Viruses

Obligate intracellular organisms

Bypass barriers - insects vectors, animal bites, trauma, ulcerations

Exploit mucosal M cells

Co-evolution with receptors drives narrow host specificity

Viremia needed to seed organs required for transmission - kidneys (urine), skin, salivary glands (secretions), respiratory (sputum) and digestive tracts (feces)

Immune cells make good targets…

Viruses

Flavors: ssRNA, dsRNA, DNA

Encoded within virally encoded capsid proteins

Enveloped or not

Classes: Lytic (cytopathic) (polio, flu) versus nonlytic (hepatitis B, LCMV)

Latency: special property of some lytic viruses

Micro-evolution: RNA viruses near mutational thresholds/many defective particles; DNA viruses can use transient gene amplification

Innate response to viruses - nucleic acid recognition

Pichlmair and Reis e Sousa, Immunity 27:370, 2007

cGAS

STING

Cytosolic dsRNA detectors - RNA helicases/RIG-I/MAVS (Mda5)

Li S et al, MAVS recruits multiple ubiquitin E3 ligases to activate antiviral signaling cascades. eLIFE 2013;2:e00785

Cytosolic DNA detectors – the cGAS/STING pathway

Diner EJ, RE Vance. Taking the STING out of cytosolic DNA sensing. Trends Immunol 2013

The cGAS/STING pathway is essential for the cytosolic DNA interferon response

Li X-D et al. 2013. Pivotal roles of cGAS-cGAMP signaling in antiviral defense and immune adjuvant effects. Science 341:1390-4.

Key players: interferonsIssacs and Lindemann, Proc R Soc London B Biol Sci 147:258-67, 1957

Type 1 interferons: interferon-/interferon- (14)

Type 2 interferon: interferon-

Hybrid interferons: interferon- (3) {IL-28A, IL-28B, IL-29}

Auto-enforcing loop: IRF-3 > IFN > Stat1/2 + IRF-9 > IRF7 > IFN’s

IFNs induce multiple genes with anti-viral activities

Nature 472:481, 2011

Why all the interferons and what do they do?

The ‘bleb’ hypothesis

M

DC

Immune system activation

Apoptosis - cell turnover, tissue development, etc.

Tolerance

Type 1 IFNs overcome inability to respond to apoptotic ‘blebs’

MpDC B

Clearance - ligands, opsonins, receptors

Apoptosis thresholds Nucleic acid sensors -TLRs 7,8,9/helicases

DC and B cell activation

Immune system activationCell activation inhibitors

Tolerance

Type 1 IFNs

X

X

Interferonopathies – exogenous and genetic

1. Exogenous – type 1 IFN treatment (MS, HCV, etc.)

5-30% of patients receiving type 1 IFNs get auto-antibodies (ANA, etc) and ~5% get autoimmune disease (anti-thyroid Ab’s, vitiligo, diabetes).

2. Disease ‘signatures’ of elevated type 1 IFNs

Systemic lupus erythematosisPre-activation state of latent tuberculosis

3. Genetic interferonopathies (high serum type 1 IFN, autoantibodies, cranial calcifications, mycobacterial susceptibility)

Aicardi-Goutieres (Trex1 mutation – DNA exonuclease)SpondyloenchondrodysplasiaISG15 deficiency (negative regulator of IFN signaling)SAVI (STING-associated vasculopathy with onset in infancy) - a gain-of-function STING mutation

Viruses attack common cellular defense pathways

Medina RA, A Garcia-Sastre, Influenza A viruses: new research developments. Nature Rev Microbiol 9:590, 2011.

Relevant Life Cycle Issues

1. An intestinal infection of wild waterfowl.

2. Crosses to mammals through close contact.

3. Multiple ‘crosses’ enhance capacity to establish

mutants and reassortment variants

adapted to mammalian hosts.

4. HA species specificity: sialic acid -2,3 galactose linkage (avian intestine; human LRT)

sialic acid -2,6 galactose linkage (human trachea)

both (pig trachea)

5. NA compatibility: human viruses gain -2,6 activity

stalk length (longer NA enhances activity in humans)

6.HA, NA Adaptations HA glycosylation; HA1/HA2 fusion domain (expanded basic amino acid repeat in highly pathogenic chicken H5/H7/H9 flu -HPAI- enhances spectrum of proteases that can activate HA fusion event; may explain pathogenicity of co-infection with bacteria)

Medina RA, A Garcia-Sastre, Influenza A viruses: new research developments. Nature Rev Microbiol 9:590, 2011.

Mutation and reassortment drive influenza A epidemics and pandemics

Influenza Pandemics

Year Common Name Subtype OriginDeaths

1889 - H2N2 ?Europe 6 million

1898 - H3N2 ?Europe 0.5 million

1918 Spanish Flu H1N1* ?Eurasia 40 million

1957 Asian Flu H2N2* China 4 million

1968^ Hong Kong Flu H3N2* China 2 million

1977^ Russian Flu H1N1+ China/Russia 1 million

2009^ Swine Flu H1N1* N. America >18,000

* Contained elements from avian viruses

+ Laboratory-derived from frozen stock (persons pre-’50s immune)

^Antigenic variants continue to co-circulate

Live chickens and ducks in same cages

Asian Live-Animal Markets -

The Great Zoonotic Mixer

A new pandemic influenza virus, H1N1/09

USA estimates: 22 million infected, 3900 deaths

Relevant Immunology

Innate immunity: Type 1 IFNs, TNF-, MxA, IFIT and IFITM proteins

HA antibodies: Neutralize infectivity, protective

NA antibodies: Restrict viral spread

Cytotoxic CD8 T cells: M2, PB2, HA, NP specificity common M2 specificity almost universal

CD8 TCR / chains

V17/V10.2

HLA-A2 (A*0201)

Influenza A Matrix Protein amino acids 58-66

Stewart-Jones et al. Nature Immunol 7:657, 2003

The Most Common Human TCR in the World

Why do they die?…

Human Immunodeficiency Virus

Worldwide: 35 million infected

29 million dead

14,000 new infections/day

2/3 infected persons in Africa

U.S.: ~1 million infected including 400,000 dead

(appeared 1983)

Worldwide Estimates of Numbers of HIV-Infected Persons

Origins of HIV(9 genes)

Chahroudi A, et al. Science 335:1188, 2012.

HIV Origins - Primate Lentiviruses

HIV-1

SIVcpz - West equatorial Africa = M group (chimps)

Cameroon = N group (chimps)

Gabon = O group (gorillas)

HIV-2

SIVsm (sooty mangabey)

Infection/Disease in areas of active bushmeat trade.

HIV Origins

SIVcpz - Asymptomatic infection of chimpanzees (up to 1% in areas of west Central Africa)

HIV-1: M group consists of 11 clades

Last common ancestor entered human population around 1890 (+ 30 yrs)

Spread and recombination among founder HIV clades

HIV is a primate lentivirus

Lentiviruses can infect nondividing cells

Replication driven from long terminal repeats

Structural genes - gag, pol, env

Regulatory genes - tat, rev

Accessory genes - vif, vpr, vpu, nef

HIV life-cycle

TRIM5, TREX1, SAMHD1

APOBEC Tetherin

Innate HIV Resistance by APOBEC3G

Arias JF et al., Frontiers Microbiol 3 (275):1-12, 2012.

HIV vif sequesters

APOBEC enzymes from

the budding virions

Martin-Serrano J, SJD Neil. Host factors involved in

retroviral budding and release. Nature Rev Microbiol 9:519,

2011.

HIV Pathogenesis

M

DC-SIGN

1. Entry at sites of M cells or trauma (STDs)

2. Transit to LN via C-type lectins* on dendritic cells

3. Peak CD4+ T cell infection days 4-7

4. Viremia peaks day 14

5. All lymphoid tissues infected by day 23

*DC-SIGN, MR, Langerin

HIV infection occurs predominantly at mucosa

Dendritic cells mediate transit of virus to regional lymph nodes via CLRs

Massive loss of mucosa-associated lymphocytes of the small intestine precedes systemic CD4 T cell loss

Proposed epithelial damage mediates sustained activation of mucosal T cells after HIV infection

Brenchley, Price & Douek, Nat Immunol 7:235, 2006

HIV Receptors

CD4

R5

X4

1o Infection: M-tropic, CCR5

Turnover 1010 virions/day

Progressive CD4 T cell destruction

CXCR4

T-tropic

Syncytium-forming

Natural History of Untreated HIV Infection

Natural HIV Resistance

1. CCR532 - slow progression if infected

20% W. European Caucasians heterozygous

1% homozygous

Successful bone marrow tx

2. HLA class I homozygosity - rapid progression

3. Rare HLA class I alleles - slow progression (suggests virus near mutational threshold)

Natural HIV Resistance

Scherer A, et al. PNAS 101:12266-70, 2004.

Science 334:89-94, 2011

Why no HIV vaccine?

1. Escape variants/altered peptide ligands - virus operates near mutational threshold

2. Neutralizing antibodies low-affinity, arise late (conformationally hidden, glycan shielding, mutational escape, evolutionary escape from ‘natural antibodies’, polyclonal B cell activation may impede)

3. Loss of CD4 help required for CD8, antibody responses

4. Immune exhaustion with PD-1 expression on CD4 and CD8 anti-HIV T cells

5. Prolonged time required to develop broadly neutralizing protective antibodies (bnAbs)

Kwong PD, JR Mascola. 2012. Human antibodies that neutralize HIV-1: Identification, structures, and B cell ontogenies. Immunity 37:412-25.