Week 11 Natural History of Influenza & Pneumococcus

Influenza Virus

• Influenza (the flu) is a contagious respiratory disease caused by the orthomyxovirus influenza virus that leads to mild to severe illness, and sometimes death.

  • Directly affects 15% of the global population.

  • Causes 250,000 – 500,000 deaths (1000 deaths per year in Australia).

  • Costs estimated at 87.1 billion in the US.

  • The population at high risk of severe illness includes older people, young children, and immunocompromised individuals.

  • The 1918 influenza pandemic killed at least 40 million young people; the majority died from secondary bacterial infection (pneumonia).

  • Seasonal influenza cases increase in Australia winter with a predictable spike in reported cases around August each year; the size of spike and specific virus types found vary year to year.

  • Notable influenza viruses in humans in the 20th century included H1N1, H2N2, H3N2, H5N1, and H7N7; Highly pathogenic avian influenza.

Influenza - Classification

• Family: Orthomyxoviridae.

  • Includes several genera that affect different hosts.

• Genera: Influenza A virus, Influenza B virus, Influenza C virus.

  • Flu A and Flu B are common causes of acute respiratory illnesses.

  • Flu A is the principal cause of larger epidemics including worldwide pandemics.

• Genome: enveloped, multipartite (segmented – 8 ssRNAs), negative sense, single-stranded RNA (10-14kb), each segment encodes one or two proteins (HA) (NA).

  • The segmented nature of the genome allows for antigenic shift, leading to new viral strains.

Influenza – Structure

• Hemagglutinin (HA) and Neuraminidase (NA) are the major surface glycoproteins targeted by antibodies.

• Matrix (M1) protein forms a shell underneath the viral envelope, providing structural support.

• Nuclear export protein (formerly NS2) mediates binding to target cells and is involved in viral release from target cell.

• Proton selective viroporin (M2) maintains pH across viral envelope, and amantadine anti-viral drug block viral uncoating.

Influenza Virus Replication Cycle

• Viral entry: Binding of hemagglutinin (HA) to sialic acid (neuraminic acid sugars) on host cell, entry through endocytosis.

  • HA binds to sialic acid receptors on the surface of respiratory epithelial cells.

• Fusion: Fuses with endosomal membrane to release into cytoplasm.

  • Low pH in the endosome triggers a conformational change in HA, leading to fusion.

• Transcription / Replication: Transcription of viral proteins and replication of viral genome in nucleus.

  • Viral RNA polymerase complex (PA, PB1, PB2) carries out transcription and replication.

• Packaging / Assembly / Release: New virus assembled and released from host cells via cleavage of sialic acid by neuraminidase (NA).

  • NA cleaves sialic acid, preventing the newly formed virions from sticking to the host cell.

Influenza Pathogenesis and Clinical Features

• Transmitted from person to person in droplets released by sneezing and coughing; some inhaled virus enters lower respiratory tract.

  • Virus can spread rapidly in crowded environments, such as schools and nursing homes.

• Primary site of replication in the respiratory tract, although nasopharynx also involved.

• Liquefaction of mucus by NA may help to spread virus.

• The superficial mucosa suffers destruction and desquamation because of infection of bronchial epithelial cells.

• Non-productive cough, sore throat, nasal discharge – oedema and cellular inflammation.

• Systemic symptoms – fever, muscle aches, general feeling of illness caused by host immune mediators, rather than virus – interferon, ISGs, endogenous pyrogens (cytokine storm).

Risk Factors for Severe Influenza Infection

• Chronic respiratory diseases (e.g., asthma, COPD, bronchiectasis, lung surgery).

• Obesity.

• Pregnancy.

• Smoking.

• Diabetes mellitus.

• Chronic cardiovascular diseases.

• Renal diseases.

• Immunosuppression (such as blood disorders, malignancy).

• Delay in presentation to hospital (and hence delay in initiating antiviral therapy).

Influenza Virus Hosts

• Birds are natural hosts of influenza virus; typically have no symptoms.

  • Waterfowl, such as ducks and geese, are common reservoirs.

• Virus can transfer to humans and other species (e.g. pigs, horses, seals).

• Viral rearrangements (antigenic shift) occur between viruses in the same host.

  • Pigs can be infected with both avian and human influenza viruses, acting as mixing vessels for new strains.

Pandemic (H1N1) 2009 Influenza A “Swine Flu”: Origins

• Recombination of viral genome segments from multiple viruses occurs in single host.

• Simultaneous infection in pig host.

• Recombined virus caused severe symptom burden.

• PB2 - North American avian

• PB1 - Human H3N2

• PA - North American avian

• H1 - Classical swine

• NP - Classical swine

• N1 - Eurasian avian-like swine

• M - Eurasian avian-like swine

• NS - Classical swine

Influenza Complications

• Pulmonary:

  • Croup (young children).

  • Primary influenza pneumonia.

  • Secondary bacterial infection

  • Streptococcus pneumoniae

  • Staphlyococcus aureus

  • Hemophilus influenzae

• Non-Pulmonary:

  • Myositis (muscle inflammation).

  • Cardiac complications.

  • Encephalopathy.

  • Liver and CNS: Reye Syndrome.

  • Peripheral nervous system: Guillain- Barre syndrome.

Cytokine Storm

• Cytokines are signalling molecules that orchestrate inflammatory response and ramp up the immune responses to pathogens by a variety of mechanisms including the activation of cells of the immune system.

• Cytokines act on blood vessels leading to proteins, fluid and cellular elements of the blood to leave the circulation (exudation) and move into tissues to destroy pathogens.

• With reduction in pathogen numbers cytokine secretion subsides, and the large numbers of lymphocytes created through clonal selection also decline.

• In certain instances the immune response does not subside normally. Instead, there is uncontrolled inflammation within tissues and key organs. Certain types of infection carry a higher risk of cytokine storm: systemic infection and septic shock, SARS, bird flu (H5N1), Hanta virus infection, Ebola.

• Respiratory failure as a result of oedema in the lungs as a result of an excessive inflammatory response.

Race to Mobilise Innate Immunity

• Contain infection at mucosal point of entry.

  • The innate immune response includes natural killer cells, macrophages, and dendritic cells.

H5N1: Highly Pathogenic Avian Influenza Virus (HPAI)

• 1918 Pandemic: Likely an adapted avian H1N1 virus.

• Emergence of HPAI H5N1 in 2003.

• Striking characteristics:

  1. Young adults and children (previously well).

  2. High mortality – 60%-

  • True case fatality rate unknown (unclear how many infected).

  • 1% seropositive in Cambodian village.

• Endemic in birds in Asia: Direct exposure to source.

• Poor human-human transmission.

• \alpha-2,3 sialic acid galactose; other receptors?

  • H5N1 preferentially binds to \alpha-2,3 sialic acid receptors, which are more common in the lower respiratory tract of humans.

Controlling Influenza with Vaccination

• Vaccines

  • Seasonal quadrivalent vaccine protects against 2 influenza A and 2 influenza B strains.

  • Updated annually to keep pace with drift.

  • Based on circulating flu strains in environment and other countries.

  • Specific 2009 swine H1N1 virus pandemic vaccine.

  • Universal vaccine not available.

• Critical ‘subunit’ of the virus used as the antigen (e.g. surface protein) – Purified protein subunit purified from virus culture (eg Flu vaccine – hen eggs or cell culture) or recombinant DNA cloning

  • Subunit vaccines are safe and effective, but may require adjuvants to enhance the immune response.

• Direct administration will not induce a cell-mediated response (need to be formulated with adjuvant) – But subunit alone is not infectious.

Influenza Prevention and Treatment

• Prevention: Hand washing, facemask/respirator, nanomask, clean surfaces frequently, cook chicken and eggs properly, vaccination.

• Anti-viral Treatments:

  • Neuraminidase inhibitors - Oseltamivir (Tamiflu).

  • These drugs block the activity of neuraminidase, preventing the release of new virus particles from infected cells.

  • M2 inhibitors (adamantane derivatives) – amantadine (Symmetrel), rimantadine (Flumadine).

  • These drugs block the M2 protein, which is involved in viral uncoating.

  • Viral resistance to treatments has been noted.

Pneumococcal Pneumonia

• Caused by pneumococcus bacteria (Streptococcus pneumoniae).

  • Gram-positive, lancet-shaped bacterium.

• Most common cause of community acquired pneumonia requiring hospitalisation.

• Alveoli (air sacs of lungs) fill with fluid and pus, making breathing more difficult.

• Clinical Features:

  • Abrupt onset.

  • Fever.

  • Shaking chill.

  • Productive cough.

  • Pleuritic chest pain.

  • Difficulty breathing.

• Often fatal, if untreated.

• 1.6M deaths worldwide per year.

• Major cause of death and hospitalisation in Australia.

Mechanism of Pathogenesis

• Entry and colonisation of pneumococci into nasopharynx.

  • Colonisation can be asymptomatic.

• May cause infection of the middle ear, paranasal sinuses & respiratory tract by direct spread.

• Infection of meninges can also occur, by contiguity or through blood (leading cause of meningitis in children).

• If bacteria enters blood (bacteraemia) may also lead to disseminated infections in the heart, peritoneum or joints.

Streptococcus pneumoniae

• Streptococcus pneumoniae = Pneumococcus, formerly known as Diplococcus pneumoniae.

• Reclassified as S. pneumoniae because of its genetic relatedness to Streptococcus.

• Normal inhabitants of the upper respiratory tract in humans.

Pneumococci: Morphological Features

• Gram positive small (1\mum) elongated cocci, with one end broad & other end pointed, presenting a flame shaped or lanceolate appearance.

• Occur in pairs, with the broad ends opposing each other.

• Polysaccharide capsule encloses each pair.

• Non-motile & non-sporing.

Pneumococci: Virulence Factors

• Polysaccharide capsule (> 90 serotypes) – Provides resistance to phagocytosis and antibiotics.

  • Capsule type determines serotype.

• Pneumococci in intimate contact with lung cells show reduced capsular polysaccharide.

• Pneumolysin:

  • Pore-forming toxin.

  • Cholesterol-dependent cytolysin.

  • Interfere with cytokine synthesis and inflammatory response.

Pneumococci: Transmission

• Person-to-person infection mostly by coughing of tiny droplets.

• Some opportunistic pathogens can live in upper airway with no disease.

• May cause pneumonia if inhaled into lungs.

• Patients with underlying health issues or elderly are under greater risk of pneumonia; often healthy individuals do not develop pneumonia when exposed to pneumococcus.

Immune-Pathology of Invasive Pneumococcal Pneumonia

• Pneumococci enter lower airways.

• Disruption of epithelial barrier allows pathogen entry (primary influenza infection).

• Trigger innate immunity and inflammation.

• Neutrophil / macrophage activation and cytokine release.

• Activation of adaptive immune response.

• Activation of B cells produce protective secretory IgA.

• Invasion of S. pneumoniae into the bloodstream can lead to systemic disease.

Pneumococci: Treatment and Prevention

• Treatment: Antibiotics are the mainstay treatment.

  • Amoxicillin, cephalosporin - inhibit cell wall formation (some resistance exists).

  • Erythromycin, chloramphenicol - inhibit protein synthesis.

• Prevention: Pneumococcal vaccine.

Pneumococci: Vaccine

• 23-valent pneumococcal vaccine contains purified capsular polysaccharides derived from 23 different S. pneumoniae serotypes.

• Serotype coverage: 85-90% of serotypes responsible for all cases of invasive pneumococcal disease (IPD).

• Vaccine includes major serotypes that have developed antibiotic resistance (90%).

• Vaccine induces antibodies that enhance opsonisation, phagocytosis and bacterial killing.

Who Should get Vaccinated for Pneumococcal Infection

• Healthy elderly (over 65 years of age) particularly those living in institutions. Over 50 years of age for Indigenous population.

• Increased risk category: Patients with diabetes mellitus, chronic lung, cardiac or liver disease, Down Syndrome, alcoholism or tobacco smoking.

• High risk category: Patients with immuno-deficiencies particularly those with functional or anatomical asplenia, cerebrospinal fluid leaks, cochlear implants or intracranial shuts.

• Infants receive immunisation with a 13-valent vaccine.

• Children at high risk for disease (splenectomised children and sickle-cell disease) receive a booster of 23-valent vaccine.