Week 14 Flashcards
(88 cards)
1
Q
What is a virus composed of?
A
A simple, miniscule, infectious, obligate intracellular parasite (only reproduce within living cell)
comprising of genetic material (DNA or RNA)
surrounded by a protein coat
and/or an envelope derived from a host cell membrane
2
Q
Each virus has a ‘host range’, what is this?
A
limited range of animals which can be infected
(Since all animals have strong immune system, viruses have to antagonize these responses to be able to cause disease)
3
Q
What are the general properties of a virion?
A
Mainly Spherical
Enveloped
ssRNA (-)sense
Replication in the nucleus
Segmented genome (n=8)
4
Q
Features of Haemagglutinin (HA) virion surface protein in Influenza A?
A
Binds sialic acid receptors -> viral entry
Agglutinates RBCs
Antigenic (neutralizing)
5
Q
Features of Neuraminidase (NA) virion surface protein in Influenza A?
A
Cleaves sialic acid to release virus
Degrades mucin
Antigenic (non-neutralizing)
6
Q
Features of Matrix protein 2 (M2) virion surface protein in Influenza A?
A
Forms proton channel that facilitates uncoating and assembly
Stabilizes the virus budding
Antigenic (neutralizing)
7
Q
Structure of influenza A virion: envelope and interior?
A
Outer lipid envelope:
- Lipid bilayer from plasma membrane of infected host cell; Supported by the M1 protein, which play role in virion assembly
Nucleocapsid:
- Each of eight different single stranded RNA + nucleoprotein + RNA polymerase (PB1, PB2 and PA)
8
Q
What is a nucleocapsid in terms of influenza A virion?
A
RNA along with 4 different proteins combined to make a nucleocapsid, each is identical and is required for the virions virulency and pathogenicity
9
Q
What are the 4 different serotyes of influenza virus?
A
Four different serotypes: A, B, C, D according to internal structure proteins (nucleocapsid and matrix) – these proteins can’t cross-react.
10
Q
Antigenic structure and classification of influenza A virion?
A
Strain (subtype) specific antigen:
- Two surface glycoproteins are used to subtype the virus
- named by specific HA and NA subtype (e.g. H3N2)
- 18 HA types and 11 NA types (n=198 different combinations)
11
Q
What few subtypes of antigen strain have caused epidemics/pandemics of Influenza?
A
A/ H1N1 (Spanish flu),
H2N2 (Asian flu),
H3N2 (Hong Kong flu),
novel H1N1 (Swine Flu),
H5N1 and H7N8,
12
Q
What organism is usually the source of an influenza pandemic/epidemic?
A
Birds/bats usually are a result of these as they’re susceptible to all forms of influenza
13
Q
Stage 1 of the influenza virus replication cycle?
A
Attachment: HA-Sialic Acid on host cell - virus endocytosed; vesicle membrane and transferred to endosome
14
Q
Stage 2 of the influenza virus replication cycle?
A
Uncoating: endosome acidification - M2 increased H+ = uncoating
15
Q
Stage 3 of the influenza virus replication cycle?
A
Transcription: Nucleocapsid goes to the nucleus and transcribed mRNA are translated into proteins in cytoplasm
16
Q
Stage 4 of the influenza virus replication cycle?
A
Replication The vRNP (-s) converts to cRNP (+s), then trough replication generates vRNP (-s) -> cytoplasm
17
Q
Stage 5 and 6 of the influenza virus replication cycle?
A
Assembly: HA/NA transported to cell surface with M1 and genome segments
Budding: Virus buds off by NA
18
Q
Haemagglutinin is the major determinant of host specificity and pathogenicity, it exists as a trimer in influenza virion and each monomer possesses which two important sites?
A
The Receptor Binding site - confers host-specificity
The Cleavage site where the single chain is cut into two chains. At the N-terminus it is fusion peptide which is critical for infectivity
19
Q
Why do we continue to have influenza?
A
Influenza virus keeps changing its structure via two mechanisms:
Antigenic drift
Antigenic shift
20
Q
Influenza virus keeps changing its structure via two mechanisms: what is antigenic drift?
A
Antigenic drift – minor changes in the antigenic sites of the HA and NA, because of:
- Error prone replication
- No proofreading
- Provides a selective advantage: seasonal flu (epidemics)
- Influenza A, B, and C
21
Q
Influenza virus keeps changing its structure via two mechanisms: what is antigenic shift?
A
Antigenic shift - major changes due to a re-assortment of genes that occurs when two different influenza viruses infect the same host. This occurs due to:
- Segmented genome
- Wide host ranges
- Complete change of HA, NA or both
- Only occurs in Influenza A
- Usually, requires non-human intermediate
22
Q
How vaccine strains are selected for influenza?
A
- 100 National Influenza Centers -> year–round surveillance (Just in 2004, more than 5000 strains have been sequenced)
- 5 WHO Collaborating Centers (UK, USA, Australia, Japan & China)
- Recommend vaccine twice a year
- Each country make their own selection for next year vaccination
23
Q
How do adamantanes work as antiviral treatment against influenza?
A
Adamantanes: Amantadine and Rimantadine are M2-ion channel inhibitors:
- Blocks viral uncoating
- Treatment or Prophylaxis
- Influenza A only
- CNS + anticholinergic effect, teratogenic
- The gene for M2 is susceptible to mutations, so strains are developing resistance (90 % viruses are now resistant to this category).
24
Q
How do neuraminidase inhibitors work as antiviral treatment against influenza?
A
Oseltamivir and Zanamavir
- Influenza A+B
- Generally well-tolerated, some nausea/vomit
- Most effective within 48h of onset
- Relief from symptoms for ~1-2 days or less
- Treatment or prophylaxis (oseltamivir)
- Oral or inhaled (zanamavir)
25
Serotype A influenza
Infects: Human, swine, birds, horses, bats, dogs
Cause severe clinical diseases
Most likely to cause epidemics and pandemics
26
Serotype B influenza?
Infects: Human, Seals
Causes generally mild but could be severe
Generally causes milder epidemics only
27
Serotype C influenza?
Infects: Human, swine, dogs
Usually only mild or asymptomatic
Doesn't cause epidemics or pandemics
28
Serotype D influenza
Infects: Swine, cattle
No further information has been gathered on this type.
29
Receptor specificity of influenza virus, and how do they change to infect other vessels?
- Human viruses preferentially bind to N-acetylneuraminic acid- α2,6 linked galactose
- Avian viruses preferentially bind to N-acetylneuraminic acid- α2,3 linked galactose
- Avian influenza replicates less efficiently in humans.
- Human influenza replicates less efficiently in birds
- Swine can act a mixing vessel.
30
How did SARS-COV-2 begin?
- A cluster of pneumonia cases appeared in Wuhan wet market
- Sequencing of nasal samples identified coronavirus patients
- Phylogenetic and genetic analysis showed coronavirus is closely related to SARS-COV-1 and previously isolated bats coronavirus called RaTG13
- Due to closer association with SARS-COV-1, the new coronavirus was called SARS-COV-2
31
What is the SARS-COV-2 Genome?
Single-stranded
non-segmented
positive sense
~30 kb long genome.
32
SARS-COV-2 genome encodes for 27 proteins which are either 1 of 3 categories. What are these categories?
Structural: Constitute the virion, Include S, E, M, N
Non-structural: Not structural components of virion (but essential for replication), Include NSP1, NSP2, NSP3, NSP14 etc
Accessory proteins: Produced only in infected cells, Includes ORF3b, ORF6, ORF7a etc
33
Genomic composition of SARS-COV-2?
SARS-COV-2 undergo discontinuous transcription
Non-structural proteins make Replication-Transcription Complex (RTC)
Error rate for RNA replication = reduced by proof reading enzyme NSP14.
RdRp/E/N genes = targeted for qRT-PCR - diagnostics
34
Function of the Spike (S) protein in Coronavirus?
Entry of SARS-COV-2 into cells
Host tropism
Protective immune responses (vaccines)
Virulence – severity of the disease
35
Function of the Nucleocapsid (N) protein in coronavirus?
Component of nucleocapsid
Virus transcription efficiency
Protective immune responses (vaccines)
36
Function of the Membrane (M) protein in coronavirus?
Most abundant amongst structural proteins
Assembly of virus particles
37
Function of the Envelope (E) Protein in coronavirus?
Smallest amongst all the structural proteins
Virus assembly, and release
38
What proteins is coronavirus virion made up of?
Spike (S)
Nucleocapsid (N)
Membrane (M)
Envelope (E)
RNA viral genome
(~125 nm diameter; enveloped virus; numerous surface-projected - spikes )
39
Step 1 of SARS-COV-2 replication cycle: viral attachment and entry?
Spike protein interacts with cell surface protein ACE2 to enter the cells
40
Step 2 of SARS-COV-2 replication cycle: replication and synthesis?
The viral genomic RNA acts like an mRNA – it can directly make proteins
Genomic RNA produces proteins and RNA necessary for viral reproduction by hijacking host cell machinery
41
Step 3 of SARS-COV-2 replication cycle: replication and synthesis?
Polyproteins (pp1a and pp1ab) are cleaved by PL proteinase and 3CL proteinase
NSPs and RdRp make replication-transcription complex (RTC)
42
Step 4 of SARS-COV-2 replication cycle: viral assembly and release?
Protein synthesis happens in double membrane vesicles budding off from ER
Structural proteins (S, E, M, N) and newly formed RNA are modified, packaged, and assembled before release from the host cell by exocytosis.
43
Three routes of transmission for SARS-COV-2?
1. Droplets
2. Aerosols - produced by breathing, speaking, singing, sneezing, coughing, etc.
3. Smear infection
44
What is a key prevention method used to reduce transmission of SARS-COV-2?
N95 masks (best option), Surgical masks, Cotton masks.
= 11% drop in risk of COVID-19 if mask is properly applied
45
What are the treatment methods for SARS-COV-2 for individuals who don't have a vaccine?
How do these methods work?
Monoclonal antibody/convalescent plasma for ACE-2 (Prevent the virus into the host cell.)
Camostat mesylate (Prevent SARS-CoV-2 into the cell by acting on TMPRSS2.)
Lopinavir-Ritonavir (HIV): (Inhibition of protease activity of SARS-CoV-2.)
Ribavirin (HCV): (May inhibit mRNA capping.)
RNA Synthesis Inhibitors (Remdesivir): (Inhibits SARS-CoV-2 RNA synthesis and replication.)
Chloroquine group: (Interfere with the release of progeny from infected host cells.)
46
What family does SARS-COV-2 virus, causing COVID-19 belong to?
Coronaviridae family
47
What was the spillover reservoir and transmission hub for SARS-COV-1/SARS and SAR-COV-2/coVID-19?
SARS-COV-1/SARS = civet cats, mainly in the hospital setting, no transmission until 24-36hrs after symptoms
SAR-COV-2/coVID-19 = Unknown reservoir, widespread community transmission, possible abundant asymptomatic/mild cases
48
What are the two different types of routes a spike protein can take, enabling SARS-COV-2 to enter a cell?
- ACE2-TMPRSS2 Route (Delta variant) (needs protease)
- Endocytosis Route (Omicron variant) (requires no protease, it simple sinks into the cell via endocytosis)
(The differing routes show that the type of spike protein on the virion determines what route of entry is entertained)
More info:
- TMPRSS2 protease cleave S protein at the S1/S2 site and an additional S2’ site
- Cleavage of S protein is marker of disease severity
49
Innate immunity against SARS-COV-2 is named what process and what occurs?
Cytokine storm
1. Lung cells infected,
2. Immune cells identify virus and produce cytokines
3. Cytokines attract more immune cells creating a cycle of inflammation, damaging lung cells
4. Damage can occur through formation of fibrin
5. Weakened blood vessels allow fluid to seep in and fill lung cavities = respiratory failure
50
Why is antibody immunity is important for long term protection against SARS-COV-2?
(Adaptive immunity against SARS-COV-2)
Important in almost all currently licensed human COVID vaccines
Most COVID recovered patients have antibodies within 1-3 weeks
Severe disease correlates with higher level of antibodies
51
Why is CD4 T cells Helpers immunity is important for long term protection against SARS-COV-2?
(Adaptive immunity against SARS-COV-2)
Critical for antibodies responses
Protection independent of antibodies in SARS
Cross reactive immunity against pan-coronaviruses
52
Why is CD8 T cells Killers immunity is important for long term protection against SARS-COV-2?
(Adaptive immunity against SARS-COV-2)
Important in many viral infections
May prevent re-infection
53
Describe the anatomy of adaptive immunity against SARS-COV-2?
Mostly immunity (antibodies) measured in blood
Local sites of infection and/or portals of entry are important.
Local immunity in lungs, nasal passages, and the oral cavity and salivary glands can consist CD8+ T cells, CD4+ T cells, and IgG and IgA antibodies
Additional: IgG and IgA are secretory antibodies found in the nose/mouth, important as when infection occurs, these are the first and ready to catch on
54
What is the principle of immunisation?
Vaccines contain antigens found on pathogens causing disease BUT exposure to these antigens in the vaccine does not cause disease.
When natural infection occurs, the body has already made memory cells so a quicker response occurs and a higher level of antibodies are produces.
55
What does vaccination refer to versus immunisation?
Vaccination = having received vaccine
Immunisation = Receiving a vaccine and becoming immune to the disease as a result
56
How do vaccines work?
Induces active immunity immunologic memory similar to exposure to natural infection but without the risk of disease
Immunological memory = rapid recognition and response to infection; prevents or modifies effects of disease
57
What are the features of a vaccine, making it useful?
Elicit a response giving same immune protection following a natural infection without causing disease
Safe – no side effects or contraindications
Stability – no requirement for ‘cold chain’ storage for faster distribution
Cost – cannot be too high for use in developing countries
Ease of administration eg oral/nasal
Long term protection (single shot)
Interrupt spread of infection
58
What are the different types of vaccines?
Live vaccines (whole pathogen where virulence is reduced - attenuation)
Inactivated vaccines (killed organism)
Subunit vaccines (components of pathogen are purified)
Passive immunotherapy (antibodies from one person and inject them into another person - own immune response is unneeded)
59
What is poliomyelitis?
a viral disease that mainly affects children < 5 years of age
1 in 200 infections result in irreversible paralysis - 5-10% of those affected by paralysis die when muscles aiding breathing are immobilised
Polio cases have decreased by >99.9
60
WHO estimates how many childhood deaths are prevented by vaccine against poliomyelitis?
~1.5 million childhood deaths prevented by vaccination and predicts eradication of polio would save US$ 40–50 billion (1988 to 2035) - mostly in low-income countries
By 2017 only 3 countries remain polio-endemic (Nigeria, Afghanistan, Pakistan)
61
What are the 3 different serotypes of poliovirus? What does this mean for vaccines?
Type I – Brunhilde
Type II – Lansing
Type III – Leon
The disease caused a indistinguishable but antibodies produced don't provide protection against other serotypes: the vaccine contains all three!
62
How was the live attenuated polio vaccine originally produced?
by allowing polio virus to grow in non-optimal conditions and selecting randomly occurring mutants that had lost neuro-virulence (Medical Microbiology Mims et al).
63
Advantages of the live attenuated polio vaccine?
Induces both systemic and mucosal immunity:
- Antibodies in blood prevent spread of poliovirus to CNS
- Mucosal immune response prevents viral replication in gut and interrupts poliovirus transmission
Short-term shedding of Oral Polio Virus in faeces ca result in passive immunity
Immunity is life long
64
Disadvantages of live attenuated polio vaccine?
May reproduce features of the disease as subclinical or mild form of the infection so cannot be given to immunosuppressed or pregnant patients
Unstable (live virus so has to be at certain temperatures/conditions)
May revert to virulent form (T1 needs 57 base substitutions to remove virulence, T2/3 have 2 base substitutions relating to loss of virulence)
65
Features of inactivated polio vaccine (Salk) (Killed organisms)?
Consists of 3 serotypes – chemically inactivated so cannot cause circulating Vaccine Derived Polio Virus (cVDPV)
Antibodies - prevent spread of poliovirus to CNS, preventing paralysis
But not delivered orally, does protect individual but wild polio virus can replicate in gut wild virus can be spread to infect others (Mucosal immune response not protected)
66
Advantage and disadvantage of inactive vaccines?
Advantages
- Cannot cause infection
- Can be given to immunosuppressed and pregnant individuals
Disadvantages
- Less immunogenic and require addition of adjuvants and booster doses
67
What is the role of an adjuvant?
For example aluminium hydroxide (Alum)
To enhance immune response to the antigens included in the vaccine
Mode of actions not precisely defined:
- To carry the vaccine antigen and slow its release
- To provoke a local inflammatory response
68
Why can polio be completely eradicated?
- Poliovirus cannot survive for long periods outside of the human body
- Type 2 eradicated (1999) and Type 3 eradicated (2019)
- Cheap and effective vaccines are available
- OPV can be administered by anyone - even volunteers
(Involves largest public-private partnership for health but eradiation campaigns can be compromised eg Taliban targeted workers carrying out polio vaccination causing a rise in cases)
69
Toxoid vaccines are an example of sub-unit vaccines. What is tenatus caused by, how does it occur?
- caused by the bacterium Clostridium tetani
- caused by a neurotoxin produced when C. tetani grows in anaerobic conditions
- characterised by muscle spasms - initially in the jaw muscles (lock-jaw)
- As it progresses mild stimuli trigger tetanic seizures, prolonged skeletal muscle contraction and eventually death.
70
Surface protein vaccines are an example of sub-unit vaccines. What is Hepatitis B virus vaccine?
Originally the surface coat protein (HBsAg) produced by the virus was purified from the blood of carriers:
- Purified and inactivated (95% protective)
- Derived from human blood – risk of viral transmission
- Extremely expensive to produce
71
Surface protein vaccines are an example of sub-unit vaccines. How is Hepatitis B virus vaccine now produced?
produced using recombinant DNA technology – gene encoding HbsAg has been cloned into a plasmid vector and is expressed in either yeast or Chinese Hamster Ovary (CHO) cells, then purified
Advantages: safer, cheaper
72
DNA vaccines are an example of sub-unit vaccines. What do these involve?
injecting nucleic acids encoding antigens, uptake by host cells resulting in the expression in situ and stimulation of an immune response.
DNA is usually delivered in a plasmid vector, so it can go to the nucleus produce mRNA and be expressed.
73
DNA vaccines are an example of sub-unit vaccines. What are potential advantages of this approach?
absence of any infectious agent
improved vaccine stability
relative ease of large-scale manufacture
stimulation of both B- and T-cell responses
insertion multiple variants of antigens into single vaccine
However, possible genomic incorporation of immunising DNA might activate oncogenes
74
mRNA vaccines are an example of sub-unit vaccines. How do these work?
RNA is usually encapsulated in a lipid vesicle to protect it and facilitate direct uptake into the cytoplasm where is it expressed.
RNA is a relatively labile molecule (compared to DNA) so requires careful long term storage – Pfizer vaccine at -70°C and Moderna vaccine at -20°C
75
mRNA vaccines are an example of sub-unit vaccines. Give an example of the first mRNA vaccines deployed for mass immunisation of humans?
Moderna & Pfizer Covid19 vaccines were the first mRNA vaccines to be deployed for mass immunisation of humans
They encode full length or the receptor binding domain of the SARS-CoV-2 viral spike protein
76
What is primary vaccine failure?
an individual fails to make an adequate immune response to initial vaccination and so infection is possible any time post vaccination
77
What is secondary vaccine failure?
an individual makes an adequate immune response initially, but then immunity wanes over time (this is a feature of most inactivated vaccines, hence the need for booster vaccinations)
78
How is HIV a Biological and financial challenge for vaccines?
- HIV has an incredibly high mutation rate, with variants arising within a single infected individual – which has frustrated efforts to make an effective HIV vaccine
79
How are parasites a Biological and financial challenge for vaccines?
- Parasites are “master immunologists” – because of the chronic nature of their infections they each have various ways to evade the immune response
80
How is the majority affected population a Biological and financial challenge for vaccines
- most of the people affected by these diseases live in poorer countries so there has not been sufficient financial incentive or investment to develop vaccines
81
What is 'Herd immunity'?
The more immune the population = the less likely a susceptible person will come into contact with person who has infectious disease
It prevents spread of disease and protects groups who cannot be vaccinated, these people get some protection as spread of contagious disease is contained.
82
Why are vaccination rates declining?
Due to vaccine hesitancy - vaccination is proven to be one of the most effective ways of avoiding disease, however vaccine hesitancy threatens to reverse significant progress made in tackling vaccine-preventable disease.
83
Define vaccine hesitancy?
"The reluctance or refusal to vaccinate despite the availability of vaccines"
It is reported in more than 90% of countries in the world and has been identified by WHO as one of its top ten priorities.
84
One example as to why vaccine hesitancy may occur?
MMR and autism incident. Study was published in 1998 by Dr Andrew Wakefield claiming to show a link between the MMR vaccine and autism and bowel disease - this work is completely discredited but if may put people off getting vaccines as a whole;
His claim lead to a rise and still is leading to a rise in measles due to the lower uptake of MMR vaccine, despite his claim being false
85
Human influenza virus strains preferentially bind to...?
sialic acids with alpha2-6 linkage
86
True or false:
Rimantadine blocks M2-ion channel to inhibit virus release
False
87
The Sabian Polio vaccine is what type of vaccine?
A live attenuated vaccine
88
In order to bind to the surface of a cell, the SARS-CoV-2 virus spike protein binds to what receptor on the surface of the cell?
ACE-2 receptor
