Micro study guide by FN4Cq68t


									Viruses vs. Cellular organisms, comparatively:
    Simple organization
    DNA or RNA but not both
    Unable to reproduce outside of living cells, obligate intracellular parasites
    A lot smaller and more diverse shapes
           o Polio is tiny 27 nm, while Influenza is 85 nm.
           o Shape/capsid structure can be: filamentous, geometrical, regular cell shape,
    Cellular organisms:
           o Have DNA and lots of RNA (90% rRNA-huge role, 10% mRNA)
           o Cell division
           o Some are obligate intracellular orgs

Cultivation of virus requires inoculation of living host cell
    Studies limited until find suitable animals (ex. Influenza and mink)
           o Using Koch’s postulates to study microbes and how to treat
    Embryonated eggs- for growing vaccine strains, some viruses replicate better in diff
           o Chorioallantoic membrane inoculation (more superficial)
           o Allantoic cavity inoculation (deeper)
    Tissue (cell) cultures- now vaccines moving toward cultures
           o Monolayers of animal cells
                    Plaques – Put virus in area of petri dish and create localized area of
                       cellular destruction and lysis
    Cytopathic effects (CPEs)- even if don’t create plaques, might have microscopic effects,
       cells might grow in dense colonies instead of monolayer. Micro or macroscopic
       degenerative changes or abnormalities in host cells and tissues.

Structure and Classification of Viruses
     Delivery system = Structural components (allows survival & binding)
     Payload = Genome and enzymes (enzymes required for initial steps)
     Naked capsid virus (just a nucleocapsid)
     Enveloped virus (nucleocapsid + glycoproteins and MEMBRANE)
     Nucleocapsid components
           o Capsid
           o Capsomers (proteins)
           o Nucleic acids
     In helical nucleocapsid: have monomeric units of protein coating nucleic acids.
           o More linear type
     Icosaheral capsid shape
           o Regular polyhedron with 20 equilateral triangular faces
           o 12 pentamers/vertices
     Enveloped viruses have:
           o Glycoprotein spikes on very outside
           o Lipid bilayer membrane
      Classified by:
          o Type and structure of nucleic acid for viral genome (RNA or DNA), (+/-)
          o Presence or absence of envelope
          o Type of capsid symmetry
          o Replication strategy
      Positive sense- Can read directly from it like mRNA molecule
          o Replication: Will make negative sense to synthesize copies of positive sense
               strands for repackaging
      Negative/anti sense- Must have enzyme packaged with it to synthesize positive strand
          o Translate proteins from newly synthesized positive stand
          o Replication: Synthesize negative sense from positive strand

Virus Replication
    Adsorption of virus onto host’s cells
            Viral surface proteins and/or enzymes mediate attachment to host receptors
                    More picky tissue tropisms than bacteria because receptors more specific
                       to certain tissue types.
    Penetration and Uncoating
           1) Injection of nucleic acid, direct Ex. Naked virus, bacteriophage
           2) Fusion of envelope with host membrane  nucleocapsid delivery into cytoplasm
           3) Active endocytosis  Forms endosome around capsid  Fusion of two once
               inside releases nucleocapsid into cytoplasm (Clatherin based entry Ex. Semliki
               forest virus)
    Synthesis of viral proteins and nucleic acids
    Assembly of virions/virus capsids
            Capsid proteins encoded by late genes
            Assembly of naked viruses – empty procapsids formed then nucleic acid inserted
            Assemby of envelope viruses – same as naked viruses
            Site of morphogenesis varies
    Release (in order to infect more cells)
            Naked viruses – usually by lysis of host cell, damaging
            Envelope viruses – formation of envelope and release usually occur concurrently
                    Virus-encoded (glyco)proteins incorporated into host membrane, then
                       buds off around nucleocapsid
Route of Transmission
    Respiratory
           o Small droplet (Ex. Influenza, Measles, Smallpox, Varicella Zoster)
           o Large droplet (Ex. Adenovirus, Parainfluenzavirus, Parvovirus, Smallpox)
           o Direct contact w/ resp. secretions : (Ex. RSV, Rhinovirus)
    Gastrointestinal
           o Fecal-Oral (Ex. Enteric adenovirus, Hepatitis A, Norwalk, Polio, Enteroviruses,
    Contact with lesions (Ex. Herpes simplex, smallpox, varicella-zoster)
    Blood and body fluids (Ex. CMV, Epstein-Barr, Hep B, Hep C, HIV)
    Insect bites (Ex. Dengue, E & W Equine, encephalitis, West Nile, Yellow Fever)
   1. Parechovirus
   2. Hepatovirus
   3. Enteroviruses- Largest picornavirus group, 5% become viremic, live in GI, can survive
      acidic environments, Echoviruses (enteric cytopathic human orphan viruses – viruses w/o
      disease), replication in lymphoid tissue
          o Polio virus
                   3 antigen types for different capsids: PV1-3
                   Icosahedral
                   Attaches to CD155 poliovirus receptor (PVR) AND possibly an unknown
                      coreceptor because has very specific tissue tropism.
                   RNA alone can cause infection
                           Covalently attached 5’ VPg protein on RNA so will be transported
                              to nucleus for replication
                   Lytic virus, so persists after symptoms disappear weeks-months
                   Transmission is fecal-oral  ingestion  viral replication in oropharynx
                      and GI tract
                   Translation from 5’ end, with large non-coding region preceeding start
                      codon at internal ribosome entry site (IRES).
                   Symptoms: mild fever, headache, loss of appetite, vomiting, sore throat
                   Sometimes viremic, if so  brain & meninges
                           CNS disease
                                  o Flaccid paralysis (destruction of ant. horn in spinal cord)
                                  o Bulbar poliomyelitis (most severe form, respiratory muscle
                                      paralysis due to distruction of medulla oblongata, 25%
                   Factors increasing severity of infections:
                           physical exertion
                           trauma
                           tonsillectomy
                   Vaccine very successful
                           Salk- killed vaccine. “Hero” because first introduced, given to
                              children and immunocompromised now
                           Sabin- attenuated live strain. Better because can get small amount
                              of recombination and wild strains
          o Coxsackieviruses
                   Group A: Herpangina
                           Sudden fever
                           Vesicles, ulcers on tonsils, palate
                           A16: Skin  foot and mouth disease
                   Group B:
                           heart  myocarditis
                           respiratory tract  pleurodynia
                           eye mucous membrane  hemorrhagic conjunctivitis
                   Also can affect brain and spinal cord  aseptic meningitis
   4. Rhinoviruses
          ~100 serotypes
          Habitat is upper respiratory epithelium
          causes 50% cases of common cold
          binds to ICAM-1 or VLDL receptor on respiratory epitheliam cells
          acid sensitive and ≤33 degrees optimum for replication
          No tissue destruction or lysis upon leaving host cells
          Infection duration only a few days, complications include:
                o Sinusitis, otitis media
                o Worsening of asthma (50% of attacks)
          Poor prospects for vaccine bc too many variants
          TX:
                o Alpha-IFN nasal spray
                o Prevention for rest of family
       Enveloped, (+) RNA, helix nucleocapsid
       Largest viral RNA genome
       Brought into cell by absorption
       Causes 30% of common colds
            o SARS-CoV (Severe Acute Respiratory Syndrome)
                    Outbreak 2002-2003
                    Atypical pneumonia
                    Animalshumans
       Genome packed densly, very efficient
       Cytoplasmic replication
       2 phases of translation

       arthropod borne viruses, by insect vector
       multiplication in vector without producing disease
       humans are dead end host
       causes viremia of short duration & blood viral levels low (except dengue and yellow
       transported in used tires
       not much regionality to disease since travel so popular and easy.

       Enveloped, linear (+) RNA
   1. Arboviruses
          a. Alpha virus (Endocytosed, fusion and release of nucleocapsid into cytoplasm)
                  i. Eastern equine encephalitis by mosquito in Eastern US
                 ii. Western equine encephalitis by mosquito in Western US
   2. Rubivirus (Rubella- German Measles)
          a. 1 of 5 rash causing diseases in children
          b. Others: Measles, roseola, chickenpox, and fifth disease
   1. Enveloped, linear (+) RNA
   2. Arboviruses
          a. Flavivirus
             o St. Louis encephalitis by mosquito in North America
             o West Nile  encephalitis by mosquito (worldwide)
             o Dengue
                      Most prevalent disease cased by arbovirus
                      Doesn’t produce significant mortality, but bad symptoms
                      4 serotypes
                      When partial immunity exists (from prior infection), worse than naïve
                             Because immune enhancement, virus readily enters
                               macrophages & increases its viral load
                             Activates memory T cells creating hypersensitivity 
                               vasculature rupture  internal bleeding
                             More severe symptoms
                                  o DHS- dengue hemorrhagic shock
                                  o DSS- dengue shock syndrome
             o Yellow Fever
                      First human disease found to be caused by virus, army digging Panama
                      Mosquito (Aedes aegypti) vector
                      Monkey or Human  Human
                      Clinical manifestations:
                             Fever, chills, headach, backache, nausea, vomiting
                             Severe: Jaundice, lesions and hemorrhaging of infected organs
                      TX, prevention, control
                             Serological tests
                             Symptomatic/supportive therapy
                             Attenuated live vaccine & insect control

Disease progression for Togavirus and Flavivirus:
    2-3 days: Mild or asymptomatic
    3-7 days: Mild systemic disease, fever, chills, ache
    Antibody block, unless not enough to defend and then severe, life threatening:
           o Encephalitis
           o Yellow fever hepatitis
           o Hemorrhagic fever

      Enveloped, linear (-) RNA, one segment, small
      Helical nucleocapsid inside pleomorphic envelope (variable shape)
      Replication: Viral RNA polymerase transcribes (-) into (+)RNAs, cytoplasmic
      Can induce syncytia formation
     1. Morbillivirus (Measles virus)
         Hemagglutinin membrane glycoprotein on envelope binds sialic acid on host
          cell surface glycoproteins
       Binds CD46 protein (on most cells)  some bind more making giant cluster
       F protein causes membranes to fuse together  viral entry
               Expression on infected cells causes cell-cell fusion  giant cells
       Respiratory tract entry  lymphatic spread  viremia  dissemination 
          rash  recovery (with life-long immunity) or rarely fatal
                 Skin involvement (epidermal inflame due to host response)
                 Humoral and cellular response modulate outcome, most recover
       Extremely contagious
       Symptoms: 3 C’s (Cough, coryza, conjunctivitis)
                 Coryza- inflamm of nasal mucous membranes giving rise to
                    congestion and loss of smell
                 Koplik spots in oral cavity – look like vesicles
                 Morbilliform appearance (rash=exanthema)
       Complications:
                 Pneumonia (giant cell pneumonitis)
                 Bacterial superinfections of middle ear and lung
                 Pneumococci, staphlycocie, and meningococci (life-threatening)
                 Subacute sclerosing panencephalitis
                       rare
                       progressive degeneration of CNS
       TX, prevention, control
                 Symptomatic/supportive therapy
                 Live, attenuated measles vaccine since 1993
                       MMR
                       Initial vaccine in 1960’s and rates dropped rapidly
                               a. Recent increased incidence ~1990
2. Rubulavirus (Mumps and parainfluenza)
       Very rare now due to vaccine
       Swelling, infection of parotid salivary glands
       Respiratory tract entry  local replication  viremia  systemic infection 
          1) Parotid gland eventually
          2) testes (orchitis), ovaries, periph. nerves, eye, inner ear, CNS (meningitis)
       Incubation 16-18 days
                 Fever, swelling, tenderness of salivary glands
       TX, prevention, control
                 Symptomatic/supportive therapy
                 Live attenuated vaccine (MMR)
3. Respirovirus (Respiratory syncytial virus, RSV)
       G Protein (NO hemagglutinin)
                F protein  syncytia
                Respiratory tract entry  spreads down along resp. mucosa (doesn’t spread
                        Necrosis of lung epithelial cells  increased mucous production
                        Infiltration of lymphocytes
               Most dangerous resp. infection in young children – hand contact spread
               Symptoms:
                        Acute onset of fever
                        Cough, rhinitis, nasal congestion
                        Often quickly  severe bronchiolitis (bronchiole obstruction that
                           can lead to respiratory failure) and pneumonia
                        Host response accounts for serious symptoms
               TX, prevention, control
                        Rapid immunologic tests
                        RSV-immune globulin injections
                        Isolation, protective clothing, hand washing
       4. Human metapneumovirus (Newly discovered common lower respiratory infection

Rhabdoviruses (Enveloped, non-variable bullet-shape, linear (-) RNA)
     1. Lyssavirus (Rabies)
             One segment of (-) RNA packaged tightly inside envelope
             Highly neurotropic
             Transmitted by:
                      Bites of or contamination of open wound by infected animal’s saliva
                           40% Raccoon
                           30% Skunk
                           14% Bat
                           Domestic animals: very rare
                           Vaccine-containing food drops in wild areas to decrease wild
                              animal infection, decrease our exposure risk
                      Aerosols in bat caves
             Progession of symptoms:
                      Incubation can be up to 12 months (depending on proximity of bite
                        to CNS)
                           Face bite – shorter incubation
                      Viral replication in muscle  peripheral nervous system  sensory
                        fibers to dorsal root ganglia where replicate again  ascend spinal
                      2-16 wks after exposure show symptoms
                           Pain or paresthesia at wound site
                           Anxiety, irritability,
                           Depression fatique, loss of appetite
                           Fever
                               Sensitivity to light and sound
                               Hydrophobia – swallowing muscle contractions (even at sight
                                of water)
                             Quick progress to paralysis
                        Negri bodies – masses of nucleocapsids in cytoplasm of brain tissue
                          (70-90% or infected cases)
                        Death (if not treated) from destruction of regions of brain that
                          regulate breathing
                 TX, prevention, control:
                        Numerous tests, rapid immunodiagnostic tests
                        Passive admin. of antibody (antiserum or human rabies immune
                          globulin, HRIG, collected from immunized persons)
                        Postexposure vaccination
                        Preexposure vaccination if high risk/exposure lifestyle/career

    Enveloped, segmented genome, (-) RNA, replication in nucleus
   1. Influenzavirus
   1. Types:
                  Virus A (8 segments)
                  Virus B (8 segments)
                  Virus C (7 segments)
   2. “Cap-snatching” – Steals 5’ end cap and part of beginning sequence from host mRNA to
      prime viral mRNA synthesis
   3. Process of packaging after replication is very disorganized, “random packaging” of the 8
      segments, more like 11 segments (over packaging occurs).
   4. Glycoprotein surface spikes (peplomers, which elicit immune response)
                  Hemagglutinin (HA) - trimer
                          For attachment to sialic acid on epithelial cell surface
                          Promotes viral-cellular membrane fusion
                          Binds & aggregates RBCs (agglutination assay can diagnose)
                          Elicits protective neutralizing antibody response
                  Neuraminidase (NA)
                          Release of virus from envelope
                          Cleaves sialic acid so virus can bind to new cells and host
                  Reason for H & N serotypes of virus, Ex. H1N1.
   5. Aerosol inoculation  replication in resp. tract  antibody response  desquamation of
      mucus-secreting and ciliated cells  influenza syndrome
                  Typical flu symptoms (fever, headache, muscle aches, malaise) due to
                     interferon induction
                  Less frequently  Secondary bacterial infection  pneumonia
                   primary viral pneumonia (Spanish influenza)
                  Rarely  CNS, muscle involvement
                  Symptoms appear in 2 days along with interferon induction, secondary
                     bacterial infection can occur in 7 days.
                           Pneumonia may result from bacterial, viral or immuno-
   6. TX, prevention, control
                 Rapid immunologic tests
                 Symptomatic therapy
                 RX:
                          Virus A – Amantidine or rimantidine
                          Virus A or B – Ribvirin
                 Killed virus vaccine
   7. New virions of influenza
                 If host is coinfected, host has mixed infection with both viruses in which
                    reassortment can occur (mixing and matching of segments to create new
                    viruses), and the new resulting virus can be transmitted to humans
   8. Novel types of surface epitopes form
                 By antigenic drift, human and domestic animal segments can mix.
                    Worried about wild flus (bird flu) mixing with ours.
                          Also, mutations or errors during replication can produce different
                            surface epitopes of hemagglutinin (figure shows 6 antigenic sites
                            that undergo drift)

Reoviruses (Respiratory enteric orphan viruses)
    Rotaviruses
          o Identified in 1973
           Naked/non-enveloped, but double capsid around double-stranded RNA (11
                 o Inner and outer capsids makes double protein coat around RNA
                 o Replication in cytoplasm, assembly in rER
                 o Lysis of cell upon release
           Diarrheal agent, although 50% of diarrhea cases still have unknown etiology
           Cause viral gastroenteritis
                 o Inflammation of stomach or intestines
                 o Infants and children
                          Leading cause of childhood death in developing countries
           Types:
                 o Group A – wintertime, major cause of diarrhea in children 6-24 mo. old
                 o Groups B & C – rare in United States
           Fecal-oral transmission
                 o Only 10 virus particles needed to cause infection, easily transmitted
                 o Found very concentrated, 10^12 particles per mL in stool
                 o Potentially fatal dehydration, fluid loss (within a couple hours)
           Detection: Viral antigen in stool by electron microscopy
           TX, prevention, control
                 o Live, attenuated vaccine since 2006
                 o Supportive/hydration therapy

      Norovirus
          o Norwalk virus 1st virus identified from stool samples by ElectronMic in 1972
                   Viruses are pretty concentrated in stool
          o Naked/non-enveloped, single-stranded (+) RNA
                   Very hard to combat & extremely hardy bc has no membrane to damage
          o Cause of viral gastroenteritis
          o Winter peak, year-round occurrence
          o Major cause of diarrhea outbreaks in children and adults, “Cruise ship” virus
              (explosive outbreaks)
                   Takes 1 day for fever, vomiting, diarrhea, cramps, nausea
          o Replication similar to picornaviruses (poliovirus), except 2 phases of translation
              (like coronaviruses)
                   Covalently attached 5’ VPg protein on RNA so will be transported to
                      nucleus for replication (like picorna)

    Naked/non-enveloped, linear double-stranded DNA
         o Icosahedral capsid
         o Fairly big genome (36,000 bp)
    Many serotypes (1-41)
         o Respiratory infections (1, 2, 5, 6)
         o Pharyngoconjunctivitis (3, 7, 14)
         o Acute resp. disease (4, 7, 21)
         o GI infection (40, 41)
         o Assoc. with celiac disease (12)
         o Conjunctivitis (2, 3, 5, 7, 8, 19, 21)
         o Epidemic keratoconjunctivitis (8, 19, 37)
    Attaches to CAR receptors on surface of host cells (CAR, coxsackievirus adenovirus
         o Most cells express CAR
         o Receptor-mediated endocytosis (Clatherin coated pit formation)
         o pH drop in endosome  viral uncoating  endosome rupture  contents into
            cytoplasm  viral nucleoprotein complex delivered into nucleus
    Transcription in nucleus, translation into proteins in cytoplasm
         o 3 stages, temporal regulation (Intermediate-early, early, and late)
                 Transcriptional regulators produced at each stage act to promote
                    transcription of subsequent phase. These proteins enter nucleus after
         o Complicated genome
    Replication in nucleus
         o Adenovirus was the model system where gene-splicing was discovered to happen
         o 5’  3’ synthesis
                 Only one of the 2 DNA strands copied at each fork, only continuous
                    replication, no lagging strand
                 Priming event by viral protein, pTP (preterminal protein)
    Capsid assembly in nucleus
      Causes “common cold”
          o 5-10% of all viral infections (really widespread)
          o 75% occur before age 14, and >50% before age 5
      Symptoms resemble common cold
          o Systemic symptoms: Chills, headache, fever, muscle aches
          o Conjunctivitis
          o Severe: Pneumonia
          o Latent infections common – asymptomatic, low level that lasts long time
                   Recover virus from 80% of tonsils and adenoids (asymptomatic pts)
          o In immunocompromised: Can be lethal
      TX, prevention, control
          o Live, attenuated vaccine given to new military recruits (for serotype 14)
      Characteristics:
          o Interferes with host cell gene expression
                   Prevents transport of host mRNAs from nucleus  cytoplasm
                   Inhibits translation of host’s cytoplasmic mRNA
                    Host protein synthesis inhibited
          o Evades host defense
                   Blocks MHC class I mRNA production specifically
                   And/or blocks their transport to the cell surface
                   So,  infected host cell cannot signal
                   E3 region of genome codes for many proteins for evasion of host defense
                          Inhibits killing by cytotoxic T cells
                          ADP (adenovirus death protein)- Promotes virus release
                          RID complex (Receptor Internalization and Degradation):
                                o Inhibits Tnf-induced apoptosis, translocation of
                                    phospholipid to membranes
                                o Inhibits inflammation
                                o Reduces expression of Fas and epidermal growth factor

    Naked/non-enveloped, circular double-stranded DNA genome
          o Smaller, and codes fewer factors than adenovirus
    E1 protein binds DNA at ori and promotes viral DNA replication, has helicase activity.
    E2 protein binds DNA, helps E1, and activates viral mRNA synthesis
    E5 oncoprotein that activates the EGF (epidermal growth factor?) receptor to promote
    E4 disrupts cytokeratins to promote release
    E6, E7, of HPV-16, -18 can become immortalizing genes
    HPV-16 is associated with cervical cancer
    L1 and L2 gene products are late structural capsid proteins
    Found everywhere in nature (humans, monkeys, cattle, fish, birds), large group of viruses
    Human Papilloma Viruses (HPV): ~100 types, 16 groups A-P based on DNA sequence,
       cutaneous or mucosal HPV
o   Some have no specific disease associated with them.
o   HPV-16, Bowenoid papulosis; cervical carcinoma
o   HPV-18, Cervical carcinoma
o   Infection process (3-4 months, longer process than others)
         HPV accesses basal layer through breaks in skin
         Basal keratinocyte (dividing cells) infected  induces cell division using
            cell’s DNA pol
                 Koilocytes – enlarged keratinocytes with clear halos around
         Viral early genes stimulate cell growth and viral replication
         Replication takes long bc linked with stages of epithelial layer
         Maturation of virus (in granulosum layer), virus produces capsid before
            cell becomes anuclear, only made in differentiated layers (When L1 and
            L2 are made)
         Assembly of virions in nucleus
         At top of stratum corneum the nuclear remnant with viral particles are
            shed at skin surface  left on doorknobs for others to be infected
         Clinical progess: Inoculation of epithelium  hand, foot, throat, or cervix
             local multiplication  wart  resolution (latency) OR cell
o   Non-lytic release of virus
o   Viral genome does not integrate into human genome (episomal)
o   Virions present on warts
         Spread easily by touch, even spread to other areas of body this way
         Warts differ in appearance depending on the site
         Mucous membranes more susceptible (sexual contact)
                 During birth
o   HPV-6 and -11
         Warts of oropharynx: laryngeal papillomas
                 Respiratory papillomatosis (obstruction)
                        o Hoarseness of voice
                        o Respiratory distress due to blockage (secondary bacterial
                           pneumonia in children)
                        o Obstructing lesions due to HPV infection
         Anogenital warts: condylomata acuminata (90% caused by HPV -6 and -
o   Oral papillomas (single) are the most benign epithelial tumors of the oral cavity
         On tongue, inside of lip, on inside corner of lip
o   Cervical papillomas
         HPV presenting ~100% of cervical cancers
         >85% of cervical carcinomas contain integrated HPV DNA
         HPV 16 and 18 (and 31 and 45) are high-risk types
         Second leading cause of cancer deaths among women
o   >5 million new infections per year
o   Most common STD in U.S. along with Chlamydia infections
                    Often infections are asymptomatic
                    50% population is positive for HPV DNA but no visible sign of infection
          o DX:
                  Pap smear – look for koilocytic cells (enlarged nucleus with halo)
                  Visual inspection of cervix
                  PCR, but sample contamination prevents use in diagnostic labs
                  HPV’s not routinely cultivated, warts confirmed microscopically by
                   hyperplasia of prickle cells (in spinosum layer), excess keratin production
          o TX, prevention, control
                50% of cutaneous warts regress spontaneously within 2 years
                Ablation tx:
                       Surgical excision
                       Laser beam destruction
                       Liquid nitrogen
                Stimulators of innate and inflamm responses
                       Imiquimod
                       Interferon
                       Cidofovir
                Intact skin is an effective barrier
                Latex condoms
                New vaccine

    Enveloped, (+) RNA genome
          o Contains reverse transcriptase enzyme to copy RNA to DNA
    Causes chronic disease long after infection
          o Integration of viral DNA into host chromosome
    HIV
          o HIV-1 most geographically widespread
                  Americans have plateaued since the 90’s due to public health measures
          o HIV-2 most prevalent in West Africa
    Structure:
          o Type B- Conical shaped capsid (made of p24gag proteins), surrounded by a matrix
             (made of p17gag proteins), all within a spherical membrane.
          o Envelope membrane has glycoproteins gp41 and gp120 on the outside.
    Retroviruses re ubiquitous in animals including fish.
    Genome: Packs a lot of info into a small space
          o Simple retroviruses only have regions coding for gag, pro (protease), pol (reverse
             transcriptase & integrase), and env (gp41 & gp120)
          o Complex retroviruses have additional coding regions. Accessory factors in HIV:
                  Tat & rev are transactivating factors – enhances viral RNAs & protein
                          Tat enhances viral RNA transcription
                          Rev enhances viral RNA export from nucleus into cytoplasm
                  Nef decreases expression of MHC class I molecules by cell, preventing
                     cytotoxic T cell killing
                Vif promotes viral assembly and inhibits cellular antiviral factor
                Vpu reduces cell surface CD4 expression  viral release
                Vpr promotes viral replication in non-diving cells like macrophages
   Replication cycle – More diversity in retroviruses
       o Attaches to CD4 receptor + coreceptor
       o Penetration
       o Reverse transcriptase codes dsDNA from ssRNA  integration into host DNA
       o Transcription of DNA into ssRNA for assembly into virions and for translation
           into proteins
       o Enveloped nucleocapsid release by budding off membrane
   HIV adsorption and penetration
       o Initial infection: M tropic
                Env protein gp120 binds to macrophage cells using receptor/coreceptor
                   CD4/CCR5  brings virion closer for gp41 to interact (essential for
                   fusion)  fusion and delivery of virus still encapsulated
       o Later parts of infection: T tropic
                Env protein gp120 binds to naïve T cells by receptor/coreceptor
                   CD4/CXCR4  brings virion closer for gp41 to interact (a 6-helix bundle
                   essential for fusion)  fusion and delivery of virus still encapsulated
       o **Some people virally resistant because lack the coreceptor molecules
   HIV replication
       o Viral RNA is shorter than the DNA the reverse transciptase synthesizes.
       o RT enzyme is major target for anti-HIV drugs
       o RT enzyme is more error prone than our replication, RT: 1 error per 10,000 nts
           (creates lethal defects sometimes or non-functional errors)
                Part 1: Synthesis of DNA
                        Begins at 5’ end using a cellular tRNA used to prime 3’ end to add
                           onto by reverse transcriptase (RT)
                        Then, degrades first part of RNA strand after it is copied
                        Moves up before remaining PPT region, then tRNA + newly synth
                           DNA is added onto/finished by reverse transcriptase
                        Original RNA almost completely degraded except for PPT region
                           which serves as a primer when reverse transcriptase synthesizes
                           the 2nd DNA strand.
                        tRNA primer removed and extension of both strands 3’ end until
                Part 2: Integration of DNA into host
                        Promoted by viral integrase enzyme because host DNA cut so
                           virus can insert and appear invincible, looking like another gene
                Part 3: Transcription to create more RNA
                        Viral DNA inserted into host is transcribed into ssRNA by host’s
                           RNA polymerase II
                               o Promoter and terminator recognized at LTRs (Long
                                   terminal repeats of the HIV DNA insert upstream and
                                   downstream, respectively)
                              o Promoter responds to host cell signals and can also be
                                  relatively dormant creating the latent state.
   HIV protein expression and viral assembly:
       o Viral RNA serves as mRNA for translation  polyproteins synthesized then
          cleaved to final mature sizes by viral protease enzyme
       o Then, the viral RNA molecule is packaged into nucleocapsid composed of the
          viral proteins
       o Viral assembly occurs at the plasma membrane where virions acquire their
          membrane by budding  release
   AIDS – acquired immune deficiency syndrome
       o Retrovirus caused by HIV
       o Mostly young gay men
       o Believed to have evolved in Africa from eating infected monkeys
   HIV inoculation:
       o Sequencing hard with HIV because mutates so readily, “quasi” species, because
          every type has different islets within
       o Entry of virus:
               Direct exposure of person’s bloodstream to body fluid containing virus
                       microabrasions on mucosal surfaces
                       needle puncture
                       intact mucosal surfaces
                       recipients of blood transfusions before the 1980’s
               Not transmitted by casual contact (touching, kissing, sneezing, bug bite)
       o May enter as:
               Infected macrophage, lymphocyte, or spermatozoa
               Free virus
       o Groups most at risk (in descending order):
               Homosexual/bisexual men (Comprise 48% of AIDS victims)
               IV drug users (27%)
               Heterosexuals that have intercourse with drug users, prostitutes, or
                  bisexuals (15%)
               Transfusion pts and hemophiliacs
               Children born of infected mothers (preventable with drug therapy)
               Healthcare worker needle exposure
                       Totally changed how we protect ourselves
                       Less than 1% of needle exposures show seroconversion
       o Initial infection of small amount of macrophages  stick to dendritic cells 
          transport to lymph node where infect CD4 T-cells
               Normal CD4 T-cells activate IFN-gamma which mediates delayed type
                  hypersensitivity (DTH, type IV)
                       With DTH compromised, infected persons are very susceptible to
                          other intracellular bacterial, viral, and fungal pathogens (Ex.
                          Kaposi’s sarcoma, lymphoma)
               Normal CD4 T-cells also activate IL-2 which controls growth of tumors,
                  but this compromised once infected.
       o After initial infection  burst of viral replication  chronic phase of infection
                  In chronic phase, 99% of replication occurs in activated CD4
                   lymphocytes (CD4+ T-cells), and 1% occurs in macrophages & resting t-
                        Macrophages and resting CD4 lymphocytes are the reservoir cells
                           responsible for viral latency
   Neurological symptoms of HIV:
        o Affects glial cells
        o Not well understood but possibly due to viral infection of neurons and release of
           substance by other cells that promote inflammation in the brain
   Blood serum levels
        o Between initial infection and 12 months, burst of p24 capsid protein in blood
           (indicator of viral levels). After 12 months, plateaus until late AIDS where rises
           again near death
        o CD4 and T-cell count falls constantly from initial infection until death
        o Anti-HIV-1 antibody stays high in blood after initial infection, but as T-cell
           population is eliminated, this titer disappears (near death of patient).
   HIV pathogenesis (complicated)
        o Depletion of T-cells by:
                Disruption of plasma membrane permeability
                Destruction by immune system cells due to presence of gp120 in
                Syncytia formation
                Integration and transposition of HIV provirus DNA into host DNA
                Apoptosis
        o May cause disruption of balance between different T-cell populations
        o May destroy or disable dendritic cells
        o HIV mutates rapidly, so that it evades immune system
   Clinical manifestations:
           1. AIDS-related complex (ARC)  Term not in use anymore
                        Fever, malaise, headaches, macular rash, weight loss, lymph node
                           enlargement, oral candidiases, and presence of antibodies to HIV
                        Occurs in first few months after infection, lasts 1-3 wks
                        Can develop to full-blown AIDS
           2. AIDS (Full-blown)
                        Progressive destruction of CD4+ cells ultimately leads to collapse
                           of immune system
                        Patient susceptible to opportunistic infections
                                o Long list including:
                                o Pneumocytis jiroveci pneumonia –unheard of in healthy
                                o EBV- Epsein Barr virus
                                o Hairy leukoplakia on the mouth
           3. Central nervous system disease:
                        Headaches, fever, subtle cognitive changes, abnormal reflexes, and
                           Dementia and severe sensory and motor changes observed in
                            advanced cases
                         Autoimmune neuropathies, cerebrovascular disease, and brain
                            tumors are common
              4. AIDS-related cancers
                         Kaposi’s sarcoma – dark spots on body, skin
                               o Cause by human herpes virus 8 (HHV 8)
                         Carcinoma of mouth and rectum
                         B-cell lymphomas
 Diagnosis:
       o Immunodiagnostic tests for HIV antibodies or antigens (ELISA followed with
          Western Blot)
       o RT-PCR (method for detecting RNA-based viral genomes)
 Treatment:
       o Antiviral agents
              Nucleoside analogue reverse transcriptase (RT inhibitors) Ex. AZT
              Non-nucleoside RT inhibitors (Ex. delavirdine)
              Protease inhibitors (Ex. indinavir)
              Fusion-penetration inhibitors (target gp41)
       o Treatment of opportunistic infections and cancer
 Prevention and control
       o Screening and treatment of blood and blood products
       o Education
       o Protected sex
       o Search for vaccine –
              maybe not good idea because this virus attacks immune cells so an antibody
                 presenting this virus more rapidly to immune cells would just increase the
                 rapidity of their infection
              Just found glycoprotein protects 30% of individuals
 Article about the monthly progression of HIV infection:
       o Neutralization assay
              Took a sample each month for 39 months?
              Used PCR to amplify region coding for glycoprotein for each sample
              Also looked at immunoglobulins/antibodies every month
              If luciferase high, means antibody couldn’t neutralize virus
              Antibody neutralization titer chart
                      High numbers means getting higher neutralization with antibody
                             o Produce an effective antibody 12 months after exposure and by
                                 that time, it has created new variant
                      Patient will never mount effective response against virus at the same
                         time the specific one is infecting
 Retrovirus caused leukemias
              Long latency period (30+ years, extremely long)
              Spread by contaminated blood transfusions, needle sharing, sexual contact,
                 across placenta, from mother’s milk, (not by mosquitos)
       1. Adult T-Cell leukemia
             -Caused by retrovirus: human T-cell lymphotropic virus I (HTLV-I)
                      -First one identified in 70’s
                      -integration of virus into host genome activates growth-promoting genes
             -Death caused by proliferation of leukemia cells or from opportunistic infections
             -No treatment available
       2. Hairy-cell leukemia
             -Caused by retrovirus: HTLV-II
             -Chronic progressive lympho-tropic proliferative disease
                      -death usually caused by opportunistic infections
             -IFN-alpha n3 used for treatment

 Human herpesviruses
       Enveloped, double-stranded DNA linear genome
             o Fragile because enveloped  subject to heat, detergent, drying
       Very large genome (up to 236,000 bp)
       Lots of space between core and envelope
       Infects many different cell types
       Share 4 significant biological properties:
         1. Encode a large array of enzymes involved in:
                 a. Nucleic acid metab
                 b. DNA synthesis (DNA pol, helicase, primase)
                 c. Protein processing (protein kinases)
         2. Synthesis of viral DNAs and capsid assembly occur in the nucleus, while final
             processing of virions occurs in the cytoplasm
         3. Production of virus results in destruction of the infected cell
         4. Able to exist in a latent state (not producing virus in infected cells) but retaining
             the capacity to replicate and cause disease upon reactivation.
       Types:
             o Alpha herpesviruses
                     Herpes simplex virus 1 (HHV-1) – Fever blisters
                              Ocular and oral herpes (ocular “herpes keratitis” can lead to
                                 scarring and blindness from dendritic ulcer of cornea)
                              Transmitted by direct contact  epithelial cells
                     Herpes simplex virus 2 (HHV-2) – Sexually transmitted genital
                              Genital, neonatal, meningoencephalitis herpes infections
                              By direct contact  epithelial cells
                     Varicella-zoster virus (HHV-3) – Chicken pox and shingles
                              By aerosol inhalation or direct contact  epithelial cells
             o Beta herpesviruses
                     Cytomegalovirus (HHV-5)
                              By saliva, blood, urine, semen, or parent to child  blood
                                 system cells targeted
                     Human herpesvirus type 6 (HHV-6) – Roseola (Childhood rash)
                        Blood system targeted
                Human herpesvirus type 7 (HHV-7) – Roseola (Childhood rash)
                        Blood system targeted
        o Gamma herpesviruses
                Epstein-Barr virus (HHV-4) – Infectious mononucleosis
                        By saliva, blood  blood system targeted
                Kaposi’s sarcoma-associated herpesvirus (HHV-8)
                         death usually moreso because other HIV/AIDS problems
   Most humans become infected with 1+ herpesviruses because very infectious,
        o Generally require direct inoculation
                Mucous membranes more susceptible than skin
                CMV & EBV can be transmitted thru infected leukocytes
                VZV mostly transmitted by aerosols
        o Hard to pick up herpesviruses on toiletseats, doorknobs, etc because very
   Herpes lytic cycle
        o Initiate binding of HSV-1 & -2 to heparin sulfate chains on cell surface
                Several cellular receptors for HSV-1 & -2
                Binding of virus triggers membrane fusion
        o Active recruitment of cellular cytoskeleton that brings capsid into nuclear pore
           & genome allowed in nucleus
        o Cascade of gene expression
                3 stages: Immediate-early, early, and late
        o Viral proteins:
                VHS (Viral shutoff factor) – inactivates host mRNAs
                VP16 – Transcription factor, promotes early viral gene transcription
        o Predominant localized spread is hallmark of HSV-1 & -2:
                Attach to and infect adjacent cells upon release (instead of floating off)
                Budding directly onto/into adjacent cells
                Syncytia can form because virus inserts its membrane proteins onto
                   cell’s membrane which adheres to adjacent cells
   Virus replicates and assembles in the cell nucleus
        o This creates havoc on the infected cell
                Get changes in nuclear structure  chromatin shifted to margins of
                “Cowdry type A acidophilic intranuclear inclusion bodies” – dense
                   structures in nucleus, host’s own DNA marginating
        o Evolved to have extra proteins because it:
                shuts down host’s replication functions
                provides own proteins to replicate itself
                provides own proteins for coactivation of other processes (Ex. VP16 &
                   others produced at each wave of transcription)
        o The high level of mRNAs produced allows virus to exceed its own VHS
           proteins so some mRNAs get translated, then the rest from that round are
           degraded and VHS is used up entirely. When more VHS is produced in the
           last wave of transcription, it’s in the inactive form and packaged with the
           newly synthesized virions.
   Host response to alpha-herpesvirus infections (HHV-1, -2, and VZV/HHV-3)
       o Innate responses
                Production of IFN and other cytokines
                Activation of neutrophils and NK cells
       o Adaptive responses
                Antibodies to viral proteins appear within several days
                        Minor role in recovery from primary or recurrent disease
                        can use as vaccine to prevent VZV primary disease
                        Antibodies limit viremic spread of virus
                Activation and amplification of T-lymphocytes
       o Major role by cell-mediated recovery
                MHC I and II displaying viral antigens on surface activate T-
                        Directly kill infected cell
                        Secrete cytokines and chemokines to attract macrophages
                Cell mediated recovery varies with age
                        Neonates: problems with HSVs
                              o Don’t have cellular mediation response maturity so bad
                                   if infected
                        Elderly: problems with VZV
                              o Recurrence of VZV ~70-80 to giving rise to shingles
                                   from childhood chickenpox
                              o Primary infection of VZV in adults more severe
                                         Causes interstitial pneumonia in 30% of adults,
                                            can be fatal
       o Immune evasion by herpesviruses
                Alpha herpesviruses glycoproteins on the envelope bind the Fc domain
                  of antibodies and complement components, and block their ability to
                  promote an antiviral response.
                HSV (HHV-1 & -2) proteins can reverse antiviral effects of IFNs
                HSV (HHV-1 & -2) proteins can prevent MHC proteins from being
                  expressed on the surface of infected cells
                Latency results in no expression of viral proteins, therefore no peptides
                  for MHC proteins to display
   Usual course or HSV infection and disease
    1. Acute disease
           o Facial or genital herpes, stomatitis, or keratitis localized
                   Exposure of skin, mucosa, or cornea to secretions containing virus
                    Replication of virus in epithelial cells causing vescular
                       mucocutaneous lesions, stomatitis, or keratitis
                    Spread to peripheral sensory or autonomic nerve endings and
                       ganglia (for latent state)
                      HSV-1 acquired very early in life (from kissing), 2/3 or adults test
                      HSV-2 mostly transmitted by genital contact, uncommon before
                       adolescence, 1/5 of adults test positive
                      HSV-1 & -2 infections –
                           2/3 are asymptomatic
                           1/3 have recognizable symptoms
    2. Recovery
           o Healing of lesions but establishment of latent infections in neurons
               (expressed very little, lariat mRNA but no protein associated)
    3. Latency
           o Maintenance of latent infections in neurons
    4. Recurrent disease
           o Reactivation of latent virus and distal spread
                    In same tissue as primary infection- reemerging and reinfection of
                       original site’s epithelial cells
                    Cold sores, fever blisters, keratitis, or genital lesions (localized)
                    Cause by sunburn, emotional stress, etc.
                    Virus damages tissue and host response from lesion causes damage
                       to tissue.
   Herpetic stomatitis
       o Most common viral infection of the mouth
       o HSV-1 & -2
       o Vesicles on oral mucosa, the tongue, and gingivae
                Gingivae inflammation confused with ANUG
   Herpes labialis (cold sore)
       o Due to reactivation of latent HSV-1 & -2
   Herpetic dermatitis and herpetic whitlow
       o HSV-1 & -2
   VZV/HHV-3:
       o Smallest genome of all HHVs
       o Aerosol transmission (90% of adults test positive)
       o Local viral replication in respiratory tract epithelium
                Viral progression to phagocytic cells via blood and lymph
                Secondary viremia spreads through body & skin 11-13 days
                        Skin lesions appear over entire body (chicken pox)
                        Systemic spread is different from HSVs
       o Virus spreads cell-to-cell like HSVs
                Except epithelial cells of lung keratinocytes of skin lesions, which
                   can’t release virus (shedding)
       o VZV replication
                similar to HSVs but slower
                establishes latent infection of neurons but more viral RNAs and
                   proteins detected, whereas HSVs just have 1 LAT gene in latency.
                        In dorsal root ganglia or cranial nerve ganglia
       o VZV reactivated in older adults with impaired cell-mediated immunity
               Causes rash along entire dermatome (whereas HSV release only at end
                   of nerve)
               Postherpetic neuralgia in 30% of cases – Pain for months to years after
   Epstein-Barr virus (HHV-4)
       o More limited cell tropism
       o Infects B lymphocytes and epithelial cells
       o Adsorption
               Initial nonspecific interaction to glycosaminoglycans
               Secondary interaction with high affinity cell surface receptor CD21
       o Latent infection
               In memory B cells
               Virus proteins produced during latency (unlike HSV latency) promote
                   B cell proliferation
               Basis for viral reactivation is not known, maybe decreased cell-
                   mediated immunity leads to recurrence
   Cytomegalovirus (HHV-5)
       o Infects wide variety of cells
       o Adsorption
               Same as Epstein Barr, but the specific secondary cell surface receptor
                   is unknown
       o Establishment of CMV persistent/chronic infection
               Not a true latent infection  produce at very low level  more like
                   chronic virus
               Possibly in hematopoietic progenitor cells and macrophages but not
                   well understood
   Host defenses against CMV and EBV
       o Both innate and adaptive immune responses are important
               Patient with primary immunodeficiencies have increased risk of severe
                        NK cell defects
                        T-lymphocyte defects
                        AIDS
                        Transplant procedure antirejection therapy patients (High % of
                           virus in population, so if get an organ there’s good odds donor
                           had virus.
               NK cells and virus-specific CTLs control virus during primary
                        Also provide surveillance during latency/chronic infection
       o Evasion of host defenses
               Many mechanisms similar to HSV-1 & -2
                        CMV encodes cytokines IL-8 & IL-10 and chemokine
                           receptors to modulate inflammatory response, favoring viral
                       EBV encodes glycine-alanine repeats in its major target
                        antigens restricting antigen processing, reducing antigen
                        presentation on MHC I or II.
   CMV and EBV infections very common
      o 95% of adults in developing world test positive
      o 50-60% of adults in the U.S. test positive
      o Usually asymptomatic when acquired early (Early in life, disease is no
      o CMV acquired early through breast milk or saliva
              Also sexually transmitted
              Also through blood transfusion or transplantation
                     Significant morbidity and mortality
              Congenital CMV (infected mom  fetus)
                     Most common viral infection of the fetus in humans
                     Leads to severe disease and permanent neurological damage
                            o Hearing loss
                            o Learning disabilities
      o EBV acquired by saliva or sexually transmitted
              Often get after childhood
                     Symptomatic infections: infectious mononucleosis
              Also through blood transfusion or transplantation
                     Significant morbidity and mortality
      o Persistent CMV and EBV infections associated with chronic inflammatory
         diseases and cancer
              EBV:
                     Hodgkin disease
                     African Burkitt lymphoma
                     Nasopharyngeal carcinoma
                     Possibly breast cancer, but no causal relationship yet
      o Diagnosis:
              CMV
                        1. Large inclusions in tissue specimens (“owl eye” inclusions)
                        2. Antigenemia assay – detection of CMV antigen by
                            microscope with fluorescent antibodies (detects actively
                            replicating virus)
                        3. PCR
              EBV
                        1. PCR
                        2. Heterophile antibody or “monospot” test (easy in clinics)
                             EBV produces large number of antibodies that
                                recognize RBC antigens of other species (characteristic
                                of active infection)
              Other serological tests?
                    o IgG – Would be no good because would have no idea when got
                    o IgM – Would mean got it more recently, but still not great
o Oral manifestation of other herpes virus infections
     o Chickenpox (VZV) – lesions may be found in mouth before skin rash (typical)
     o Shingles (VZV reactivation) – If trigeminal nerve affected (15% of cases)
             Opthalmic>maxillary>mandibular divisions involved
             Oral pain precedes rash and mimics toothache pain
             Common intraoral sites affected:
                     Anterior half of tongue
                     Soft palate
                     Cheek
     o Epstein-Barr – Infectious mononucleosis (very common)
             Painful sore throat at onset of infection
             Rash may be present at junction of hard and soft palate (fine petechial
             White pseudomembrane on tonsils and other oral mucosa
                     But this is non-specific (can be for other reasons too)
     o HHV-8 (Kaposi’s sarcoma-associated virus)
             Lesions (endothelial tumor)
             Patient knows and usually tells you they’re in late AIDS
     o Herpesviruses and periodontal disease
             CMV and EBV present in majority of advanced perio lesions
                     CMV ~60% in active disease sites, 12% in stable disease sites
                     EBV ~44% in active disease sites, 12% in stable disease sites
                     Coinfection ~1/3 of active cases (29%), but none in stable sites
             HSV-1, HHV-7, HHV-8 also detected in some lesions
             Presence of herpes virus correlated with presence of perio bacteria:
                     Prev. gingivalis
                     P. intermedia
                     Tannerella forsynthia
                     Trep. Denticola
                     P. Nigrescens
             Possible roles for herpes viruses in perio disease:
                     Viruses may cause direct cytopathic effects  tissue damage
                         further disease
                     Gingival viruses may promote bacterial
                        attachment/colonization  cause cells to express proteins for
                     CMV & EBV can infect monocytes, macrophages, and
                        lymphocytes in lesions and impair cell function (function
                        normally to prevent perio bacteria from take-over)
                     Viruses induce a proinflammatory response that can result in
                        tissue destruction
                     Viruses can suppress host defenses locally and systemically
                            1. Downregulate MHC I expression
                            2. Sequester chemokines (or produce them)
                            3. Inhibits MHC II expression
                                    4. Inhibit NK cells
                                    5. Suppress cytotoxic T-lymphocyte functions
                        Same trend seen in the following (?)
                             Localized juvenile periodontitis (LJP)
                             Rare types of aggressive periodontitis in young individuals
                                    1. Papillon-Lefevre syndrome
                                    2. Fanconi’s anemia periodontitis
                             Acute necrotizing ulcerative gingivitis (ANUG)
                             HIV-periodontitis
                        Herpesviruses latency and reemergence
                             Could be responsible for burstlike episodes of periodontal
                                disease progression
                             More frequent vs. less frequent reactivation could parallel
                                disease progression
                             Consequences for transmission of herpesvirus
                                            relationship between gingival health and viral

      o Clinical syndrome characterized by inflammation of the liver
            o Causing hepatocyte cell death  bilirubin release  jaundice
                     Bilirubin is byproduct of heme metabolism/detox in liver
      o Causes of hepatitis:
            o Viral
                     Hepatitis viruses A – E
                     Herpesviruses (HSV, EBV, CMV)
                     Adenovirus
                     Yellow fever virus
                     Others
            o Alcohol
            o Toxins (amanita toxin in mushrooms)
            o Drugs, pregnancy, autoimmune disorders
      o Hepatitis viruses A – E
            o Have strong tropism for liver, replicating in hepatocytes
                     85% of liver cells are hepatocytes  so viruses cause liver disease
            o Hep A
                     Picornavirus family
                     Naked, no envelope
                     Icosahedral
                     Linear (+) RNA
                            VPg at 5’ end of RNA
                     Spread by fecal-oral contamination of food, drink, shellfish
                            Shed into bile ducts  intestine  out of body in feces
                     Directly kills hepatocytes
                     Clinical manifestations:
                            Usually mild intestinal infection
                             Anorexia
                             General malaise
                             Nausea
                             Diarrhea
                             Fever
                             Chills
              Occasionally  viremia  liver infection
                             Jaundice
              Period of infection lasts a few weeks (longer than most acute
              In highly endemic regions (S. Amer, Africa), almost all
                children become infected in first years of life
                             Most are asymptomatic
              Adults in nonendemic regions usually show symptomatic
         Treatment, prevention, control
              Immunodiagnostic test for HAV antibodies
              Hygienic measures, sanitary disposal of excreta
              HAV vaccine for high-risk groups (military, travelers, child
                care staff)
              Post-exposure immune globulin
o Hep B
      Hepadnavirus family
      Enveloped
      Nicked circular ssDNA & mostly dsDNA
           3 distinct viral particles
                  1. 22 nm particle
                          Empty, spherical envelopes but present in large
                  2. Variable tubular/filamentous particle
                  3. 42 nm Dane particle (infective form of virus)
                          Spherical
                          Surface antigens (small, medium, large)
                             embedded in lipid bilayer
                                  HBsAg-S (small) – main component
                                  HBsAg-L (large) – for receptor binding
                          Core antigens (capsid-type proteins)
                                  HBcAg
                                  HBeAg (processed form of HBcAg)
                                        o Secreted from infected celled
                                           into blood stream (useful
                                           marker of infection)
      Cannot grow in cell culture
           Can grow in fresh primary hepatocyte cell cultures but only
             remain infectable for a few days (limits studying)
           Perform most studies with animal hepadnaviruses (duck,
   Fusion to host cell, delivery of core
        dsDNA  nucleus
        transcription by host RNA polymerase
                         cap and poly A tail attached to protect and
                            signal for translation
                         overlapping reading frames (make more from
                         contains a secondary binding site for reverse
                            transcription into DNA that will be packaged
                            into virion
        ssRNA  reverse transcription into DNA form  packaged
           into capsid
   Virus doesn’t directly kill hepatocytes, cytotoxic T-cells kill infected
        Killing also occurs by cytokine release promoting
           inflammation and tissue damage
   Cell-mediated immune response determines course of infection
        Effective response  acute disease  resolution (no long
           term effects)
                         4 clinical periods
                                 Incubation
                                 Preicteric
                                 Icteric (jaundice)
                                 Convalescent
                         Serology: 4 months after infection see
                            antibodies in blood to HBcAg, HBsAg, &
                         Serology: Serum aminotransferase levels
                            correspond to liver damage, which tapers off at
                            5 months
        Ineffective response  chronic disease  too many
           hepatocyes killed  fulminant hepatitis, carcinoma, cirrhosis
                         90% of infants infected become chronic
                                 Most adult cases will resolve (acute)
                         Hepatocellular carcinoma can result because:
                                 Increased cell division due to
                                    regeneration  increased mutation risk
                                 Peroxides and free radicals from CTL
                                 Integration of HBV DNA into
                                         o Alteration of growth regulatory
                                 HBV X gene is transcriptional activator
                                    of host genes (proliferation)
                                Serology: No antibodies produced for HBsAg
                                 after infection
                              Serology: Serum aminotransferases in small
                                 amounts until years down the road when
                                 significantly increase right before liver failure
         Shedding of virus so transmittable by sex, blood
         Serology is better diagnostic tool for HepB, because PCR can’t tell
          you what stage of infection patient is in.
         Treatment, prevention, control
              Vaccination for all infants
                              HBsAg particles produced in yeast
                              1st recombinant/artificial vaccine approved for
              Passive immunotherapy within 7 days of exposure
              IFN-alpha for chronic carriers
                              Expensive, toxic, limited efficacy
              Reverse transcriptase inhibitors (originally anti-HIV drugs)
              Discouraging contact with contaminated materials (serum, IV
                 drug use, prostitutes)
o Hep C
         Flavivirus family
         Enveloped
         Linear (+) RNA
         Transmitted by:
               Mother  fetus
               Fecal-oral
               Organ transplants or blood transfusions
         Does not directly kill hepatocytes, damage by immune response to
          infected cells (same as Hep B)
         More persistent infection than Hep B, 70% develop persist infection
               Of those, 40% asymptomatic, 60% Chronic hepatitis
               Chronic cases  Liver failure, cirrhosis (more often),
                  hepatocellular carcinoma
         Can lead to: Mixed cryoglobulinemia – immune complex disease of
          kidney and other sites (disease outside of liver)
               Type III hypersensitivity
         Treatment, prevention, control
               ELISA diagnosis for antibodies
               IFN-alpha 2b or IFN-alpha 2a (interferon treatments)
                              Lasting response in half of patients
                              Expensive and toxic- hard to tolerate, but
                                 without, will get liver failure
               No vaccine bc many genotypes and hypervariable envelope
o Hep D
                       Deltavirus – subviral species because requires Hep B coinfection to
                             HBV + “delta factor” (deltavirus)  “coinfection,” longer
                             Chronic HBV + “delta factor”  “superinfection,” shorter
                             3 possibile outcomes from both coinfection or superinfection:
                                    1. Cirrhosis
                                    2. Fulminant hepatitis (extensive damage, liver failure)
                                    3. Chronic delta infection
                       Circular (+)RNA (very small genome, ~length of 1 gene)
                             Only encodes a single protein, HDAg, that binds viral RNA
                             Depends on HBV to replicate, HBV provides envelope protein
                       Surface antigen same as Hep B : HBsAg
                             Also has delta particle/antigen (supposedly Hep B does too)
                       Treatment, prevention, control
                             Serological tests for anti-HDAg antibodies
                             No satisfactory treatment
             o Hep E
                        Calcicivirus (group that can cause diarrheal symptoms)
                        Naked, no envelope
                        Linear (+) RNA
                        Transmission:
                              Contaminated food and drink (like Hep A), fecal-oral
                      Virus directly kills hepatocytes (like Hep A)
                      Resolves after jaundice
             o   Hep F – recent
                      Leads to fulminant hepatitis
             o   Hep G – recent
                      Leads to syncytia of hepatocytes  giant cell hepatitis
             o   Transfusion transmitted virus (TTV)Post transfusion hepatitis when blood
                 wasn’t screened for this
             o   Infectious hepatitis: A & E (all vowels)
                      Hit and run
                      Transmission: fecal-oral
             o   Serum hepatitis: B, C, and D
                      Hide and infiltrate chronic infections
                      Transmission: Blood and sexual fluids

Viruses and Cancer
    Families and associated cancers:
           o Flavivirus
                  Hepatitis C  Hepatocellular carcinoma
           o Retroviruses  Hematopoietic cancers, sarcomas, and carcinomas
           o Hepadnaviruses
                  Hepatitis B  Hepatocellular carcinoma
           o Papovavirus
                    Papillomaviruses  Papillomas and carcinomas
                    Polyomaviruses  Various solid tumors
           o Adenoviruses  Various solid tumors
           o Herpesviruses  Lymphomas, carcinomas, and sarcomas
           o Poxviruses  Myxomas and fibromas
      How retroviruses can make cells cancerous
               1. Make DNA insertion into host chromosome & downstream portion is
                   promoter for gene inserted before (sometimes proto-onco gene)
               2. Virus carries around a gene that gets inserted into viral genome and
                   transcribespromoter protein
      Cell cycle factors:
           o cyclin-CDK complex: Phosphorylates the Rb-E2F complex breaking it apart into
               E2F and Rb.
                    E2F then enters nucleus and binds upstream to polymerase and associated
                       enzymes to prepare for DNA replication (progresses cell cycle)
                    But, as long as Rb is bound, inhibits progression of cell cycle
           o If DNA damage during G1 phase:
                    p53 (checkpoint controller) recognizes DNA damage and activates p21
                    p21 binds and inactivates the cyclin-CDK complex so it cannot break
                       apart Rb-E2F
                    DNA gets repaired, p53 decreases, p21 no longer blocks cyclin-CDK
                    Cell cycle progression
      Inactivation of p53 by papillomavirus proteins
           o HPV-16 or -18’s E6 protein:
                    Binds to p53, targets for ubiquitin  p53 degraded by proteasome 
                       progression of cell cycle (BAD!)
           o HPV’s E5 protein:
                    Increases EGF (epidermal growth factor) receptor concentration
                            Does so by preventing receptors endocytosis for degradation
                            Prevents endocytosed receptors from being dissociated/degraded
                                  o E5 binds vacuolar ATPase and inhibits acidification of
                            Basically, promotes recycling of used EGF receptors, so end up
                              with increased receptors on surface, and increased sensitivity
                              to EGF
           o HPV’s E7 protein:
                    Binds to Rb and prevents Rb’s negative regulation on E2F
                    Similar to proteins of other viruses
                            SV40 virus LT protein (Large T antigen)
                            Adenovirus E1a protein
                                  o Adenovirus not oncogenic in humans, but is in hamsters
                                  o A defective virus might be oncogenic in humans

Antiviral Treatment Strategies
    Inhibitors of viral replication
o Every step in viral replication can be potential target
      Viruses are very particular in each step (Ex. viral assembly occurs in
          either nucleus or cytoplasm) so hard to design a broad spectrum antiviral
o Not able to target host cell functions because toxicity to host cells
o IFN treatment developed by empirical approach
      Natural products discovered in 1957
      IFNs assist the immune response
               Inhibit viral replication in cells
               Activate NK cells and macrophages
               Increase antigen presentation to lymphocytes
               Induce resistance of host cells to virus
      Treatment for Hep C
      Formerly used for Hep B
      Type I IFNs
               IFN-alpha (produced by leukocytes; induced by viruses)
               IFN-beta (produced by fibroblasts & epithelial cells; induced by
      Type II IFNs
               IFN-gamma (induced by antigens and mitogens)
o IFN treatment effects
      Fatigue
      Fever
      Myalgias
      Bone marrow suppression
      Neuropsychiatric problems
o Viral absorption, penetration, and/or uncoating targeted by:
      Enfuvitide (fusion inhibitor)
               Specific to HIV
               Binds to gp41 region to prevent fusion of membranes
      Amantadine (Rimantadine=analog)
               Blocks penetration and uncoating of influenza A virus
                      o By blocking M2 ion channel function, prevents the
                      o M2 ion channel allows acidification of endosome after
                          endocytosis of virion, driving virion disassembly
               Used to prevent influenza infections
                      o 75% effective if given prior to exposure (prophylactic)
                      o 50% effective if given after first signs of infection
o Viral replication targeted by:
      Acyclovir (nucleotide analog)
               Very similar structure to the molecule deoxyguanosine, which is
                  used as substrate for DNA synthesis
               Acyclovir doesn’t contain a 3’ OH group, so when is mistakenly
                  used in viral DNA synthesis, the process “dead ends” and it cannot
                  add any more substrates, halting viral replication.
                      o Inhibits herpes virus DNA polymerase
                 Drug is specific to infected cells, targeting herpesviruses
                      o Effective for most, but ineffective for CMV (HHV-5)
               Has no effect on latency, so if reemergence occurs, have to retake
                  drug again.
                      o If continue taking, ~80% stay free of recurrence of genital
      Ganciclovir (nucleotide analog)
               Also similar structure to deoxyguanosine
               Much more effective against CMV
               More toxic
      Adenine arabinoside
               Inhibits herpes virus enzymes involed in DNA & RNA synth
      Foscarnet (DNA polymerase inhibitor, not full nucleotide analog)
               Directly inhibits herpesvirus and CMV DNA polymerase
o Viral RNA synthesis targeted by:
      Ribavirin
               Purine nucleoside analog
               Lack of potency at nontoxic levels, but broad-spectrum like
               Inhibits many RNA viruses, some DNA viruses including:
                      o Influenza A & B
                      o Measles
                      o Respiratory Syncytial Virus (RSV)
               Mechanism of action
                         1. Inhibits viral polymerases
                         2. Reduces GTP levels
                         3. Impairs 5’ capping of viral mRNAs
 Viral release targeted by:
     o Neuraminidase (NA) inhibitors
               NA usually releases virus from envelope and
               NA cleaves sialic acid (enzymatic activity)
               Inhibits above, thus prevents spread of virus from cell to cell
               Effective against influenza virus
 Cidofovir (Broad-spectrum like anti-DNA virus drug)
     o Inhibits viral DNA polymerase
     o Effective on:
               Papillomaviruses (papovaviruses)
               Adenoviruses
               Herpesviruses
               Iridoviruses
               Poxviruses
 Anti-HIV drugs
     o Nucleoside reverse transcriptase inhibitors (NRTIs)
               AZT (Azidothymidine)
                       First drug on market
               Lamivudine
                               Nucleoside analog that inhibits virus but not host cells
                 o Non-nucleoside reverse transcriptase inhibitors (NNRTIs)
                       Delaviridine
                       Efavirenz
                       Nevirapine
                 o Protease inhibitors
                       Peptidomimetic inhibitor – mimics region of protein at cut site
                          where protease is supposed to cleave, and blocks this
                               Inhibits cutting of polyproteins
                               Inhibits assembly of virions
                       Ritonavir
                               Also has an additional unexpected activity:
                                       o Cytochrome P450 3A4 inhibitor
                                              Cytochrome is a detoxifying enzyme in
                                                body so the drug has longer half-life in body
                       Saquinavir
                 o HAART – Highly active antiretroviral therapy
                       At least 3 drugs in combination (bc resistance is common)
                               (2) nucleoside inhibitors + (1) NNRTI or protease inhibitor

Vaccines and antisera
    Protection against microbial pathogens by public health measures
      1. Public sanitation
          o Portable water supplies, sewage disposal, improvements in housing
      2. Vaccines
          o Prevention of infectious diseases by inducing immune responses
    Immunization strategies depend on:
          o Type of microorg
          o Age of individual (Young have immature cell-mediated immune system)
          o Time frame of contact between individual and the pathogen
    Types of immunization, “immunotherapy”
          o Active immunization (vaccine)
          o Passive immunization (exogenously produced or preformed antibodies)
    Active immunization (Vaccines) – Immunizing agent derived from microorg or parasite
          o (1) Live, attenuated microorganism vaccines
                   Advantages:
                          Immunization resembles the natural infection
                               o Host reaction progresses through TH1 and TH2 immune
                               o Humoral, cellular, and memory immune responses
                          Immunity is long-lived
                          No adjuvant is required
                          Only single does usually required
                   Disadvantages:
                          Vaccine may still be dangerous for immunosuppressed
               Vaccine microorg may revert to a virulent form (viruses, but rare)
               Viability of the vaccine must be maintained
       Examples of bacterial vaccines:
               Calmette-Guerin bacillus (TB)
                      o Cow strain, not used in U.S. because then people show
                           false-positive for PPD test.
               Salmonella typhi (Ty21a)
               Francisella tularensis (tularemia)
       Examples of viral vaccines:
               MMR (measles, mumps, rubella)
               Varicella-zoster virus (HHV-3)
               Influenza virus
                      o Nasal mist because replicates at lower temperature so won’t
                           further down in respiratory tract
               Polio virus (after 50-60 point mutations)
                      o Not virulent in humans after passed through multiple
                           animal cells
o (2) Killed (irreversibly inactivated) microorganism vaccines OR (3) Products
  or derivatives of microorganisms (Components)
       Advantages:
               No risk of infection
                      o Inactivated or killed by chemical treatment (formalin) or
                           heat for bacteria, viruses, or bacterial toxins
                      o Purify or synthesize subunits or components of the
                           infectious agent
               Can use large amounts of antigen
       Disadvantages:
               Adjuvants required to boost the immunogenicity of the vaccines
               Immunity isn’t long-lived (generates TH2 response that doesn’t
                  elicit effective immune memory)
               Immunity may be humoral and not cell-mediated
               Doesn’t usually elicit a local IgA response
               Booster shots required
               Larger doses must be used
       Adjuvants:
               Aluminum salt (common, acts like cage around compound)
               Some mimic PAMPs (pathogen associated molecular patterns)
                      o Bacterial cell wall components
                      o Synthetic polymers – mimic surface polymers
                      o Bacterial toxins (attenuated)
               Influence the type of immune response
                      o TH1 or TH2
                      o Secretory IgA (for cholera toxin-linked vaccine admin
       Examples of Bacterial vaccines:
                          Inactivated (killed bacteria)
                               o Vibrio cholera
                               o Bacillus anthracis
                        Toxoids
                               o Corynebacterium diphtheriae
                               o Clostridium tetani
                        Capsule of bacteria
                               o Capsular polysaccharide vaccines:
                                        Haemophilus influenzae B
                                        Neisseria meningitides
                                        Salmonella typhi
                                        Streptococcus pneumonia
                                        Conjugate these because polysacc are poor
                        Subunit vaccine
                               o Borrelia burgdorferi – Lyme disease (outer membrane
                Examples of Viral vaccines:
                        Inactivated viruses
                               o Polio [Salk is main one used now, opposed to Sabin (live
                                        Sabin vaccine is better for nasal and duodenal IgA
                                           response though
                               o Hepatitis A
                               o Influenza
                               o Rabies
                        Protein subunits of viruses
                               o Hepatitis B
   Passive immunization (post exposure treatment)
       o Injection of purified antibody or antibody-containing serum to provide rapid,
           temporary protection or treatment
       o Newborns receive natural passive immunization from maternal immunoglobulin
           that crosses the placenta and is present in breast milk
       o Used because the incubation period for most pathogen-associated diseases is too
           short for post-exposure vaccination to be effective in preventing disease
       o Administration:
                Immunoglobulin (IG) + Specific (hyperimmune) IG
                        Intramuscularly
                        Intravenously (IVIG)
                Human plasma + antibodies from animal origin
       o Uses of passive immunization:
                To prevent disease after a known exposure
                To ameliorate the symptoms of an ongoing disease
                To protet immunodeficient individuals
                To block the action of bacterial toxins and prevent the diseases they cause
                   (Ex. Clostridium tetanus)
       o Human immune globulins used against:
                CMV
                Hep A, B
                Rabies
                RSV
                Smallpox
                Varicella zoster (HHV-3)
                Tetanus
       o Animal antitoxins used against:
                Botulism
                Diphtheria
       o Limitations:
                Sometimes antiviral antibody titers are not high enough
                Contamination with other infectious agents
                Need to use early after exposure
                        And often this is not possible
                Some viruses have a limited extracellular phase
                        Ex. Herpesviruses, enteroviruses
                Should not be used at same time as vaccine because can inhibit vaccine’s
                   elicitation of an immune response
                        Should admin vaccine after antibodies have had time to degrade
                        Both active and passive immunization used for postexposure of:
                                o Hep B
                                o Rabies
                                o Tetanus
   Definining the “correlates of protection” in developing a vaccine
       o The host immune responses associated with disease protection
                Vaccines that protect solely or principally by induction of serum IgG
                        Hepatitis A, polio, rabies, yellow fever, depth, Lyme, pertussis,
                            tetanus, and extracellular encapsulated bacteria
                Both antibody levels and their function are important for signaling within
                   the immune system
                        Mumps, rubella, meningococcal, and pneumococcal vaccines
                Secretory antibodies play a role in protection against infections caused by
                   agents that must first replicate on mucosal surfaces
                        Influenza virus, polio, and rotavirus
                Vaccines for which T-cell responses are essential include
                        Measles, varicella, and TB
                        Induction of T-cell immunity is goal of current efforts in
                            developing HIV vaccine
   Immunization schedules for babies-children and then a catch-up schedule
       o Pertusis added in 2005 due to increased incidence in adults and adults
                Previously was just Td (tetanus & diphtheria toxoids)
   Immunization schedule for special populations
       o Healthcare workers:
                Hep B
                   MMR
                   Influenza
      Future directions for vaccines:
          o Genetically engineered attenuation
                   Inactivate or delete a virulence gene
                   Current method: Random attenuation by passage through tissue culture
          o Hybrid virus vectors
                   Genes from infectious agents that cannot be properly attenuated can be
                      inserted in to safe viruses (vaccinia, canarypox) to form hybrids
                           Could create polyvalent vaccines: protection agains several agents
                              in single hybrid vaccine
          o Defective infectious single-cycle (DISC) virus
                   One round of virus replication may be sufficient for immunization for
                      many viruses
          o Genetically engineered subunit vaccines
                   Need to identify appropriate subunit or peptide immunogen that can elicit
                      protective antibody and, ideally, T-cell responses
                   Need to have the antigen presented in the correct conformation, then use
                      bacterial or eukaryotic plasmid vectors to express large amounts of the
                      protein subunits
          o Peptide subunit vaccines
                   Specific epitopes of microbial proteins that elicit neutralizing antibody or
                      desired T-cell responses
                           Peptide must bind MHC I or II proteins for presentation
          o Anti-idiotype antibodies
                   Antibody that recognizes the variable regions of a monoclonal
                      antipathogen antibody (like a cast of the original pathogen epitope)
          o Adjuvants
                   New generation adjuvants that activate toll-like receptors
                   Also tailor immune response (TH1 and/or TH2)
          o DNA vaccines
                   Naked DNA injected into muscle or skin, taken up by cells, and genes
                   Proteins produced elicit immune responses (TH1 and TH2)

Prion diseases:
     Rare, fatal, rapidly progressive neurodegenerative diseases that occur in humans and
       animal species
     Presence of small vacuoles within the neuropil, which produces a spongiform
           o Neuropil: The complex net of axonal dendritic and glial branchings that forms
                the bulk of the CNS gray matter of the brain and in which the nerve cell bodies lie
     Animal prion diseases:
           o Bovine spongiform encephalopathy (BSE) in cattle
                     Spiked in 1992-93, slaughtered lots of cattle to control
                 At time tapered off (~1995), variant CJD started appearing
       o Scrapie in sheep and goats
                 Fatal
                 Demonstrated to be transmissible disorder in 1930’s (sheep to goats)
                 Thought to be caused by slow virus
                        Incubation period months-years
       o Chronic wasting disease in deer and elk
       o Transmissible mink encephalopathy in farmed mink
       o Feline spongiform encephalopathy in zoological and domestic cats
       o Transmissible spongiform encephalopathy in zoological ruminants and nonhuman
   Human prion diseases:
       o Kuru
                 Fatal, occurring among the Fore people of New Guinea
                 Transmission by ritual cannibalism (brains of deceased)
                 Also proved transmissible from human to chimps in 1960’s
                 Cannibalism outlawed in 1950’s but reached epidemic levels again in
                   1980’s and 90’s because still occurring
       o Creutzfeldt-Jakob disease (CJD)
                 Recognized since 1920, fatal
                 Demonstrated to be transmissible in the 1960’s (humans to chimps)
                 LONG incubation period (30 years)
                 Median age of death 68 y.o.
                 Rapid progression 4-5 months
                 Dementia, early neurologic signs
                 Sharp waves present on electroencepthalogram (EEG)
                 Signal hyperintensity in the caudate and putamen on MRI, also in parieto-
                   occipital cortical regions
                        Non-invasive, avoids biopsy
                 Variable accumulation of PrPSc in brain tissue
       o Variant CJD
                 Median age at death: 28 y.o.
                 Longer progession ~13 months
                 Psychiatric/behavioral symptoms, painful dysthesias, delayed neuro signs
                        Depression, anxiety, eventually can’t shower or dress themselves
                 Sharp waves on EEG absent
                 Hyperintensity in caudate nucleus on MRI absent
                        But, pulvinar sign on MRI in 75% of cases
                        And, dorsalmedial thalamus “hockey-stick”
                 Marked accumulation of PrPSc in brain tissue
       o Gerstmann-Straussler-Scheinker syndrome (GSS)
       o Fatal familial insomnia (FFI)
   Early research:
       o Infectious agents were filterable meaning not cellular, therefore possibly a virus
       o Used ionizing radiation, which destroys DNA and RNA, but this did not affect
            transmission of scrapie and CJD
                   So, hypothesis in 1960’s that scrapie and CJD are cause by infectious
                    agents consisting solely of proteins
                The term “Prion” (protein + infectious) coined in 1982 by Stanley Prusiner
   Endogenous normal protein PrP: more alpha helical character
        o Surface protein
        o Reasearch published January 2010 show PrP might help maintain myelin sheath
           of nerves because when recognize wear and tear, PrP is cleaved, and the
           fragments signal activation for myelin repair by Schwann cells.
   Exogenous scrapie conformation of protein (PrPSc) : more of a beta sheet character
        o Resistant to degradation
        o Accumulates in amyloid fibrils
        o Promotes normal protein to change into abnormal, scrapie conformation
                Inhibits PrP (normal), and decreases its synthesis
        o Possibly involved in MS, multiple sclerosis
   Prion diseases and clinical practice:
        o WHO and disease control & prevention recommend instrumentation be destroyed
           after use
        o Or secondary to destruction, suggest combination decontamination to process
           instruments that come in contact with high-infectivity tissues
        o No cases of iatrogenic transmission of CJD have been reported since current
           sterilization procedures adopted in 1976

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