Influenza viruses Holly Shelton holly.shelton@pirbright.ac.uk - - PowerPoint PPT Presentation

Influenza viruses Holly Shelton

holly.shelton@pirbright.ac.uk

Preventing and controlling viral diseases

Influenza Viruses

• Orthomyxoviridae
• Negative sense RNA virus
• 7 or 8 segments
• Enveloped
• 4 Subtypes; A,B, C, D

Subtype Natural Host Disease Other Species Infected A Wild aquatic birds Frequent, Mild – Severe, pandemic potential Humans, Poultry, Horses, Pigs, Dogs, Tigers, Cats, Ferrets, Seals, Whales &

• thers

B Humans Frequent - Mild Seals C Humans Rare – Mild Pigs D Cattle Mild Pigs

Electronmicrograph of influenza virus

• particles. (Courtesy of Linda M. Stannard,

University of Cape Town). http://virology-

• nline.com/viruses/Influenza.htm

Influenza virus structure

A transmission electron micrograph of MDCK cells infected with influenza A/Netherlands/602/2009 (H1N1) virus is shown at a magnification of ×40,000. (Seladi-Schulman et al. Journal of Virology Nov 2013, 87 (24) 13343-13353; DOI: 10.1128/JVI.02004-13 )

Influenza A virus proteins

Core Proteins Accessory Proteins HA PB1-F2 NA PB1-N40 M2 PA-X M PA-N155 PB1 PA-N182 PB2 M3 PA M42 NS1 NS3 NEP NEG8 NP PB2-S1

Birds are natural hosts for influenza viruses

Haemagglutinin Neuraminidase

H16 H17 H18 N10 N11

Influenza A virus host range

H17N10 H18N11

Bat

Swayne, D.E. Epidemiology if Avian Influenza in Agricultural and Other Man-Made Systems. In: Avian Influenza. Wylie-Blackwell (www.blackwellpublishing.com). 2008

Human Infection

Symptoms

• Fever & Chills
• Lethargy
• Aches – headache & muscular
• Coughing & Sneezing
• General discomfort
• Conjunctivitis
• Pneumonia
• Death

H1N1 and H3N2 co-circulate in humans.

1918 ‘Spanish flu’ H1N1 1957 ‘Asian flu’ H2N2 1968 ‘Hong Kong flu’ H3N2 1977 ‘Russian flu’ H1N1 1997 H5N1 2003 H7N7 2006 H7N3 2009 ‘Pandemic H1N1 2009’ H1N1

= pandemic

1918 – Spanish flu pandemic

The influenza pandemic of 1918 killed 50 million people. Case fatality rate of 2%.

2009 - Swine flu pandemic

The influenza pandemic of 2009 killed 250,000 people. Case fatality rate of 0.03%.

M2 inhibitors

• Amantidine & Rimantadine

No use as most viruses resistant. Neuramidase inhibitors

• Oseltamivir (Tamiflu)
• Zanimivir (Relenza)

Increasing resistance being

• bserved.

Inhibitors of RNA-dependent RNA polymerase

• Favipiravir; Pimodivir;

Baloxavir acid

Treatment

UK Annual influenza vaccine Split virion inactivated vaccine 2 Influenza A strains and 1 Influenza B strain. Grown in hens eggs Live attenuated vaccines Intra-nasal administration Routine in the USA for years 2013 first introduction in the UK for children 2+ (Fluenz). Grown in hens eggs

Vaccines

Influenza virus entry is blocked by antibodies

Error prone replication leads to mutation accumulation.

x x x

Antigenic Drift

• Slow accumulation of mutations
• Can alter the epitopes which Abs

recognise.

• Immune evasion results.

Human impact from human virus infection

Report from Norway published in 2012 suggests that influenza virus sick leave rate is around 1950 per 100,000 with around 10,300 days of work lost annually. ECDC 10th Oct 2012. USA Centre for disease control reported in Feb 2018 that influenza causes US employees to miss approximately 17 million workdays which is estimated at $7 billion a year in sick days and lost productivity. Research by Longevity Centre UK (ILCUK) found that influenza vaccination prevents up to 626,000 infections per year in England and therefore approximately 6,000 premature deaths.

Avian influenza in birds

Natural avian influenza cycle Aquatic birds

• inc. shorebirds

Domesticated poultry Farm animals

Avian Disease

Wild aquatic bird symptoms

• No outward disease symptoms
• Sudden death

Poultry symptoms

• Coughing/ sneezing
• Decreased egg production
• Soft shells and misshapen eggs
• Nasal discharge
• Swelling of eyelids, head, comb & wattle
• Cyanosis
• Diarrhoea
• Lethargy
• Fever
• Lack of coordination (neurological signs)
• Sudden death without warning

Prevalence of avian influenza in domesticated birds

H9N2

H5Nx outbreaks in Europe 2017-2018

Wild bird migration brought the H5Nx virus to Europe from Asia.

• During October 2016 and August 2017 29 European

countries experienced poultry outbreaks.

• 1.6 million birds culled in Europe over the 2016/2017

winter because of H5N8 outbreaks.

• In winter 2016/2017 mandatory to keep poultry inside

resulting in free-range status of some eggs and chicken being affected.

Impact of H5Nx in Europe

Chickens are one of the major livestock species used for food

Economic Impact

• H5N1 caused >$20 billion in economic losses since 2003
• H7N9 resulted in $6.5 billion loss for china in 2013
• LPAI losses often incalculable

Control mechanisms;

• Stamping out – culls and quarantine
• Can only take place in non-endemic countries
• Leave livestock susceptible to future incursions
• Vaccination in endemic countries
• Virus variability means a limited to what protection is afforded
• Cost of vaccination
• How long it takes for immunity to develop, average meat birds have a life

span of 6 to 8 weeks.

• Differentiation between infected and vaccinated animals (DIVA) hard

meaning certain trading routes cut off.

How do we deal with outbreaks of avian influenza virus?

Making better vaccines – viral vectors

Vector HVT – Herpes Virus of Turkeys DEV – Duck Enteritis Virus

Making better vaccines – protecting against multiple strains or pathogens

Zoonotic risk from avian influenza virus

HPAI LPAI Wild Aquatic Birds Domestic Poultry Humans Natural Reservoir

Virus Number of human cases Number of human deaths Case fatality rate H5N1 860 454 52.8% H7N9 1625 623 38.3% H6N1 1 0% H9N2 42 0% H10N8 1 0% H7N7 85 1 1.1% H5N6 19 6 31.5% H7N3 2 0% H7N4 1 0%

Human cases of avian influenza infection since 2003.

No human to human transmission of avian influenza viruses

What characteristics do Influenza viruses require to replicate and transmit

efficiently in the human population?

Receptors

Attachment – HA binds sialic acid receptors.

Sialic acid

Linkage of sialic acid to the sugar chain

Sialic Acid-(a-2,3)-Lactose AcHN O O H O O H OH COOH Protein O O O H OH OH OH O OH OH O H Sialic Acid-(a-2,6)-Lactose AcHN O O H O O H OH COOH Protein O O O H OH O H OH O O H OH O H

OH AcHN O H O O H OH O H COOH Sialic Acid

OH O O O H OH O H OH O O H OH OH Lactose

Avian Human

Cell α-2,3 2,3 Cell α-2,6 2,6

Avian and human influenza viruses bind to different types of sialic acid receptors. Why are the receptors different for human and avian influenza viruses?

Site of replication differs Human infection: Upper respiratory tract Avian infection: Intestinal tract - Colon

Sialic acid in chickens

Trebbien et al., Virology (2011) 8:434

Sialic acid in humans

Eriksson et al., Scientific reports (2018) 8:12215

Amino acid residues in the HA receptor binding site can alter the preference for sialic acid linkage.

Source: Stevens et al., Science, 2004

H3 subtype (1968) – Matrosovich et al. 2000 Amino acid 226 228 a2,3 a2,6 Avian Q G ++

• Human

L S + + H1 subtype (1918) – Tumpey et al . 2007 Amino acid 190 225 Avian E G ++

• Human

D D + +

Some H5N1 avian strains found in Egypt and some H7N9 isolates contain molecular signatures that predict binding to human receptors.

Stability

PH 5-6 Transmission mechanism is different between human and birds

• Humans - respiratory droplets
• Aquatic birds – Faecal/ oral.

PH 7.5-8.4

Influenza virus membrane fusion

Figure with thanks to Dr Thomas Peacock: Schematic for proposed mechanism of influenza A HA- membrane fusion. A) Binding of HA to SA on surface of host cell. B) as pH drops HA head domain moves away and fusion peptide is inserted into host membrane. C and D) The HA fusion peptide and transmembrane domain contract together pulling the host and viral membrane together forming the fusion pore.

Host Range Restriction of Influenza A virus – Stability

Human viruses more stable at low PH. Shelton et al 2013

mRNA

mRNA vRNA cRNA

Host Range Restriction of Influenza A virus – Replication

Temperature Sensitivity

• Polymerase complex is a enzymatic complex – Optimal temperature for activity.
• Human upper respiratory tract is ~ 33°C.
• Avian gut is ~ 41°C.

Interaction with host factors

• Polymerase complex recruits host factors in the nucleus.
• Differences between interaction partners in humans verus birds.

Changes in PB2 adapts avian influenza for growth in mammalian cells.

Avian virus Human virus Avian virus + PB2 (human) Avian virus + PB2 (human) E627K mutation in avian PB2 sufficient to allow growth in mammalian cells

Some H5N1 and H7N9 strains already contain the E627K mutation.

Gain of function studies

• scientists have generated an avian H5N1 so it

transmits in the lab in a model of human influenza infection….

Ferrets

• Best model for looking at human influenza infections apart from humans!
• Same viruses infect and transmit.
• Same symptoms are seen.

Ron Fouchier – Erasmus Centre in Rotterdam Yoshihiro Kawoaka – University of Wisconsin