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.