Orthomyxovirus-2023v2.pptx

Orthomyxoviridae Influenza Debra Bramblett, PhD Burrell College of Osteopathic Medicine 2023 The 3 days after Thanksgiving, Earl White presents to the Virtual BCOM family clinic with a major complaint of respiratory illness and difficulty breathing. He said he was feeling fine on Thanksgiving when his grandchildren came to visit but he noticed that little Jamie was “coughing up a storm” and fell asleep on the couch. The next day he had a sudden on-set of a Considering his past medical history sore and his clinical high fever (103֯ F), chills, myalgias, throat and a cough. presentation what is most likely wrong with Mr. Earl? What places him at greater risk? testing is performed on a Rapid influenza diagnostic nasopharyngeal specimen and is found to be positive for influenza A (H3N2) which had been circulating in the community that year. On the third day, Mr. Earl went to the hospital because his sputum appeared bloody and he had chest pain. Chest radiographs were notable for extensive bilateral infiltrates with focal areas of consolidation. Indicating what? Mr. Earl was hospitalized and treated with ceftriaxone but his condition quickly worsened. Blood and sputum cultures yielded Gram positive cocci. The cultures demonstrated beta-hemolysis. PCR analysis confirmed the presence of the Mec gene in the isolated pathogen. What bacterium is most likely causing his pneumonia and what antibiotic should be used now? Objectives:  Describe and classify Influenza virus based on genome composition, virion structure, viral proteins and antigens, envelope, modes of replication, receptor, disease, and mode of transmission and compare this to Rhinovirus  Compare and contrast the pathology of Rhinovirus and Influenza viruses in terms of replication and the preferred region of entry in the respiratory tract, how they evade the interferon host defenses and differences in the adaptive immune response.  Differentiate between antigenic shift and antigenic drift and explain how these two mechanisms of genetic variation can lead to epidemics and pandemics.  Describe the mechanism of action of antiviral drugs amantadine and rimantadine and how they inhibit influenza A replication.  Describe the mechanisms of action of the antiviral drug zanamivir and how it inhibits influenza A and B. Spanish Flu Pandemic in 1918 The influenza pandemic that swept the world in 1918 was the deadliest single event in recorded human history, killing an estimate 40-50 million people, more than the WWI itself. In the US, 675,000 died. The pandemic lasted two years. A,B Public warning posters From Fenner and Whites’s Medical Virology 5e Figure C. Mass graves in Philadelphia 25.6 Globally, as of November 8, 2023, there have been 771,820,937 confirmed cases of COVID-19, including 6,978,175 deaths, reported to WHO. In United States of America, from January 3 2020 to, November 8, 2023, there have been 103,436,829 confirmed cases of COVID-19 with 1,138,309 deaths, reported to WHO. OMT during influenza epidemics 1918 Spanish Flu: the most outstanding example of the efficacy of OMT on record in the Unitedrelated States. Original estimates placed fatalities at 21 million, 1% of the world’s population at that time. In the United States, more than 28% of the population succumbed to the disease overall. In US military hospitals, the mortality rate averaged 36%, while the mortality rate in US medical hospitals fell between 30% and 40%, with the exception of a rate of 68% in 2445 osteopaths responding in treating 110,122 medical hospitals in New York City. patients with influenza, with a resulting mortality of 0.25%. They used lymphatic pump techniques and also taught these techniques to laymen. JAOA, Vol 104 , No 10; October 2004 Slide provided by Dr. Gabor Szalai The Recurrence of Influenza Pandemics • In the United States, influenza results in approximately 200,000 hospitalizations and 36,000 deaths in a typical endemic season • The worst pandemic on record, in 1918, killed approximately 50 million people worldwide. • The last influenza pandemic in 2009 was associated with 151,700 to 575,400 deaths worldwide 29 10 11 9 20 We are due! Pandemic influenza occurs every 10-15 years and is characterized by the introduction of a new influenza A virus strain that is antigenically very different from previously circulating strains; the lack of pre-existing immunity in humans is often associated with the severity of the infection and an increase in mortality Clinical presentation of Influenza: “It is not the same as a cold!” • Incubation can be very short: 1 day to 4 days • Symptoms of the flu : • Prodrome: malaise and headache lasting a few hours and followed by…. • Rapid and intense onset of high fever, chills, severe myalgia, loss of appetite, weakness and fatigue, sore- throat, and a non-productive cough • Respiratory symptoms progress to lower respiratory tract. • In most cases, pneumonia is not clinically prominent This virus does not • The fever lasts 3 to 8 days and recovery is usually within 7 to 10 days surrender to the innate immune • Fatigue may linger for weeks. system quickly! • Complications can occur: Bacterial pneumonia, Myositis, Reye syndrome, Transverse myelitis • People with chronic pulmonary or cardiac diseases or diabetes mellitus are at high risk of complications • severe complications from influenza A viruses, which may include hemorrhagic bronchitis, pneumonia (primary viral or secondary bacterial), and death. • Hemorrhagic bronchitis and pneumonia can develop within hours. • Fulminant fatal influenza viral pneumonia occasionally occurs; dyspnea, cyanosis, hemoptysis, pulmonary edema, and death may proceed in as little as 48 hours after the onset of symptoms. Pathogenesis of Influenza Replicates in the epithelial cells through the respiratory tree. The takeover of infected cells by influenza is so devastating that these cells die as newly made viruses are released.-cytolytic Tracheobronchial changes Multifocal destruction and desquamation of the pseudostratified columnar epithelium of the trachea and bronchi. Edema and congestion of the submucosa Hemorrhagic trachealis and bronchitis can occur Ciliated pseudostratified epithelium of trachea and bronchi Ciliary beat frequency is decreased, and ciliary motion become uncoordinated Shrinkage and vacuolization followed by desquamation of these cells into the luminal space Degeneration of epithelial cells in the tracheal and bronchial mucus glands Combined with the release of fibrinous materials and the secretion of mucins, small airways become obstructed leading to dead space, decreased oxygen and carbon dioxide diffusion capacities and lung dysfunction. Some neutrophil infiltration but not massive without bacterial infection The alveolar epithelial cell lining is as much a target of influenza infection as the epithelial covering of the bronchi and bronchioles. – Viral pneumonia ensues Davis, J.D., Wypych, T.P. Cellular and functional heterogeneity of the airway epithelium. Mucosal Immunol 14, 978–990 (2021). Influenza bacterial co-infection With a lack of ciliated epithelium, swallowed/ aspirated oral and nasal bacteria (e.g., Staphylococcus aureus) cannot be expelled and may cause pneumonia. Viral infection promotes bacterial adhesion to the epithelial cells. Viral infection Increases receptor availability for bacterial adherance Exposing sites for bacterial attachment Fibronectin binding protein A of S. aureus as well as factors capable of binding to EMC, fibrin, fibrinogen, and collagen by other bacterial receptors (review Staphylococci in MSKI) Bacterial co-infections In 1918, the “flu” killed approximately 50 million people worldwide. Clinical case an autopsy series suggests that more than 95% of all severe illnesses and deaths were complicated by bacterial pathogens, most commonly by S. pneumoniae. S.aureus, Haemophilus influenza and S. pyogenes were all identified as the predominant pathogens in various individual studies suggesting regional variation. NOW, S. aureus is the emerging cause of fulminant pneumonia in association with influenza H. influenza less prominent because of the H. influenza type B conjugate vaccine in 1985. Prominence of S. aureus in the 2009 H1N1 pandemic was likely due to emergence of certain clonotypes such as the CA-MRSA which has Panton Valentine leukotoxin ( PVL) coupled with increased penetrance of pneumococcal vaccination. Influenza A/B Genome composition and structure of the influenza virion • The Virion is enveloped (pleomorphic) surrounding 8 helical nucleocapsids. • It often appears spherical ranging from 80 to 120 nm in diameter • The envelope contains two glycoproteins: hemagglutinin (HA) and Neuraminidase (NA) and one additional protein the M2 protein in the membrane • The envelope is lined with the matrix protein (M1) • The genome is ss(-)RNA with 8 helical nucleocapsid segments • Each ss (-)RNA segment is associated with nucleoproteins and the transcriptase Describe and classify Influenza virus based on genome virion structure, viral proteins and antigens, components (PB1, PB2,composition, PA) disease, and mode of transmission and compare this to Rhinovirus envelope, modes of replication, receptor, Influenza Virus Genome Components of RNA polymerase All the proteins are encoded on separate segments except the Nonstructural proteins: NS1 and NS2 and the M1 and M2 proteins Fields Virology fifth edition, Vol II Section II Chapter 47 Eds. Knipe and Griffin, Lippincot Williams & Wilikins, 530 Walnut Street, Philadelphia, PA 19106 USA https://doi.org/10.1038/ s41572-018-0002-y Influenza proteins and their functions • HA: Spikes on cell surface with hemagglutinin activity. It is responsible for attachment to the host cell binding via sialic acids on cell surface • NA: Neuraminidase also on viral surface. Assists release from the host cell by clipping sialic acid. NA is a target for two antiviral drugs, zanamivir (Relenza) and oseltamivir (Tamiflu) • M1: Matrix protein, links with NP to assist budding • M2: Matrix protein, serves as a proton pump, acidifying the viral envelope context breaking the NP and M1 linkage to release the RNA into the cytosol • The M1, M2, and NP proteins are type specific and are therefore used to differentiate influenza A from B or C viruses • NP: Nucleoprotein • PB1, PB2, PA, Polymerase components • NS1 nonstructural protein- inhibits cellular messenger RNA translation Hemaglutinin (HA) has several functions • HA forms a spike-shaped trimer; each unit is activated by a protease and is cleaved into two subunits held together by a disulfide bond. • The protease is a serine protease expressed by Club cells secreted into the mucus 1. Serves as the viral attachment protein binding to sialic acid on epithelial cells 2. Promotes fusion of the viral envelope to the cell membrane of the endosome at acidic pH 3. Hemagglutinates (binds and aggregates) human red blood cells (as well as chicken and guinea pig) 4. Elicits the protective neutralizing antibody response 5. undergoes minor (drift) and major (shift) changes in receptor specificity and antigenicity Influenza Virus Replication Viral RNA polymerase carried in with RNP Sialic acid M2 Stage Influenza (-RNA) 1. Binding HA binds sialic acid Endocytosis Fusion of membranes via HA 2. Uncoating Acidification by M2 in the viral envelop contents breaks NP and M1 linkage and promotes fusion with endosome 3.Transcri ption (-) RNA to (+ ) RNA nucleus “Cap – Stealing” 4. Translatio n 8 (+) RNAs exit nucleus to be translated in cytoplasm or rER One RNA one protein HA Acidification Cap Stealing 5. Genome 2nd Round of Transcription in the Replicatio nucleus(+) RNA to (-)RNA n 6. Release Assembly at the membrane Stage Comparison of Rhinovirus and influenza replication Influenza (-RNA) Rhinovirus (+ RNA) Binding HA binds sialic acid Endocytosis Fusion of membranes Binding to ICAM or LDL Capsid conformation change VP1 Uncoating Acidification of the viral envelop contents breaks NP and M1 linkage Transmission of RNA across the cell membrane and vesicle association Transcriptio n (-) RNA to (+ ) RNA nucleus “Cap – Stealing” Requires translation of viral RNA polymerase Translation 8 (+) RNAs exit nucleus to be translated in cytoplasm or rER One RNA one protein Immediately after un-coating to generate a poly-protein that must be cleaved into VP1, VP2, VP3, VP4, 2A, 3D Genome Replication 2nd Round of Transcription in the nucleus(+) RNA to (-)RNA (-)RNA to (+) RNA by viral polymerase Release from Cell Assembly at the membrane Buds from Surface Escape by NA cleavage of sialic acid Encapsidation -Provirion Virion formation Cell lysis Influenza Virus Replication Sialic acid M2 HA Viral RNA polymerase carried in with RNP X8 segments Acidification Cap Stealing Approximately one protein for each segment Escape by way of Neuraminidase Review Rhinovirus Replication Capsid Conformation Change Figure 24.4 Fields Virology fifth edition, Vol I Section II Chapter 24 Eds. Knipe and Griffin, Lippincot Williams & Wilikins, 530 Walnut Street, Philadelphia, PA 19106 USA ICAM or LDL receptor Cap-Stealing by PA, PB1 and PB2 • Polymerase synthesizes viral messenger RNAs using short capped primers derived from cellular transcripts. • PB2 binds to the 5’ cap of host pre-mRNAs • PA subunit has the endonuclease activity • Provides the virus with a ready-made cap. • Helps focus the protein synthesis machinery of the cell on the production of viral proteins This is different from Rhinovirus in that Rhinovirus doesn’t use a Cap and Rhinovirus uses Vpg to prime and the IRES is recognized by the ribosome. It blocks protein synthesis from Capped RNAs by proteolytically cleaving Drugs: Amantadine and Rimantadine • Amantadine and rimantadine only have activity against influenza A. • Used daily are 70-90% protective in the prevention of clinical illness • Begun 1-2 days after onset of illness systemic symptom are reduced by 1-2 days • Due to high rates of resistance these drugs are no longer recommended for prevention or treatment • MOA: • bind to and block the hydrogen ion (H+) channel formed by the viral M2 protein. • Without the influx of H+, the M1 matrix proteins do not dissociate from the nucleocapsid (uncoating), so movement of the nucleocapsid to the nucleus, transcription, and replication are prevented. • Can also inhibit the acid-mediated change in conformation in the hemagglutinin protein that promotes fusion of the viral envelope with cell membranes Describe the mechanism of action of antiviral drugs amantadine and rimantadine and how they inhibit Influenza virus faces an escape problem • The infected cell has receptors on its surface that contain sialic acid molecules to which the hemagglutinin protein of the virus can bind. • The exiting virus can be “captured” by the infected cell when the viral hemagglutinin molecules “re-bind” to the hemagglutinin receptor on the cell surface. • The Neuraminidase protein functions as a “razor” that enzymatically shave off sialic acid residue from the surface of an infected cell, releasing the virus. Antiviral Drugs Zanamivir (Relenza) and Oseltamivir (Tamiflu) NA Cleaves of sialic acid on glycoproteins on the cell receptor and on the virion HA. • Prevents clumping of the viruses • Facilitates the release of virus from infected cells Thus this makes NA a target for these two anti-virial drugs Zanamivir and Oseltamivir can inhibit influenza A and B by inhibiting the enzymatic activity of neuraminidase. If taken within the first 48 hours of infection will reduce the length of illness Can also be taken prophylactically as an alternative to vaccination. Describe the mechanisms of action of the antiviral drug zanamivir and how it inhibits Influenza replication movie “Flu” symptoms are associated with interferon and cytokine induction • Early in a viral infection the innate immune system responds first. Type I Interferons (INF-α and INF-β), which are anti-viral cytokines are produced by a variety of cells. • They are very important in resistance because they render neighboring cells resistant to viral infection. • They are the response to double stranded RNA intermediate of virus replication and other structures that bind to Toll-like receptors and PAMP receptors • During influenza replication there are stretches of double stranded RNA present during transcription (due to 5’ cap-stealing and RdRp) and this triggers high level interferon production by the infected cell to warn neighboring cells. • High levels of cytokines and interferon are responsible for the fever, severe myalgia, chills and headache associated with the “Flu” This is different from Rhinovirus in that Rhinovirus blocks secretion of interferon The antiviral response Type I interferons are induced by dsRNA, and other viral components The virally infected cell releases interferons leading to viral inhibition of cellular protein synthesis. Type 1 Interferon binds to a specific cell surface receptor on another cell inducing the “antiviral state” • 2’,5’ oligoadenylate synthetase- activates ribonuclease L which degrades viral mRNA • Protein kinase R (PKR)- inhibits protein synthesis by phosphorylation of eIF-2α blocking protein synthesis NK cells are activated by INF-α and INF-β and Il-12 to kill virally infected cells. IFN-α and INF-β also increase the expression of class I MHC antigens, enhancing the cell’s availability to present antigen and make the cell a better target for cytotoxic T cells. INF-γ (type II interferon) activates macrophage inducing more INF-α and INF-β production. INF-γ increases expression of class II MHC on macrophage to promote antigen Describe the presentation to cellular T-cells. response of interferon production as a result of In most cases, cells that have been “warned” by the interferon signal will shut down protein synthesis. Warned cells have elevated levels of PKR (RNAdependent protein kinase) PKR will be stimulated by the presence of ds viral RNA to phosphorylate eIF2blocking protein translation. The influenza virus protien NS1 blocks the interferon response in multiple ways. 1. It blocks INF production by interfering with IRF3 and it prevents interferon pre-mRNA processing. 2. NS-1 binds to PKR and blocks its activation by autophosphorylation. 3. It also has dsRNA binding activity as some feel it prevents the activation of PCR by masking dsRNA. Do you remember how Adenovirus interferes? Rhinovirus interferes with the production of interferon by disrupting the cellular transport system so much less interferon is secreted. http://www.nature.com/nri/journal/v2/n9/fig_tab/nri888_F2.html Interfering with Interferon What’s the difference between influenza AD? • Influenza A is unique in that it not only circulates in humans but also in domestic animals, pigs, horses, poultry and wild migratory birds(>100 species) • New antigenically diverse HA and NA genes can be exchanged between viral strains by reassortment after co-infection of the same host, sometimes leading to pandemic influenza virus strains. • Influenza B and influenza C are not divided into different subtypes and are restricted to humans with no know animal reservoirs. • Influenza C causes a mild disease • Influenza D infects primarily pigs and cows. • The 2009 pandemic came from a type A H1N1 reassortent previously circulating in pigs https://www.nature.com/articles/s12276-021-00603-0/figures/1 Shift and Drift: Segmented genomic structure fosters genetic diversity and antigenic changes Shift and Drift • HA and NA proteins elicit the neutralizing antibody response • HA and NA undergo minor (“drift”) and major (“shift”) changes in receptors and antigenicity. HA • Minor being point mutations • Major being large, involving an entire genomic segment • Shifts occur only with influenza A virus, not B NA • Different HAs are designated H1, H2…H16 • Different NAs are designated N1, N2… N9 • Antigenic drift (A & B) & Antigenic shift (type A only) allows the virus to avoid immunity and can result in pandemics. •Differentiate between antigenic shift and antigenic drift and explain how these two mechanisms of genetic variatio • Yearly vaccinations can lead to epidemics and pandemics. needed due to drift In 1968 there was coinfection between an avian influenza A virus H2Nx and the seasonal human influenza A H2N2. The hemagglutinin was derived from the avian virus as was the PB1. Vaccination • The inactivated subunit influenza vaccines are a mixture of extracts or purified HA and NA proteins from three or four different strains of virus. • Studies of healthy young adults have shown influenza vaccine to be 70% to 90% effective in preventing influenza A illness, with moderately lower efficacy rates in the elderly. • However, vaccines normally protect only for a matter of months while natural immunization by infection lasts much longer. • continuous viral antigenic drift of influenza A viruses make once effective vaccines ineffective after a few years' time. • Ideally, the vaccine incorporates antigens of the A and B influenza strains that will be prevalent in the community during the upcoming winter. • A live attenuated influenza vaccine (LAIV) is also available for administration as a nasal spray instead of a “flu shot.” The quadravalent vaccine consists of reassortant viruses that contain the HA and NA gene segments of the desired influenza strains within a master donor virus that is cold adapted for optimum growth at 25° C. Were do Avian and Swine flu pandemics come from? Antigenic shift! • Influenza A is zoonotic • Avian, Human and swine influenza A each have 8 independent genomic segments 1-8 • Coinfection of swine cells allows for re assortment of segments from different species-specific strains • This results in H1N1 influenza A capable of infecting immunologically naïve humans. • Influenza B and C do not have a non-human host so do not undergo shift. Changes in the annual influenza vaccine 2019-2020 Flu season The quadrivalent vaccine (egg-based ) was recommended by the FDA's Vaccines and Related Biological Products Advisory Committee (VRBPAC) A/Hawaii/70/2019 (H1N1) pdm09-like virus; A/HongKong/45/2019) (H3N2)-like virus; B/Washington/02/2019- like virus; (B/Yamagata lineage) B/Phuket/3073/2013-like virus (B/Yamagata lineage). For 2019-2020, trivalent (threecomponent) vaccines were recommended to contain: A/Brisbane/02/2018 (H1N1)pdm09-like virus (updated) A/Kansas/14/2017 (H3N2)-like virus (updated) B/Colorado/06/2017-like (Victoria lineage) virus. The quadravalent vaccine also contained: B/Phuket/3073/2013-like (Yamagata lineage) virus The cell or recombinant based influenza vaccine contains: A/Hawaii/70/2019 (H1N1) pdm09-like virus; A/HongKong/45/2019 (H3N2)-like virus; So last year and this year the vaccine was directed against an H1N1 virus and H3N2 but the B/Washington/02/2019- like virus (B/Victoria strains were different due to subtle changes caused by anti-genic drift. lineage); B/Phuket/3073/2013-like virus (B/Yamagata https://www.cdc.gov/flu/weekly/index.htm#ILIActivity lineage) Map Flu vaccines for the U.S. 2023-2024 season will contain the following: • Egg-based vaccines • an A/Victoria/4897/2022 (H1N1)pdm09-like virus; (Updated) • an A/Darwin/9/2021 (H3N2)-like virus; • a B/Austria/1359417/2021 (B/Victoria lineage)-like virus; and • a B/Phuket/3073/2013 (B/Yamagata lineage)-like virus. •Cell- or recombinant-based vaccines • an A/Wisconsin/67/2022 (H1N1)pdm09-like virus; (Updated) • an A/Darwin/6/2021 (H3N2)-like virus; • a B/Austria/1359417/2021 (B/Victoria lineage)-like virus; and • a B/Phuket/3073/2013 (B/Yamagata lineage)-like virus. These recommendations include one update compared to the 2022-2023 U.S. flu vaccine composition. The influenza A(H1N1)pdm09 vaccine virus component was updated for egg-based and cell- or recombinant-based flu vaccines. Quadrivalent flu vaccines protect against four different influenza viruses: one H1N1 virus, one H3N2 virus, one B/Victoria virus and one B/Yamagata virus. All current flu vaccines in the United States are quadrivalent vaccines. Trivalent flu vaccines are formulated to protect against three flu viruses (an A(H1N1) virus, an A(H3N2) virus, and a B/Victoria virus • Hybrid viruses are created by coinfection of a cell with different strains of influenza A virus, allowing the genomic segments to randomly associate into new virions. An exchange of the HA glycoproteins may generate a new virus that can infect an immunologically naïve human population Avian, Human and swine influenza A each with 8 genomic segments 1-8 Coinfection of swine allows for re assortment of segments from different species-specific strains Resulting in H1N1 influenza A capable of infecting immunologically naïve humans. Influenza B and C do not have a non human host so do not undergo shift. 2 3 1 8 41 5 7 6