Highly Pathogenic Avian Influenza
Avian Influenza & Pandemic Basics
Zoonotic spillover: domestication of animals and more interaction between vectors is a source of new virus infection in
humans – a human getting an infection from an animal
- Wild aquatic birds are the natural viral reservoir for influenza viruses
- The aquatic bird can spread the virus to other farm animals but also sea life, poultry and humans
Characteristics of pandemic:
- Associated with introduction of virus into human circulation with no pre-existing immunity
- Sudden onset, no warning
- Rapid global spread, easy human to human
transmission
- Get waves of infection, increasing virulence
Influenza A virus’s structure and replication
cycle
- Structure enveloped, segemented, single-
stranded negative-sense RNA virus
- HA (haemagglutinin): mediates binding to host cells and NA (neuraminidase): assists in viral release
- Replication cycle: attachment endocytosis uncoating RNA replication in nucleus assembly budding
and release
- Haemagglutinin (HA) protein determines host range and tissue tropism (the range of cells and tissues of a host that
support growth a of particular pathogen) through sialic acid binding
- The influenza’s HA attachment point is a trimer that can recognise sialic acids
- The distinct influenza Has can distinguish between different sialic acid linkages – i.e. alpha 2,3 linkage vs alpha 2,6
linkage
- Hemagglutinin (protein that causes red blood cell clumping)
binds to sialic acid groups on cell surface proteins
- Human viruses bind to sialic acid in an alpha 2,6 galactose
linkage and bird viruses bind to alpha 2,3
- The HA is then cleaved by the host protease which enable
penetration and uncoating
- Influenza A viruses can generate new pandemic strains primarily because their RNA genome is segmented which
allows reassortment of the gene segments when a host cell is co-infected by two different viruses – process enables
creation of new virus with unique combination of gene segments
- Allows host jumps and rapid evolution
Influenza – Transmission, Immunity and Antigenic Drift
Characteristics of human flu:
- Spread by aerosol and/or droplet
- Rapid spread of infection
- Several days before onset of symptoms
- Virus shed before onset of symptoms
Influenza A virus infection induces a robust immune response
- Symptoms: fever, pneumonia (5-7 days) – due to production of cytokines
- Most a risk are young, elderly, immunocompromised
- Generate excellent antibody response to spike (HA>NA) proteins – provide protective immunity
- Generate good T cell responses – cell mediated immunity
, - B cell = antibody production, CD4+T cell =
maturation of adaptive responses, CD8+T
cell = recognition and removal of virus
infected host cells
- Influenza A virus infection induces a robust
immune response
Antigenic Drift: the gradual accumulation of small genetic changes, or point mutations in a virus’s protein surface
change in hemagglutinin and neuraminidase for influenza A
Accumulation of mutations in antibody binding sites of HA immunity to previous year’s strain not as effective
- Protection from influenza infection is primarily via
neutralizing antibody
Antigenic shift (process where two or more
different strains of a virus combine to create a
new subtype with a mix of surface antigens) can
result in a new human subtype = H2N2 – human
circulation, spreads human to human infects
intermediate host (pig) as well as H3N? – bird
circulation, virulent but can’t spread to humans
Creation of H3N2 – not in circulation, highly
virulent, acquires ability to spread human to human – mixture of both
A lack of population immunity, asymptomatic shedding and internation air travel = an influenza strain spreads worldwide
within three months despite initial containment measures (rapid dissemination)
Host immune responses:
- Protective: Neutralising antibodies against HA/NA prevent reinfection; CD8+ T cells clear infected cells.
- Pathogenic: Dysregulated cytokine release (“cytokine storm”) causes inflammation and tissue damage (seen
in 1918 and H5N1 infections).
Influenza Pandemics
Flu pandemic after introduction directly from animal species – no need for reassortment
- There was direct introduction from host species into humans
- The 1918 Spanish influenza pandemic had waves of outbreaks – as the outbreaks occurred the virulence increased
across the waves
- The pandemic flu demonstrated adaptation to the human host
- Result of viral evolution and immune drive selection
- During the pandemic, high mortality among healthy young adults were primarily associated with severe immune-
mediated inflammation in the lungs
H5N1
Two types of bird flu
- Low pathogenic avian influenza (LPAIs) – minor or no symptoms
- The haemagglutinin (HA) protein must be cleaved by the host enzymes to activate it
- Normally done by trypsin-like proteases only found in respiratory and intestinal tract
- Infection stays localised to those tissues
- Highly pathogenic avian influenza viruses such as H5N1 have a mutlibasic amino acid insertion at the HA
cleavage site
, - There are several amino acids added in a row and this allows for different proteases to cleave HA
- Makes for easier activation in many cell types and the virus can spread beyond the respiratory tract to
multiple organs
- Increased virulence = more severe disease and higher mortality rate
Characteristics of HPAI outbreaks: direct transmission from birds to human, no need for pig as intermediate host
(Spanish flu)
- H5N1 – endemic in wild aquatic bird populations
- Continuing to evolve in bird reservoir in S.E Asia, Southern China
- H5N1 viruses have not yet acquired the ability to spread human to human efficiently
H5N1 pathogenicity is multi-factorial and constantly evolving
HA: Increased efficiency in cleavage – still has preference for the alpha 2,3 galactose linkage
- PB2: more efficient growth in human cell lines and mice
- NS1: resistance to anti – viral cytokines; IFN-alpha, IFN-gamma and
TNF- alpha
- Human infection is inevitable
Risk mitigation strategies:
- Surveillance in poultry and wildfire
- Limiting live bird markets
- Vaccination development and antiviral stockpiling
- Rapid response and biosecurity measures
Summary
- Influenza pandemics arise when novel viruses emerge to which humans have little or no immunity.
- Influenza A viruses possess a segmented RNA genome and surface proteins (haemagglutinin and neuraminidase)
that determine host specificity and transmission.
- Binding preferences for different sialic acid linkages explain why avian and human influenza viruses infect distinct
hosts and tissues.
- Antigenic drift produces gradual seasonal variation, whereas antigenic shift through genome reassortment can
generate pandemic strains.
- Highly pathogenic avian influenza viruses such as H5N1 continue to evolve in animal populations, posing an ongoing
pandemic threat through potential human adaptation and spillover.
Clostridial Infections
Common Characteristic of Clostridial Species
It is a gram-positive rod, obligate anaerobes, form heat resistant
endospores, common inhabitants of the gastrointestinal tract
- Important in agriculture (soil maintenance) and industry
(biofuels)
- Important human and animal pathogens
Anerobic culture methods: Anerobic chamber: chamber filled with a has
mix, walls made of material with low oxygen permeability equipment located inside the chamber where all
manipulations are carried out entry port capable of oxygen evacuation which is used for entry/exit of materials
Avian Influenza & Pandemic Basics
Zoonotic spillover: domestication of animals and more interaction between vectors is a source of new virus infection in
humans – a human getting an infection from an animal
- Wild aquatic birds are the natural viral reservoir for influenza viruses
- The aquatic bird can spread the virus to other farm animals but also sea life, poultry and humans
Characteristics of pandemic:
- Associated with introduction of virus into human circulation with no pre-existing immunity
- Sudden onset, no warning
- Rapid global spread, easy human to human
transmission
- Get waves of infection, increasing virulence
Influenza A virus’s structure and replication
cycle
- Structure enveloped, segemented, single-
stranded negative-sense RNA virus
- HA (haemagglutinin): mediates binding to host cells and NA (neuraminidase): assists in viral release
- Replication cycle: attachment endocytosis uncoating RNA replication in nucleus assembly budding
and release
- Haemagglutinin (HA) protein determines host range and tissue tropism (the range of cells and tissues of a host that
support growth a of particular pathogen) through sialic acid binding
- The influenza’s HA attachment point is a trimer that can recognise sialic acids
- The distinct influenza Has can distinguish between different sialic acid linkages – i.e. alpha 2,3 linkage vs alpha 2,6
linkage
- Hemagglutinin (protein that causes red blood cell clumping)
binds to sialic acid groups on cell surface proteins
- Human viruses bind to sialic acid in an alpha 2,6 galactose
linkage and bird viruses bind to alpha 2,3
- The HA is then cleaved by the host protease which enable
penetration and uncoating
- Influenza A viruses can generate new pandemic strains primarily because their RNA genome is segmented which
allows reassortment of the gene segments when a host cell is co-infected by two different viruses – process enables
creation of new virus with unique combination of gene segments
- Allows host jumps and rapid evolution
Influenza – Transmission, Immunity and Antigenic Drift
Characteristics of human flu:
- Spread by aerosol and/or droplet
- Rapid spread of infection
- Several days before onset of symptoms
- Virus shed before onset of symptoms
Influenza A virus infection induces a robust immune response
- Symptoms: fever, pneumonia (5-7 days) – due to production of cytokines
- Most a risk are young, elderly, immunocompromised
- Generate excellent antibody response to spike (HA>NA) proteins – provide protective immunity
- Generate good T cell responses – cell mediated immunity
, - B cell = antibody production, CD4+T cell =
maturation of adaptive responses, CD8+T
cell = recognition and removal of virus
infected host cells
- Influenza A virus infection induces a robust
immune response
Antigenic Drift: the gradual accumulation of small genetic changes, or point mutations in a virus’s protein surface
change in hemagglutinin and neuraminidase for influenza A
Accumulation of mutations in antibody binding sites of HA immunity to previous year’s strain not as effective
- Protection from influenza infection is primarily via
neutralizing antibody
Antigenic shift (process where two or more
different strains of a virus combine to create a
new subtype with a mix of surface antigens) can
result in a new human subtype = H2N2 – human
circulation, spreads human to human infects
intermediate host (pig) as well as H3N? – bird
circulation, virulent but can’t spread to humans
Creation of H3N2 – not in circulation, highly
virulent, acquires ability to spread human to human – mixture of both
A lack of population immunity, asymptomatic shedding and internation air travel = an influenza strain spreads worldwide
within three months despite initial containment measures (rapid dissemination)
Host immune responses:
- Protective: Neutralising antibodies against HA/NA prevent reinfection; CD8+ T cells clear infected cells.
- Pathogenic: Dysregulated cytokine release (“cytokine storm”) causes inflammation and tissue damage (seen
in 1918 and H5N1 infections).
Influenza Pandemics
Flu pandemic after introduction directly from animal species – no need for reassortment
- There was direct introduction from host species into humans
- The 1918 Spanish influenza pandemic had waves of outbreaks – as the outbreaks occurred the virulence increased
across the waves
- The pandemic flu demonstrated adaptation to the human host
- Result of viral evolution and immune drive selection
- During the pandemic, high mortality among healthy young adults were primarily associated with severe immune-
mediated inflammation in the lungs
H5N1
Two types of bird flu
- Low pathogenic avian influenza (LPAIs) – minor or no symptoms
- The haemagglutinin (HA) protein must be cleaved by the host enzymes to activate it
- Normally done by trypsin-like proteases only found in respiratory and intestinal tract
- Infection stays localised to those tissues
- Highly pathogenic avian influenza viruses such as H5N1 have a mutlibasic amino acid insertion at the HA
cleavage site
, - There are several amino acids added in a row and this allows for different proteases to cleave HA
- Makes for easier activation in many cell types and the virus can spread beyond the respiratory tract to
multiple organs
- Increased virulence = more severe disease and higher mortality rate
Characteristics of HPAI outbreaks: direct transmission from birds to human, no need for pig as intermediate host
(Spanish flu)
- H5N1 – endemic in wild aquatic bird populations
- Continuing to evolve in bird reservoir in S.E Asia, Southern China
- H5N1 viruses have not yet acquired the ability to spread human to human efficiently
H5N1 pathogenicity is multi-factorial and constantly evolving
HA: Increased efficiency in cleavage – still has preference for the alpha 2,3 galactose linkage
- PB2: more efficient growth in human cell lines and mice
- NS1: resistance to anti – viral cytokines; IFN-alpha, IFN-gamma and
TNF- alpha
- Human infection is inevitable
Risk mitigation strategies:
- Surveillance in poultry and wildfire
- Limiting live bird markets
- Vaccination development and antiviral stockpiling
- Rapid response and biosecurity measures
Summary
- Influenza pandemics arise when novel viruses emerge to which humans have little or no immunity.
- Influenza A viruses possess a segmented RNA genome and surface proteins (haemagglutinin and neuraminidase)
that determine host specificity and transmission.
- Binding preferences for different sialic acid linkages explain why avian and human influenza viruses infect distinct
hosts and tissues.
- Antigenic drift produces gradual seasonal variation, whereas antigenic shift through genome reassortment can
generate pandemic strains.
- Highly pathogenic avian influenza viruses such as H5N1 continue to evolve in animal populations, posing an ongoing
pandemic threat through potential human adaptation and spillover.
Clostridial Infections
Common Characteristic of Clostridial Species
It is a gram-positive rod, obligate anaerobes, form heat resistant
endospores, common inhabitants of the gastrointestinal tract
- Important in agriculture (soil maintenance) and industry
(biofuels)
- Important human and animal pathogens
Anerobic culture methods: Anerobic chamber: chamber filled with a has
mix, walls made of material with low oxygen permeability equipment located inside the chamber where all
manipulations are carried out entry port capable of oxygen evacuation which is used for entry/exit of materials
