?

Answer 3

Based on the appearance of the diseased plant

Ex: TMV

Question 4

How were mammalian viruses mainly named initially?

Answer 4

By location of identification or the disease the virus causes

Question 5

What are the 3 main viral naming strategies seen throughout history?

(AND provide examples)

Answer 5

Naming by:

1) Location (Ebola Virus + West Nile Virus)
2) Disease (Hepatitis A Virus + Tobacco Mosaic Virus)
3) Physical Characteristics (Coronaviridae + Picornaviridae)

Question 6

What are the current WHO recommendations for naming INFECTIOUS DISEASES?

Answer 6

1) Names should NOT include locations, names of individuals, or cultural references

2) Names SHOULD contain: descriptive terms, reference to causative pathogen, time of 1st reports of disease
(Ex: COVID-19 = Corona Virus Disease 2019)

Question 7

What are the 2 main virus classification systems?

Answer 7

1) ICTV system

2) Baltimore system

Question 8

What does the ICTV system classify viruses by?

Answer 8

Classifies them by:

1) Order
2) Family
3) Subfamily
4) Genus
5) Species

Question 9

What is the problem with assigning species to viruses?

(what is the typical definition of species?)

Answer 9

Typical definition of a species = A group of interbreeding individuals

Problem –> Viruses do not breed

Question 10

What is the definition of a viral species?

Answer 10

A group of viruses whose members share several properties and occupy a common ecological niche

Question 10

What are the 3 main attributes considered by the ICTV in their classification?

Answer 10

1) Viral morphology

2) Genome structure

3) Biological features

Question 11

Baltimore System

Answer 11

A classification system for viruses in which all are separated into SEVEN classes based on HOW viral mRNA is generated from a viral genome

Question 12

What are the 7 classes of the Baltimore System?

Answer 12

I = dsDNA viruses
II = ssDNA viruses

III = dsRNA viruses
IV = (+) sense ssRNA viruses
V = (-) sense ssRNA viruses

VI = ssRNA with REV. T
VII = ssDNA with REV. T

Question 13

Example of a Class I virus:

Answer 13

Human Herpes Virus (dsDNA)

Question 14

Example of a Class II virus:

Answer 14

Parvoviruses (ssDNA)

Question 15

Example of a Class III virus:

Answer 15

Rheoviruses (dsRNA)

Question 16

Example of a Class IV virus:

Answer 16

Poliovirus (+ ssRNA)

Question 17

Example of a Class V virus:

Answer 17

Influenza (- ssRNA)

Question 18

Example of a Class VI virus:

Answer 18

HIV (ssRNA with REV. T)

Question 19

Example of a Class VII virus:

Answer 19

Hepatitis B (ssDNA with REV. T)

Question 20

Generation of mRNA is a….

Answer 20

COMMON FEATURE among ALL viruses!

Question 21

What are the 2 main methods of viral identification?

Answer 21

1) Electron Microscopy

2) Nucleic Acid Analysis (mainly PCR + RT-PCR)

Question 22

How is electron microscopy used for viral identification?

Answer 22

EM allows us to see distinct physical characteristics of viruses and physical differences between viruses

Question 23

What are 2 main problems with viral identification using EM?

Answer 23

1) Not always precise enough (sometimes can’t get a clear image of intricate and small structures)

2) Many viruses often exhibit similar physical features
(can be hard to distinguish between viruses of the same groups)

Question 24

What are the two common methods of nucleic acid analysis (for viral identification)?

Answer 24

1) PCR 2) RT-PCR

Question 25

For which viruses would we use RT-PCR for viral identification?

Answer 25

For RNA viruses!

Question 26

What is the process of RT-PCR?

Answer 26

1) Total RNA is isolated from a viral sample 2) Primers, Rev. T, and nucleotides are added to the RNA sample 3) Rev. T makes a DNA complementary strand from the RNA template (forms a heteroduplex of cDNA:RNA) 4) Heat is applied to separate strands of the heteroduplex 5) Taq Polymerase, nucleotides, primers are added to synthesize double stranded cDNA 6) ds-cDNA undergoes PCR amplification 7) Gene sequences analyzed

Question 27

What are all the viral-like particles we currently know of:

Answer 27

1) Viroids 2) Satellite Viruses 3) Satellite RNAs 4) Virophages 5) Prions

Question 28

Viroid

Answer 28

An infectious agent of PLANTS that is composed of non-enveloped (naked) RNA

Question 29

Viroid Defining Characteristics

Answer 29

1) Consist ONLY of naked RNA 2) Extremely small (<400 NTs) 3) Exhibit a good amount of intramolecular BP 4) Exhibit increased resistance to ribonucleases

Question 30

Viroid genomes are...

Answer 30

CIRCULAR and ssRNA

Question 31

What was the first identified viroid?

Answer 31

PTSVd (Potato Spindle Tuber Viroid)

Question 32

What may be responsible for the ribonuclease resistance of viroids?

Answer 32

Their RNA secondary structure!

Question 33

Viroids DO NOT contain _______ and therefore DO NOT carry out ________

Answer 33

Viroids DO NOT contain **GENES** and therefore DO NOT carry out **PROTEIN SYNTHESIS**

Question 34

How are viroids hypothesized to replicate?

Answer 34

By using host cell RNA polymerase

Question 35

How are viroids hypothesized to cause host cell damage (via RNA polym.)?

Answer 35

By diverting the function of RNA polymerase away from essential cellular pathways (and occupying its use for viroid replication)

Question 36

What is a potential explanation for viroid pathogenesis (ER)?

Answer 36

Viroids may bind to SRP RNA preventing proteins from being directed to the ER for processing (causing symptoms due to improper proteins in cells)

Question 37

Viroids contain regions that are complementary to what eukaryal seuences?

Answer 37

Eukaryal SRP RNA (specifically 7S RNA)

Question 38

SRP RNA

Answer 38

Signal Recognition Particle RNA == RNA that directs cytoplasmic proteins to the ER for processing

Question 39

How are viroids spread?

Answer 39

Mainly through human activities and insects

Question 40

Similarities between Satellite RNAs/Viruses and Viroids

Answer 40

1) Both have small RNA genomes 2) Both infect PLANTS

Question 41

Differences between Satellite RNAs/Viruses and Viroids

Answer 41

**Viroids** = 1) can replicate on their own in a host cell 2) NOT encapsulated **Satellite RNAs/viruses** = 1) CANT replicate on their own in a host cell (require a helper virus) 2) ENCAPSULATED by a protein coat

Question 42

What is the difference between satellite RNAs and satellite viruses?

Answer 42

**Satellite RNAs** = Coat is made of proteins produced by the HELPER virus **Satellite Viruses** = Coat is made of proteins IT encodes for

Question 43

What is the human infectious agent similar to satellite RNAs/viruses?

Answer 43

HDV (Hepatitis Delta Virus)

Question 44

How is HDV similar to satellite RNAs/viruses?

Answer 44

Require COINFECTION! == It is an ssRNA virus that can only replicate in cells ALREADY infected with Hepatitis B

Question 45

Virophages

Answer 45

Infectious agents like satellite viruses BUT their replication HARMS the helper virus!

Question 46

All currently known virophages infect...

Answer 46

AMOEBAS that are coinfected with Giant viruses

Question 47

Prions are AKA...

Answer 47

Proteinaceous Infectious Particles

Question 48

Prion

Answer 48

Infectious agent composed of JUST PROTEIN that can replicate within a host cell + cause transmissible spongiform encephalopathies

Question 49

Prions contain NO _____________ BUT can STILL _________

Answer 49

Prions contain NO **DNA or RNA** BUT can STILL **replicate on their own**

Question 50

What diseases are caused by prions?

Answer 50

Transmissible Spongiform Encephalopathies (TSEs)

Question 51

What are Transmissible Spongiform Encephalopathies?

Answer 51

Progressive neurodegenerative diseases characterized by mental impairments and sponge-like holes in the brain

Question 52

What are two HUMAN TSEs?

Answer 52

1) Kuru 2) CJD (Creutzfeldt-Jakobs Disease)

Question 53

What are two ANIMAL TSEs?

Answer 53

1) Scrapie (sheep) 2) Bovine Spongiform Encephalopathy (Mad cow disease)

Question 54

Prions are __________ forms of __________ occurring proteins found on the surface of ___________

Answer 54

Prions are **misshapen** forms of **naturally** occurring proteins found on the surface of **neurons**

Question 55

Prion proteins can exist in one of two states:

Answer 55

1) Cellular State (PrP^c) 2) Pathogenic Form (PrP^Sc) NOTE: Sc = scrapie (letters will correspond to the TSE)

Question 56

Prion replication process:

Answer 56

1) Pathogenic form interacts with the cellular form prion protein 2) Interactions causes the cellular form prion protein to change conformation and become a pathogenic prion protein 3) Process repeats as the pathogenic form proliferates 4) Pathogenic prion proteins polymerize into FIBRILS (which are thought to contribute to the TSEs)

Question 57

What role do genetics play in prion replication?

Answer 57

Mutations in the prion protein gene/s can make a given prion protein more susceptible to taking on the pathogenic form! **== We can INHERIT prion disease from mutation in a PrP gene!**

Question 58

Prion diseases can be BOTH

Answer 58

Infectious AND hereditary