Virology Antigenic Variation Vaccine Development Microbial Pathogenicity Dec

Virology Antigenic Variation Vaccine Development Microbial Pathogenicity Dec. 4, 2012 Kevin Coombs kcoombs@cc. umanitoba. ca

Overview Host defense mechanisms General considerations of viral variation 3 Examples; Virus replication; Poliovirus Influenza Coronavirus Vaccine considerations When things can go wrong

Whitton & Oldstone (2001) in Fields Virology, p. 287

Kinetics of endogenous immune responses Biron & Sen (20017) Fields Virology, p. 332

Viral-induced Signaling pathways Biron & Sen (2007) In Fields Virology, p. 251

Summary of innate immune responses Biron & Sen (2007) In Fields Virology, p. 270

Class I Antigen Processing Yewdell & Hill (@002) Nature Immunol 3: 1019 Mc. Michael & Hanke (2002) Nature Rev. Immunol. 2: 283

Class II Antigen Processing Nature Reviews Immunology 1; 126 -134 (2001) CROSS-PRESENTATION IN VIRAL IMMUNITY AND SELF-TOLERANCE Youtube Class I: http: //www. youtube. com/watch? v=HYAmlm. Xf. Lu. Y&feature=related Class II: http: //www. youtube. com/watch? v=taq. Re. Kl. CEEg&feature=related

Humoral Immunity Pazner (2004) Nature Rev. Immunol. 4: 199

What is antigenic variation ? Y

Reoviridae Some viruses have segmented genomes: Orthomyxoviridae Allows “assortment” Ritchey et al (1976) J. Virol. 20: 307, in Krug (1989) The Influenza Viruses T 1 L T 2 J T 3 D

Segmented Genomes Allow Assortment X

Viruses with Segmented Genomes n … 2 Influenza (8 genes) = 256 possibilities Rotavirus (11 genes) = 2048 possibilities

RNA viruses with segmented genomes have capacity to generate altered genomes by both random mutation (where rates are high) and by assortment In Orthomyxoviridae random mutation leads to “Genetic drift” and assortment leads to “Genetic shift” Influenza pandemics generally* result from assortment of human and avian influenza viruses in a pig “mixing vessel” which results in new virus

SPECIFIC VIRUSES Basic Virology

The Baltimore Classification Scheme +- DNA Class VII ex. Hepatitis B virus +/- DNA + RNA +- DNA Class VI ex. HIV Rous sarcoma virus - RNA m. RNA Class II ex. parvoviruses bacteriophage f. X-174 Class I ex. herpesviruses polyomaviruses adenoviruses bacteriophage T 4 + RNA Class V Class IV ex. rabies virus measles virus influenza virus Ebolaviruses ex. poliovirus West nile virus rubella virus TMV +- RNA Class III ex. reoviruses Revised from: Baltimore (1971) Bacteriol. Rev. 35: 235

m. RNA Protein synthesis Nucleus

Antigenicity Type-specific (Neutralizing) Group-specific Modified from Stewart et al (1991) Cell 67: 145

Virus – Host Interactions Nucleus

Virus – Host Interactions Nucleus

Virus – Host Interactions Lytic Infection Persistent Infection Latent Infection (Lysogeny) Transformation

Tyler & Nathanson (2001) In Fields Virology, p. 201

Pico rnaviridae Very small ~30 nm non-enveloped icosahedral particles 60 copies each of VP 1, VP 2, VP 3, VP 4 Genome ~ 7 -8 kb ss(+) RNA 5 genera: Enteroviruses [111 strains](poliovirus) Rhinoviruses [105](common cold) Hepatovirus [2](hepatitis A) Aphthovirus [8](Foot and mouth) Cardiovirus [7](Encephalomyocarditis) http: //virology-microbiology-b. blogspot. ca/2009/01/picornaviridae-and-orthomyxoviridae. html

Modified from Hollinger & Emerson (2007) In Fields Virology, p. 914

Overview of picornavirus life cycle Baltimore Class IV Cytoplasmic Polyprotein cleavage All proteins = amounts No glycosylation No splicing RNA replication through full-length (-) strand Racaniello (2001) In Fields Virology, p. 693

Translation and processing of picornavirus proteins Racaniello (2001) In Fields Virology, p. 691

Translation and processing of picornavirus proteins P 1 2 A P 1 P 2 3 C 3 CD L Modified from: Racaniello (2001) In Fields Virology, p. 691

Genes and cleavage sites in various picornaviruses Rowlands (2001) Encyclop. Life Sci. - Picornaviruses

Orthomyxoviridae http: //www. google. ca/imgres? q=big+picture+book+of +viruses&um=1&hl=en&tbo=d&biw=1237&bih=557&t bm=isch&tbnid=RRu. Hdh. Pz. Vl 2 Gw. M: &imgrefurl=http: / /bakerinstitute. vet. cornell. edu/publicinfo/view. php%3 F id%3 D 347&docid=fme 5 LMu. PEHkdv. M&imgurl=http: // bakerinstitute. vet. cornell. edu/contentimages/2006121 1_105014046626. jpg&w=200&h=177&ei=umm 1 UIW HL 6 ftyg. GPh. YCICQ&zoom=1&iact=hc&vpx=379&vpy =174&dur=3303&hovh=141&hovw=160&tx=81&ty=81 &sig=112302969421377156868&page=1&tbnh=134& tbnw=152&start=0&ndsp=23&ved=1 t: 429, r: 2, s: 0, i: 88 Current genera: Influenza A Influenza B Influenza C Thogotovirus Isavirus ~100 nm virion Pleomorphic Segmented Genome (7 -8 segments) ss(-) RNA Enveloped

History and Impact • Epidemics documented since 1173 AD • 1918 Pandemic – “Spanish Flu” (HINI) Influenza and Pneumonia Mortality Rates - Killed 20 – 100 Million • 1957 “ Asian Influenza” ( H 2 N 2) • 1968 “ Hong Kong Flu” (H 3 N 2) • 2004 - ( H 5 N 1) – 272 cases so far “Avian Flu” / 166 deaths (WHO, Feb 6) • 2009 “Swine origin” H 1 N 1; WHO reported 1225 deaths as of Aug 2010; CDC re-estimates suggest up to 0. 4 M • Yearly Epidemics lead to approx. 2000 deaths in Canada, ~ 1 M deaths globally Figure 3. U- and W- shaped combined influenza and pneumonia mortality rates, by age at death, per 100, 000 persons in each age group (United States, 1911 to 1918). Influenza- and pneumonia-specific death rates are plotted for the interpandemic years (1911 to 1917, dashed line) and for the pandemic year (1918, solid line). Reprinted from Grove RD, Hetzel AM. Vital Statistics Rates in the United States: 1940 -60. Washington: U. S. Government Printing Office, 1968, and Linder FE, Grove RD. Vital Statistics Rates in the United States: 1900 -1940. Washington: U. S. Government Printing Office, 1943.

• For Both Flu types - the virus came directly from birds - young and healthy make up most fatalities - The human immune system creates “cytokine storm, ” filling the lungs with fluid newfluwiki 2. com/

• Unlike H 5 N 1 and 1918: - p. H 1 N 1 is a quadruple reassortant; not directly from birds • Like 1918 and H 5 N 1: - young and healthy make up most fatalities - The human immune system creates “cytokine storm, ” filling the lungs with fluid • The 1918 flu had a Case Fatality Ratio of 2. 5% • H 5 N 1 has a Case Fatality Ratio of 60% • p. H 1 N 1 had a Case Fatality Ratio of ~ 1% newfluwiki 2. com/

Wright, Neumann & Kawaoka (2007) In Fields Virology, Supplemental

B A Gene Segment # Protein Size (nt) Name MW (k. D) Copy # per virion Function(s) 1 2 3 2341 2233 PB 2 PB 1 PA 87 96 85 30 -60 4 1778 HA 63 500 5 1565 NP 56 1000 6 1413 NA 69 100 7 1027 M 1 27 3000 Matrix, interacts with v. RNPs, nuclear export, budding M 2 14 20 -60 Ion channel, assembly NS 1 26 NA NS 2 14 130 -200 8 890 + + RNA polymerase; cap recognition RNA polymerase; elongation RNA polymerase, protease Hemaglutinin, receptor binding, major antigen, fusion activity Noda et al. , (2006) Nature 439: 490 RNA binding & nucelar import Neuraminidase activity, surface glucoprotein Multi-functional; IFN antagonist Nuclear export of v. RNPs Nomenclature: A/PR/8/34 (H 1 N 1) Type Subtype Isolate # Country of Origin Puerto Rico Year of Isolation Figure 1. Influenza A/PR/8/34 genetic and structural organization. A. Gene – protein coding assignments & characteristics. B. Virus structure; Top, electron micrograph; Bottom, Diagrammatic cartoon of virion, with proteins designated as in A, middle column.

Phylogeny of Influenza A H and N Genes Palese & Shaw (2007) In Fields Virology, p. 1648 A new “H 17 N 10” virus described from bats (Tong et al (2012) PNAS 109: 4269)

Wright, Neumann & Kawaoka (2007) In Fields Virology, Supplemental

Wright & Webster (2001) In Fields Virology, p. 1542

1 Amantadine 4 2 3 5 AA 6 7 10 a AA m. RNA 8 v. RNA 11 m. RNA Leptomycin B c. RNA NP PB 2 M 1 PB 1 9 a 12 NS 1 PA NS 2 13 HA NA M 2 15 9 b Oseltamivir® 10 b 14

Orthomyxoviruses generate 2 distinct (+)RNA; 1 for message that Cap snatches host 5’ end to serve as primer and has 3’ end truncated (loss of packaging signal); plus 1 for template to faithfully transcribe progeny Lamb & Krug (2001) In Fields Virology, p. 1507

Influenza Variation: From: Lamb & Krug (2001) In Fields Virology, Supplemental

Influenza virus transmission/assortment From: Wright & Webster (2001) In Fields Virology, Supplemental

• The recurring nature of influenza is due to its ability to vary surface antigen expression Antigenic Drift: • Due to subtle changes of the viral genome • Changes antigenic character of H and N • Responsible for epidemics Antigenic Shift: • Due to rearrangement of viral gene segments when two different influenza viruses infect the same cell • Produces major changes in the antigenic nature • Responsible for epidemics and pandemics Ritchey et al (1976) J. Virol. 20: 307, in Krug (1989) The Influenza Viruses

Adenoviridae Orthomyxoviridae Coronaviridae Dr. Linda Stannard Dept. Med. Micro. University of Cape Town http: //web. uct. ac. za/depts/mmi/stannard/emimages. html

Anther prototypic Class IV ss(+) RNA virus (ex. Coronaviridae) www. microbiologybytes. com Different Coronavirus transcripts are produced by differentially transcribed messages; The genome is copied into a fulllength (-) copy, from which various sub-genomic (+) are transcribed www. microbiologybytes. com

Sites of maturation also influence antigenicity & presentation Hunter (2001) In Fields Virology, p. 184

Vaccine Development Considerations • • Which agents should be targeted ? Who should be vaccinated ? What constitutes a “good” vaccine ? Live vs Dead

Vaccines are available for all of the following vaccine-preventable diseases (unless otherwise noted): Vaccines & Preventable Diseases: List of Vaccine-Preventable Diseases The following links will lead you to the main page that describes both the • Monkeypox disease and the vaccine(s). There is NO monkeypox vaccine. The • Anthrax • Cervical Cancer (Human Papillomavirus) • Diphtheria • Hepatitis A • Hepatitis B • Haemophilus influenzae type b (Hib) • Human Papillomavirus (HPV) • Influenza (Flu) • Japanese encephalitis (JE) • Lyme disease vaccine no longer available in the United States. • Measles • Meningococcal smallpox vaccine is used for this disease. • Mumps • Pertussis • Pneumococcal • Polio • Rabies • Rotavirus • Rubella • Shingles (Herpes Zoster) • Smallpox • Tetanus • Typhoid • Tuberculosis (TB) • Varicella (Chickenpox) • Yellow Fever http: //www. cdc. gov/vaccines/vpd-vac/vpd-list. htm

Genetic Relatedness Between Vaccinia Virus and Variola major Brunham & Coombs (1998) CJIDMM

Ogra & Karzon (1971) Prog. Med. Virol. 13: 156 Pallansch & Roos (2001) In Fields Virology, p. 764

Polio Eradication Program (WHO) Year 1988 1997 2003 WHO, 2004

Reliefweb. int

Are all Antibody Responses “Good” ? Antibody-mediated enhancement of Dengue leads to worse disease if Ab mismatch Whitehead et al (2007) Nat. Rev. Microbiol. 5: 518

from: Ponnuraj et al. , J. Gen. Virol. (2001) 82: 2663 -74