Respiratory Viruses

Question 1

Describe the features of the coronavirus

Answer 1

• Corona – ‘Crown’
  
  • (+)ssRNA virus
  • Large RNA genome ~29kB
  • 14 ORFs (both large and small)
  • Ribosomal frameshifting
  • 29 gene products
• Host-derived envelope ^[i.e. stolen]
• Spherical
• 100-160nm
• Protruding spike proteins ^[critical, binds to ACE2 receptor, target of vaccination]

Question 2

Describe the notable features of the coronavirus genome

Answer 2

The multiple orfs and the spike protein.

Question 3

Describe and distinguish between the features of SARS-CoV-1 and 2, and describe why SARS-CoV-2 spread more

Answer 3

SARS-CoV-1 v SARS-CoV-2
- SARS-CoV-1
- 8110 cases, 811 deaths: CFR ~10%
- SARS-CoV-2
- 608m (confirmed) cases, 6.5m deaths: CFR ~1% (falling)

Note that the CFR for SARS-CoV-2 is much lower than SARS-CoV-1.

• SARS-CoV-2
• Higher tropism for the URT
  - With evolution increases affinity
  - More efficient host-cell invasion
  - Increased spread
• **Higher virus loads prior to symptoms
  
  • Pre-symptomatic/asymptomatic spread - it is this factor that contributed to the much greater spread of SARS-CoV-2
  • Note also that CoV1 cases are much easier to identify and isolate given that symptomatic individuals had higher load ^[this idea contributed to complacency in COVID-19]
• BOTH
  
  • Attach via ACE-2
  • Respiratory pathogens
  • Stronger binding to ACE-2 = virus is now adapting to avoid ACE-2, or bind less well, in favour of another receptor

Question 4

Describe a notable feature regarding the infective period of SARS-CoV-2

Answer 4

The notable feature in this diagram is the viral genome which peaks in the pre-symptomatic phase (within the URT).
Consider also that a proportion of the population will be complete asymptomatics.
Note also that those with severe illness are theorised to have poorer innate immune systems (IFN). Viral genome curve shifts to the left.

Question 5

True or False: SARS-CoV-2 solely resides in the respiratory tract

Answer 5

• SARS-CoV-2 does not stay in the respiratory tract
• Found viral RNA at autopsy:
  
  • Digestive tract tissue – (-ve RNA)
  • Brain tissue + CSF
  • Heart tissue– 2/3rds of patients who died of pneumonia!
• Multisystem disease (severe illness) ALSO includes:
  
  • Renal insufficiency
  • Reduced liver function
  • Blood clotting ^[treat to drastically improve outcomes]
  • Arrhythmias, hypertension, and cardiac dysfunction in long COVID
  • Direct invasion of cardiomyocytes
    
    • Damages/destroys the cells
    • Dampens ACE-2 function: Usually plays a role in regulating blood pressure.
  • Cardiac tissue immunopathology
    
    • Myocardial injury – 5 of the first 41 patients in Wuhan

Question 6

Describe the diversity of outcomes of COVID-19

Answer 6

• SARS-CoV-2 can cause:
  
  • Asymptomatic
    
    • Never develop COVID-19 symptoms
    • • RNA test
  • Mild
    
    • Symptoms self-limiting
  • Severe
    
    • Life-threatening
    • Requires critical care
  • Long-COVID ^[note also that long COVID fairly common, poorly understood and not well acknowledged]
    
    • Symptoms beyond 4 weeks
    • RNA test

Question 7

Describe long COVID and issues of its classification

Answer 7

There are multiple syndromes under the umbrella of long COVID. These syndromes produce diverse symptoms in patients.

Note also that the relationship between infection and long COVID risk is not well understood.

Question 8

Describe the basic principles and different features of CIOVID-19 vaccines

Answer 8

• All COVID-19 vaccines…
  
  • Aim to generate antibodies to the spike
  • Probably also T cells that recognize the spike too
• The different COVID-19 vaccines differ in…
  
  • How the spike gets introduced to the body
  • How much of the spike is included
  • The things other than Spike
    
    • that might stimulate B and T cells ^[e.g. adenovirus]
  • How the innate cells are activated

Question 9

Describe the treatment options for COVID-19

Answer 9

• All for use in at-risk people only
  
  • Paxlovid is the main modality
    
    • Nirmatrelvir and ritonavir (combination of antiviral and anti-metabolite)
    • Best efficacy
    • Lots of drug interactions due to anti-metabolite
    • Note also the rebound risk - largely attributable to normal rebound pattern
  • Lagevrio
    
    • Molnupiravir
    • No impact on hospitalisations
    • May be useful in very severe disease
  • Evusheld
    
    • Tixagevimab and cilgavimab
    • Long lasting (6 months)
    • But outrun by variants

Question 10

Describe the future of coronavirus vaccine development

Answer 10

• Variant-specific vaccines
  
  • Moderna Spikevax Bivalent
    
    • Original/Omicron BA.1 vaxx
    • Now in Australia as dose 3 or 4
    • Circulating strains are BA.5
    • And still changing
• Pan-coronavirus vaccines
• Intranasal vaccines?
  
  • Mucosal immunity (at the site of infection, thus in theory more likely to stop infection)

Question 11

Describe the criteria for diagnosing flu solely based on symptoms

Answer 11

• central: headache
  
  • systemic: fever
  • muscular: tiredness (due to IFN effect)
  • joint aches
  • coughing
  • GI upset
  • nasopharyngeal symptoms

Question 12

Describe the features of the influenza virion

Answer 12

• segmented ssRNA genome
• Haemagglutinin = HA = H
  
  • adheres to cell receptors and enters cell
  • RNA synthesis in nucleus
• Neuraminidase = NA = N
  
  • enables release
    Note that it is the balance of HA to NA to mediate entry and exit from the cell - in order for infection to be most efficient.

Question 13

Describe influenza nomenclature

Answer 13

• Divided into A, B, and C
  
  • A is the most prevalent cause of human infection
  • B also circulates

Influenza A viruses split into serotypes based on:
- Haemagglutinin (H) – H1 to H16 known
- Neuraminidase (N) – N1 to N9 known
- H1, H2 & H3 + N1 & N2 in viruses adapted to humans

Isolates Named After Place of Isolation, Year & Type:
- A/Brisbane/59/2007 (H1N1)
- A/Uruguay/716/2007 (H3N2)
- B/Florida/4/2006

place of isolation =/= origin

Question 14

Describe sources of immunity to influenza

Answer 14

• innate immunity is strong e.g. via IFN action
• T cells have a minor role
• most of adaptive response exerted via antibodies: recognise HA (neutralising) and NA (protective) to prevent re-infection with the same strain

Question 15

Describe the two processes by which new strains emerge

Answer 15

Genetic and Antigenic Drift - Evolution in Action
- A low fidelity polymerase + high replication rate result in a relatively rapid mutation rate.
- A high percentage of infectable individuals have protective antibodies to HA and NA, creating strong selective pressure to change these proteins, evade antibody recognition, and reinfect.

Genetic and Antigenic Shift - Flu as a Genetic Engineer
- If two strains co-infect a single cell, segmented genomes can ‘re-assort,’ creating new strains ^[just a byproduct of assembly, cell cannot distinguish between strain A and B].
- Co-evolution of a strain and its host creates a species barrier, and genetic shift can break or lower species barriers.
- note that statistically only a small amount is pathogenic
- with multiple rounds of replication becomes more feasible

Question 16

List the three different classifications for strains of influenza

Answer 16

• seasonal
• incidental
• pandemic

Question 17

Describe seasonal influenza

Answer 17

Seasonal
- Several strains circulate globally in humans.
- Each year these strains drift.
- Significant immunity remains on a population basis, requiring approximately 5 years of change to escape immunity.

Question 18

Describe incidental influenza

Answer 18

• Some bird/pig adapted strains can infect people.
• These can sometimes be highly lethal.
• Do not necessarily transmit well between people.

Question 19

Describe pandemic influenza

Answer 19

• A reassortant between bird/pig and human viruses.
• HA/NA from Bird/pig mean no immunity in humans.
• Human-adapted parts are required for human-human spread e.g. RNA polymerase
• May require more than a reassortment event. Further human adaptation might be required.
• Low or no immunity in the population leads to a greater number of people being infected, and morbidity and mortality are expected to rise.
  
  • morbidity and mortality are not necessarily expected to rise on case fatality basis ^[may not be elevated, proportional, or causes havoc due to the numbers]
  • pandemic strains may or may not have unusual properties
  • may or may not be more pathogenic

Question 20

Describe the species barrier and its levels

Answer 20

1st Level is required for incidental infection:
- The ability to infect another species.
- Many factors can contribute to this barrier, such as receptor differences, differences in host proteins required for infection, and the inability of the virus to counter key immune defenses.
2nd Level is required for pandemics:
- The ability to maintain spread through another species, which is a higher barrier.
- The virus must be made at a site that allows spread, such as the upper versus lower respiratory tract for influenza viruses.
- Spread between hosts defines evolutionary fitness, and circumstances and societal factors play a role in spread (Ebola in W Africa vs developed nations)

Question 21

Describe the epidemiology and clinical presentations of RSV

Answer 21

• Very frequent respiratory pathogen, almost all children will have had RSV by age 2.
• Characteristic seal bark or croup-y cough
• Reinfections are common, and infections in infants can be serious, making it the most important cause of bronchiolitis and pneumonia.
• RSV can also be associated with childhood wheeze.
  
  • note: unclear if this extends to atopy
  • note 2: does not predict asthma in adults

Question 22

Describe the biology of RSV

Answer 22

RSV – From the Family: Paramyxoviridae
- A big family with two branches: Paramyxovirinae and Pneumovirinae.
- RSV belongs to the Pneumovirinae branch, along with Human Metapneumovirus.

RSV shares similarities in types of surface proteins with orthomyxoviruses e.g. influenza

Respiratory Syncytial Virus (RSV)
- Enveloped capsid with helical symmetry.
- Negative (-ve) sense RNA genome.
- note two forms when cultured: spherical or filamentous (which could constitute infectious form)
- Makes 10 mRNAs, one for each gene, and replication is entirely in the cytoplasm.
- no splicing or polyproteins

Question 23

Describe the disease burden of RSV

Answer 23

How Much of a Problem Is RSV?
- Highly seasonal in temperate climates, with RSV ‘season’ coinciding with winter – early spring.
- On first exposure, 25% to 40% have bronchiolitis or pneumonia, and 0.5% to 2% will require hospitalization.
- Hospitalizations with RSV mostly involve infants less than 6 months old.

Who Gets Sick with RSV and When?
- Highly seasonal in temperate climates, with RSV ‘season’ coinciding with winter – early spring.
- On first exposure, 25% to 40% have bronchiolitis or pneumonia, and 0.5% to 2% will require hospitalization

Hospitalisations:
- Most (~60%) are infants < 6 months old
- Nearly all (>90%) are < 1 year old
- Anything that compromises breathing, cardiac, or immune function predisposes to the risk of severe RSV (premature babies at risk)
- These risk factors exist in adults as well.

Question 24

Describe RSV pathogenesis and spread

Answer 24

RSV Pathogenesis
- Virus-induced
- Immunocompromised individuals are at risk.
- But direct virus damage is limited.
- Disease is largely caused by immunopathology. ^[an over-reaction as opposed to histological changes]
- The narrowing of bronchioles is due to inflammation and not direct virus damage.
- Appropriate immune response is a tricky balance.

Transmission
- Transmitted by droplets, large particles, and fomites.
- Incubation time is 4-6 days.
- Infectious for 3-8 days after symptoms.
- Not especially stable but can survive a few hours on nonporous surfaces.
- Medical personnel transmit these viruses readily.
- Also childcare.
- Toys can be good vectors too.
- Nosocomial infection is an enormous problem, especially as many infants at high risk of severe infection are already in the hospital.

Question 25

Describe treatment options for RSV

Answer 25

Treatment
- Supportive care.
- Use of antivirals (ribavirin) not well supported by evidence.
Prophylaxis
- No vaccine.
- Early trial of formalin-inactivated vaccine a disaster.
- Immunized kids had more severe infections.
- Potentially the wrong ‘type’ of immunity generated.
- Palivizumab (Synagis) given monthly to babies at high risk. ^[e.g.?]
- Studies mixed as to the reduction of disease.
- Costs approximately $1000 a shot and is not on the PBS.

Question 26

Describe rhinoviruses

Answer 26

Rhinovirus – A Picornavirus
- Picornavirus (literally ‘very little RNA virus’).
- A large family of very small +ve sense RNA viruses.
- Collectively they are a nasty bunch, with rhinoviruses accounting for more specimens tested than influenza.
- Other members include Polio, Coxsackievirus (causes myocarditis), and Foot and Mouth Disease Virus (of livestock).
- note rhinoviruses are more of an economic problem than a cause of serious disease, but account for more specimens tested than influenza
Rhinovirus (Picornavirus) Genome
- Genome is translated immediately upon entry.
- Viral RNA pol is not carried in the virion.
- A single open reading frame generates a polyprotein, processed by a viral enzyme.
- Note: 5’-UTR has many AUGs therefore ribosome cannot start at the beginning and scan for first AUG
- therefore has to jump onto RNA at rifht place– has IRES which allows ribosome to bind at internal position, which differes mechanistically from host translation
- this enables virus to stop host translation but preserve its own
- IRES has biorech appliactions

Rhinovirus – A Family Affair
- Most frequently isolated agent from people with the ‘common cold.’
- Children have more frequent infections than adults.
- “The family unit is a major site for the spread of rhinoviruses in contemporary society.”
- “Infections are generally brought into the home by children.”
- Secondary attack rates are 30-70%, with spread most common for other children and mothers.
- Secondary infections appear at 2-5 day intervals, most within a few days of the index case.
- The greater the symptoms of the index, the higher the attack rate.

Note that rhinoviruses are not enveloped and thus harder to disinfect.

Question 27

Describe adenoviruses

Answer 27

Adenoviruses
- Adenoviruses (AdV) were found in the 1950s using cell culture and were associated with human respiratory disease.
- Human AdV has 6 species (A-F) and 51 serotypes.
- Characteristics include a linear, dsDNA genome ~35 kb, non-enveloped virion, and replication in the nucleus.

Adenoviruses Do Lots of Nasty Things
- Diseases caused by Adenoviruses include upper respiratory infections, gastroenteritis, meningoencephalitis, hepatitis (in kids with transplants), myocarditis, acute hemorrhagic cystitis, and more.
- Different serotypes cause different disease

Adenovirus – An Example of Tropism
- Tropism = predilection for certain cell types or tissues.
- Adenovirus fiber directs cellular tropism.
- Swapping fibers between serotypes redirects tropism. ^[but does not explain the full picture]
- Most serotypes seem to get to the GI tract, but why only a few cause disease is not known.
- Tropism can be altered in immunocompromised individuals.

Question 28

Describe tests and samples used to detect viral infection, and tests for past exposure

Answer 28

Samples to Detect Virus:
- Throat swabs.
- Nasopharyngeal aspirates (NPA) or washes.
Tests to Detect Virus:
- PCR, often a combined test for multiple pathogens.
- Immunochromatographic (ICT) tests (dip sticks).
- ELISA.
- Immunofluoresecence on cells from samples
Tests for Past Exposure:
Test serum for antibodies (ICT, ELISA).
- Remember, it takes time, especially IgG, and is complicated by maternal antibodies in very young individuals.