CD

Viruses and Influenza A Notes

Viruses – Including ‘Flu

What is a Virus?

  • A virus consists of:
    • Genome – RNA or DNA
    • Capsid – a protein shell (or nucleocapsid)
    • +/- Envelope - a lipid membrane
    • Proteins (enzymes, polymerases etc), ion channels, immune modulators
  • Viral genomes are packaged inside particles that mediate their transmission between cells and hosts.
  • Key to virus survival: transmission and replication.
    • Escape, Survive, Infect & Replicate.
  • Disease is a common but unnecessary side effect of virus replication and host immune response to infection.

Modes of Virus Transmission

  • Direct contact
  • Aerosols & droplets
  • Contaminated surfaces
  • Vector
  • Bodily fluids
  • Mother to child
  • Zoonosis – animal to human

Virus Routes of Entry to the Body

  • Skin – cuts and bites
  • Mucosal surfaces (respiratory tract, gastrointestinal tract, urogenital tract etc.)
  • Eye – conjunctiva
  • Blood – needle reuse, contaminated blood products, mother to foetus

Virus Replication Cycle

  • Attachment & Entry
  • Uncoating
  • Genome Transcription & translation
  • Genome replication
  • Proteins Assembly & Maturation
  • Virion release

Common Patterns of Infection

  • Acute Infections (sprint)
    • Rapid onset of disease
    • Rapid production of virions, followed by clearance and elimination of infection by host immune response
    • Examples: Poliovirus, Influenza virus, Norovirus, Coronavirus
  • Persistent Infections (marathon)
    • Virions produced either continuously or intermittently for months/years/lifelong
    • Infection not cleared by host
    • Examples: HIV, Varicella zoster virus (chickenpox), Human papilloma virus

Persistent Viral Infections

  • Chronic infection with low-level replication of viruses in tissues which regenerate.
    • Example: Papillomaviruses cause warts/cervical cancer
  • Latent infection - viral genomes are maintained but virions are not formed until episodes of reactivation
    • Examples: Herpes Simplex in cold sores; Varicella zoster virus chickenpox and shingles

Factors That Can Affect Disease Severity

  • Pyramid of disease severity:
    • Asymptomatic infection – no symptoms
    • Mild symptoms – don’t need to see a doctor
    • Sick – requests medical help
    • Very sick – hospitalised
    • Succumbs to infection
  • Factors:
    • Amount of virus at infection
    • Co-infections with other microbes
    • Viral genome sequence/virulence
    • Immune response – too much/too little vs just right
    • Previous infection
    • Route of infection
    • Age of host – young/old
    • Other health problems/medications

Acute Measles Infection

  • (-)ssRNA genome
  • Transmission via respiratory droplets/aerosols
  • Symptoms: fever, cough/respiratory infection, rash
    • Leukopenia – destruction of immune cells – “immune amnesia”
  • In the absence of vaccination – case fatality rate of 3-6%
  • 2018 EU: 12,352 cases reported, 34 deaths

Rare Persistent Measles Infection

  • Subacute Sclerosing Panencephalitis (SSPE)
    • Manifests approximately 7 years after acute measles infection
    • Neurological impairment – difficulties controlling limbs, behavioural problems, impaired eyesight
    • Weeks-months – mental deterioration, seizures, paralysis, blindness.
    • Death within 1-3 years of onset
    • Caused by persistent defective measles virus infection of CNS
    • Age-dependent incidence rate: estimated 1:600 – 1:5000
    • 2018 EU: 12,000 cases measles = SSPE? 2-20?

Viral Load

  • The first person in the family to contract a viral illness often has a milder illness than other people in the household.
  • This may be because within the household there is closer/ prolonged interaction, and people become infected by a higher dose of virus.

Pathogenicity and Virulence

  • Pathogenicity is the ability of the virus to cause disease
    • Some commensal microbes are not pathogenic.
    • Ebola virus is more pathogenic than common cold viruses.
  • Virulence describes the capacity of a virus to cause disease
    • Some influenza strains encode non-essential genes that encode immune evasion proteins.

Virulence Determinants

  • Enhance replication – better interactions with host proteins needed during virus replication
  • Modify/block host immune defence responses - inhibit cytokines, prevent apoptosis etc.
  • Facilitate spread – better receptor binding, lower minimum infectious dose, additional routes of transmission
  • Direct toxicity – diarrhoea, vomiting

Viral Sequence

  • Two strains of poliovirus might vary in their virulence.
  • A single mutation in the genome separates 2 very different strains
    • One is attenuated and used as a live attenuated vaccine
    • the other invades the motorneurones and causes flaccid paralysis (poliomyelitis).

Unpredictable Influenza A Virus

  • Infects many hosts, aquatic birds, adapts to humans, pigs, horses etc.
  • Acute infection - causes influenza/the ‘flu’
  • Seasonal epidemics – winter ‘flu’
  • Occasional pandemics – 2009 swine flu pandemic
  • Transmission - Respiratory droplets, aerosols, close contact, contact with contaminated surfaces

Usual Symptoms of Influenza Infection

  • Most of the symptoms we associate with “the flu” are caused by the immune response activate to control and remove the infection.
    • Example: interferons induce fever, headache, muscle pain, fatigue

Influenza A – Virion Structure

  • Haemagglutinin (HA)
  • Neuraminidase (NA)
  • Envelope/Lipid bilayer
  • RNA polymerase -ve ssRNA genome ~100 nm diameter
  • A/Thailand/8/2022 (H3N2)
    • Virus type Geographic location Strain number Year of collection Virus subtype

Influenza Virus A – Segmented Genome

  • PA-X Genome replication
  • Non-essential virulence factors
  • Receptor binding/entry
  • Genome protection
  • Cell entry/exit
  • Nucleus entry
  • Modulate immune response

Currently Circulating Seasonal Influenza A & B Virus Strains

  • Influenza A:
    • H1N1 – circulating since 2009
    • H3N2 – circulating since 1968
  • Influenza B:
    • Late 1990s B/Yamagata B/Victoria
    • Post-COVID pandemic

Why Do We Need Annual Influenza Vaccinations?

  • Antigenic drift

Antigenic Drift

  • Accumulation of point mutations in surface antigens – HA and NA
    • Amino acid changes cause:
      • Localised changes to protein structure
      • Localised changes to charge (acidic amino acid changed to neutral amino acid)
      • Addition/removal of a glycosylation site (sugar modification)
    • Changes antibody binding sites so that pre-existing/memory antibodies no-longer efficiently neutralise virus and block infection.
    • Annual vaccination of people at risk of severe influenza infection

Unpredictable Influenza Pandemics

  • 1918 H1N1 pandemic killed over 50 million people.

Transmission of Influenza A Subtypes

  • Seasonal Human Influenza: H1N1, H3N2
  • Avian Influenza: H5N1, H7N9, H7N7, N9N2, H6N1, N9N2, H3N8, H1-H16, H17-18, H5N1
  • Swine Influenza: H1N1, H3N2

Two Ways to Start an Influenza A Pandemic

  • Zoonotic transmission of a human-adapted avian or swine (cattle?) influenza A virus
  • Antigenic shift
    • Genetic mixing between 2 or more strains of virus → introduction of novel HA

Genetic Reassortment: Antigenic Shift

  • Co-infection of a host AND host cells with two+ different subtypes of influenza A viruses.
  • Produces virus with “novel to humans” HA.

Antigenic Shift and Influenza Pandemics of the 20th Century

  • 1918 H1N1
  • 1957 H2N2
  • 1968 H3N2
  • 2009 H1N1

Why are Influenza A Virus Pandemics Rare?

  • Host restriction barriers:
    • Viruses adapt to their host species
    • Small differences in host receptors inhibit efficient infection
      • Exposure to more virus needed to cause infection
    • Small difference in host proteins needed during the replication cycle inhibit efficient virus replication
      • Replication is less efficient / unsuccessful
    • Animal to human infection occurs relatively frequently BUT human to human transmission is much harder

Examples of Influenza Viral Proteins That Affect Zoonotic Transmission

  • HA – binds to cellular receptor
    • α2,6 linked sialic acid – human receptor
    • α2,3 linked sialic acid – avian receptor
    • Pigs and cattle have both in the same locations
  • NA – influenza in chickens have shorter NA, that don’t function efficiently in people
  • Viral polymerase (PB2) – interacts with host proteins – needs to acquire specific point mutations to adapt to mammals

A Small Difference Can Have a Big Effect on Receptor Specificity

  • Sialic acid attached to glycoprotein – receptor for influenza virus

Receptor Specificity Determines the Types of Cells a Virus Can Enter

  • α2,6 (Human)
  • α2,3

Mixing Vessel Theory for Influenza A Virus Antigenic Shift and Mammalian Adaption

  • Could cows also become mixing vessels?

H5N1 Influenza – The Next Pandemic?

  • First identified in 1996 in domestic waterfowl in China.
  • 1997 – H5N1 poultry outbreaks in China and Hong Kong, including 18 human infections (6 deaths).
  • 2003 – widespread poultry outbreaks in Asia.
  • 2005 – wild birds spread H5N1 to poultry in Africa, the Middle East and Europe.
  • 2021- H5N1 detected in wild birds in the USA and Canada
  • 2022 – H5N1 detected in poultry farms in USA
  • 2024 – H5N1 detected in cattle* in USA
    • First detection of influenza A virus in cattle

H5N1 Influenza Viruses – Now a Panzootic Virus

  • Panzootic virus:
    • A virus that can infect many species of animals throughout the world;
    • A pandemic in wild animals
  • Lots of viral genetic variation (reassortment & point mutations throughout gene segments)

Current H5N1 Influenza Virus Situation in the USA

  • Multiple spillover events from wild birds into poultry farms throughout USA
  • 100+million domestic birds culled since 2022
  • egg shortage
  • March 2024, first instance of H5N1 in cattle
  • As of 18/3/2025: 989 cattle herds affected, in 17 states
  • 3 spillover events
  • High amounts of virus in milk
  • Mostly mild symptoms to asymptomatic in cattle
  • 70 confirmed human H5N1 infections
    • 41 – exposed to infected cattle
    • 24 – exposed to infected poultry
    • 2 – exposed to other type of infected animal
    • 3 – exposure unknown

Will We Have an H5N1 Influenza Pandemic?

  • H5N1 influenza viruses:
    • Are now infecting a wide range of bird and mammalian species, and causing sporadic human infections.
    • Have lots of genetic diversity – so H5N1 virus infecting poultry in Ireland is currently quite different from H5N1 virus infecting cattle in USA.
    • Are currently not able to transmit from person to person.
    • Are currently not able to efficiently bind the receptor that influenza use to enter human cells – requires more mutations in HA.
    • H5N1 viruses in USA are developing mutations in the viral polymerase that adapt influenza to efficiently replicate in human cells.
    • H5N1 viruses in USA have acquired the usual “long” NA (not the shorter “chicken adaptation” version)

Summary

  • Viruses are packages of genomic material transmitted from one host to another.
  • Viruses are intracellular obligate parasites that MUST infect cells for replication.
  • There are a wide range of transmission routes that different viruses use.
  • Some viruses cause acute infections, others cause persistent/chronic infections.
  • Multiple host and viral factors affect disease severity
  • Influenza A viruses cause annual seasonal epidemics (antigenic drift) and occasional pandemics (zoonosis or antigenic shift)
  • Avian influenza viruses need to acquire host adaptation mutations to efficiently transmit between mammals.
  • H5N1 influenza viruses are now considered to be panzootic – infecting many different wild animal species throughout the world.