Viral disease Flashcards
What disease does Epstein Barr virus cause?
Infectious mononucleosis (IM)
also known as glandular fever or the kissing disease
what are the main symptoms of infectious monocleosis?
extreme fatigue.
fever.
sore throat.
head and body aches.
swollen lymph nodes in the neck and armpits.
swollen liver or spleen or both.
rash
Breifly describe the Herpes Life Cycle
REPLICATION = NUCLEAR
Lytic replication:
1. * * 1. Attachment of the viral gB, gC, gD and gH proteins to host receptors mediates endocytosis of the virus into the host cell.
1. * * 1. Fusion with the plasma membrane to release the core and the tegument proteins into the host cytoplasm.
1. * * 1. The capsid is transported to the nuclear pore where viral DNA is released into the nucleus.
1. * * 1. Transcription of immediate early genes which promote transcription of early genes and protect the virus against innate host immunity.
1. * * 1. Transcription of early viral mRNA by host polymerase II, encoding proteins involved in replication of the viral DNA.
1. * * 1. A first round of circular genome amplification occurs by bidirectional replication
1. * * 1. Synthesis of linear concatemer copies of viral DNA by rolling circle.
1. * * 1. Transcription of late mRNAs by host polymerase II, encoding structural proteins.
1. * * 1. Assembly of the virus in nuclear viral factories and budding through the inner lamella of the nuclear membrane which has been modified by the insertion of herpes glycoproteins, throughout the Golgi and final release at the plasma membrane.
Latent replication : replication of circular viral episome in tandem with the host cell DNA using the host cell replication machinery.
Herpes virus produce three temporal classes of mRNAs and proteins, what are they?
IE immediate early
E Early
L Late
what are the three phases of gene expression in the Herpes Lytic phase?
1) tegument proteins regulate production of mRNAs and proteins of IE immediate early genes; they
protect the virus against innate host immunity and promote transcription of early genes
2) production of E early
mRNAs / proteins; they are involved in viral replication
3) production of L late
mRNAs / proteins; they are involved in virus assembly
what is the EBV genome like in the lytic phase?
linear dsDNA
what is the EBV genome like in the latent phase?
circular dsDNA
how many members are there of the herpes family
There are eight currently identified members of the herpesvirus family. They are ubiquitous and extremely well adapted pathogens. The name comes from the Greek ‘herpein’ - ‘to creep’, describing the chronic, latent or recurrent nature of infections.
breifly how do herpesviruses regulate host immunity
– can down-regulate pro-inflammatory responses
– can down-regulate MHC-II complex in infected cells
– Herpes and EBV can infect B and T-cells
how large are the herpesviruses?
120-200nm
relatively large but still smaller than a bacterial cell
what seven points can you use drugs to interfer with viral replication?
① receptor binding
② entry
③ mRNA function
④ DNA/RNA synthesis
⑤ Assembly
⑥ Release (still infected but the virus particles aren’t released)
what chemicals orchestrate viral defence?
interferons - mainly type II INFg
what interferons do virus infected cells produce?
type 1IFNa and IFNb
what type of interferon do T cells and Natural Killer cells respond to?
what are the autocrine and paracrine effects of this?
type II INFg
* autocrine: inhibition of virus replication, apoptosis
* paracrine: up-regulation of MHC-I and NK-cell activation
how many cases and death were there in the 2002/3 SARS outbreak?
what was the % fatality?
over 8000 cases
almost 800 deaths
nearly 10% fatality
how many cases and death were there in the 20012/13 MERS outbreak?
what was the % fatality?
in the middle east
over 1300 cases
over 400 deaths
nearlly 40% fatality
how many cases and death were there in the COVID19 outbreak?
what was the % fatality?
over 750,000,00 cases,
6,900,000 deaths,
0.9% fatality
define epidemic
geographically and temporally restricted disease
define endemic
geographically limited disease over a long period
define pandemic
temporally restricted disease, occurring worldwide
define incidence
number of new infections (typ. per year per 100,000)
define prevalence
number of diseased at a given time (typ. per 100,000)
define morbidity
number of diseased (typ. per 100,000)
define mortality
number of deaths (typ. per 100,000)
what does the R0 number mean?
R0 indicates the # of individuals one sick person will infect
what is the R0 of Ebola?
2
what is the R0 of HIV
4
what is the R0 of Pox
6
what is the R0 of SARS
4
what is the R0 of Mumps
10
what is the R0 of Measles
18
what is Dexamethasone?
how was it involved in COVID19?
Dexamethasone is a corticosteroid used in a wide range of conditions (anti-inflammatory, immunosuppressant).
People realised in the hospital setting that COVID19 patients were suffering from inflammatory problems
It was tested in hospitalized patients with COVID-19 in the United Kingdom’s national clinical trial RECOVERY and was found to have benefits for critically ill patients.
For patients on ventilators, the treatment was shown to reduce mortality by 1/3rd; for patients requiring only oxygen, mortality was cut by about 1/5th
what is Paxlovid also known as?
Nirmatrelvir/ Ritonavir
What Paxlovid mechanism of action?
an inhibitor of Mpro, a protease critical in viral replication
what is sotrovimab
Sotrovimab (Xevudy) is a monoclonal antibody recognising the spike protein that the covid19 virus uses to attach to cells.
* used to treat symptomatic acute covid-19 infection in adults and adolescents (12 years or older, weighing at least 40 kg)
* overcome an infection and prevent serious illness
what are viral factories
Viral factories are intracellular compartments of the host cell that contain viral replication organelles and necessary elements for assembly and maturation of new infectious viral particles
give two examples of viruses with cytoplasmic viral factories
- Coronaviridae use double membrane vesicles (DMVs)
in the cytoplasm where the dsRNA is produced - Poxvididae form a viruplasm for viral replication and assembly
give an example of a virus with a nuclear viral factory
- Herpesviridae form nuclear replication compartments (RCs) for viral DNA replication and late gene transcription
what is the reason viruses create viral factories?
Reason: for undisturbed viral replication and assembly, shielding this process from host defenses.
(not exposed to cellular machinery that wound react against it)
which epidemics coincided with the fall of the roman empire?
Epidemics in the years 165-180 and 251-266 coincide with the fall of the Roman Empire
– smallpox: Poxvirus
– measles: Paramyxovirus
Paramyxovirus causes what disease
Mumps and measles
what features are viruses classified by?
How they look: capsid, envelope
Their genome: This can be either DNA or RNA
what is baltimore classification?
Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis.
Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.
what are the 7 baltimore classifications?
(how do they produce mRNA?)
double or single stranded DNA viruses
I. dsDNA: all mechanisms like DNA genomic host cell
II. ssDNA: convert to dsDNA first, then like host cell
(can produce mRNA, just normal host mechanism, easy)
double or single stranded RNA viruses
III. dsRNA: RNA used as template for mRNA
IV. ssRNA: a positive strand has the same orientation as mRNA; requires synthesis of complementary RNA first;
mRNA is then synthesized from the complementary RNA strand (plus RNA, llooks like mrna?)
V. ssRNA: a negative strand is complementary to mRNA; mRNA can be synthesized directly from the genome template (minus RNA)
VI. RNA genome but dsDNA intermediate
VII. DNA genome but ssRNA intermediate
what is the most common drug hypersensitivity reaction?
Morbilliform drug eruption
what happens when someone presents with pharyngitis and is misdiagnosed with a Streptococcal infection (when it was glandular fever) and treated with amoxicillin?
morbilliform drug eruption
(bad rash)
what is unusual about the Herpes Virus lifecycle?
It has a lytic (linear dsDNA) and latent phase (circular dsDNA)
It is assembled in the nucleus and buds out through the nuclear membrane
what is cell tropism?
Tropism of a virus pertains to the types of cells, tissues, and animal and plant species in which it can replicate. Because various replication steps of viruses require host proteins, the expression levels of such host proteins in a cell affect tropism.
what does tegument protein do?
- protect the virus against innate host immunity (dampens immune repsonse to help virus survive)
- promote transcription of early genes
what percentage of people have been infected with the Herpes virus?
> 60%
what percentage of epople have been infected with cytomegalovirus?
> 90%
How many gene products do stage 1 interferon response produce?
> 300
what cells release type 1 interferon alpha?
dendritic cells
what cells release type 1 interferon alpha?
dendritic cells
what cell releases type 1 interferon beta?
fibroblasts
what does autocrine mean
?
the production and secretion of an extracellular mediator by a cell followed by the binding of that mediator to receptors on the same cell to initiate signal transduction
what does paracrine mean?
cells communicate with each other by releasing signaling molecules that bind to and activate surrounding cells.
the type 1 interferon response stimulates what cells to release what?
T-cells & Natural Killler cells to produce type II INFg
what cells can interferon gamma kill?
INFg can kill virus infected cells or cancerous cells
what is the antiviral state
The antiviral state is the result of a signaling pathway induced by IFN-alpha or IFN-beta following viral infection. It leads to the transcription of various cellular antiviral genes coding for host defense proteins.
what are the major autocrine effects triggered by interferons part of the antiviral state?
- Degredation of RNA (viral and cellular)
- Shutdown of protein synthesis
- inhibition of RNA virus replication
- Apoptotic cell death
what does Protein kinase R do in the antiviral state?
phosphorylate eukaryotic initiation factor 2 (ELF2) and other proteins to shutdown protein synthesis
stimulate cell death via apoptosis
what do effectors such at TRIAL do in the antiviral state?
stimulate cell death via apoptosis
what do effectors such at TRIAL do in the antiviral state?
stimulate cell death via apoptosis
what are the major paracrine repsonses triggered by interferons in the antiviral state?
increased synthesis of MHC-1 proteins which increases presentation of antigens to adaptive cellula rimmune repsonse to increase killing of virus infected cells
activation of NK cells to increase killing of virus cells
how are NK cells targeted to the site of virus infection?
cytokines
how do NK cells kill virus infected cells?
by release of perforin (which disrupts the integrity of the target cell membranes) and granzyme to induce programmed cell death (apoptosis) in the cell
what happens when viruses come into contact with macrophages?
virus binds to specialised cellular recepotrs stimulating uptake (phagocytosis)
the phagosome fuses with the lysosome and digestion of phagocytosed material occurs.
Digested viral proteins are then presented onto MHC-2 (for stimulation of CD4+helper T cells), the rest are released by exocytosis
other than phagocytosis what happens when macrophages come into contact with viruses
produce a characteristic pattern of cytikines to initiate a localised immune response, includign migration of neutrophils into the tissues from the blood
neutrophiils are another type of phagocytotic cells
what other cells are involved in the phagocytotic repsonse?
neutrophils
subset of dendritic cells (help activate adaptive immune repsonse aswell)
what three ways can the complement system be activated
- by antigen bound antibodies (classical)
- by specific binding of a lectin to a mannose sugar residues on bacteria or viruses (MB lectin pathway)
- by specific structures on the surface of some pathogens which stabilise the intitial enzymes of the activation process (alternative pathway)
what three ways can activated complement act?
- binding to the surface of pathogens and making them better targets for phagocytosis by cells bearing complement receptors (opsonisation)
- providing a chemokine-like (proinflammatory) attractant activity for phagocytes
- creating pores in the membrane via the membrane attack complex (often targeted by bound antibody)
how can viral proteins influence NK function?
- directly
- by inhibiting expression of the MHC-1 protein involved in cell killing (to limit the cell mediated response)
why is the viral influence on MHC-1 expression problematic?
a range of viruses inhibit the expression of the MHC-1 protein, but the lack of MHC-1 can actually enhance killing by NK cells
This effect of NK activity is moderated by a second consequence of virus induced interferon produciton: upregulation of class 1 MHC gene trasncription - maybe serving to balance the stimulation of NK activity by interferon
what enhances the cytotoxicity of NK cells?
alpha and beta interferon and Interleukin 12
what ways can NK cells be targetted?
by cytokines
by bound antibodies (antibody dependent cellular cytoxicity)
NK cells are controlled by a balance of activatory and inhibitory signal/receptors
Give an example of each
inhibitory: presence of autologous major hisocompatibility complex 1
activatory: NK receptor complex (composed of C-type lectin homologs) and the KIR (killer cell immunoglobulin like receptor) proteins
give some examples of active immune evasion mechanisms by viruses
infection of immune cells
interference with complement functin
interfererence with MHC1/2 presentation
inhibition of NK cells (via MHC-1 homolog)
interference with toll-like receptor function
interference with cytokine production or fucntion
interference with interferon function
interference with apoptosis
interfereonce with inflammatory repsonse
give some examples of passive immune evasion mechanisms used by viruses
antigenic drift
antigenic shift (segmented genomes only)
molecular mimicry
masking of virus
latency
what is reverse transcriptase?
also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into DNA. This enzyme is able to synthesize a double helix DNA once the RNA has been reverse transcribed in a first step into a single-strand DNA.
what three reactions does reverse transcriptase catalyse?
① RNA dependent DNA synthesis
② RNA degradation
③ DNA dependent DNA synthesis
very breifly describe reverse transciptase production of DNA double helix
- RT converts single stranded RNA to a duplex - hybrid RNA-DNA molecules
- complex dissociates and RT synthesises the second DNA strand that replaces the RNA
integration of the HIV genome into host genome requires what enzyme
integrase
What are the two ingrediants in Paxlovid?
what is the mechanism of action
Nirmatrelvir and Ritonavir Inhibit protease Mpro critical in viral replication to stop the virus maturation process
give an example of a monoclonal antibody against covid19
– Sotrovimab (Xevudy)
give two examples of drugs that intefere with viral RNA replication
– Remdesivir (Veklury, nucleotide interfering with viral RNA replication)
– Molnupiravir (Lagevrio, nucleoside interfering with viral RNA replication)
how effective was Paxloid in reducing hospitalisation rate and mortality?
6.3% of the control group were hospitalised and 12 died
0.3% of the Paxlovid group were hospitalised wiht no deaths
give to benefits of Paxlovid
orally available and prevents transmission
how does Nirmatrelvir work?
(component of paxlovid)
inhibits cysteine protease to specifically inhibit the COVID maturation process (from polyprotein chains to mature viral proteins)
at what stages might protease inhibitors affect the viral lifecycle?
Proteases are required on virus entry (step 1b) and endosomal release
Proteases are required to cleave polyprotein (step 4
when/ why is Sotrovimab given?
to treat symptomatic acute covid-19 infection in adults and adolescents (12 years or older, weighing at least 40 kg)
overcome an infection and prevent serious illness
what structure is targeted by neutralising antibodies against COVID19
Spike receptor binding domain (RBD) targeted mAb to neutralise the virus attachment to the cell surface
how are neutralising monoclonal antibodies porduced against SARS
take (infected) human B cells and combine with tumour cells to produce hybridoma
Test effectivity against antigen, here SARS spike protein
Sotrovimab was engineered to have potent and lasting effects against SARS-CoV-2 and other CoVs
What were design principles?
- improved lung bioavailability
- extended half life
- low dose to allow for 1M formulation
- blocks viral entry into healthy cells (neutralisation)
- clears infected cells by recruiting the immune system
- high barrier to resistance potential to address future pandemic
give two pieces of evidence for the effectivity of sotrovimab
85% reduction in hospitalisation or death in high risk outpatients versus placebo
70% relative reduction in Persistent high viral load in low risk outpatients versus placebo
give some examples of viruses in the HerpesViridae family
Cytomeglovirus, herpes simplex virus types 1 and 2, varicella-zoster virus, and Epstein-Barr virus.
what characteristic do herpesviridae viruses share?
lifelong latency
what happened upon first contact of the eropeans with the indians in North America 17th century
10 out of 12 million Indians died after first contact with Europeans (17th century), historically often falsely attributed to armed conflict
* Insufficient knowledge + religion: “Lord put an end to this quarrel by smiting them with smallpox” (William Wood, New England, 1634)
* Europeans “relatively” immune through exposure to the virus
describe the genome and sturcture of Paramyxovirus
- negative strand (mRNA complement)
- linear ssRNA– genome, 15.3 kb (medium)
- enveloped, size 150 nm
what is Parotitis?
what virus can cause it?
Parotitis is a term used to describe parotid gland swelling. Your parotid glands are salivary glands located between your jaw and ear
can be caused by mumps (paramyxovirus)
how does Paramyxovirus protects itself against the immune system?
Paramyxovirus down-regulates innate immunity by interfering with interferon responses
why is mumps so dangerous?
the mumps virus can cross the brain blood barrier and infect ependymal cells.
That’s why you can get a lumbar puncture to confirm diagnosis
why was the discovery of HIV considered the founder of a new class of viruses?
HIV – a retrovirus that is able to convert RNA into DNA
it violated the Central Dogma
give two examples of DNA viruses
poxvirus
herpesvirus
give four examples of RNA viruses
HIV (AIDS virus)
influenza virus
coronavirus
mumps virus
give an example of a group 6 virus
HIV
how do class 1 viruses make proteins for assembly?
dsDNA viruses
use the noraml cellular machinery
dsDNA->mRNA>protein>assembly
give examples of class 1 viruses
adeno, herpes, papilloma, polyoma, pox
give example of class 2 viruses
parvo
how do class 2 viruses make proteins for assembly?
ssDNA viruses: convert to dsDNA first.
then mRNA>protein
how do class 3 viruses do to make proteins for assembly
dsRNA viruses
use the normal cellular mechanism (use just one template strand to produce mRNA from dsRNA then protein then assembly)
give examples of class 3 viruses
reo, picobirna
how does class 4 viruses make proteins for assembly
ssRNA+ viruses must synthesise complementary strand 1st .
start by synthesizing a negative sense strand form the plus RNA strand, from which we then synthesize the mRNA. However you can also make protein from the plus RNA genome directly, if it is released from the virus
give examples of class 4 viruses
astro, calici, corona, flavi, hepe, picorna, toga
how does class 5 viruses make proteins for assembly
ssRNA- viruses use the normal cellular mechanism
from negative strand RNA make positive strand RNA then it makes protein
(copies it again into negative for progeny)
how does class 6 viruses make protein for assembly
Retroviruses convert their genome to DNA
from ssRNA they generate a DNA/RNA hybrid then dsDNA then integrate into the host genome and use the normal host clel machinery to generate mRNA which is turned into protein
give examples of class 6 viruses
retroviruses
give examples of class 5 viruses
borna, filo, orthomyxo, paramyxo, rhabdo (bunya, arena)
when did David Baltimore win the Nobel prize “for their discoveries concerning the interaction between tumour viruses and the genetic material of the cell”?
1975
how many viruses are estimated to be on earth?
10^31
of the known species… how many infect humans?
Known species: 2000
≈250 infect humans
what is the most common class of virus?
class 4
what type of genome does Influenze have
RNA-
8 segments
describe the lifecycle of Influenza
- Binding of HA glycoprotein to the sailic acids at cell surface
- uptake via clathrin coated and other vesicles
- M2 protein mediates entry of H+ ions into virion
- Acidifcation exposes HA2 fusion peptide
- fusion with vesicle wall and release of (genomic RNA as) ribonucleoprotein into the nucleus
- viral mRNAs are made for viral protein synthesis, the viral RNA polymerase and shuttles out of the nucleus spliced and into the ER
- NP transported back into the nucleus and helps assembly into ribonucleoprotein
- oligomerisation and shuttling of HA and NA to the golgi for glycosylation.
- assembly of NP and genomic RNAs into ribonucleoprotein and transport out of the nucleus where to associate with M proteins and HA and NA glycoproteins create a lipid raft for the particle to bud off from the cell
- release from cell by NA glycoprotein
how do influenza escape the endosome?
upon endocytosis there is acidifcation of the endosome
this causes a pH induce conformational change of Hemagglutinin surface protein
It exposes hydrophobic domains on the trimer
as it opens up the hydrophobic parts grabs the endosome membrane and fuses it with the viral membrane to release the viral genome and destroying the endosome
Step 1: binding glycosylated surface protein
step 2: reoritntation exposure of fusion peptide
step 3: membrane fusion
describe how the influenza virus buds off the membrane
Hemagglutinin - glycosylated protein binds to sialic-acid
Neuraminidase - hydrolyses sialic-acid glycosylation, active against Hemagglutinin as well as surface proteins, cleaving them off allowing viruses to leave the cell
give two examples of drugs that hinder virus release
INfluenza neuraminidase inhibitors
Tamiflu (Oseltamivir) & Relenza (Zanamivir)
how do new variants of influenza come about
when you get infection in an organism with more than one influenza variant you get swapping of RNA segments to create a new viral variant
Influenza has 8 RNA segment
what is the typical method of naming influenza variants
HxNx
where Hemagglutinin = H and Neuroaminidase = N
which viral variant of influenza was bird flu
H1N1
what variants cause human flue infections today
H3N2
H1N1
which hemagglutinin are specific for human surface proteins?
H1/H2/H3 specific for human surface proteins
orthomyxovirus also know as…
influenza
what virus causes the common cold?
corona virus
what type of viruses infect bacteria (most commonly)
DNA mostly dsDNA
what type of virus infects plants (most commonly)
RNA virses mostly ssRNA
animal are infected by what types of viruses
Animals are infected by all (but ssDNA) viruses
ebola is also known as..
Haemorrhagic fever
how is ebola transmitted?
Ebola spreads through human-to-human transmission - contact
what proteins does the ebola virion contain?
glycoprotein on the outer surface
nucleoprotein (genome)
polymerase and polymerase cofactor VP35
VP24 and matrix VP40 on the inner surface for structure
transcription factor VP30
what is the fatality (%) of ebola
40-90%
what are the two most common countries where ebola outbreaks happen?
Democratic republic of congo
Uganda
why do we see the geographical distribution of Ebola virus disease outbreaks that we do
Pteropodidae fruit bats are the natural hosts of Ebola – we see Ebola within their home range
why is it that bats are always infected with viruses
it has one of the most advanced immune systems, it can protect itself against lots of viruses. They are an incubator for new virus forms they survive them and spread.
when did ebola first appear and where did it come from
- Ebola virus disease (EVD), formerly known as Ebola haemorrhagic fever, is transmitted to people from wild animals (fruit bats)
- Ebola first appeared
in 1976 in two simultaneous outbreaks (Sudan/Zaire)
what are the symptoms of ebola
what causes death?
- Early symptoms are non-specific; impaired kidney / liver function and eventually you die (the blood vessel of all skin organs fail)
- Ebola has a wide tropism (type of cell in which infection is established)
– internal / external bleeding lead to case fatality rate of up to 90%
why can HIV be a lifelong infection?
because HIV integrates into the genome
how is the viral DNA integrated into the host genome
- Integrase cuts viral DNA to generate reactive OH on the ends,
- It then bends the host DNA putting a lot of stress onto it,
- Integrease brings viral DNA to the target chomosome and facilitates the attack of viral DNA on target DNA -
- The reactive OH ends opens up the host DNA and we get a cross over binding with the host an dviral DNA strands.
- Two remaining free ends get repaired. (gap filling by DNA repair)
- Release enzyme and the viral DNA is integrated into host genome. This reaction is occurring using the short direct repeats of target DNA sequence
what is required for DNA only transposons
Short inverted repeats at each end
(elements moves as DNA cut and paste mechanism)
Transposase enzymes
what is required for nonretroviral retrotransposons
Poly A 3’ end of RNA transcription; 5’ end is often truncated
Reverse transcriptase and endonuclease
LINE: long interspersed nuclear element (~7000Bp)
Not a retroviral transposition – no tRNA binding site, need an endonuclease
what is required for retroviral like retrotransposons
doirectly repeated long terminal repeated (LTRs) at each end
Reverse transcriptase and integrase
Elements move via RNA intermediate, replicative.
what is required for retroviral like retrotransposons
doirectly repeated long terminal repeated (LTRs) at each end
Reverse transcriptase and integrase
Elements move via RNA intermediate, replicative.
how much of the genome is protein coding exons
5%
how much of our genome is repeated sequences
50%
how much of our genome is repeated sequences
50%
what are SINEs?
Short interspersed nuclear element (SINE) sequences are short repetitive, non-coding sequences ranging in size from 100–600 bp. SINE sequences are widely distributed in eukaryotic genomes and have crucial roles in genome organization, genome evolution and modulating gene expression
what are LINEs?
Long interspersed nuclear elements (LINEs) (also known as long interspersed nucleotide elements or long interspersed elements) are a group of non-LTR (long terminal repeat) retrotransposons that are widespread in the genome of many eukaryotes. They make up around 21.1% of the human genome
describe how transposition happens with human genome
- inverted repeats required (min 20 bp)
- transposase monomers recognises the short inverted repeat sequences in chromosome A
- transposase brings the ends together (looping it out)
broken donor A is rejoined - this creates a central intermediate which the 3´OH groups can attack the target chromosome resulting in integration in chromosmoes B within its short direct repeats
how many nt is the HIV genome?
9700nt
wwhat are the three main polyproteins ar ein the HIV genome?
Gag – encodes capsid proteins
Env – encodes envelope proteins
Pol – encodes reverse transcriptase and integrase
flanked by long terminal repeats with a 5’ cap
what proteins are encoded by Pol?
- protease: proteolytic processing of the polyprotein
- integrase: retro-transposition
- reverse transcriptase: RNA intermediate
- ribonuclease H: degrade RNA
what are the LTRs?
LTR are repetitive sequences, several 100 bases in length
* tRNA binding sites in LTR help reverse transcription
* LTR recognised by integrase for retro-transposition
what are the smaller regulatory proteins encoded in the HIV genoem
- Vif, Vpr, Vpu are regulatory proteins with various functions
- Rev regulates nuclear export of the RNA (spliced together from two transcripts)
- Nef interferes with protein trafficking, regulating host immunity, modulates the cell
- Tat regulates transcription
describe the HIV lifecycle
- attachment to cellular receptor – two stage binding
- Fusion with plasma membrane (endocytosis may also occur)
- Viral particle released
- Reverse transcription creating dsDNA genome and digestion of RNA genome
- DNA funneling into cell nucleus
- Integration of ds DNA into preferred sites within the cellular genome (may be stable stage)
- Activation signals needed to get out again
- If make mRNA then splicing occurs to make polyproteins (but splcingin destroys the RNA interfering with progeny)
- Progeny RNA genomes need to be intact – they are generated and assemble in the cytosol
- Approches plasma membrane and then buddling
mature RNA must not be spliced. how does the HIV virus control this
- Integrated viral DNA becomes unspliced RNA (by cellular transcription machinery) Unspliced RNA has a retention signal (to prevent it from being degraded) while spliced RNAs do not have this.
- RNA is spliced; Rev, Tat and Nef are translated first. Spliced RNAs are exported out of the nucleus, in cytosols they are made into protein
- One protein made is the Rev protein, this protein is then shuttled back into the nucleus. It has a structure that bind the Rev response element (RRE)(retention sequence), and subsequently protects that RNA from being spliced or degraded.
- Then shuttled out of the nucleus and both the viral proteins and the genome are in the cytosol – so progeny viruses can be assembled
what is the structure of GAG and how does it aid its function
has multiple proteolytic sites, with larger domains at the N terminal and smaller ones at the C terminal so that the structure is broadly triangular
this results in a circular capsid when the proteins come together
In the early assembly it is spherical, in late HIV assembly the proteolytic sites have been cleaved and the capsid assumes a cone shape, form ed of hexamers and pentamers (of the same protein, due to diff context/splicing)
what secondary receptor does HIV use for entry in first phase AIDs
CCR5
Macrophages/B cells
what secondary receptor does HIV use for entry in second phase AIDs
CXCR4
Helper T cells
what primary receptor does HIV use for cell entry
Env protein binds CD4
why is HIV able to develop specific infection of macrophages and helper T cells
by variation of the secondary receptor
give examples of virus and the immune adhesion moelcules they bind
what virus can bind to CD4?
MHC2 ligand
HIV
what virus binds to MHC-1
Adenovirus
what virus can bind CR2
complement C3D receptor
EBV
what virus can bind IgA-R
Hepatitis B
what virus can bind IgG
Dengue
why is is advantagous fo virus to infect immune cells?
- blood / immune cells are generally good vessels to travel the body
- cells of the immune system end up in lymphoid organs – more cells to infect here!
- strategies to suppress immune response needed
give three examples of viruses with icosahedral capsids
- Papillomavirus, herpes virus, bacteriophage
what is the advantage of having an icosahedral capsid
- Advantage: make the capsid up from many copies of a few proteins (efficiency)
describe the structure and compostion of an icosahedral capsid?
Icosahedral – 20 triangular faces
- each triangle has at least three proteins
- the simplest virus contains 60 proteins, always the same construction principle –
- Largest viruses would have more than three proteins per triangle - T number increase
what is the T number?
The triangulation number (T) indicates the number of structural units per face of the icosahedron. In a T = 1 virus, one structural unit create the icosahedron face.
: we know T number of T= 1, 3, 4 ,7, 9, 16 ,25
(can be a way of classifying)
what are the three domains of an icosahedral capsid protein monomer?
P = Protrusion
S = (beta) Sheet
R = RNA (nucleic acid) binding
describe the assembly of an icosahedral capsid
Bring two of these domains together and form a dimer
Dimerization is almost automatic
Then form the trimer
These things are self-assembling (can just put proteins into Eppendorf and they will self assemble into little baby capsids)
Trimers assemble further until they form a sphere – automatic
breifly describe the composition of bacteriophages
Construction:
head: icosahedral capsid
tail: helical
typically dsDNA genome
sizse and genome vary massively
brefily describe the tobacco mosaic virus construction
Construction:
helical capsid, Ø 15-18 nm,
length 300 nm
single protein subunit
associated with ssRNA+
(long stick thing)
why are tobaco mosaic viruses always exactly 300 microns in length?
Protein subunits on the outside and the rna genome on the inside, and the genome is a certain length
Curled up RNA genome gives the size of the virus. Only single protein subunit to make
what structural feature of virus most commonly infects plants
Helical
also see icosahedral and enveoped rarely
what structural feature of virus most commonly infects bacteria
head + tail
sometimes enveloped
what structural feature of virus most commonly infects animals
icosahedral and enveloped
what are the differences between Vaccinia and Variola pox viruses?
Vaccinia - smallpox vaccine (Edward Jenner, 1796), does not cause smallpox, causes cowpox, L. vacca – cow
Variola - is the disease virus – cause small pox disease, the infectious and dangerous version
what is the genome of the pox virus like
- linear dsDNA genome, covalently closed, 130-375 kB
what is the structure of the pox virus
- enveloped, size 240-260 nm diameter (very large)
where does replication and protein synthesis occur for the pox virus
cytosol
how do the two main froms IMV and EEV of pox virus differ
They differ only in the number of membranes (2 or 3 membranes)
how does the pox virus acquire its many membranes
(1) budding to give 1st coat of 2 Golgi membranes (2 membranes)
(2) engulfed to give a 2nd coat of 2 membranes (4 membranes)
(3) fusion with plasma membrane leaves 3 membranes
when is the pox virus known as intracellular mature virion (IMV)
after the immature virion has been assembled and matured in the viral factory (with 2 membranes)
when is the pox virus known as an immature virion
when it has just been assembled in the viral factory (2 membranes)
when is the pox virus known as the extracellular enveloped virion?
After the intracellular enveloped virion fuses with the plama membrane to exit the cell (3 membranes)
when is the pox virus known as the extracellular enveloped virion?
After the intracellular enveloped virion fuses with the plama membrane to exit the cell (3 membranes)
why is it advantagous for the pox virus to exist as two different types with different number/type of membranes
The membranes that the virus presents to its environment are different!
both forms of pox are infectious which is more virulent?
EEV
describe the phases of gene expression in the pox virus
– Early phase: essential viral proteins transcribed by viral RNA polymerase; uncoating and release of viral genome into cytoplasm
– Immediate phase: 2 hrs post infection triggers genomic DNA replication
– Late Phase: structural proteins; viral assembly
breisfly describe the lifecycle of the small pox virus
- attachment to the surface
- fusion with plasma membrane (so you have two membranes inside)(endosomal entry may also occur)
- genomic dsDNA is released and virion proteins are expressed (early intermediate and late mRNAs are transcribed and translated). Then the immature virions is assembled and matured – occurs completely in the viral factory
- The virions are release from the viral factory as intracellular mature virions. These can be released directly or pass through the golgi to acquire 2 more membranes
- After ‘wrapping’ in transgolgi membranes then the intracellular enveloped virion is released from the cell, losing one membrane and becoming the extracellular enveloped virion
which virus has the most advance viral factory
smallpox
what two locations can viral factories be located?
cytoplasmic or perinuclear (next to nucleus)
what is the mortality (%) of small pox
30%
how do viral factories form
why are viral factories advantagous for viruses
increase the efficiency of viral replication assembly and protect it from host defense
why are viral factories advantagous for viruses
increase the efficiency of viral replication assembly and protect it from host defense
when was smallpox officially eradicated?
1980
when did Edward Jenner first use cowpox agasint small pox
1796
when was the DTP vaccine developed?
it vaccinates against what three pathogens (when were their individual vaccines developed)
1948
DTP vaccine against diphteria (1926), tetanus (1938) and pertussis (1914)
when was the MMP vaccine first administered
1971
MMR vaccine against mumps (1967), measles and rubella (1969)
when was HPV vaccinated widely against
2011
what are the four types of vaccines?
give two examples for each
- Live attenuated; tuberculosis, measles
- inactived (killed antigen); whole cell pertussis, inactived poliovirus
- subunit (purified antigen); Haemophillus influenzae type B, hepatitis B
- toxoid (inactivated toxins); tetanus toxoid, diptheria toxoid
what were the two approaches to COVID vaccines?
- Adenovirus - gene therapy and vaccination
- RNA vaccines
describe how the RNA vaccine was used for COVID19 vaccination
viral RNA was contained in a lipid nanoparticle
1. vacine delivered and enters cell
2. mRNA is release
3. immunogens are built
4. APCs present immunogens
5. T helper cell binds antigen bound MHC
6. activates T and B cells
breifly describe the lifecycle of human papilloma virus
- Docks on surface on cells then waits for cells to engulf it (clathrin dependent endocytosis)
- When inside cell, uncoating and release of genetic material, dsDNA
- L2 protein goes into cells (epithelial cell prone to infection, progression restricted)
- dsDNA progeny genome maintained in episomes (long time, dormant), 50-100m copies per cell. however some can integrate directly into host DNA
- then phases of production of proteins, Immediate early phase proteins E1, E2 and E5 protein
- then the early proteins, the E4 and E6 nd E7 which go back into the nucleus and requires cellular transformation)
- assembly virus with late protein and release (occurs only in terminally differentiated epithelial cells where late (L1+2) proteins are expressed)
breifly describe the structure and geome of HPV
- icosahedral capsid
- 55 nm diameter
- dsDNA
- 8 kB circular genome
the HPV genome encades what proteins
- L1 + L2 capsid proteins (L2 has another function)
- E1 + E2 replication
- E4 + E5 assembly / release
- E6 + E7 oncogenic proteins
how many strains of HPV are there
between 100-200
how can vaccination against HPV prevent against cancer
persistant HPV infection can propagate the risk of cancer
we need to vaccinate against the virus before exposure
(the onset of sexual activity)
Have to vaccinate before the onset of sexual activity then avoid onset of HPV and risk of cancer is lowered
what are the four ways a virus can exist/act in a cell
Lytic: EBV
* acute
* linear dsDNA
Latent: EBV
* genome inactive
* circular dsDNA form
Chronic: Hepatitis B
* long term
* low levels of virus production
Transforming: Pappilloma
* altering cell growth
what 2 HPV strains cause 70% of all cervical cancer
HPV16/18 cause 70% of all cervical cancers
what two HPV strains cause 90% of all genital warts
HPV6/11 causes 90% of all genital warts
cervarix protects against which HPV strains
Cervarix protects against HPV16/18
gardasil protects against what strains of HPV
- Gardasil protects against HPV16/18 & HPV6/11
who won the Nobel prize for HPV vaccination against cancer
- Nobel Prize 2008 to Harald zur Hausen
how does HPV propagate the risk of cancer?
- influence the cell cycle regulation
– E6 dependent ubiquitination and degradation of p53
– E7 deregulates the tumor suppressor pRb - P53 and pRb control onset of cell cycle, knockout would increase dna damage and make more prone to cancer
what is the difference between fusion and endocytosis?
In fusion, the virus membrane becomes contiguous with the cell membrane. In endocytosis, the host cell internalizes the virus by wrapping it in an endosomal vesicle. A number of viruses are known to enter cells via either fusion or endocytosis
why would a virus inhibit IRF3
IRF3 is a key transcriptional factor involved in the signaling pathway leading to establishment of antiviral state in infected cells. Under normal conditions, IRF3 exists in a latent form in the cytoplasm. Viral infection triggers the phosphorylation of IRF3 C-terminal region. The activated IRF3 migrates to the nucleus, where it complexes with the transcription coactivator CBP/p300, leading to the transcriptional activation of the IFN-alpha and IFN-beta genes
Due to its crucial role in innate response, IRF3 is the target of many viral proteins. Some viral proteins interact with IRF3 and prevent its phosphorylation such as SARS coronavirus PLpro protein, while others target IRF3 for proteasome-dependent degradation, like bICP0
egm papilloma
