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4.1 Medical Microbiology > Viral Pneumonia > Flashcards

Viral Pneumonia Flashcards

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1
Q

What are the two main types of viruses?

A

DNA viruses

RNA viruses

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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)

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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

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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

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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

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6
Q

Give an example of a DNA virus

A

Adenovirus

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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

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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

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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

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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

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11
Q

What does Haemagglutinin do, why is it significant?

A

HA binds to host cell receptors: key vaccine target

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12
Q

What does neuramidase do?

A

It facilitates the release of new vira particles

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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

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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

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15
Q

What are the structural components of influenzae

A

Lipid envelope

Surface glycoproteins: HA and NA

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16
Q

What are the structural components of influenzae

A

Lipid envelope

Surface glycoproteins: HA and NA

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17
Q

Talk about the lipid envelope of influenza

A

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

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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

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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

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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

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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

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22
Q

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

A

Internal ribonucleoprotein (RNP)

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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)

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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

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25
Q

What is the definition of antigenic drift?

A

A gradual process where minor mutations occur in the genes encoding HA and NA over time

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26
Q

What are the results of an antigenic drift?

A

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

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27
Q

What are the impact of antigenic drift?

A

Antigenic drift is responsible for seasonal influenza epidemics and the need for annual updates to flu vaccines

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28
Q

What is the definition of antigenic shift?

A

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

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29
Q

What is the result of an antigenic shift?

A

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

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30
Q

When does shift usually occur
(2)

A

Usually occurs in pigs

This is because pigs can bi infected by both birds or humans

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31
Q

What is the impact of antigenic shift?

A

Leads to pandemics as the population mayhave little to no pre-existing immunity against the newly formed virus

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32
Q

Who does influenza A infect, why is this significant?
(3)

A

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

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33
Q

What are the symptoms of Influenza A?

A

Fever, cough, sore throat, body aches, fatigue

Sever illness in vulnerable populations

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34
Q

Comment on the serotype of influenza A

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)

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35
Q

Comment on the trends of influenza A and B

A

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

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36
Q

Comment on the trend in influenza serotypes

A
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37
Q

Comment on the trend in influenza A serotypes (2017-2024)

A

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
Q

Why does prevalent influenza serotypes change year on year?

A

Its all down to coverage by the flu vaccine

Some years we do a better job at predicting strains then others

39
Q

What are the two ways antigenic drift occurs?

A

Genetic reassortment

Change of species specificity

40
Q

How can genetic reassortment cause antigenic drift?

A

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
Q

How can a change of species specificity result in antigenic drift?

A

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
Q

How can antigenic drift cause a pandemic
(4)

A

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
Q

How can antigenic drift cause a pandemic
(4)

A

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
Q

How did the swin flu originate?
(4)

A

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
Q

Talk about the global impact of influenza A, when is it prevalent, how prevalent is it, mortality?

A

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
Q

When is considered to be influenza season

A

October through to May

But we generally say october through to March 31st

47
Q

Who is most susceptible to influenza outbreaks?

A

Young and old

48
Q

Comment on influenza epidemiology, how is it spread, who does it affect
(3)

A

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
Q

Comment on the mortality of Influenza

A

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
Q

What are some pulmonary complications of influenza
(6)

A

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
Q

What are some non-pulmonary complications of influenza
(5)

A

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
Q

What are some non-pulmonary complications of influenza
(5)

A

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
Q

What four methods are there to diagnosing influenza

A

Provisional clinical diagnosis

Isolation using tissue culture or culture in eggs

Serology

Molecular

54
Q

Why is detection of influenza so difficult?

A

They are extremely thermo-labile

Transport at 4 degrees to lab ASAP is required for a quality sample

55
Q

How do we isolate influenza in the lab

A

Nasal, nasopharyngeal or throat swabs

Tissue culture or egg culture

56
Q

What serological methods do we use to edtect influenza

A

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
Q

What molecular methods do we use for influenza

A

NAATs
Real time PCR

Multiplex PCR most common - Gene xpert etc etc

58
Q

What molecular methods do we use for influenza

A

NAATs
Real time PCR

59
Q

Talk about the egg culture method of isolating influenza

A

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
Q

How can we use tissue culture to fetect influenza?

A

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
Q

What is DFA for influenza, what are some pros and cons

A

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
Q

What moelcular method is available for influenza, how sensitive is it, main downfall?

A

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
Q

How does the GeneXpert compare to the NVRL PCR method of detecting influenza?

A

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
Q

Why is GeneXpert considered such an advantage in influenza diagnostics?

A

Really quick turn around time

Great for bed management -> can isolate patients quickly

Patient can be put on antivirals quickly

65
Q

Why is GeneXpert considered such an advantage in influenza diagnostics?

A

Really quick turn around time

Great for bed management -> can isolate patients quickly

Patient can be put on antivirals quickly

66
Q

What is another molecular platform used for the detection of influenza?

A

Biofire film array only 84% sesntive though

67
Q

How do we develop the influenza vaccine?

A

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
Q

Who should get the annual influenz vaccine?

A

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
Q

what kind of influenza vaccine do we give kids between 6 and 23 months

A

a nasal spray

70
Q

How does B compare to A in terms of epidemiology

A

B just has drift not shift

B has similar symptoms but usually milder than A

71
Q

How do we detect C?

A

We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab

72
Q

How do we detect C?

A

We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab

73
Q

What is bronchiolitis?

A

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
Q

What is bronchiolitis?

A

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
Q

What causes bronchiolitis?

A

Viral infection most common cause:
- Respiratory syncytial virus (RSV) most common
- Adenovirus, influenza, human metapneumovirus also implicated

76
Q

How is bronchiolitis/RSV transmissed?

A

Spreads through respiratory droplets or direct contact with contaminated surfaces

RSV can indirectly survive several hours on surfaces

77
Q

How does RSV get its name?

A

Respiratory syncytial virus

Its ability to cause cells lining the RT to merge into large, multinucleated cells called syncytia

78
Q

What family is RSV a part of and what is characteristic of this family?

A

Paramyxoviridae

These are enveloped viruses

79
Q

What family is RSV a part of and what is characteristic of this family?

A

Paramyxoviridae

These are enveloped viruses

80
Q

How does RSV cause infection
(3)

A

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
Q

What RNA does RSV use to hijack host cells?

A

A negative-sense strand

82
Q

How is the immune system involved in RSV pathogenicity?
(6)

A

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
Q

Comment on the epidemiology of RSV
(6)

A

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
Q

How many cases of RSV is there per year worldwide

A

33 million

85
Q

Comment on the mortality of RSV i children

A

Second leading cause of infant mortlity, 6.7% of deaths under 1
Causes 60k deaths annually in kids under 5

86
Q

Comment on RSV trends in Ireland

A

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
Q

Explain the huge increase in RSV numbers in recent years

A

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
Q

What is the basis for an RSV diagnosis?

A

Symptoms: Cough, wheezing, respiratory distress

Time of year: Circulates october to march

Age: <2

OR LAB Based diagnosis e.g. RSV

89
Q

What is the basis for an RSV diagnosis?

A

Symptoms: Cough, wheezing, respiratory distress

Time of year: Circulates october to march

Age: <2

OR LAB Based diagnosis e.g. RSV

90
Q

How is RSV transmitted?

A

Through droplets, fingers and fomites
HCAI
Community outbreaks

91
Q

How is RSV treated?

A

Supportive therapy, mainly consisting of oxygen and hydration

92
Q

How is RSV prevented?
(2)

A

Vaccine now available babies 6 months or younger but not for older kids

Infection control

4.1 Medical Microbiology (9 decks)

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