Virology

Question 1

Group I

Answer 1

dsDNA viruses e.g herpes virus family

Question 2

Group II

Answer 2

ssDNA viruses e.g Parvovirus

Question 3

Group III

Answer 3

dsRNA viruses e.g Rotaviruses

Question 4

Group IV

Answer 4

+ sense RNA viruses e.g HCV, Polio

Question 5

Group V

Answer 5

• sense RNA viruses e.g influenza, Ebola, measles, rabies

Question 6

Group VI

Answer 6

RNA reverse transcriptase viruses (Retroviruses) e.g HIV

Question 7

Group VII

Answer 7

DNA reverse transcribing viruses (DNA Retrovirus) e.g HBV

Question 8

DNA virus groups?

Answer 8

I, II, VII

Question 9

Names of all the DNA virus families?

Answer 9

HHAPPPy
Hepadna
Herpes
Adeno
Pox
Parvo
Papova

Question 10

Which DNA viruses have naked capsids?

Answer 10

DNA gets naked for her PAP smear…

Parvovirus
Adenovirus
Papovavirus

Cervical cancer

Question 11

Which viruses have SEGMENTED genomes?

Answer 11

Bunyavirus, Orthomyxovirus, Arenavirus, Reovirus

Question 12

What is the definition of a Virus?

Answer 12

• Obligate intracellular parasite: Depend ENITRELY on the cell they infect for ALL functions i.e replication, to make energy or utilise nutrients

Question 13

Problems with new emerging viruses?

Answer 13

Zoonotic origin (transmitted from animals)

Question 14

Viroids and Prions

Answer 14

• Viroids (no protein) and Prions (no nucleic acid); resistant to radiation damage, heat inactivation, sensitive to urea, SDS and other protein-denaturing chemicals

Question 15

Capsid

Answer 15

• Protein coat that protects virus from the environment (Helical capsid most common (made up of one type of protein)
o Isosahedral capsid Each triangle identically spatial

Question 16

Nuceloproteins

Answer 16

• ALL viruses have NUCLEOPROTEINS (nucleic acid bound to protein)

Question 17

Assembly of a bacteriophage

Answer 17

STALK (helical) Head (Icosaherdal)

Question 18

Virus replication cycle

Answer 18

• Virus replication cycle: ENTRY (major determinant of tropism), REPLICATION, ASSEMBLY, RELEASE (major determinant of pathogenesis)
o Host cell receptors define: tissue tropism and species tropism i.e is a cell lacks the receptor, it can’t be infected
o Tissue tropism the cells and tissues of a host which supports growth of a particular virus or bacteria
o Pigs can act as an intermediate host (then transfer virus to humans)

Question 19

LOCK AND KEY

Answer 19

interaction of virus will host cell surface receptor is a major determinant of the subsequent events i.e replication/ outcome of infections

Question 20

HIV cell interactions

Answer 20

o CD4 HIV receptor (virus has proteins on its surface which interact with the cell surface)
o Virus tends to have slightly opposite charge to the cell (GAGs) sticks to the cell via static interaction
o 2nd receptor = CCR-5 (lock turns) membrane at the top bought down to meet the membrane at the bottom
o GP41 contains fusion peptide which joins the two membranes together virus inside host cell

Question 21

PENETRATION

Answer 21

• PENETRATION: pH dependent or pH independent
• pH dependent: EC virus receptor binding (virus triggers internalisation; instantly transported into a vesicle) viral entry into cytoplasm requires the bursting of the endosome (usually requires acidification by viral proton pumps)
• pH independent: virus binds to receptor molecule translocated across PM by receptor Virus released into cytoplasm (receptor recycled)

Question 22

Lytic/Chronic release

Answer 22

• Lytic release destruction of infected cell and its membrane (tend to be naked particles
• Chronic release Budding borrowing from the cell membrane to create the viruses own membrane (envelope) e.g HIV, Flu

Question 23

Famous 1 step growth curve

Answer 23

Eclipse: Virus inside cell, not detectable, synthesing enzymes, nucleic acid etc
Maturation/Release: MASSIVE increase in growth curves as viruses lyse cells, releasing virion
Plateu: all cells in the culture have been lysed and virus released

Question 24

RNA viruses

Answer 24

• RNA unstable clover shape protects the end; No poly-A tail (stabalising factor)
• All proteins that do manufacture assembly are together; all proteins going into the capsid are together; entire virus is one OFR which is cut down to give mature gene products

Question 25

+ Strand RNA virus genomes

Answer 25

* SS, no anti-sense; single START and STOP codon; UTR at start and end; cassette (compartmentalise) their genes like bacteria * Sometimes no poly-a-tail (knot up ends into clover leaf structure) Poly-a-tail prevents the degradation of the message

Question 26

- strand RNA virus genomes

Answer 26

• ANTI-SENSE strand cannot make RNA into protein, therefore the virus has to replicate BEFORE you can get expression of a protein (replication produces sense strand) • Has a polymerase INSIDE the capsid; piece of RNA in the virion • Some SEGMENT their genome more stable/can get more information inside (simple and multi-partite viruses) Fairly simple genetic organisation • ORF..GAP..ORF..GAP • RNA pol, Trimeric envelope, Glycoprotein, Nucleoprotein • Filovirus 1 genome FRAME SHIFTING signals cause it to move around with each frameshift, different protein thrown off PARA and ORTHO myxovirus • Myxo = mucus; ss anti-sense viral genome; causes common cold; effects UPPER RT

Question 27

Influenza

Answer 27

• Ss anti-sense RNA: 7/8 segments (all segments necessary for replication of genome) o These pieces can be moved around and swapped vast majority of influenza particles are defected (lot less viability in particles) o Reassortment of strains can occur in wild ducks, pigs etc NEW flu epidemic o If you infect an organism with two different viruses at the same time, they will MIX at random • Viruses don’t proof read their own polymerase doesn’t check as it goes along ‘genetic drift’ • HN: Neuraminidase found on surface of influenza, enables virus to be released from host cell o Hemagglutinin glycoprotein found on the surface of influenza virus responsible for binding the virus to cells with sialic acid on the membranes

Question 28

Viral Sex

Answer 28

‘’Reassortment’ and swapping of chromosomes massive evolutionary

Question 29

ssRNA replication

Answer 29

* ssRNA needs to form ds RNA replicative intermediate however dsRNA is just plain wrong so ALL RNA viruses will tell you that you are infected as the body recognises this as a foreign agent * 4 basic lifestyle steps total un ivolvement of the nucleus (90-95% of cases)

Question 30

Ds viral replication

Answer 30

* Capsid never fully releases the genome; replication takes place in a partially disassembled shell or ‘skeleton’ never free floating nucleic acids around * Rioviruses very stable on EM can watch what happens during infection

Question 31

Routes of viral entry/Retroviruses

Answer 31

Routes of Viral Entry • PM; endosomes (majority) Retroviruses • Very simple architecturally; very similar to one another; DNA polymerase, reverse transcriptase

Question 32

Why are DNA viruses of interest?

Answer 32

• Why are they of interest? Can cause cancer in humans (apart from adenovirus respiratory disease) o Human adenoviruses infect rodent cells and can turn them cancerous (model system) • HPV16 Papilloma cervical cancer, head and neck cancers • However can have therapeutic uses anti-cancer Herpes simplex to treat solid tumours

Question 33

HOW bad are these viruses?

Answer 33

* 12.7 in 2008 2 mill were infection by virus (approx. 10% = all BC cases) * Causing cancer is not NORMAL part of virus life cycle; DEAD END as new viruses are not made; virus often altered so doesn’t finish life-cycle * Virus-host interactions formed during virus life cycle contribute to carcinogenesis to understand this we need to understand HOW DNA viruses replicate in the host

Question 34

Common persistent infections

Answer 34

* Herpes (e.g Epstein Barr Virus) asymptomatic; stays with us for life; only small % of individuals develop cancer (infection alone not sufficient) other factors involved such as malaria infection (causes Burkitt lymphoma) Nasopharyngeal cancer eating salty fish (nitrosamines) * HPV Hyperproliferative warts (200 genotypes) STI; only small % go on to get cancer; 610,000 cancers caused by HPV usually other factors involved in pathogenesis e.g gene defect, smoking, sun exposure

Question 35

Immune surveillance control

Answer 35

* HIV individuals have MORE cancers caused by these viruses than the general population; HIV patients have a compromised immune system enabling persistence of other infections including cancer causing viruses * These viruses have evolved strategies to hide from our immune system * Organ transplant patients high incidence of cancer caused by genetic viruses

Question 36

Viral DNA replication

Answer 36

* All replicate in the nucleus- except poxviruses; all have different strategies for replication * Requirements: Polymerase + other factors (e.g thymidine kinase) induce the host to express the polymerase * If virus does not encode these factors, has to get them from host if host not making these has to induce host replication factors

Question 37

Where do the replication proteins come from?

Answer 37

• Small DNA viruses do not encode an entire genome replication system encodes proteins that orchestrate the host (polyoma,papilloma,parvo)

Question 38

Viral gene expression

Answer 38

* E + L genes expressed at different times in the life cycle * Viral DNA replication early viral proteins/genes * Once virus has replicated see expression of LATE genes (i.e structural proteins such as capsids) * Replication machinery will only be on and active when our cells are proliferating need to prevent cells dying early proteins stimulate cell growth and stop cell death

Question 39

HPV orchestrates the host cell

Answer 39

• Replicates in squamous epithelia (multi-layered structure) life cycle dependent on differentiation of epithelia • Gains access to basal compartment (parts that are still growing) through cuts/breaks in the epithelia • Virus amplifies its DNA to form new virions in the upper layer of the epithelia virus hits problem as these aren’t proliferating o Proteins E6/E7 upper layers lots of proliferation as lots of new virus is being produced • E7 causes proliferation; in response to this host cell induces apoptosis pathways (problem for virus as it needs to divide) E6 blocks induction of cell death (targets cell regulators which cause cell death) BOTH DEREGULATE TUMOUR SUPPRESSOR PATHWAYS • Targeting TSG lots more host genomic instability therefore increased risk of one of those mutations being an oncogenic mutation proliferation • CERVICAL CANCERS only viral E6 and E7 being expressed.. bad news • Can control E6/E7(viral oncogenes) in lab cancer cells than restore their normal growth

Question 40

Cancer- accumulation of genetic mutations

Answer 40

* Need more than one ‘hit’ ie genetics, diet, chemicals; could be mutations in oncogenes initiates proliferation * Oncogenic viruses: Herpesviridae;Hepadaviridae(HepB vaccine liver cancer; where incidence is high) ;Papillomaviridae;Polyomaviridae,Adenoviridae

Question 41

HPV

Answer 41

* HPV vaccine HPV16L1 protein expressed in insect cells assembled into virus like particles basis for HPV vaccine * Pentamers made up of L1 capsid protein * Very difficult to grow this virus in cell cultures * Took the gene encoding the late protein L1 expressed in bacteria when they looked down the electron microscope saw particles icosahedral capsid just by expressing late protein would assemble spontaneously into a viral capsule form the basis of HPV vaccine * Cervatix, Gardasil * Cervatrix 2 virus like particles * When individuals are vaccinated virus like particles stimulate antibodies can then block infection with infectious HPV 16 and 18. * When the girl is exposed to the actual infectious virus won’t be able to infect * Won’t know true effect for decades