Virus

Question 1

where are viruses? what can they cause

Answer 1

• found everywhere: in all ecosystems, all cellular organisms are infected by them

* if theres a host they can ifnect they’ll be there

• big impacts on ecosystems, evolution, human/animal health and history
• some can generate serious global diseases: SARS COVID-19, Zika, human and avian influenza, HIV-AIDS etc

Question 2

how are Viruses used in research?

Answer 2

• serve as tools and model systems in molecular biology and genetic engineering including vectors for gene clonging, delivery devices for gene therapy and CRISPR antiviral defense system
• Attenuated and genetically engineered viruses used as vaccine
• Bacteriophages are being used to treat infections by multi-antibiotic resistant bacteria
• Buculoviruses (infect specific insects) are used for bio-control of insect pests

Question 3

what is the ecological role of viruses

Answer 3

• viruses are the tiniest of biological entities, they have huge roles in ecosystems
• sum of viral populations in an ecosystem = virome
• virus-to-bacteria ratios range from 1:100 in marine and aquatic environments to 1:1000 (100-1000 virsues for each species of bacteria)

*play role in controlling microbial densities -> they pray on bacteria

• on global scale they are critical players in carbon balance and in the global recycling of nutrients
• marine bacteriophages and eukaryotic viruses infect numerous aquatic hosts, when host organism dies their organic matter provides them carbon and nitrogen for growth to toher organisms in env

Question 4

describe the ‘host range’ of a virus

Answer 4

• viruses are obligate intracellular pathogens (must infect a host cell to reproduce)
• each species infect a particular group of host species known as their host range
• Chronic viral ifnections are more common than acute disease
• we have far more antibacterials then antivirals (viruses typically cause chronic infections though, would be more lucrative to have mroe antivirals)

Question 5

what is a virus

Answer 5

• virus particle or VIRON is a ‘bag’ of genomic material protected by protein coat that:
• must infect a host cell where itll reproduce
• typically subverts the cell’s machinery and directs it to produce viral particles
• consists of nucleic acid (DNA or RNA) contained usually within a protective protein CASPID coat
• genome typically codes for 10-100 genes

* cna argue that viruses are non living bc lack metabolism and not able ot reprudoce wihout a host

Question 6

What are giant viruses

Answer 6

• simple definitions based on size can be problematic
• ‘giant’ viruses have genomes of double stranded DNA comrpised of 500-2500 genes

*more genes than some free lving bacteria and aerchaea

• the mimivirus which infects amoebas is as large as some bacteria (can actually be infected by smaller viruses called virophages)

Question 7

what are viroids

Answer 7

• Viroids (not virions) are extreamely simple RNA viruss that infect plants

*double stranded RNA virus

*basically just naked RNA, no protein cpaid and replicated by the hosts RNA polymerase

• some have catalytic ability: cleave specific RNA sequences
• transmitted by sap feeding insects, throguh damaged tissue and infected seeds

Question 8

what are prions

Answer 8

• shape chainging proteins
• occur naturally in the brain fo animals: in normal conformation cause no problems

*infectious proteins, NO RNA or DNA, not in a capsid

• cahnge in conformation due to spon mutation, can then recruit and bind to the normal protein causing it to change shape
• abnormal conformation is pathogenic (disease causing) and can be transmitted

•Highly resistant to chemical, heat, radiation inactivation

* multiple prion proteins aggregae and cause sponge like holes/plaques in the brain

*prions are not viruses, cause disease by abnormal protein shape not be nucleic acids

Question 9

describe the gneral anatomy of a virus

Answer 9

• two general formats: caspid & genome (RNa and DNA) or caspid, genome & envelope

*envelope is composed of cytoplasmic/cell membrane derived fromt he host cell

• the viral caspid protects the genome (present in all virsues)
• capsid composed of repeated protein subunits, this maximized the capacity while minimizing the number of genes required
• caspid packages of the viral genome and delivers it to the host cell

*different virsues make different caspid forms: symmetrical and asymmetrical

Question 10

What is an icosahedral virus

Answer 10

• symmertrical virus
• ef: herpes simplex virus (HSV-1)
• polyhedral with 20 identical triangular faces- largest possible (making up the caspid)
• structure has rotational symmetry
• caspid is packed with viral DNA genome *not all icosahedral viruses have a DNA genome, but this is the case with herpes
• some icosahedral virsues ahve an envelope surroudning/encolsing the caspid

Question 11

what is a filamentous virus

Answer 11

• symmetrical virus
• ex: tobacco mosaic virus (TMV), ebola
• elongated shape
• caspid consists of long tube of caspid monomers with the genome coiled inside
• vary in legnth depenging on genome size
• include bacteriophages as well as animal viruses

Question 12

what are asymmetircal viruses

Answer 12

ex: influenza, poxvirus - lack capid symmetry
- have large genomes surrounded by several layers: core envelope studded with PSIKE proteins and an outer membrane
- also contain a large number of accessory viral proteins

*encoded for by viral genome

• accessory proteins are required immediately upon infection of the host cell, faciliates survival of virus and subvert host cell functions

Question 13

describe complex / asymmertircal viruses

Answer 13

• ahve multipart structures
• T4 bacteriopahges
• have icosahedral “head” and helical “neck”
• neck acts as an elaborate injectisome devide
• looks like an apollo lander
• middle pic is an electromicrograph shoing bacteriophage infecting an ecoli cell, entire virus contracts as the DNA in injected through the neck adn cell wall into e coli

Question 14

describe viral genomes

Answer 14

• DNA or RNA not both
• varations: double standed (ds) or single standed (ss) RNA or DNA
• ssDNA or ssRNA can be + (sense) or - (antisense)
• can be linear, ciruclar or segmented: some viruses ahve one piece of DNA/RNA while others may have multiple pieces
• messanger RNA encoded using antisense as the template so the nucleotide seq of mRNA matches that of the coding strand
• genes in viruses encode: capsid proteins, the accessory proteins, spike protiens

Question 15

how are viruses classified

Answer 15

• classifed based on :
  1. genetic material: DNA or RNA genome, strandessness (ss or ds), if ss then either +sense or -antisense
  2. morphological/host range characteristics: shape, size, enveloped, non enveloped, host range

*baltimore classification scheme uses only (1) while international committee on the taxonomy of viruses (ICTV) uses (1) and (2)

Question 16

what is the central dogma

Answer 16

DNA -> mRNA -> protein

*information flows different pathways in RNA genome viruses

-ssRNA <–(rdRP)–> + ssRNA —(host ribosomes)–> viral proteins

RdRP = viral RNA-dependent RNA polymerase, this viral enzyme is packaged in the viron

+ssRNA = positive (+) single strang (the +ssRNA serves directly as mRNA)

-ssRNA = negative ss RNA, template to make a +sense copy
*all cells and vriuses nee to make mRNA (+ssRNA) to produce proteins

NOTE +ssRNA is teh same as mRNA

Question 17

describe the baltimore classification of viruses

Answer 17

• research-wise is the most used
• HOW mRNA is produced by a virus is central to the baltimore virus classification
• 7 fundamental ways shown in fig 6.19

Question 18

how to retroviruses make mRNA

Answer 18

• integrate their genomes into the host genome
• have (+)ssRNA genomes, equivalent of an mRNA is used for translation into viral proteins using host cell machinery
• retroviruses are RNA reverse transcribing viruses : they package thier own reverse transcriptase (RT) enzyme
• the +ssRNA is injected into the host and used as template and transcribed into -ssDNA (intermediate)
• accomplished by RT enzyme trascribes the virus (+)ssRNA genome into a ss(-)DNA (start with RNA to get DNA)
• the ss(-) DNA strans if then generated using host DNA polymerase generating dsDNA
• the dsDNA is inserted into the host genome and directs the expression fo the viral genome
• includes HIV, SIV and FIV

*read more in textbook on how

Question 19

naming viruses

Answer 19

• Family name: ends with viridae
• Genus name: ends with virus

*Members of the same family share similar characteristics but each member (genus) has other unique characteristics

E.g. FAMILY: Hepadnaviridae

Genera: Hepadnavirus

Can you tell the type of genetic material? Disease the virus causes?- hep = liver cells, also contains DNA

Question 20

how do you grow viruses - bacteriophages

Answer 20

• culturing bacteriophaes quite easy, just need bacteria and palte on agar medium and evenutally get a lawn
• infect wiht bacteriophage that infects these
• if lytic will see plaques (zones of clearance), if you took a sample from middle of plaque where there is a lawn would make another zome of cleance (plaques contin lots of the virus)
• can then washt eh plate with buffer to collects lots of baceria phages

Question 21

howd o you culture eukaryotic viruses

Answer 21

• culturing viruses reuqires groth in a susceptable/ appropraite host cells: plant and simal viruses are especially diffuclt to cultuure bc they show tropism for particular cells/host tissues
• host cell must have the right receptors (maybe specific to liver cell)

ways to clulture:

1. living animals: rabbits, mice, chimps
   * ensures cirus maintains original virulence, but this is expesnvie and laborious and ethics
2. embryonic eggs
   * inject virus into developing enbryo, this is hw you culture influenze virus for vaccinations
3. Tissue culutre

• in liquid media (complex and specialized media, doesnt work for all)
• in transformed/culture adapted cells, gow a layer and infect

Question 23

decribe how bacteriophages/viruses infect the cell

Answer 23

• to start infection cycle bacteriophages need to contct and attach to the surface of an appropriate bacterial host cell
• contact and attachemnt mediated by cell surface receptors
• phages have proteins/glycoproteins on their caspids that recognize specific proteins or polysaccharides on the bacterial cell surface
• receptors determine the phage tropism
• cell surface receptors are proteins wiht important functions for the host cell that have been co-opted by the virus
• host bacteria can evolve resistance to phage attachment by mutating the aa seq on receptors

Question 24

what are teh stages of the lytic cycle of bacteriphages

Answer 24

APUBARM

1. Attachemnt to a bacterial cell surface receptor (host ‘tropism’)
2. Penetration of the genetic material thorugh bacterial cell wall (w/o lysis of the cell)
3. Uncoating: DNA drawn into celll (caspid ghosts stays outside, ins ome animals viruses can use with the membrane)
4. Biosynthesis: temporal regualtion of transcription, viral protein synthesis, genome replication
5. Assembly of virion proteins and genome
6. Release (+/- lysis of the cell ) through cell membrane/wall
7. Maturation (final activation of virion proteins

Question 25

what is a lytic phage cycle

Answer 25

- lyse the host to release new progeny - the injected phage genome is replicated within the cytoplasm - synthesis fo phage protiens, capsids - assembly of progeny phages - phage protiens digest the host cell membranes/wall to release progeny - can be observed as clear plaques on a bacterial lawn on agar plates

Question 26

describe the lysogenic lifecycle

Answer 26

- lysogenic or temperate life cycle of DNA genome phage - injected phage DNA integrates into the host chromosome (ie prophage) - prophage replicates with the host genome, spreading in the population - fi the host cell is exposed to stress conditions, the prophage can **direct its excision** then initiates a lytic cycle

Question 28

what types of anti-phage defence do bacteria have?

Answer 28

- genetic resistance: altered phage receptor proteins - Restriction endonucleases: cleave viral DNA lacking methylation - CRISPR integration of phage DNA sequences: Clustered Regulatly Interspaced Short Palindromic Repeats: a bacterial immune system to cleave bacterial DNA

Question 29

describe animal virus life cycles

Answer 29

- bidn to specific recepotr proteins on host cell/cytoplasmic membranes: receptor determines **tropism** - most animal virus enter the host as virions (include the caspid) - internalized virions undergo uncoating, where the genome (and any accessory proteins) are released from its caspid - uncoating can occur in several diff ways and in diff sites/organelles ex: uncoated at cytoplasm, endosome or nuclear membrane - mature viruses exit the host cell via PM via cell lysis, budding (naked viron exists without lysis), or budding (membrane surrounds caspid forming the envelope

Question 30

what are oncogenic viruses?

Answer 30

- many human cancers are caused by oncogenic viruses ie: epstein-barr virus (which cause lymphomas) and hepatitis C virus (which causes liver cancer) - oncogenic viruses transform the host cell to become cancerous - transformed cell undergoes unregualted cell dsivisiona dn growth

Question 31

Baltimore Classification Group 1: Double standard DNA virus

Answer 31

- herpes - make own DNA polymerase or use host genome for replication - genes can be transcribed by standard RNA polymerase whihc can be of the host cell or encoded in virl genome

Question 32

Baltimore Classification Group II: Single stranded DNA

Answer 32

- require host DNA polymerase to generase complementary strand - dsDNA then transcribed by host RNA pol

Question 33

Baltimore Classification Group III: double stranded RNA viruses

Answer 33

**require a viral RNA dependent RNA pol** to generate mRNA - RNA pol is required immediately upon infection so packaged with genome before existing host cell ex: reoviruses

Question 34

Baltimore Classification Group IV: + sense single stranded RNA virus

Answer 34

- have the coding strand that can serve as mRNA to be translated - to replicate RNA genome need the - sense uses **viral RNA dependent RNA polymerase** to make the double stranded RNA intermediate ex: hepititis C

Question 35

Baltimore Classification Group V: - sense single stranded RNA viruses

Answer 35

- ex: influenza - only have the template - package **viral RNA dependent RNA polymerase** to transcribe -RNA to +mRNA \*- strand is often segmented

Question 36

Baltimore Classification Group VI: retroviruses or RNA reverse transcribing viruses

Answer 36

- HIV - have a + RNA and package a **reverse transcriptase** that transcribed the RNA into ds DNA to be integrated into host genome

Question 37

Baltimore Classification Group VII: double stranded DNA Pararetroviruses

Answer 37

- require reverse transcriptase - use plant host - can first copy ds DNA genomes into RNA then reverse transcribes RNA to progeny DNA - reverse trancriptase can come from original virus or host