Respiratory Viruses - Influenza, RSV, Parainfluenza, hMPV Flashcards
What are the two main types of viruses?
DNA viruses
RNA viruses
What are some differences between RNA and DNA viuses?
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)
Why do only DNA viruses cause latent infection?
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
Give some examples of RNA viruse
Orthomyxoviridae -> influenza A, B, C
Paramyxoviridae -> Parainfluenza, RSV
Picornaviridae -> Rhinoviurs, Coxsackie virus, Enterovirus (echovirus), Parechovirus
Coronaviridae -> coronavirus, SARS CoV, MERS
Bunyaviridae -> hantavirus
What kind of infection does coxsackie A cause?
Hand foot and mouth
-> similar to chickenpox
Everyone has had this at some point -> its highly contagious and spreads rapidly in playschools etc
Give an example of a DNA virus
Adenovirus
When do we usually ID enterovirus in the lab?
Usually flags for meningitis
Usually the most common flag on the film array in the lab
What are othomyxoviridae, what viruses are in this family?
(4)
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
What influenza strains are we concerned with?
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
What are the different components of an orthomyxoviridae?
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
What does Haemagglutinin do, why is it significant?
HA binds to host cell receptors: key vaccine target
What does neuramidase do?
It facilitates the release of new vira particles
What makes up an RNA nucleocapsid?
A segmented RNA genome composed of eight RNA segment whic encode viral proteins
Surrounded by a nucleoprotein, forming a helical structure
What matix proteins are found in orthomyxoviridae, what do they do?
M1 proteins which maintain viral stucture and aid assembly
M2 proteins which facilitate viral uncoating in host cells
What are the structural components of influenzae
Lipid envelope
Surface glycoproteins: HA and NA
What are the structural components of influenzae
Lipid envelope
Surface glycoproteins: HA and NA
Talk about the lipid envelope of influenza
It has a protective outer layer made of lipids (fats) that encase the virus
Talk about the haemagglutinin of Influenza, how many on cell, what is the function
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
Talk about the neuraminidase of Influenza, how many on cell, what is the function
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 do we make use of HA and NA combinations?
(2)
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 can influenza use HA and NA to evade our immune system?
(4)
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
What is an antigen found on group A, B and C influenza?
Internal ribonucleoprotein (RNP)
How do we name viruses, according to WHO
Virus type, geographic origin, strain number, year of isolation, virus subtype
Virus subtype (H3N2)
Talk about antigenic variability in influenza viruses, why does it happen and what is it?
(3)
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
What is the definition of antigenic drift?
A gradual process where minor mutations occur in the genes encoding HA and NA over time
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
What are the impact of antigenic drift?
Antigenic drift is responsible for seasonal influenza epidemics and the need for annual updates to flu vaccines
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
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
When does shift usually occur
(2)
Usually occurs in pigs
This is because pigs can bi infected by both birds or humans
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
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
What are the symptoms of Influenza A?
Fever, cough, sore throat, body aches, fatigue
Sever illness in vulnerable populations
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)
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
Comment on the trend in influenza serotypes
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
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
What are the two ways antigenic drift occurs?
Genetic reassortment
Change of species specificity
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
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
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
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
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
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
When is considered to be influenza season
October through to May
But we generally say october through to March 31st
Who is most susceptible to influenza outbreaks?
Young and old
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)
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
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
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
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
What four methods are there to diagnosing influenza
Provisional clinical diagnosis
Isolation using tissue culture or culture in eggs
Serology
Molecular
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
How do we isolate influenza in the lab
Nasal, nasopharyngeal or throat swabs
Tissue culture or egg culture
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
What molecular methods do we use for influenza
NAATs
Real time PCR
Multiplex PCR most common - Gene xpert etc etc
What molecular methods do we use for influenza
NAATs
Real time PCR
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
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)
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
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
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
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
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
What is another molecular platform used for the detection of influenza?
Biofire film array only 84% sesntive though
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
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
what kind of influenza vaccine do we give kids between 6 and 23 months
a nasal spray
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
How do we detect C?
We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab
How do we detect C?
We have to send any query Cs out to the NVRl as molecular methods dont detect it in lab
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
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
What causes bronchiolitis?
Viral infection most common cause:
- Respiratory syncytial virus (RSV) most common
- Adenovirus, influenza, human metapneumovirus also implicated
How is bronchiolitis/RSV transmissed?
Spreads through respiratory droplets or direct contact with contaminated surfaces
RSV can indirectly survive several hours on surfaces
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
What family is RSV a part of and what is characteristic of this family?
Paramyxoviridae
These are enveloped viruses
What family is RSV a part of and what is characteristic of this family?
Paramyxoviridae
These are enveloped viruses
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
What RNA does RSV use to hijack host cells?
A negative-sense strand
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
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
How many cases of RSV is there per year worldwide
33 million
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
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)
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
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
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
How is RSV transmitted?
Through droplets, fingers and fomites
HCAI
Community outbreaks
How is RSV treated?
Supportive therapy, mainly consisting of oxygen and hydration
How is RSV prevented?
(2)
Vaccine now available babies 6 months or younger but not for older kids
Infection control
Monoclonal antibody treatments
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
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
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
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
What percentage of LRTI in paeds is caused by hPIV
40%
What percentage of croup is caused by hPIV?
75% of croup
hPIV accounts for what percentage of respiratory illness in adults?
15%
How does hPIV affect our elderly and immunocomprimsed?
50% of acute hPIV result in death
75% mortality in our 6months post stem cell recipients
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
What three methods do we have available for the detection of human parainfluenza?
RT-PCR
Viral culture
Serological detection
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
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)
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
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
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
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
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
