Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

4.1 Medical Microbiology > Respiratory Viruses - Influenza, RSV, Parainfluenza, hMPV > Flashcards

Respiratory Viruses - Influenza, RSV, Parainfluenza, hMPV Flashcards

1
Q

What are the two main types of viruses?

A

DNA viruses

RNA viruses

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are some differences between RNA and DNA viuses?

A

RNA viruses replicate in the cytoplasm ,use RNA-dependent RNA polymerase

DNA viruses in the nucleus, uses host DNA replication machinery

RNA has a high mutation rate while DNA has a lower mutation rate as it has proofreading mechanisms

RNA undergoes rapid evolution and is less stable, DNA has a more consistent genome and is more stable

RNA only cause acute infections while DNA cause both acute and latent (think chickenpox)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Why do only DNA viruses cause latent infection?

A

RNA viruses tend to mutate quickly meaning you can repeatedly get RNA viruses but you never get the same one e.g. flu

DNA viruses dont mutate and have more stable genomes so you build immunity against them such as chickenpox

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Give some examples of RNA viruse

A

Orthomyxoviridae -> influenza A, B, C

Paramyxoviridae -> Parainfluenza, RSV

Picornaviridae -> Rhinoviurs, Coxsackie virus, Enterovirus (echovirus), Parechovirus

Coronaviridae -> coronavirus, SARS CoV, MERS

Bunyaviridae -> hantavirus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What kind of infection does coxsackie A cause?

A

Hand foot and mouth
-> similar to chickenpox

Everyone has had this at some point -> its highly contagious and spreads rapidly in playschools etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Give an example of a DNA virus

A

Adenovirus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

When do we usually ID enterovirus in the lab?

A

Usually flags for meningitis

Usually the most common flag on the film array in the lab

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are othomyxoviridae, what viruses are in this family?
(4)

A

A family of RNA viruses primarily known for causing influenza, Influenza A, B, C and D

Characterised by their segmented, single stranded RNA genomes and unique surface proteins: Hemagglutinin and neuraminidase

They exhibit a remarkable ability to mutate and re-assort, this contributes to their virulence and emergence of new strains

Constatly pose ongoing challenges for public health, continuous surveillance and vaccine development to mitigate impact and control influenza outbreaks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What influenza strains are we concerned with?

A

A = most common strain, causes seasonal epidemics(not flu), can infect multiple different species such as birds and pigs
B = only affects humans, seasonal flu
C = causes mild illness, not much diagnostics done on this as it usually goes away on its own
D = doesnt infect humans so we dont care

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the different components of an orthomyxoviridae?

A

Shape = spherical or filamentous
Size = 80-120 nm in diameter
Envelope = lipid bilayer derived from the host cell
Surface proteins:
- Hemagglutinin (HA)
- Neuraminidase (NA)
Nucleocapsid:
- Segmented RNA genome, 8 RNA segments encoding viral proteins
- Nucleoprotein (NP) encases the RNa forming a helical structure
Matrix proteins: M1 and M2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What does Haemagglutinin do, why is it significant?

A

HA binds to host cell receptors: key vaccine target

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does neuramidase do?

A

It facilitates the release of new vira particles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What makes up an RNA nucleocapsid?

A

A segmented RNA genome composed of eight RNA segment whic encode viral proteins

Surrounded by a nucleoprotein, forming a helical structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What matix proteins are found in orthomyxoviridae, what do they do?

A

M1 proteins which maintain viral stucture and aid assembly
M2 proteins which facilitate viral uncoating in host cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the structural components of influenzae

A

Lipid envelope

Surface glycoproteins: HA and NA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the structural components of influenzae

A

Lipid envelope

Surface glycoproteins: HA and NA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Talk about the lipid envelope of influenza

A

It has a protective outer layer made of lipids (fats) that encase the virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Talk about the haemagglutinin of Influenza, how many on cell, what is the function

A

Approximately 500 spikes per virus particles

HA binds to receptors on host cells, allowing the virus to enter and initiate infection by fusing its envelope with the host cell’s plasma membrane

Allows virus to attach to and enter host cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Talk about the neuraminidase of Influenza, how many on cell, what is the function

A

There are 100 spikes per virus particle

This helps release new virus particles from the surface of infected cells so that they can go on to infect other cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How do we make use of HA and NA combinations?
(2)

A

We use specific combinations of these proteins to determine the subtype of the influenza virus e.g. H1N1 = swine flu

HA and NA are targetted by our immune system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How can influenza use HA and NA to evade our immune system?
(4)

A

Influenza can change its HA protein through mutations or genetic reassortent

This allows influenza to evade detection by the immune system

This variation can lead to new strains that the immune system may not recognise thus making it harder for the body to fight -> have to produce new antibodies now etc

The same concept applies to vaccines -> new vaccines needed yearly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is an antigen found on group A, B and C influenza?

A

Internal ribonucleoprotein (RNP)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How do we name viruses, according to WHO

A

Virus type, geographic origin, strain number, year of isolation, virus subtype

Virus subtype (H3N2)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Talk about antigenic variability in influenza viruses, why does it happen and what is it?
(3)

A

Influenza is RNA based so they are dynamic and are continuously evolving

Antigenic variability refers to the ability of these viruses to change their surface proteins, HA and NA

This happens due to either antigenic drift or shift

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What is the definition of antigenic drift?
A gradual process where minor mutations occur in the genes encoding HA and NA over time
26
What are the results of an antigenic drift?
Mutations alter the structure of the proteins, leading to changes in the virus's antigens As a result, the immune system may not recognize the virus, even if a person has been previously infected or vaccinated against an earlier strain
27
What are the impact of antigenic drift?
Antigenic drift is responsible for seasonal influenza epidemics and the need for annual updates to flu vaccines
28
What is the definition of antigenic shift?
this is a more dramatic change that occurs when two different strains of influenza viruses infectt the same host cell and exchange genetic material 2+ viruses that come together
29
What is the result of an antigenic shift?
This reassortment can lead to the emergence of a new influenza subtype with a novel combination of HA and NA proteins This new strain may be significantly different from previous strains This is how pandemics ocur as nobody has immunity May confer increased pathogenicity and/or change the ability to spread rapidly from person to peron
30
When does shift usually occur (2)
Usually occurs in pigs This is because pigs can bi infected by both birds or humans
31
What is the impact of antigenic shift?
Leads to pandemics as the population mayhave little to no pre-existing immunity against the newly formed virus
32
Who does influenza A infect, why is this significant? (3)
A subtype of the influenza virus that primarilyinfects humans and other animal species, including birds and pigs Influenza A is known to cause antigenic drift and shift every 40 years, leads to seasonal epidemics and pandemics Vaccination and antiviral treatments are crucial for prevention and management
33
What are the symptoms of Influenza A?
Fever, cough, sore throat, body aches, fatigue Sever illness in vulnerable populations
34
Comment on the serotype of influenza A
There are 18 HA subtypes and 11 NA subtypes leading to a possible 198 possible HA and NA combinations However only 3 subtypes, all derived from swine can infect and transmit among humans (H1N1, H1N2 and H3N2)
35
Comment on the trends of influenza A and B
A tends to predominate B only most common in 2017-2018 and this was due to poor vaccination cover B coverage went back up with 99% of cases being A in 2018-2019
36
Comment on the trend in influenza serotypes
37
Comment on the trend in influenza A serotypes (2017-2024)
The specific A serotype that is prevalent tends to vary year on year In 2017-2018 H1N1 and H3N2 showed similar numbers In 2018-2019 H1N1 prevailed over H3N2 In 2022-2023 H1N1 accounted for 91% and H3N2 for 9% In 2023-2024 H3N2 prevailed
38
Why does prevalent influenza serotypes change year on year?
Its all down to coverage by the flu vaccine Some years we do a better job at predicting strains then others
39
What are the two ways antigenic drift occurs?
Genetic reassortment Change of species specificity
40
How can genetic reassortment cause antigenic drift?
Viruses from different species such as avian and swine viruses infect the same host and mix with human influenza viruses This resulting hybrid virus can have new combinations of haemagglutinin (HA) and neuramidase (NA) proteins
41
How can a change of species specificity result in antigenic drift?
The reassorted virus can gain the ability to infect humans directly from animals, particularly from poultry, which is a common source of zoonotic transmission
42
How can antigenic drift cause a pandemic (4)
New subtype means no protection from old vaccines Little or no immunity to a novel virus, virus is efficently transmitted among humans -> no heard immunity Pandemic can result in widespread morbidity and mortality worldwide A good example is the 2009 H1N1 virus swsine flu
43
How can antigenic drift cause a pandemic (4)
New subtype means no protection from old vaccines Little or no immunity to a novel virus, virus is efficently transmitted among humans -> no heard immunity Pandemic can result in widespread morbidity and mortality worldwide A good example is the 2009 H1N1 virus swsine flu
44
How did the swin flu originate? (4)
It occured from the reassortment of genetic material from three influenza viruses, swine (pig), avian (bird) and human It developed in 2009 (H1N1), mixing occured primarily in pigs Virus gained ability to spread efficiently to humans Initial spread to those with direct contact with pigs, human -to human transmission
45
Talk about the global impact of influenza A, when is it prevalent, how prevalent is it, mortality?
It has been recognised since at least the early 16th century In temperate regions (countries with seasonal climates) it causes seasonal epidemics, outbreaks in colder months when people are indoors etc In tropical climates it has year round activity due to consistent weather and human interaction It causes 3-5 million severe illness cases a year It causes 250,000-500,000 deaths a year
46
When is considered to be influenza season
October through to May But we generally say october through to March 31st
47
Who is most susceptible to influenza outbreaks?
Young and old
48
Comment on influenza epidemiology, how is it spread, who does it affect (3)
Its highly contagious and quickly spreads from person to person through mist/spray of respiratory secretions -> coughing/sneezing etc It affects all age groups and causes moderate to severe illness, mostly causes loss of school and work hous Highest rates of complications among young children and elderly (90%of deaths)
49
Comment on the mortality of Influenza
Leading cause of mortality after AIDS Infects about 5-15% of population annually Causes 250-500,000 deaths Death associated with bacterial pneumonia and cardiac failure following flu 90% of deaths in those over 65
50
What are some pulmonary complications of influenza (6)
Primary viral pneumonia Secondary bacterial pneumonia Acute Respiratory Distress Syndrome (ARDS) - Sever lung injury, fluid buildup, impaired oxygen exchange Bronchitis Exacerbation of COPD or asthma Pleural effusion -> fluid in pleual space
51
What are some non-pulmonary complications of influenza (5)
Myocarditis pericarditis Reye's syndrome -> liver and brain damage Guillain-Barre syndrome -> autoimmune attacking of peripheral nerves leading to muscle weakness and paralysis Septic shock -> systemic inflammatory respnse -> low blood pressure
52
What are some non-pulmonary complications of influenza (5)
Myocarditis pericarditis Reye's syndrome -> liver and brain damage Guillain-Barre syndrome -> autoimmune attacking of peripheral nerves leading to muscle weakness and paralysis Septic shock -> systemic inflammatory respnse -> low blood pressure
53
What four methods are there to diagnosing influenza
Provisional clinical diagnosis Isolation using tissue culture or culture in eggs Serology Molecular
54
Why is detection of influenza so difficult?
They are extremely thermo-labile Transport at 4 degrees to lab ASAP is required for a quality sample
55
How do we isolate influenza in the lab
Nasal, nasopharyngeal or throat swabs Tissue culture or egg culture
56
What serological methods do we use to edtect influenza
It takes time to mount an antibody response so serology is of little use so we dont use Ab based serology DFA - direct antigen testing is carried out for type A though
57
What molecular methods do we use for influenza
NAATs Real time PCR Multiplex PCR most common - Gene xpert etc etc
58
What molecular methods do we use for influenza
NAATs Real time PCR
59
Talk about the egg culture method of isolating influenza
Involves inoculating ebryonated chicken eggs with a samples for 10-12 days Virus replicates in the cells of the amniotic membane Cytopathic effects may not be observed After 2-3 days of incubation aliquots of havested amniotic fluid are added to erythrocytes to check for agglutination - haemagglutination
60
How can we use tissue culture to fetect influenza?
Specimens are inoculated into tissue cultures such as Hela or Rhesus monkey cells (rhesus particularly sensitive to influenza) Cytopathic effects may not be observed but newly produced virsus can be detected through hemadsorption and haemagglutination assays using cultured cells Viruses can also be identified using serological or molecular methods (same for egg culture)
61
What is DFA for influenza, what are some pros and cons
Direct immunofluorescence for the detection of influenza A and B antigens Simple and quick TAT 60-80% sensitivity Concerns regarding specificity of antisera and level of background fluorescence i.e. difficult to interpret enzyme immunoassays for the detection of influenza A are easier to interpret
62
What moelcular method is available for influenza, how sensitive is it, main downfall?
Molecular RT PCR -> done for circulating strains (targets change annualling) GeneXpert Flu -> detects Flu A and FluB 98% sensitivity and specificity for A and B Only takes 21 minutes to run a test There is a chance you will miss a more uncommon/not circulating strain
63
How does the GeneXpert compare to the NVRL PCR method of detecting influenza?
GeneXpert only takes 21 mins, highly sensitive and specific (98%), might miss less common strains PCR can take 3-5 working days, highly sensitive, wont miss any strains
64
Why is GeneXpert considered such an advantage in influenza diagnostics?
Really quick turn around time Great for bed management -> can isolate patients quickly Patient can be put on antivirals quickly
65
Why is GeneXpert considered such an advantage in influenza diagnostics?
Really quick turn around time Great for bed management -> can isolate patients quickly Patient can be put on antivirals quickly
66
What is another molecular platform used for the detection of influenza?
Biofire film array only 84% sesntive though
67
How do we develop the influenza vaccine?
Developed annually by examining strains that appear at the end of the viral season in Australia We then use these to predict the strains for the following year
68
Who should get the annual influenz vaccine?
65+ 6-23 months Chronic medical conditions e.g. asthma, diabetes, heart disease and kidney failure women in 3rd trimester pregnancy any household contacts of these people health care workers
69
what kind of influenza vaccine do we give kids between 6 and 23 months
a nasal spray
70
How does B compare to A in terms of epidemiology
B just has drift not shift B has similar symptoms but usually milder than A
71
How do we detect C?
We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab
72
How do we detect C?
We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab
73
What is bronchiolitis?
Common respiratory infection that primarily affects infants and young children less than 2 It causes inflammation and congestion in the smallest air passages of the lungs, bronchioles
74
What is bronchiolitis?
Common respiratory infection that primarily affects infants and young children less than 2 It causes inflammation and congestion in the smallest air passages of the lungs, bronchioles
75
What causes bronchiolitis?
Viral infection most common cause: - Respiratory syncytial virus (RSV) most common - Adenovirus, influenza, human metapneumovirus also implicated
76
How is bronchiolitis/RSV transmissed?
Spreads through respiratory droplets or direct contact with contaminated surfaces RSV can indirectly survive several hours on surfaces
77
How does RSV get its name?
Respiratory syncytial virus Its ability to cause cells lining the RT to merge into large, multinucleated cells called syncytia
78
What family is RSV a part of and what is characteristic of this family?
Paramyxoviridae These are enveloped viruses
79
What family is RSV a part of and what is characteristic of this family?
Paramyxoviridae These are enveloped viruses
80
How does RSV cause infection (3)
RSV targets epithelial cells lining the nasopharynx - local inflammation Spread down RT to bronchioles Virus RNA hijacks host cell machinery forcing it to produce viral proteins and replicate the virus
81
What RNA does RSV use to hijack host cells?
A negative-sense strand
82
How is the immune system involved in RSV pathogenicity? (6)
Cell damage triggers immune response Natural killer cells attracted to site to eliminate virus-infected cells This repsonse leads to an increase in mucus production by epithelial cells which makes blood vessels in the affected areas more leaky This influx of immune cells and fluid causes inflammation and swelling, narrowing the airways -> very dfficult for child to breath Alveoli are no longer able to expand and therefore collapse -> loss of gas exchange Mucous plugs can form in the airways, trapping air and causing atelactasis/collapsed lung
83
Comment on the epidemiology of RSV (6)
33 million epidosed annually (huge burden) Leading cause of hospitilastion in infants and young children (3 million annually) Second leading cause of infant mortlity, 6.7% of deaths under 1 Causes 60k deaths annually in kids under 5 Almost all children <2 get at least one episode a year Seasonality - peak in winer/december
84
How many cases of RSV is there per year worldwide
33 million
85
Comment on the mortality of RSV i children
Second leading cause of infant mortlity, 6.7% of deaths under 1 Causes 60k deaths annually in kids under 5
86
Comment on RSV trends in Ireland
1,476 cases in 2018-2019 7,829 cases in 2023-2024 (Huge increase) 1,397 RSV hospitilisations in infants under one year of age (1017 were less than 6 months)
87
Explain the huge increase in RSV numbers in recent years
Pandemic -> GeneXpert brought in to detect coronavirus Anyone with respiratory symptoms being tested for Covid Lots of these patients ended up being Covid neg but RSV positive -> hence the huge increase in numbers -> pre-pandemic numbers were not very reflective of RSV burden in Ireland due to poor detection
88
What is the basis for an RSV diagnosis?
Symptoms: Cough, wheezing, respiratory distress Time of year: Circulates october to march Age: <2 OR LAB Based diagnosis e.g. RSV
89
What is the basis for an RSV diagnosis?
Symptoms: Cough, wheezing, respiratory distress Time of year: Circulates october to march Age: <2 OR LAB Based diagnosis e.g. RSV
90
How is RSV transmitted?
Through droplets, fingers and fomites HCAI Community outbreaks
91
How is RSV treated?
Supportive therapy, mainly consisting of oxygen and hydration
92
How is RSV prevented? (2)
Vaccine now available babies 6 months or younger but not for older kids Infection control Monoclonal antibody treatments
93
What monoclonal antibody treatments are available to prevent RSV?
For premature babies and high risk children the monoclonal antibdy therapy Palivizumab is available This prevents lower respiratroy tract infections (bronchiolitis) caused by RSV in infants
94
Talk about the paramyxoviriniae family of viruses, what are they and give an example of one
A family of singel-stranded, envloped RNA viruses Human parainfluenza is part of this family
95
Talk about Parainfluenza, what are the serotypes, what infections does it cause
Four serotypes of hPIV (1-4): - hPIV 1 and 2 cause croup in children - hPIV 3 causes bronchiolitis and pneumonia in children - hPIV 4 causes common cold like illness
96
Who does hPIV infect and how?
hPIV binds to and replicates in the ciliated epithelial cells of the upper and lower respiratory tract - bottle neck blockage etc 40% of paed hospitilised LRTI are caused by hPIV 75% of croup cases are caused by hPIV 15% of respiratory illness in adults Can cause severe disease and fatal pneumonia in elderly and immunocompromised adults
97
What percentage of LRTI in paeds is caused by hPIV
40%
98
What percentage of croup is caused by hPIV?
75% of croup
99
hPIV accounts for what percentage of respiratory illness in adults?
15%
100
How does hPIV affect our elderly and immunocomprimsed?
50% of acute hPIV result in death 75% mortality in our 6months post stem cell recipients
101
Comment on the epidemiology of hPIV serotypes from 2017-2019
hPIV 1 and 2 have decreased from 2017 to 2019 hPIV3 and 4 have more than doubled
102
What three methods do we have available for the detection of human parainfluenza?
RT-PCR Viral culture Serological detection
103
Talk about RT-PCR for the detection of human parainfluenza
There are several commercial available tests There is optimal sensitivity, specificity and rapidity of diagnosis It only takes 1 hour
104
Talk about viral culture for the detection of human parainfluenza
this can take up to two weeks Looking for cytopathic effect or the detection of haemadsorption Detected by monoclonal antibodies (egg culture or cell culture)
105
Talk about serologic methods for the detection of human parainfluenza
Complement fixation and EIA assays Only really a research tool/rarely used for diagnosis Cross-reactive immune responses to HPIV1 and 3 antigens Require collection of convalescent sera
106
Talk about the pneumoviridae family, give two examples
A family of enveloped, non-segmented, negative-sense, single-stranded RNA viruses Human metapneumovirus 2001 Avian metapneumovirus 1978
107
What kind of infections does HMPV cause?
Causes infections similar to RSV Manifestation ranged widely from mild upper respiratory infections to severe LRTIs such as bronchiolitis and pneumonia Can cause repeated infections
108
How frequent is human metapneumoviurs, when does it peak, who does it affect
Studies show that most children have had hMPV by age 5 hMPV causes about 15% of RTI in young children Most severe disease in young children or elderly or those with chronic conditions Cases decreased during covid years but increasing again now
109
What are the three methods of detecting human metapneumovirus?
Real Time PCR e.g. BioFire Respiratory 2.1 panel Viral culture - difficult to grow - taking 10+ days as virus replicates slowly Serology - not diagnostic just for study

4.1 Medical Microbiology (30 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions