Virology Review antiviral drug by benbenzhou


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									Virology Review

1. Virus Basics
       A. Small Obligate Intracellular Pathogens
       B. Classification based on
               a. biological properties
               b. physical properties/chemical properties
                       viral-specific nucleic acids
                       viral-specific proteins
                       lipid envelope = fragments of cell membranes with viral
                               i. created by trafficking viral envelope proteins to specific
                                        cell membrane (not necessarily PM) and then
                                        allowing them to congregate, pushing host proteins
                                        to other portions of the membrane
                               ii. extracellular portion is glycosylated and hydrophilic
                               iii. transmembrane domain is hydrophobic
                               iv. cytosolic domain is non glycosylated and hydrophilic
                               v. causes virus to be very sensitive to acids, lipid solvents;
                                        can not infect GI tract due to bile; often transmitted
                                        in dry, non-aqueous environment; in general, less
                                        stable than non enveloped viruses
                               vi. allows cell to cell fusion to create giant multinucleated
                                        cells and syncytia
                               vii. much harder to crystallize; pleomorphism more
                                        pronounced with enveloped viruses
                               vii. allow virus two pathways for entry: fusion with host
                                        membrane (these can then form giant
                                        multinucleated cells), or endocytosis of entire
                                        envelope-fusion protein expressed later, in
                       nucleocapsid = a regularly organized nucleoprotein structure
                               i. morphology can be icosahedral/spherical, helical rod, or
                                        more complex
                                        Capsomeres naturally form bagel shape
                                        Interaction with RNA causes spiral shape
                                        Size of genome determines length
                                        Can be stiff or flexible
                                        Size fixed by geometry, genome size determined by
                                        20 faces, 12 vertices
                                        May have appendages at each vertex
                               ii. condenses and confines the viral genome
                               iii. can be crystallized
                               iv. robust, yet permeable to small molecules
                                        (allows antiviral drugs such as AZT to enter)
                                        impermeable to potentially harmful proteases, etc.
                               v. rough topography – allows interaction with cell, can be
                                        epitopes for neutralizing antibody
                               vi. does NOT include the envelope, but does include viral
                                        enzymes carried with the virus
                               vii. used to classify viruses into families
                               viii. can be visualized by EM after assembly in cells
       C. Called Virions when extracellular
              VIRION CONSISTS OF
              a. nucleic acid (DNA or RNA, ds or ss, linear or circular)
                       usually in one piece, sometimes segmented
                       small genomes = simpler capsids, smaller virions, more parasitic
                       large genomes = complex capsids, larger virions, more autonomic
              b. protein
                       structural = capsid; one or a few repeating protein units termed
                                        capsomers or capsomeres
                                   = glycoprotein for envelope
                       Enzymes (replication and compaction of genome)
              c. lipid envelope (not all)
                       from host cell membrane
                       virus imbeds viral glycoproteins (external domains bear
                               carbohydrate groups and often constitute major antigens)

       D. Very important replication cycle—see main point 4
                a. structure varies during cycle and each variant = possible target of drugs
                b. no cell free replication
                c. when escaping from the cell:
                IF ENVELOPED, then cytosolic domain of glycoprotein interacts
                (sometimes via a matrix protein) with nucleocapsid and causes it to dock
                at that location before budding through this portion of the membrane—no
                damage to host membrane
                CAN CAUSE LYSIS OF CELL (all non-enveloped viruses and some
                enveloped viruses
2. Virus History
       A. first discovered as plant, animal, human, and bacterial pathogen
       B. Passed through filters used to catch bacteria
                a. seen as small, filterable intracellular pathogens
                b. later, smaller filters used to measure various sized virions
               c. now, many other types of small filterable pathogens identified
                        viroids (no protein, only single stranded circular RNA genome, no
                                ORFs, only seen in plants—transmissable RNA plasmids
                                found in plant nuclei)
                        prions (no nucleic acid, a rogue protein that acts as a template,
                                the gene for the correctly folded protein found in cell DNA)
                                some prions: scrapie in sheep and goats
                                               kuru in humans
                                               Creutzfeld-Jacob agent in humans
                                               Mad Cow disease in cows
       C. Determined to have unique infectious doses
       D. First virus to be purified and analyzed chemically = tobacco mosaic virus
3. Virus Classification
Based on characteristics listed in 1. B. (esp.genome, virion structure, replication strategy)

4. Virus Replication
Transcription – one enzyme required, one reaction
        DNA dep. RNA pol I – rRNA
        DNA dep. RNA pol II – mRNA
        DNA dep. RNA pol III – snRNA (for splicing), tRNA
RT – two enzymatic activities (RTase, RNaseH), three reactions
        ss (+) RNA – (+) RNA : (-) DNA (a hybrid duplex made by RTase)
        hybrid – ss (-) DNA (RNA is chewed up by RNaseH)
        ss (-) DNA – ds DNA (RT action going on here)
        NOTE that RT can also accept ssDNA as an initial template (fidelity is low)
        No amplification occurs at RT step—must occur at transcription step in nucleus
        Both enzymes are on one protein, coded for in one ORF
        Occurs in cytoplasm
        All processes have some infidelity, most mistakes are lethal
        For DNA based schemes, fidelity is high (1 mistake every 108 nt, 105 nt in
                genome, so 1 mistake every 1000 genomes)
                Why so low? have access to DNA repair mechanisms:
                        Cells ―do not like‖ ss DNA—this is a signal for repair enzymes
                        A nt mismatch creates torsional stress which is sensed by enzymes
                                Mismatched enzyme + area around it is excised and
                        3’ to 5’ exonuclease proofreading capability
        RNA based, RT schemes have lower fidelity (HIV, HCV esp.)
                Phenomenon can evidence itself in the following ways (good and bad):
                Development of live attenuated vaccines – virus mutates easily while in
                        animal to produce strain no longer virulent in humans
                Reverse of live attenuated vaccine to virulent strain
                 Development of drug resistance within a strain (antigenic drift)
                 Ability of same virus to re-infect individual who has previously developed
                         resistance to the virus
         Most drugs attempt to slow down replication process for many reasons, one of
                 which is to slow down the creation of drug resistant strains
         Quasispecies Concept
                 1 error/genome – all progeny are unique
                 Can take advantage of this, amplify it and cause species to be nonviable
                 Can create drug immunity within one patient
                 Creates possibility for new drug approach: incr. mutation rate to the point
                         that all progeny are non viable—but this most be very specific so
                         as to not harm the cell
Not necessarily the central dogma anymore
DNA-based (still the central dogma)
The larger the genome, the more autonomous
         Pox has its own DNA dependent DNA and RNA polymerase so it does not have
         to go to the nucleus
         Herpes, Adeno have their own DNA dependent RNA polymerase
Must make mRNA from DNA in order to make virion proteins
Because DNA dependent RNA Pol II is found in nucleus, replication takes place here
         Also: mRNA requires 3’ Cap and 5’ poly A tail, also found in nucleus
All ―flavors‖ require RNA dependent RNA polymerase which must be viral (no host cell
can provide this), and each virus except Delta codes for its own enzyme, which is specific
for each virus (attracted to a specific RNA sequence)
NO need to go to nucleus—no 3’ cap, 5’ poly A tail, splicing
Plus sense, ss: can immediately be translated
Minus sense: RNA is complement of message, must make + sense first
         No 5’ cap or 3’ tail, so must use a viral protein translated during previous
ds RNA: must use protein from previous infection (must make + sense RNA from ds
RNA before translation to protein)
Each virus must code for their own telomerase and RT/RNAseH combo enzyme
Two families
RNA – RT (in cytoplasm) – ds DNA – transcription (in nucleus) – + sense RNA
This product is both packaged and used as an mRNA for protein synthesis
In Detail: see above
Partially dsDNA – RT (in cytoplasem) – dsDNA – transcription (in nucleus) – ss (+)
RNA – RT (in virus) – partially dsDNA
In reality, the RTase and ss (+) RNA are packaged together in capsid and process
continues there. DNA does not become fully ds until next host cytoplasm
In Detail: partial ds DNA –(RTase)— ds DNA –(transcription)—ss (+) RNA – (RTase) –
partial ds DNA (this last step is synonymous to that of retroviruses)

The simplest DNA virus has one gene (capsid)
The simplest RNA virus has two genes (capsid and RNA dep RNA pol)
The simplest enveloped DNA virus has two genes
The simplest enveloped RNA virus has three genes

5. Viral Life Cycle and Targets for Drugs
Extracellular Stage
Virion provides stability
Intracellular Stage
Replicates only during this stage
Dependent on host infrastructure for: synthesis, processing of viral proteins, energy
metabolism, and membrane structures
One virus’s interaction with one cell can be divided into:
    1. Attachment/Adsorption
        Can result in tissue tropism; unique viruses for humans vs. animals, etc.
        Some cell receptors require cell co-receptors for docking and entry of virus
        Most cellular receptors have other, normal functions as well
                The receptor: protein or carbohydrate
        Normally, if a cell has the receptor it will allow the virus to replicate in it
                Exceptions: RBCs – virus enters, does not replicate, several tests
                (hemagglutination and hemadsorption) take advantage of this
        Drugs: block virus entry and docking by binding virus or coating virus
(neutralizing antibody, capsid binding drugs). This has required the solving of the crystal
structure of the virus, the cellular receptor or the viral attachment protein.
        Example: WIN compounds developed against human Rhinoviruses (common
cold), which is in the family picornavirus. 80% of the 108 serotypes of rhinoviruses have
same receptor (ICAM-1) and highly conserved receptor binding sites. Drug binds a
putative receptor binding site (a hydrophobic pocket).
        Pleconaril – treats several picornaviruses (binds a more general and conserved
spot on the virion surface). But it interferes with common birth control and does not have
FDA approval.

   2. Penetration (3 options)
         a. Receptor Mediated Endocytosis or Viropexis
                  i. if enveloped, then has a cryptic/inactive fusogenic protein, will be
                     activated within the endosome and cause fusion within the
                     endosome—no multinucleate giant cells
         b. Pore Formation
         c. Fusion
                  i. Active fusogenic protein (can create giant multinucleated cells)
   3. Uncoating
         a. Virion proteins are removed
      b. Nucleic acid transported to appropriate location (cytoplasm or nucleus)
      c. Drug Example: Amantadine and Rimantadine act on M2 protein, blocking
          ion channel pore for H+ entry into influenza A (NOT B) virion after
          endocytosis (Virion requires low pH for activation of glycoprotein HA
          which mediates the 2nd stage of uncoating in which matrix proteins are
          loosened from RNA)
4. Synthesis
      a. Replication of genome and synthesis/translation of viral transcripts
      b. Drug Examples: Inhibitors of Viral DNA Synthesis
               i. Nucleoside Analogues – chain terminators, must first be converted
                  to the triphosphate form. All but GCV lack 3’ –OH group
                      1. ACV acyclovir (dG) – HSV, VZV
                      2. GCV ganciclovir (dG) – CMV
                      3. AZT azidothymidine/zidovudine (dT) – HIV
                      4. ddI dideoxyinosine/didanosine (dA) – HIV
                      5. 3TC lamivudine (dC) – HIV, HBV
              ii. Nucleoside monophosphate analog = Adefovir (dAMP analog)
                  treats HIV, HBV; become adefovir diphosphate; chain terminator
             iii. Pyrophosphate analog = foscarnet, treats HSV, CMV, HIV
             iv. Non-nucleoside analog = neviparine which binds to HIV RT,
                  inhibits DNA Pol activity
              v. Others: Ribavirin (rG analog) treats RSV, Lassa, HCV; must be
                  phosphorylated; active in RNA reactions, GTP synthesis; also acts
                  as an immunomodulator
                           Interferons (alpha, beta, gamma) – cytokines, can be
                  induced by administration of dsRNA, result in antiviral and
                  immunomodulatory responses (incr. transcription of about 100
                  genes to block RNA and protein synthesis); most effective against
                  RNA viruses
5. Maturation
      a. Must reach certain concentration within the cell
      b. Self assembly by noncovalent protein-protein and protein-nucleic acid
      c. Packaging signals on RNA sequence binds to structural protein
      d. Segmented genomes must include all segments, each is packaged
      e. Create large aggregates, can sometimes be seen as viral inclusion bodies
                  Rabies ----- Negri bodies (cytoplasmic)
                  Smallpox – Guarnieri bodies (cytoplasmic)
                  Measles --- Nuclear and cytoplasmic bodies
                  JC ---------- nuclear (method by which it was first discovered)
      f. Drugs: use protease inhibitors to prevent maturation
      g. Examples: Indinavir, Saquinavir, Ritonavir inhibits proteases for HIV
      h. Examples: Zanamivir is an analog of the viral receptor, sialic acid; treats
          Influenza A and B
6. Release
           a. Lysis
                     i. Viral Encoded toxic products – program the death of the cell
                    ii. Metabolic stress
                   iii. Apoptosis by cell (can prevent virus from being spread—so some
                        viruses prevent apoptosis)
           b. Budding
                     i. Only seen with enveloped viruses
                    ii. Cell not damaged (if damaged, then by immune system)
Some terms for a bigger picture view:
Multiplicity of Infection – number of virions infecting each cell (at onset of infection)
Eclipse Period – no virus found in culture, ends with viral assembly
       Early – prior to genome synthesis; genes for synthesis of viral enzymes which
                will regulate late processes are transcribed
       Late – onset of genome synthesis; genes for late proteins are predominantly
                virion/structural proteins
Latent Period – includes eclipse period, from time of infection until first virions naturally
would be released from the cell
Yield – same as the burst size; the number of progeny released from one cell.
NOTE If the virion kills the cell, then it is called a plaque forming unit (PFU)
The virus’s goals:
To reproduce multiple copies of genome
To program synthesis of proteins
To package these together such that they can infect more cells
       Def: the process by which the viral lifecycle in the host produces manifestations
       of disease
NOTE: most pathogens do not have a primary goal of causing disease or death in the
       host, this is often a secondary characteristic
Exceptions: enteric viruses which cause diarrhea in order to spread via fecal oral route
                Respiratory viruses which cause coughing for spread of virion
1. Viruses which have had human hosts for a long time, or which even co-evolved with
       humans are less likely to cause life threatening disease (chronic instead)
2. Viruses which are new to human hosts are more pathogenic

Many viruses transitioned to humans during the time many humans were first
      domesticating animals

Stages in pathogenesis:
   1. entry
           a. skin
                   i. epidermal infection – localized
                  ii. dermis – dissemination after localized primary infection
                 iii. subcutaneous – animal bites, needle sticks—more likely to be
           b. respiratory tract
                   i. via aerosolized droplets
                  ii. deposited in tracheo brochial tree (largest in upper, smaller in
                      lower respiratory tract)
                 iii. barriers include mucus, ciliated epi, secretory IgA, lymphocytes,
                      neutrophils, alveolar macrophages
         c. GI tract
                   i. A formidable barrier, esp. to enveloped viruses
                  ii. Barriers: pH, maternal IgA, proteolytic digestion
                 iii. Can cross M cells to become systemic
         d. GU tract
                   i. Sexually transmitted disease entry often facilitated by abrasions or
                      tears in the mucosa
         e. Conjunctiva
                   i. Due to dirty contact lenses
                  ii. Localized if it begins here
                 iii. Can be a portion of a systemic infection that began elsewhere
2.   replication at primary site
3.   dissemination
         a. If virus undergoes basolateral membrane maturation – deeper tissues
         b. If virus undergoes apical surface maturation – release into lumen
         c. Hematogenous spread (in bloodstream = viremia), often goes from
             primary site to regional lymph nodes, to efferent lymphatics, to blood via
             thoracic duct
         d. Invasion of CNS
                   i. Blood brain barrier = tight junctions b/t capillary endothelial cells
                      + dense basement membrane
                  ii. Can enter: by replication in cells, through endocytotic vesicles, via
                      infected immune cell, through choroids plexus area, through
                      successive neurons
4.   cell and tissue tropism
         a. due to:
                   i. receptors
                  ii. transcription factors
                 iii. mitotic state of cell
                 iv. presence of needed enzymes
5.   host response
         a. Specific Immunity
                   i. Humoral antibodies (IgM (3-4 days after infection), IgG (4 days
                      after IgM), IgA) – neutralization, opsonization, iniation of
                      complement, antibody dependent complement mediated cytolysis
                  ii. Cell mediated immunity – targets viral epitopes presented with
                      MHC molecules
                          1. CTL (cytolytic T lymphocyte = CD8+), peak 7-14 days
                              after infection begins
                          2. release of cytokines, chemokines, etc.
          b. Non-specific Immunity
                    i. Cytokines
                           1. interferons (INF alpha, beta, gamma)
                           2. tumor necrosis factor (TNF alpha)
                           3. interleukins (IL-1beta, IL-6)
                   ii. NK cells
                  iii. activate 12-24 hours after infection
                  iv. can accelerate specific response
   6. cell and tissue injury
          a. virus-induced cell death
                    i. inhibition of cellular macromolecular synthesis (inhibition of CAP
                       mediated protein synthesis)
                   ii. fusion to form syncytium
                  iii. induced apoptosis
          b. immunopathology
                    i. immune complex disease (deposition in kidney)
                   ii. immune enhancement (virus:antibody complex infect macrophage,
                  iii. antigenic/molecular mimicry

   7. clearance or persistance

Questions concerning pathogenesis:
   1. Does replication cause disease?
   2. Does the virus directly cause cell death and how much cell death can be tolerated?
   3. Is the infection localized or systemic?
   4. How does the virus spread from host to host?
   5. Is the infection acute or chronic?
   6. What affect does the host response have on the infection?
   7. How does the virus avoid the immune response?


Polio Pathogenesis

Acute, systemic, enteroviral (but no significant enteritis), no immune evasion (no
persistence—remember that subsequent deterioration is due to neuron loss with age)
Mainly asymptomatic cases (90%)
Neurovirulence—kills infected neurons of CNS
Differences amongst strains
All induce protective immunity
Vaccines = OPV or Sabine (live, attenuated) and IPV or Salk (inactivated, killed) form
        Both: induce protective immune responses, encode vial protein that kills infected
        Passaged through many animal hosts, mutagenic drift taken advantage of
       Temp sensitive for replication at 37 C
       Still encodes cell-toxic protein—can produce IgA response in gut, but also can
               revert to neurotoxic form
       Now the primary vaccine used
Influenza A Pathogenesis

Acute, localized to respiratory tract
Differences amongst strains—will undergo drift and shift to enhance virulence
Pandemics in the pasts

Herpes Group Pathogenesis

Latency and Reactivation common (can occur many times within one host)
        Each reactivation allows virus to be spread and reseeds host with more latent
Latency = period in which infected cell does not produce viral progeny, no symptoms,
only a subset of viral genes is expressed
HSV and VZV – latently infect neurons
        No HLA-1 expressed on neurons, thus immune evasion is accomplished
Latency occurs during the eclipse period, no early events initiated
        The Herpes eclipse period involves:
        Immediate-Early Events
        Early Events
        Onset of Viral DNA Synthesis
        Late Events
Reactivation = virus again produces progeny, may be associated with secondary infection


Hepatitis B Viral Infection
Can cause transient and chronic infection
Determined by:
Gender (males who are infected at birth are more likely to develop chronic disease, while
females will clear infection at puberty)
Age (neonates are less likely to get acute infection because immune system is not mature)
Most liver damage is due to immune system, versus the direct viral action
       Can result in liver cancer


Caused by the variola virus
Natural portal is the oropharynx and respiratory tree
Systemic infection, 50-60% mortality
Vaccine = vaccinia (live attenuated virus that can protect against variola) or variola
Vaccinia can itself cause disease in an immunocompromised host
Variola introduced in non-natural portal, causes localized infection on skin, 1-2%

Causes respiratory infections in situations involving close quarters
        Military requires vaccines for those in boot camps
Portal of entry = oropharynx and upper respiratory tract
Vaccine = wild type, in a capsule, went directly to GI tract, enteric infection, no
pathogenesis, produced excellent immunity


Influenza virus
H = hemagglutinin, for attachment to host cell receptor (ubiquitous, polymers of sialic
acid covalently attached to cell surface glycoproteins)
H must be cleaved by protease to create H1 and H2 (linked by S-S) and expose fusogenic
peptide within H
This protease only released by specialized epithelial cells or bacteria (Haemophilus,
Staphylococcus, Streptococcus) in the respiratory tree
If H is mutated such that it is not dependent on the protease, then causes systemic disease
        The mutation = a series of basic aa’s at cleavage site, thus cleavable by a more
                ubiquitous enzyme
        This is what occurred in the avian influenza (can not be spread human to
                human so far)
        Such mutations (genetic shifts = reorganization/reassertion of segmented genes
                (vs. drift which is not such a big deal)) can occur esp. when multiple
                viruses infect one host cell
        Leads to pandemics
                Risk factors for influenza: age, underlying medical problem, immune
status, presence of new viral structural genes (shift or drift)

Hepatitis Viruses

Hepatitis = inflammatory disease of the liver

Liver Review
Bilirubin uptake
Drug Clearance
Bile secretion
Serum protein synthesis
Cholesterol and lipoprotein metabolism
Carbohydrate Metabolism and Storage

SO, it can be a gland (secretes stuff) or a ―kidney‖ (filters blood)
Liver Damage
ALT, AST in blood
Bilirubin in tissues = jaundice
Bilirubin in urine = dark urine
Reduced Bile in feces = pale feces
RUQ pain

Acute vs. Chronic
Acute: Less than 6 mo. vs. chronic: lifetime
Acute can become fulminant, with rapid onset, severe course, high mortality, mediated by
cascade of cytokines

Further Divisions of Chronic Hepatitis
Chronic Persistant Hepatitis (CPH) – Chronic Active Hepatitis (CAH) – Cirrhosis
(preliminary to liver failure) – Primary Hepatocellular Carcinoma (due to attempt by liver
to make lots more hepatocytes)

The various Hebatitis-es

HAV/Picornavirus (enterovirus)
EBV/Espstein-Barr virus (a Herpesvirus)
CMV/cytomegalovirus (a Herpesvirus)

Blue = secretion with the bile, fecal/oral transmission, acute form only, no envelope
Red = secretion into the blood, most body fluids contaiminated, parenternal (IV)
transmission, acute and chronic forms, enveloped
Green = mild hepatitis

HAV/Picornavirus (enterovirus)
No Envelope, Icosahedral (60 capsomers (3/face), each has four components, VP1-4)
ss+RNA, one ORF
has NTRs (includes packaging info) on both ends
no 5’ CAP, but does have an IRES in 5’ NTR (so uses a CAP independent pathway), and
a viral protein VPg covalently linked at 5’ terminus (for penetration, uncoating, RNA
replication, and packaging)
The IRES is a Internal Ribosome Entry Site, in the form of a loop or ―landing pad‖
The IRES is not very efficient at attracting host ribosomes, so the virus does not create a
large amount of stress on the hepatocytes--not cytolytic (unlike poliovirus, another
As a result, most of the damage is immune system-generated: CTL binds MHC 1 + viral
Viral Proteins
Viral coded proteases process polyprotein into progeny capsid and non capsid proteins
This protease does NOT inactivate host cell proteins that associate with capped mRNAs
These proteases are coded on the mRNA and work in trans—each clips the other out
P1 = structural proteins (VP1-4)
P2 and P3 = proteases, VPg
Fecal cocktail – crosses intestine epithelium (GI is probably the initial replication site) –
blood – virus spreads through liver – gets into bile, Fecal HA Ag appears – ALT levels
rise precipitously – symptoms appear – IgM Anti HAV appears – leads to IgG Anti HAV
appearance with T cell help, cytotoxic T cells (these four are almost simultaneous) –
symptoms go away, ALT levels drop -- IgM levels fall – all infected cells cleared and
Clinical Features
symptoms: nausea, vomiting, jaundice, RUQ pain, black urine, pale stools
Hepatocyte damage likely due to CTL (immunopathogenesis)
life threatening only if fulminant
If young, may be asymptomatic (possibly due to poor CMI response)
Reservoir = humans only
Difficult to control (shed before symptoms appear)
Stable in environment (no envelope)
Fecal-oral route, anal sex, changing diapers, shellfish, poor hygiene of food handlers,
contaminated blood (rare)
Hygiene, decontamination of raw sewage
Killed HAV vaccine (travelers, risk groups, school kids in some districts)
Immune serum globulin for passive immunity (not as useful as in past)

HEV/Calicivirus (very similar to HAV, differences highlighted in green)
no envelope, icosahedreal
ss+RNA, three ORFs
Viral proteins
one of the ORF’s – a polyprotein processed by a viral protease
Clinical Features
Fecal – oral route
High rate of fulminant hepatitis, 20% mortality in pregnant women (in comparison to
Endemic in third world, uncommon in US
Epidemics due to contaminated water supply
All domestic pigs in US infected
Clinical signs + history, exclusion of other causes
Serology available through CDC
Supportive only
No vaccine (a recombined vaccine is under development)

Partially ds circular DNA, four ORFs that are all overlapping w/o any non-coding bases
        + strand is incomplete, this is the one coding strand for all the ORFs
        Because all bases are used, the sequence rarely changes
        One or two ORFs are each in one of the 3 reading frames
        First transcription goes past polyA tail to make the strand 1.1 genomes long
                 Frame 1: ORF-C w/o Pre-C = capsid, HBcAg (hep B core antigen)
                         And, w/ Pre C = HBeAg (compositionally similar to HBcAg but
                         does not react with the same antibody)
                         Pre-C (a signal polypeptide) takes product to ER where Pre-C is
                         cleaved to make HBeAg
                         Also in this frame: X = regulatory protein (transcriptional
                 Frame 2: ORF-P = multifactorial protein, contains priming domain,
                         RTase, RNase. It is involved in RT w/i the nucleocapsid
                 Frame 3: ORF-S = surface proteins
                         Three different in frame start codons encode for 3 proteins, L
                                (large), M (medium), and S (small) envelope proteins
                                L = Pre S1 + PreS2 + S
                                M = PreS2 + S
                         Each is synthesized independently, S predominates, antibodies
                                directed at S can react with the other two
Virion = Dane particle, found at low concentrations w/i cell (no HBeAg)
Majority of the HBsAg in small spherical particles (excess envelope antigen) which is not
infectious, called the Australian antigen (the discovery of these spawned idea of subunit
Process observed:
Partially ds DNA – fully ds DNA, ―covalently closed circular duplex DNA‖ or
―cccDNA‖ if you will – goes to nucleus – does not integrate – host DNA dep RNA pol II
transcribes it – mRNA synthesized for protein synthesis – genome sized RNA
synthesized (the pregenome) – pregenome packaged into capsid of HBcAg =
nucleocapsid – also in capsid is the viral polymerase protein (primer + RTase + RNase) –
RT reactions occur in hepatocyte cytoplasm

The level of virus in each cell is closely regulated so as not to overstress the cell
(in HIV patients, levels get very high w/o bad side effects b/c immune system is blah)
Symptoms due to immunopathogenesis (CTLs directed at HBe or HBc Ag)
Clinical Features
Most are subclinical, even if acute (but great variability from no symptoms to fulminant)
In kids, chronic subclinical is common
In immunosuppressed, always asymptomatic and persistent
If acute, you will get:
        Strong immune response, life long immunity (anti-HBs Ab is neutralizing and
If chronic, you can get:
        Acute episode with either intermediate immune reaction or no symptoms
        Many will have low level of infection in the bile duct epi, pancreas, spleen,
                kidney, lymphocytes
        Eventually (after a long asymptomatic period):
                Recovery with anti-HBs Ab OR (the bad news)
                Chronic persistant hepatitis -- Chronic active hepatitis -- Primary
                        Hepatocellular carcinoma (NOTE that HBV DNA integration is an
                        artifact—does not cause the cancer)
        This generally takes 30+ years
If you have mutant strain:
        Pre-core mutant has no HBe Ag – causes fulminant hepatitis (cause for belief that
                HBe is a toleragen)
Polyarteritis, glomerulonephritis (if Ag:Ab complexes present)

Good clinical sign: development of anti HBe Ab
      Reduced serum infectibility (viremia)
      Less replication in liver
      Lesser rate of immune mediated damage to liver

High carriage: Asia, sub-Saharan Africa, Aleuts, American Indians, Polynesians
Low: western Europe, Caucasian Americans
In US, transmission mainly by sex
Also: perenteral inoculations, vertical transmission (highest titer in blood), saliva
        For vertical transmission, mother must be HBsAg and HBeAg + (chronic)
Highest risk group: teens and college age adults
Serology—this is the crazy window period one
Antigen – Anti HBc (IgM then IgG) –ALT/Symptoms – Antigens go away – Anti HBe –
The WINDOW: the period of time during which HBs Ag has gone away and the anit HBs
Ab has not yet appeared
No HBs Ab, but HBs Ag remains, symptoms may not appear
Vaccine! Subunit vaccine made of recombinant HBs Ag
       3 shot sequence
       Universal vaccination of newborns, jobs with infection risk
       Is effective in post exposure setting for one week
Passive immunization to:
       Neonates of carrier mom given HBIG (Hep B immune globin) along with vaccine
       Individuals exposed to infection
       Interferon (not very effective, only for non Asians)
       Those that also inhibit HIV: Lamivudine (3TC) chain terminator; inhibits RTase
                                               at both RTase steps, but effectiveness
                                               longterm is uncertain, must be
                                               phosphorylated three times
                                       Adefovir (dAMP analog) chain terminator, active
                                               after 2 phosphorylations
       Penciclovir – chain terminator, resistance arises with mutated RTases, used in
               liver transplant patients carrying HBV
       NO AZT!!! (conjugated by liver with glucuronic acid, can not be phophorylated)
       NO PROTEAE INHIBITORS—HBV does not encode corresponding viral
       Entecavir (dG analog) chain terminator; must be phophorylated three times
       All chain terminators have bad side effect of affecting hepatocyte mitochondrial
polymerases, causes hepatocytes to die

HCV/Flavivirus (formerly known as: post transfusion nonA, nonB hepatitis virus)
Enveloped, icosahedral
ss+ RNA, no 5’ CAP, IRES in 5’NTR
translated at entry into cell (no virion associated polymerase)
one ORF
much variation in exact sequence: 6 genotypes identified, 1, 2, and 3 are the most
Polypeptide cleaved by cellular and viral proteases
C = capsid
E1, E2 = glycoproteins on envelope
NS = proteases, RNA dep RNA polymerase
Not grown in cell culture so replication cycle unknown
Damage to hepatocytes from both virus and immune system (CTLs)
ALT rises – symptoms – THEN Anti HCV Ab seen – ALT fluctuates chronically (cycles
of immune attack on liver, liver damage)
Immune system can be repressed and course of infection does not change
Clinical Features
Lower serum ALT than HBV
Often presents in sequential epidsodes
Primarily asymptomatic
Most become chronic (70-100%)
If Chronic:
        40% get cirrhosis and then hepatocellular carcinoma
SO, HCV is leading cause of chronic hepatitis cirrhosis and request for liver transplants
Reservoir = humans
Blood borne (80% prevalence in IV drug users)
        Now removed from blood supply
Transmitted by blood, during sex, vertically (last two are not as common as with HBV)
Serology: positive for anti HCV means on going infection and viremia (not recovery)
ELISA used for Ab, RT PCR for viral RNA
Interferon response seems key for viral clearance
        INF-alpha licensed as a treatment, but rebounds after treatment often seen
        INF + ribavirin (rG analog) (best for genotypes 2 and 3)
Example of a quasi-species, so virus undergoes antigenic drift w/i the one patient, hard to
        develop immunity as a result
        NO vaccine, no hyperimmune serum
Vaccinate for A and B

HDV/Deltavirus (formerly known as the delta agent…fly hepatitis…D is for deficient)
Enveloped, no shape known b/c nucleocapsid is so fragile
Envelope proteins parasitized from HBV
Small circular ss- RNA
One ORF = HD antigen (internal core antigen)
The RNA is an ribozyme as well—can self cleave and self ligate
Is defective! Does not have genes for its own lipoprotein envelope or for replication of
        RNA genome
Must replicate in cells also infected with HBV
Depends on host cell DNA dep RNA pol II for replication—the RNA has a sequence in it
        that looks like ds DNA promoter (intrastrand base pairs—the molecule is ss, but it
        is collapsed so much of it forms a ds structure) so host enzyme will recognize it.
Clinical Features
When a co-infection with HBV it is more aggressive and higher mortality than otherwise
2 infection settings: Naïve patients get both HBV and HDV at the same time
                              Acute episodes for both viruses
                              Appears bi-phasic (HBV then HDV)
                              High but transient HDV viremia
                              When HBV cleared, HDV is as well
For HDV portion of infection, this looks like:
HBsAg – HDV RNA and HDAg – ALT rises and symptoms come – IgM Anti HD
comes, goes – IgG Anti HD appears – symptoms subside
                      HBV carrier gets HDV as a superinfection
                              Usually chronic for both, with faster progression than if
                              alone (but this is determined by host immune system)
For HDV portion of infection, this looks like:
HBsAg, HDAg/HD RNA – ALT rises – IgG and IgM Anti HD appear – nothing fades
Outbreaks in IV drug users
Transmission by blood, sex, saliva
Detection of HD Ag or Anit HD Ab
No vaccine or specific treatment
BUT vaccine against HBV protects against HDV (all NDV needs is the surface antigen)
A double edged sword: once infected with HBV, must get rid of all (normally
nonpathogenic) surface antigen to protect self against HDV

Childhood Diseases
Measels Virus
Pleomorphic paramyxovirus (subgroup: morbillivirus)
Helical nucleocapsid
Outer lipoprotein envelope
         Has spikes: one has hemagglutinating activity (H)
                       one has cell fusion activity (F)
                       NO neuraminidase activity
ss – RNA
viral encoded RNA dep RNA polymerase in the virion
F synthesis:
F0 (inactive) – cleaved by host protease (Golgi pathway) – fusion can now occur and
virus can penetrate
If F is displayed on surface of infected cell, fusion can occur – virus spread and formation
of giant multinucleated cells
Clinical Features
Ratcheting high fever – cough, coryza, conjunctivitis – rash (first on head and neck and
then all over body) – red lesions (Koplik’s spots) with white centers appear on buccal
Arrests childhood development, rarely are CNS infection symptomatic in children
Complications: encephalomyelitis (virus always reaches brain but does not always cause
                         infection here—this is a result of a post-infection autoimmune
                         attack on measles which have formed inclusion bodies)
                Primary measles or giant cell pneumonia (immunocompromised hosts)
                         Fusion protein causes infected cell to fuse with healthy ones
                Keratoconjunctivities (children with nutritional deficits)
                Secondary bacterial pneumonia
                Subacute sclerosing panencephalitis (SSPE) (follows primary measles 7-
                         10 years later, rare, a progressive neurological disorder, associated
                         with inflammation of the brain, due to a reactivation or improper
                         immune response to the virus
Side Effect of the old killed measles vaccine: Atypical measles
        After vaccinated, patients were infected with measles, got an atypical rash (no
        Koplik’s spots) and often a serious pneumonitis infection. If a child was
        malnourished, their ability to suckle was diminished and thus they became even
        more malnourished.
Induce both nuclear and cytoplasmic inclusion bodies
Inhalation of aerosoled droplets (survives in droplets for hours) – respiratory tract mucosa
– regional lymph nodes – primary viremia – reticuloendothelial system – secondary
viremia – lymphoid cells (including the skin) – characteristic lesions
Rash is the result of host CMI response
        if immunocompromised—no rash, but persistent infection, often w/ complications
A twist: the virus itself depresses the immune response (even the MMR vaccine)
        Latent viruses can reactivate
Only one serotype so natural infection – lifelong immunity
        Neutralizing Ab directed at H
Neonates protected by mother’s Ab for 6 months
Spread before onset of disease (4 days before rash, 4 days during rash)
High mortality due to poor nutrition, immunosuppressive nature
Must have high density of humans to become endemic
Clinical symptoms
No therapy after infection
        Two day course of Vit A reduces severity
Attenuated vaccine (part of MMR) – two doses (12 months and 24 months—do not wait
        until 16 months at which point all maternal Ab are definitely gone)
Due to poor vaccination methods, numbers of measles cases rose from 1984 to 1992, then
        changes made and now under control again
Mumps Virus
Pleomorphic paramyxovirus
Envelope with two glycoprotein spikes
        1. has both H and N activity
        2. has F activity
(-) ss RNA
Clinical Features
18 day asymptomatic incubation (virus replicates in upper resp. tract) – draining lymph
nodes – viremia – viremic spread to parotid gland and epi of various organs (kidneys,
ovaries, testes) – swollen salivary glands – cell lysis and the development of giant cells
Overview of process:
Exposure – shedding – parotitis/viruria – parotitis ends, Ab appears, shedding ends –
viruria ends
1/3 are subclinical
Usually benign, esp in children (no intervention)
Complications: orchitis (acute inflammatory reaction of the testis, can lead to sterility)
                Aseptic meningitis (usually subclinical)
                Post infectious encephalitis

Transcription, translation, assembly occur in cytoplasm
One serotype, so immunity is lifelong and complete
Neutralizing Ab directed at HN Ag
Once Ab found in saliva, virus excretion ends (begins ~6 days prior to symptoms)
Maternal Ab can cross placenta to protect the neonate
Spread via aerosolized droplets, peak in winter and spring
Clinical symptoms
Culture—antiviral Ab may be detected in the convalescent serum
Immunization with live attenuated vaccine (part of the MMR vaccine)
No antiviral therapy will work

Rubella Virus (Togavirus Family)-similar to measles
Spherical nucleocapsid
No RNA dep. RNA pol in the virion
(+) ss RNA
No fusion protein—no cell to cell spread, dependent on viremia
Clinical Course
Aerosolized droplet – Asymptomatic period (14-21 days) during which virus travels to
nasopharynx and local lymph nodes – viremia – rash (first on face, then extremities) for 3
Most are subclinical, uncomplicated
More serious when non immune pregnant woman infected: congenital rubella syndrome
       Spontaneous abortion
       If born, child may develop hearing loss and/or cataracts (not necessarily present at
       Child is usually a persistent carrier of the virus, constantly sheds virus
Replication and maturation confined to the cytoplasm
Virions bud from the cytoplasmic membrane
Natural infection = lifelong immunity
Ab cross placenta to provide some protection for the neonate
Usually is seen in springtime
Endemic worldwide
Only togavirus to not use an arthropod vector
Clinical symptoms, immune status
Culture for virus
Vaccination of children (MMR)

Human Herpesvirus 6 and 7=Roseola or Sixth Disease
Icosahedral, covered with envelope with spiked molecules embedded
ds DNA
Clinical Symptoms
Primarily found in children under 2
High fever and a red rash—v. high fever, scary to parents, but also v. common, usually
occurs around 6-12 months when mother’s immunity goes away
Usually resolves in 3-5 days w/o complications or sequelae, often asymptomatic
Infection provides lifelong immunity
Reactivation is very rare: the few that have been observed:
        Virus associated hemophagocytic syndrome (VAHS) – prominent phagocytosis of
               erythrocytes and nucleated blood cells in the BM and lymph nodes
Becomes latent after primary infection (as do all herpesviruses)
Transmitted by respiratory route – oropharynx – infects tiny fraction of many cell types
(lymphocytes, esp. CD4+ T lymphocytes, macros, epi, and endo)
Transmitted in saliva, requires close personal contact
Universal infection—most infants are seropositive by 13 months
Can occur during transplantation surgery (BM esp.)
Clinical presentation
Antivirals only used in dire circumstances:
       Ganciclovir (GCV) – intravenously suppressed HHV-6 replication in possibly
               fatal CNS infections in bone marrow transplant patients
       Acyclovir (ACV) – not as effective, but fewer side effects
No vaccine

Parvovirus B19=Fifth Disease
Small, no envelope, icosahedral
EITHER + or – ss DNA
Replication and assembly occur in nucleus, only during S phase b/c virus must utilize
host enzymes (so can not replicate in resting cell)
B19 DNA does not appear to integrate into host genome
Clinical Course
Mainly in children (1-5)
Self limiting
Slapped cheek rash, also on trunk, and accompanied with low grade fever
If in adults: asymptomatic or w/o rash – then influenza like episode – then persistent
If in patient with hemolytic disorder: life threatening transient aplastic crisis
If in utero: persistently viremic infants, with severe anemia, generally no congenital
malformations, may occasionally result in abortion (hydrops fetalis) due to anemia and
congestive heart failure
Impacts production of new erythrocytes, and reduced erythrocyte lifespan
Narrow specificity for host cells in the bone marrow, fetal liver, or heart
Directly cytotoxic (esp. kills host erythropoeitic cells)
High titer viremia (short lived) with bone marrow depression
Antibody created, clears it from the blood – but immune-complex formation is cause for
both rash and adult rheumatic syndrome
Infection leads to lifelong immunity
Spread via respiratory droplets – target cells in the URT – then on to bone marrow
Spread 5-6 days after infection, lasts until sufficient Ab created (usually 10-14 days post
Can survive in pasteurized milk products
Population: school aged kids
Clinical presentation, commonly misdiagnosed as measels
Typically not treated, if aplastic then with blood transfusion
Coxsackievirus-Picornavirus family
Naked icosahedral
RNA + ss
Replication in cytoplasm
Clinical Course
Wide range due to 30 serotypes in two serogroups (A and B)
Those in A are not as serious as those in B (B = bad)
Include infections of URT, LRT, rashes, myocardial disease, conjunctivitis, nervous sys.
For Serogroup A:
        Herpangia (fever, sore throat, vesicles in oropharynx, acute, w/ uneventful
        Hand, Foot, Mouth Disease (ulcerative vesicles on buccal mucosa, vesicular rash
                on hands and feet)
        Aseptic Meningitis (uneventful recovery)
        Epidemic Conjunctivitis (hemorrhage)
        Infantile Diarrhea
For Serogroup B
        Pleurodynia (acute, chest pain, fever, 2-14 days long)
        Myocarditis and Pericarditis (acute and chronic due to CTL response, fever, chest
        Neonatal – from inapparent to fatal, respiratory and cardiac involvement, from
                nursery or transplancentally
        Juvenile Diabetes association
Replication in oropharynx and GI lymphoid tissue – reticuloendothelial system – skin,
myocardium and the CNS
Fecal oral route, inhalation of respiratory droplets
May block effectiveness of polio vaccination
Isolated from stool samples, pharyngeal secretions, and vesicular fluids
Serum typed for presence of convalescent Ab
No antivirals or vaccines

Overview of Respiratory Tract Infections
URT infections include:
Common cold (nasal discharge, obstruction)
       Adenoviruses, non-SARS coronaviruses, rhinoviruses
       Replicate in columnar and ciliated epi of nasal mucosa
Pharyngitis (sore, red throat with or without exudates)
Laryngitis (hoarseness)
       Rhinovirus, Adenovirus, Parainfluenza
LRT infections include:
        Paramyxoviruses (parainfluenza virus, respiratory syncytial virus (RSV), human
               metapneumoniavirus), myxovirus (influenza), SARS (a coronavirus)
               penetrate further down the bronchial tree
Laryngotracheobronchitis (croup; hoarseness, barking cough, stridor—wheeze on
        Parainfluenza virus
Tracheobronchitis (nonproductive cough, substernal pain)
Bronchitis (larger airways, productive cough)
        Coronavirus (young kids)
Pneumonia (cough, chest pain, rales)
        Coronavirus (young kids)
        RSV (infants)
        Parainfluenza (kids)
Bronchiolitis (cough, dyspnea, wheezing, smaller airways)
        RSV (infants)
        Coronavirus (young kids)


The Common Cold
Clinical Features
Mild, self limited
Inflammation of mucous membranes of nasopharynx
Watery discharge (sloughed columnar epithelium), no fever
Process: nose – hand – another hand – nose (fomites such as door handles can play role)
Wash hands, ventilation, throw away used tissue
Capsid binding antivirals = WIN compounds (bind to canyon on surface of rhinovirus
       and prevent binding and entry into cell). No real beneficial effect.
Anti-receptor compounds directed at ICAM 1 (or soluble ICAM 1)
       Able to prevent binding of rhinovirus, but not helpful after symptoms
       Resistant mutants evolve rapidly
Treatment is difficult due to no early clinical recognition, no means of differentiating b/t
       types, short half lives and poor biodistribution of drugs, rapid resistance

Rhinovirus (a picornavirus)
No envelope, icosahedral capsid made from multiple copies of four different structural
ss + RNA
Replication is temperature sensitive (no cooler than 37C)
Disease is minimal and self limiting, confined to URT, but can set stage for more serious
Can survive for hours in environment
100 antigenic types
30-40% of common colds
Immunity is strain specific (but over 100 strains) so long term immunity to the group is

Coronavirus (non-SARS)
Helical nucleocapsid with envelope containing 3-4 glycoproteins in form of spikes
+ ss RNA
can result in more serious disease in young children (bronchiolitis, bronchitis,
2 types
20-30% of common colds
Strain specific immunity but limited to two years

Linear ds DNA
Genes E1A and E1B – carcinogenic in rodents (interact with pRB (retinoblastoma) gene)
Pentons and hexons make up the virus capsid
Clinical Features
Acute respiratory illness/disease and the common cold (minor)
Infection can initiate in respiratory tract, eye, GI tract, urinary bladder, liver
Persist in lymphocytes for years after initial infection with no symptoms
First discovered in adenoid tissue assumed to be uninfected
At the tip of the penton fiber, there is a portion that can interact with a receptor on the
cell, cause it to be phagosyzed. when the pH changes in the phagolysosome, the shape
of the penton changes, can then break out of the phagolysosome as a result of the action
of this altered structure
Several serotypes (A-F) divided based on ability to coagulate RBCs
Mainly affect kids and army recruits (close quarters, lots of stress, get acute respiratory
disease (ARD))
Fecal oral route (but no GI symptoms) and respiratory route
Vaccines for some types – leads to asymptomatic replication in GI tract
       Not licensed for use in civilians due to safety issues

Rhinovirus (see above for additional info)
Clinical Course
Inflammation of pharynx
Sore, scratchy throat
Edema and hyperemia of tonsils and pharyngeal mucous membranes

Clinical Features
Inflammation of the mucous membrane of larynx
Associated with common cold and influenza
Low pitched voice, hoarseness, aphonia (loss of voice)
Rhinoviruses, Adenoviruses (see above)

Parainfluenza Virus
Helical, with an envelope
- ss RNA
Virion associated RNA polymerase – replicate in cytoplasm
HN glycoprotein spike – recognizes sialic acid residues (high [] in URT and LRT)
F glycoprotein spike – can create a syncytium
Clinical Features
LRT infections in young kids, esp. Laryngotracheobronchitis (croup)
croup – high fever, blockage of larynx, dyspnea, gurgling respirations, coughs
non croup – hoarse cough, fever, resolves in 2-3 days
Infect epi of pharyngeal and nasal mucosa, spread cell to cell by fusion, then to epi of
larynx and trachea – inflammation (croup)
Details at cell level:
Entry with HN binding – viral genome transcribed in cytoplasm – several mRNAs –
nucleocapsid assembles – buds through PM
Why just respiratory tract? Here there are host cell proteases that cleave and release
virion bound by cell fusion protein to original host
Immunity: best correlated to levels of nasal secretory IgA (vs. Serum Ab)
        Only Ab to HN and F able to neutralize the virus
        Re infection can still occur but is much more mild
Virus is shed for 4-7 days post infection
Four types (PIV1-hPIV4)
Nosocomial, person to person contact, contaminated secretions
Severe cases not found in those < 4 mo due to maternal Ab
hPIV1 and hPIV2 occur in biannual epidemics (in autumn) and can then become endemic
Humidifier, racemic epinephrine, inhaled steroids or systemic corticosteroids
Vaccines: inactivated is worthless (due to importance of IgA Ab), subunit is OK
        Bovine PIV3 is protective against hPIV3
        Attenuated hPIV3 developed, but reversion to wild type is an issue

NOTE : the further down the respiratory tract you go, the more serious are the infections.

Laryngotracheobronchitis = coup
Clinical Course
Larynx, trachea, and bronchi involved
Affects those under 4 (size of airways plays a part)
High fever, blockage of larynx and perhaps bronchi – dyspnea, creaking notes of croup
on inspiration, barking cough
Parainfluenza Virus (see above)

Clinical Course
Inflammation of tracheobronchial tree
Associated with generalized respiratory infection, accompanied with a variety of viral
       infections, can be due to smoking
Due to hyperemic and edematous mucous membranes, increased bronchial secretions
Cough – to clear these secretions
Minimal to severe destruction of respiratory epithelium
Can be passed from adults to kids (rare)

Clinical Features
Can be fatal, often an URT infection also present, seen in those under 2
Acute inflammation – lymphocytic infiltration and edema – necrosis of respiratory epi in
bronchioles – wheezing and hyperaeration – tachypnea and respiratory distress
Respiratory Syncitial Virus-Paramyxofamily
Irregular in shape, helical nucleocapsid with envelope (the irregular part I am thinking)
containing three virus specific glycoproteins that look like spikes
- ss RNA
Carries an RNA dep RNA polymerase
3 glycoproteins in envelope (G, F, ?)
Transmitted by close contact (respiratory secretions), virus can survive in environment
        for hours
3-4 day incubation period, lasts 6-10 days unless immunocompromised, will shed virus
        for 3 weeks
G glycoprotein binds to receptor – penetrates by fusion of virion envelope with PM (F
glycoprotein) – replicates in cytoplasm – several mRNAs for viral proteins – F
glycoprotein mediates cell fusion to form syncytium – assembled nucleocapsids bud
through PM
Can replicate in a wide variety of cells (animal and human) but does not penetrate deeper
than the superficial layers of the respiratory epithelium (ironic for the severity of the
Most severe in infants (peaks b/t 2 and 7 months, most all infants have been infected by 2
        years) (bronchiolitis and pneumonia), young children, immunosuppressed adults
        and the elderly
Mild URT infection in adults
Spread in hospitals and day care centers, esp. In mid winter and late spring
Secretory and serum Ab and cytotoxic T cell mediate protection and recovery
Maternal Ab provide protection for the very young, along with low levels of neutralizing
Ab produced by the infant – this immaturity and maternal Ab leads to dimished response
Immunity: achieved in children with re-infection (reinfection is common in adults as
well, but not as severe), correlates best to Ab in mucosal surface
        URT – local (mucosal) immunity most important
        LRT – serum Ab most important
Wash hands!
Treatment for kids: humidifier, bronchodilator, assisted ventilation, NO ribavarin
Prophylaxis: IV immunoglobin, no vaccines (those tested not promising) – one difficulty
is trying to create a strong enough response in infants who mount poor immune responses

Clinical Course
Inflammation of the lungs
Generalized destruction of ciliated epi
Congestion of alveoli with erythrocytes and fluid
Audible rales and evidence of consolidation (=infiltrates) on radiograph

Outbreaks: Spanish flu (1918-1919; H1N1), Asian flu, Hong Kong flu
Pleomorphic, smaller diameter compared to paramyxoviruses
Enveloped with NA, HA glycoproteins – each strain IDed by these two (H3N1 for ex.)
Matrix protein
M2 ion channel
8 individual segments of ss – RNA individually wrapped by nucleoprotein (NP)
Segment 1 – Polymerase B2 (RNA synthesis, core protein)
Segment 2 – Polymerase B1(RNA synthesis, core protein)
Segment 3 – Polymerase A (RNA synthesis, core protein)
Segment 4 – HA (attachment to cell surface)
Segment 5 – NP (RNA syn, core receptor)
Segment 6 – NA (release of virus from cell envelope)
Segment 7 – Matrix 1 and 2 (scaffold, transmembrane protein)
Segment 8 – nonstructural 1 and 2 (1 regulates mRNA splicing, 2 is unknown
Viral RNA pol within virion
Clinical Features
Acute (recovery in 3-5 days, usually self limiting, though fatigue and depression may
Aching muscles (esp. In back and legs), headache, dry hacking cough, hoarseness, sore
throat, substernal pain, SOB (last five due to desquamation of the ciliated epithelium—sp
until epi is reestablished, cough may continue) fever, blocked nose (not runny)
In elderly: not as much fever; In children: often also have sinusitis, other URT infections
Most severe in the elderly and v. young (level of shedding and severity directly related)
Complications: pneumonia
                         Primary viral (more rare) esp. in older patients, cardiopulmonary
                                 Rapidly progress to hypoxemia and death (1-4 days)
                         secondary bacterial esp. in older patients, smokers, chronic
                                 bronchitis, pulmonary function deficits (may be fatal)
                                 organisms:     streptococcus pneumoniae
                                                haemophilus influenzae
                                                staphylococcus sp.
                 Abscesses in lung (staph associated)
                 Reye’s Syndrome (aggravated by aspirin) esp. in children
                         Cerebral Edema (inc. in ICP)
                         Fatty degeneration of the liver (hepatic necrosis)
                         High fatality rate
                         Seen mainly with Influenza B, as well as varicella
Person to person spread by aerosol droplets created with sneezing and coughing
Droplets deposited throughout tracheobronchial tree, initiates replication in superficial
cells of respiratory tract (no stomach flu—does not replicate in the GI tract)
2 day incubation period, then symptoms appear
The Process:
Entry into host cell mediated by binding of HA to sialic acid – HA cleaved into 2
peptides by extracellular proteases (the more virulent, the more easily cleaved) – reveals
fusion protein – virus is phagosyzed into cell – phagosome fuses with lysosome – pH
drops in phagolysosome – M2 channels pump H+ into virion – HA changes conformation
– buried portion now exposed – causes fusion with vesical membrane – due to low pH in
virion, RNP loosens its interaction b/t RNA and the RNP – virus dumped into cytoplasm
– travels to nucleus – viral RNA steals CAPs from mRNA so now can proliferate – viral
RNA copied by viral RNA polymerase (error prone) – so progeny are not identical – the
8 unique segments packaged individually encapsulated – then assemble at random
together into virion (up to 12-15 nucleocapsids/virion to make sure one of each of the
eight are incorporated, if two different strains (so far only seen w/i types, such as w/i A or
w/i B) infect the same cell, then a mixture of genome segments can combine into one
virion) – virion escapes from cell, NA cleaves sialic acid on outside of cell so that HA not
caught and virus can move on to next cell

Virus is shed 2-3 days before and after symptoms (children shed more than adults)

The Pandemics (a world wide epidemic)
Excess mortality, result from emergence of Influenza A novel to human population
Most deaths among the elderly and chronically ill
Huge cost to societies
Several types:
Influenza A – humans and animals, most severe, pandemics (shifts and drifts)
Influenza B – humans only, children the most, more likely to cause Reye’s syndrome, has
        genetically stable HA and NA, epidemics (drifts)
Influenza C – humans (sporadic URT infections) and swine (not a reservoir), sporadic
Antigenic Drift: due to high mutation rate in influenza (high RNA Pol error rates, no
proofreading enzymes) and selective pressure created by antibodies made for a current
strain. Result: persons previously infected by earlier strain will not be immune; every
two-three years an endemic and epidemic outbreak occurs
SO: new vaccines are necessary each year!
Antigenic Shift: due to 1) zoonotic nature of Influenza A (reservoirs include birds, horses,
and swine) 2) ability of one cell to be simultaneously infected by multiple strains in birds,
swine, or humans 3) the genome is segmented.
All pandemic strains have originated in Asia where ducks, swine, and humans coexist
closely; conditions are favorable in S. and C. America

Currently: 3 H and 2 N antigenic subtypes are circulating in humans; 15 H and 8 N
antigenic subtypes identified in birds—so new subtypes are possible!

Ab to HA block viral infection of cell, clinical illness in humans
Ab to NA limits spread and lessens severity of clinical illness
1) Supportive – can not shorten duration
       Acetaminophen, instead of aspirin, used to combat Reye’s syndrome
2) Antiviral Drugs
        Amatadine (related compound, Rimantadine) – inhibits viral Uncoating, effective
        against Flu A if begun in 48 hours. Lessens severity, shortens course, reduces titer
        and duration of excretion, shortens period of pulmonary disfunction (not effective
        against Flu B or H5N1 avian flu). Drug blocks the M2 channel, inhibits HA
        Neuraminidase Inhibitors (ex: Zanamivir-spray, Oselamivir-oral) – effective
        against A and B; binds sialic binding site of NA so that virus cannot release from
        original infected cell, so it blocks replication, symptoms, nontoxic – also called
        TamaFlu. Note that zanamivir is NOT for COPD or asthma b/c it is deliver
        through URT
        Prophylactic Amatadine – for Flu A, can induce side effects; must be taken
throughout period of risk
        Vaccine: formaldehyde-inactivated virions purified from embryonated eggs; two
doses separated by a month or more; induce protective levels of anti-HA Ab in 85%;
minimal side effects; short lived immunity (6-12 mo). This vaccine does NOT fully
protect against the disease but drastically reduces the severity and frequency of
complications. Developed by the info gained from surveillance by WHO.
        Trivalent vaccine: against three different types of flu, for 2004-05
        FluMist: cold-adapted, live attenuated trivalent vaccine; for those 5-49
        Molecular vaccines: production of HA antigens in genetically engineered bacteria
                                 Development of live attenuated vaccines by creation of Flu
                                 A and B chimeric viruses

Zoonotic Viruses

In General: these are viruses that are spread from animals to humans, with humans being
dead end hosts. About 50% of viruses are zoonotic. Many zoonotic viruses have been
recently discovered, due to people going new places, viruses transferring from animal
host to human host (they are ―EMERGING‖!!)

Can be spread by vertebrates (bites or contaminated excreta) or invertebrates

Slight changes in the viruses themselves, their human hosts, the vector, or the
environment can have drastic effects on the course of the disease and epidemics. Viral
changes are the least important.

All zoonotic viruses have similar pathogenesis, diagnosis, and treatment once in a human
host, but all kinds of clinical symptoms

Injection, ingestion, or inhalation – replicates locally – transient viremia – infection of
reticuloendothelial cells – secondary viremia – prodromal symptoms (common to all
zoonotic viruses: fever, chills, headache, muscle ache, malaise. Prodromal means initial-
not unique to the disease)– possible organ involvement, more serious disease
The incubation period (2-14 days) involves the initial replication, transient initial viremia,
infection of the reticuloendothelial cells, up to the prodromal symptoms.
NOTE: some zoonotic viruses may be self limiting and asymptomatic, not even
producing the prodromal symptoms.
Clinical Features:

Very variable: inapparent (most common), OR fever, chills, headache, back pain, muscle
and joint pain, w/ or w/o rash (on 3-4th day) – if w/ rash, then slow convalescence OR if
w/rash: hemorrhagic fever, targeting of specific organs (kidney, liver), thrombocytopenia,
leukopenia, and death OR w/o rash, acute respiratory syndrome and pulmonary edema
OR w/o rash: encephalitis


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Hemorrhagic Fever Viruses = Lassa fever, Argentine HF, Bolivian HF, Hantavirus,
Yellow Fever, Dengue, Rift Valley Fever, Ebola, Marburg

Arena Viruses: can treat with ribavirin early in disease
Lassa Fever (rodents, human to human spread) – treat with ribavirin
Argentine HF (rodents)
Bolivian HF (rodents)

Bunya Viruses: can treat with ribavirin early in disease
Hantavirus (renal syndrome) (rodents)

Flavi Viruses:
Yellow fever, dengue (arthropods), Rift Valley (arthropods)
Vaccines for yellow and rift valley
Need one for dengue—but difficult b/c must achieve simultaneous protection against 4
strains. If not, then the vaccine makes you susceptible to enhanced symptoms with
another infection (same with infection with one strain—2nd infection is worse). Method
to the madness: The Ab to the first strain acts as an opsonization for 2nd Ag and facilitates
entry into macrophage
Remember that also in this family: Heb C

Yellow fever extras: cycles b/t mosquito and small vertebrate and (if mosquito species is
correct) b/t mosquito and man. This type of mosquito likes traveling in old tires

Dengue extras:

Filo Viruses:
Ebola, Marburg (uknown vector, human to human spread)

rift valley fever

Treatment and control
Supportive, when younger than 1 yoa, then maternal Ab protect against infection

Pulmonary Viruses-Sin Nombre Hantavirus and SARS (coronavirus)
Sin Nombre Hantavirus – mice in Americas (esp. the West) excrete virus in urine,
transmitted thru air to humans; so when mice overpopulate, don’t clean house. Also
human to human. Remember that hanta also cause hemorrhagic fever. Treat hanta with
SARS coronavirus – palm civet cats; also spread human to human

Treatment and Control
Rodent control, no drugs
SARS—only supportive, initial symptoms too vague

Clinical Symptoms:
Fever malaise – SOB, respiratory difficulty

SARS—get a COMPLETE history

Encephalitis Viruses-Togaviridae (Eastern/Western Equine Encephalitis, St. Louis
Encephalitis, West Nile Encephalitis), Rabies (but details below)
Mosquito vector (so seasonal)
Human is a dead end
Migratory bird extend range, maintain it over the winter

Clinical symptoms:
Somnolence, altered mental status
NO: headache, stiff neck, WBC in spinal tap—these are more indicative of meningitis

Treatment and Control
Rodent control, supportive care, immune serum (?), no drugs

Infected animal – saliva – wound – replicates in striated muscle/connective tissue – nerve
endings – to spinal ganglia and replicates – to spinal cord (now moves quickly) – brain
(replicates) – salivary glands via efferent nerves
Clinical Features
3-8 week incubation period (multiplying in muscle/connective tissue) -- Prodromal period
for 2-4 days -- Fever, headache, malaise, sensations at wound site (pins and needles) –
irritability, anxiety, depression, sensitivity to sound/light (now replicating in brain) –
difficulty swallowing (hydrophobia) – generalized encephalitis – always fatal

In poor countries it is found in domesticated animals, 90% of cases are due to dog bites
In developed nations, it is found in wild animals 74% of cases due to bats
Growing in prevalence in raccoons and foxes

Post mortem examination of animal (suspect wild animals are euthanized), neck biopsy
        of symptomatic human
Creates darkly staining viral nucleocapsids (Negri bodies) in the cytoplasm of cells in
Viral inclusions seen with fast acid stain of brain tissue

Mandatory vaccination of domestic animals
Inactivated vaccine for humans at high risk, or for post exposure prophylaxis
If exposed: wound site immediately cleaned, area injected with human rabies
hyperimmune globulin (neutralize any virus not yet to nerves—20 IU/kg—no more),
vaccine to develop active immunity (booster several times)

Transmissible Spongiform Encephalopathies (TSEs)-Kuru, Creutzfeld-Jakob Disease,
Mad Cow Disease (BSE)
Transmitted by ingestion or inoculation of diseased nervous tissue
Infectious agent referred to as a ―prion‖ (PrP) – NOT a virus!!!!—a small, proteinaceous
        infectious particle that resists inactivation by procedures that modify nucleic acid
the altered prion (PrPsc) forces normal prions (PrPc) to go from alpha helix to beta sheet
        and then causes them to form fibril and amyloid plaques
Clinical Features
Incubation – decades
Symptoms: loss of motor control, dementia, wasting, loss of brain function
Once symptoms appear, death occurs in months
Post mortem analysis reveals large vacuoles in the cortex and cerebellum
Creutzfeldt-Jakob Disease
        Rapidly fatal
        Presenile dementia, memory loss, confusion, vertigo, blurred vision,
        motor dysfunction
       60-70 years old (sporadic or familial due to mutated amyloid precursor protein),
       younger if by iatrogenic transmission (surgical instruments, transplanted dura
       mater, corneas, GH from pituitary)
Transmissible Bovine Spongiform Encephalopathy (BSE)
       Scrapie is naturally occurring in sheep
       BSE developed from feeding cattle scrapie infected sheep by products or
               contaminated feed = Mad Cow Disease
       May have adapted to infect humans (this is called vCJD, see below)
Variant Creutzfeld-Jakob Disease (vCJD)
       Ataxia and memory loss v. common (more so than CJD)
       Young age group, mainly UK
       Genetic component – methionine homozygosity at position 129 of the prion
Connection b/t vCJD and BSE still unclear:
       Temporal and geographic link, similar glycosylating patterns, same distinct
plaques, similar clinical symptoms

Viral Infections of the Nervous System
These viruses infect the nervous system for either further replication of establishment of
latency after replication at the portal of entry.
Three Classes: Arthropod Borne, Enteroviruses, Herpes Simplex Viruses
Arthropod Borne
From bird and rodents (highly viremic but rarely die) – arthropod (replicates in gut) –
human (transmission occurs when mosquito population incr. and start feeding on us)
Peak incidence in mid to late summer
No human to human spread, no human reservoirs
Classified as the family Togaviridae Alphavirus genus OR family Flaviviridae
        These are similar to Picornavirus (Heb A, rhino, polio, coxsackie)
+ ss RNA
Replication in cytoplasm
Icosahedral, one capsid protein
Envelope, two viral proteins (M and E), target of most protective humoral immunity
ADCC, CTLs (play part in inflammation)
Clinical Features:
Mostly subclinical, only detected by serology or epidemiology (often not diagnosed)
Factors enhancing reaction: manner of inoculation, non specific host immunity, strain
Alphaviruses (family Togaviridae, also in this family: Rubella-not vector borne)
Include: Eastern/Western/Venezuelan Equine Encephalitis
Inoculation – blood – endothelial cells – nerve cells
Buds PM
Symptoms a result of viral and host inflammatory response action
Clinical Features
Severity is dependent on penetration into CNS
Virus in blood spreads to endothelial cells – acute febrile illness
More penetration – encephalitis (headache), malaise, dizziness, seizures, coma
Recovery can be very prolonged (must develop specific antibody to viral envelope
Wide physical and host range, but each virus may be limited
Reservoir is birds (mostly asymptomatic, some may develop fatal CNS disease)
       Sentinel birds bled to determine antibody titers
Replication occurs in mosquitoes, so best control is focused on mosquitoes (no
       pathogenesis in mosquito)
       Virus goes from gut to salivary glands to next vertebrate
Serological tests (IgM ELISA), clinical symptoms
Eastern Equine Encephalitis—most common in SE USA
Clinical Features:
Low attack rate (2% of population during epidemic), mostly subclinical infections
Steps of an infection: 10-12 day prodromal febrile illness – acute fever, stiff neck,
dizziness, loss of consciousness – seizures, coma, death OR symptoms resolve
Cytolytic; some impact due to host defenses (interferons)
Populations maintained in wild birds (the amplifying host), same for WEE (vs. enzootic
       and epizootic strains for VEE)
Humans and horses are dead ends, human to human spread via aerosol has occurred in
       laboratory setting
Mosquitoes can become persistently infected; recently a new mosquito vector arrived in
       US, the Asian tiger mosquito, that more aggressively feeds on humans—bad news
Along eastern seaboard (vs. S and C America for VEE, western America for WEE)
Clinical presentation, epi fit, comparison of paired sera, rarely virus isolation
No vaccine (vs. vaccine for WEE and VEE through military)
Equine vaccine is available

Flaviviruses (also in family: Hep C)
Include: St. Louis/Japanese/Tick-Borne Encephalitis, West Nile, Dengue virus, Yellow
Buds at internal membranes
St. Louis Encephalitis (SLE)
Clinical Features:
Most are subclinical
Course of infection: fever – malaise – headache – drowsiness – then either 1)
encephalitis, 2) meningitis, 3) febrile headache
Most prevalent arthropod borne virus in the US
Elderly more prone death, more severe symptoms
Maintained in mosquitoes, amplified in birds, human disease peaks from July – Sept.
EXCEPTION: the urban cycle goes b/t humans and mosquitoes when titer in humans is
high enough, around and around
Epidemics every 5-15 years
PCR of blood or CSF or tissue
ELISA for ID of specific IgM in serum or CSF
Ab testing of paired (acute and convalescent) sera
Immunofluorescence for SLE antigen in urine or CSF
Prevention and Treatment
No vaccine, supportive treatment, reduction of vector populations
Very similar to Equine Encephalitis

West Nile Virus
In birds, humans, and horses in US
Vector: mosquito
Also seen in organ and blood transfusions
        Now US blood bank is screened for WNV RNA sequences
Most cases and deaths seen in older patients
Clinical Features
Infection during pregnancy: formerly it was rarely associated with spontaneous abortion,
neonatal illness, never with birth defects. Now this is under investigation

Japanese Encephalitis
Underreported, most in rural Asia
Seen in pigs, birds, humans
Vaccine available

Tick Borne Encephalitis
Europe and Russia
Seen in ticks, goat and sheep milk
Vaccine available


Picornaviridae Family
       Genus Enterovirus – acid stable (unlike rhino)
               Enteroviruses—these cause very mild encephalitis and often go
       Genus Rhinovirus (cold) – if you swallow crap, it is killed in stomach
       Genus Hepatovirus (Heb A)
The family in general:
Have 4 proteins on capsid, each member has varying amounts of these

Stands for: enteric, cytopathic, human orphan virus
10 serotypes, fecal oral route

Small, spherical, icosahedral
+ ss RNA with a 3’ poly A tail and a VPg protein covalently attached to 5’ end
Protein coding region is flanked on each end by a NTR
Virus encoded RNA dep RNA pol – asymmetric replication (many + strands made from a
few – strands…so if you see more + than -, it is (+) RNA, if you see 1:1 than it is (-) or ds
RNA virus
Clinical Features
Most: subclinical
Some: abortive poliomyelitis (malaise, fever, headache, nausea resolve in a few days)
A few: aseptic meningitis (stiff neck, back) resolves in 2-10 days
rarely: paralytic polio (the worst paralysis is at onset, then gradually improves to varying
levels over 6 mo.) = poliomyelitis
again, rarely: progressive, post-poliomyelitis muscle atrophy (often seen in legs)
Additional muscular deterioration decades after initial illness, due to aging – NOT the
No one: GI symptoms
On a grand scale:
Virus enters via mouth and multiplies locally at tonsils and Peyer’s patches or lymph
nodes – appears in throat and feces – hematogenous spread to other lymph nodes, brown
fat, cardiac and skeletal muscle and CNS (the spread in the blood creates a race b/t virus
and immune system…interesting note that virus that reaches CNS is never transmitted, so
of no advantage to virus to do this) – w/i CNS, the virus travels along the nerves –
paralysis due to direct destruction of neurons OR edema induced damage (reversible),
fatalities seen once damage reaches the circulatory and respiratory centers of the medulla
Virus esp. attacks neurons of legs and lungs (iron lungs common)
NOTE: feces spread for weeks, not dependent on reaching CNS
On a cell scale:
Attachment of virus to cell receptors (determines tropism—the gene for this receptor has
been cloned and produced in the polio mouse) – penetration and uncoating via viropexis
(receptor mediated endocytosis, energy dependent) – translation is CAP independent,
host cap binding complex is inactivated – initiation at IRES (strong) in 5’ NTR –
polyprotein proteolytically cleaved by 3 virus encoded proteases (makes 11 to 12
This protease cleaves the host cell protein involved in CBC (cap binding complex), so
now all ribosome available for virus replication—same with ECHOvirus, coxsackie
Heb A vs. Polio – both are fecal oral, but Polio infects a few cells and makes a ton of
progeny in each, while Heb A infects a ton of cells and makes a few progeny in each
Replicates in GI tract (acid stable to pH of 3.0 or even lower)
Virus is cytotoxic—so when it kills GI cells, not a big deal, but when it kills CNS cells, a
much bigger deal
World split into two areas in relation to state of polio there:
1) vaccine era (N, S America, former USSR, Europe, Australia)
2) endemic polio (remainder, esp. SubSaharan Africa and S Asia
The few cases in US due to:
--Immunocompromised vaccinees vaccinated with virus that reverted to wilds type
--Imported wild type (travelers from area with wild type)
--Immunocompromised individuals exposed to vaccinee shedding the reverted virus
For Non-poliomyelitis enteroviruses:
Cases are mild or asymptomatic, mainly in the summer, target poorer kids, sweeps
through every few years, found in water with shellfish
Diagnosis—can be difficult, esp. for enteroviruses as a whole
Tissue culture, immuno-serological techniques (many serotypes)
Specimens: stools, rectal swabs, throat swabs – virus isolation
Mixed infections common—one may win out, and immune system may only target one
of them.
Unfortunately, virus shedding has already occurred once isolation can occur
Resistant to disinfectants, stable in water (polio virus found in water supply while using
live vaccine)
VACCINES!! (both are trivalent for the three serotypes)
1) killed = Salk (IPV)
First one to be developed; salk believed serum immunity to be sufficient (used proof of
        kids protected by mother’s antibodies); initiative due to FDR and his polio
Created by denaturing it in phenol
Can be combined with other injected childhood vaccines—inoculated intermuscularly,
        two boosters required
Excludes potential for mutation and reversion to wild type
Safe for Immunocompromised individuals
Reduces spread of live viruses
BUT: low percentage develop Ab after three doses
        Does not induce immunity in the gut—only serum IgM to IgG response, no IgA
                (so you can still get infection in the gut, and spread it via feces)
        Expensive, growing scarcity of monkeys for kidney tissue virus propagation
2) attenuated = Sabine (OPV)
Vaccine created by passing it through alternate host many times until variant created that
        is temperature sensitive and passes through host very slowly, giving it time to
        mount immune response.
Produces mucosal IgA, duodenal IgA, serum IgG
Immunity can be life long
Large % get Ab very quickly—stops epidemic quickly
Oral administration – must be given three times (each time may create Ab to 2 of the 3,
        dependent on who starts replication first; three doses assures that if host was
        currently fighting off another asymptomatic enterovirus infection, and did not
        create a response he will be abe to next time.)
Potent for long time, under difficult field conditions
BUT: viruses may mutate and revert to neurovirulence—actually all will eventually
                revert, but usually it is after host has developed strong immune response
        Spreads to other persons and environment via feces (if not reverted, then can
                inoculate those around you…but if reverted then very bad)
        Not for the immunosuppressed
Current Use: only IPV (the killed version) b/c poliomyelitis was occurring in vaccinees
receiving OPV. Get at 2 mo, 4 mo, 18 mo, and 4-6 years

The change of epidemiology:
1920’s: hygiene not that great, so humans would be infected early on, while still
protected by maternal Ab, and would not be seriously harmed, but would develop
intestinal immunity—it was ubiquitous
1950’s: hygiene improves, infants not infected early on, but only later, once maternal
antibodies were depleted, and thus they were more seriously affected

Papovavirus—a combo of three families:
        Human papillomavirus
        Simian Vacuolating virus
        Polyomavirus (JC, BK, monkey)
Circular, ds DNA
Replicates in cell nucleus, does not encode a viral DNA dep DNA pol
Uses host DNA pol and RNA pol II
Progeny also assemble in nucleus
Naked, icosahedral
NOTE: if it infects a non-natural host cell that is non-permissive, then the cell is not
killed, but instead transformed to neoplastic growth
        If it infects a permissive cell (a natural host), the host cell is killed by viral
                 cytolytic infection, leads to a cryptic, inapparent infection-not latent,
                 just can reappear if immunocompromised
BOTH JC and BK are distantly related to SV 40, which has been found in 40% of tumors
        in non-Hodgkins lymphomas as well as in brain and bone tumors and
        mestheliomas (rather moot point it seems except that one case of PML was due to
Clinical Features
Progressive multifocal leukoencephalopathy (PML) – a fatal neurodegenerative disease,
intrinsically immunosuppressive
Inclusion bodies seen in brain biopsy
Spread via respiratory route
no disease if immunocompetent
1-10% of AIDS patients develop PML associated with JC
Can occur after renal transplant + immunosuppression
No disease if immunocompetent
Viremia occurs in about 50% of patients after bone marrow transplantation
Isolated in urine

Herpes Simplex Viruses-Herpesviridae family

In General: best known as the cause of vesicular skin lesions, which periodically recur

Also in the family:
Varicella zoster (chicken pox)
Epstein-Barr virus
HHV 6 and HHV 7 (roseola)
HHV 8 (Kaposi sarcoma associated virus)
Monkey B virus (serious neurotropic virus for humans)
       No virus particles made; No lysis
       Minimal expression of viral genome (only RNA’s, no protein)
       Virus can be isolated
       This gives the virus another chance to be transmitted
       But virus must hide from immune system (one way = make no protein)

Two types of HSV: HSV-1 and HSV-2
Both: the primary infection is more severe than the recurrence

A study of the two:
Icosahedral capsid, surrounded by the tegument—very big
Envelope—from nuclear and ER membranes
Large, ds DNA
Transcription, replication, assembly occur in nucleus
Uses host DNA dep RNA Pol, viral DNA dep DNA pol
Maturation and acquisition of envelope occurs in cytoplasm
Clinical Features
Primary Disease – HSV 1
Often asymptomatic, esp. if <10 yoa
If symptomatic: gingivostomatitis, with vesicular eruptions on buccal mucosa, gums, and
lips which progress to form ulcerative lesions; lasts for 2-3 weeks then heal over—
―above the belt‖
Primary Disease – HSV 2
Usually symptomatic: painful, vesicular lesions on genitals and extra genital region
which progress to pustules and ulcers, systemic symptoms shorter lived than local
symptoms, lesion heals in 20 days—―below the belt‖
Can become systemic (aseptic meningitis)
Virus shed for first 12 days of symptoms
Reactivated Disease – HSV 1
Latent infection established in sensory neurons (exists as extra chromosomal episome
        with few genes expressed)
Reactivation due to stress (many types) – at first: altered sensation at initial site (hours) –
        1 to 2 days later: appearance of vesicles (often fewer in number, located on
        mucocutaneous border)
Reactivated Disease – HSV 2
Fewer lesions, virus shed for shorter time period (latent in sensory neurons as well)
The more severe the initial reaction, the more frequent the reactivation (at initial site)
HSV 2 in Pregnancy
Transmission during delivery when mother is asymptomatically shedding
In utero cases tend to be systemic, high mortality—C section performed
Other clinical Presentations:
Acute Necrotizing Encephalitis – usually in the Immunocompromised, high mortality
rate, sporadic—HSV is primary cause
Herpes simplex keratoconjunctivitis – second to trauma as a cause of corneal blindness
A superinfection—when doc touches a lesion and gets lesion on finger
Invades epithelial cells, forms giant multinuclear cells—like paramyxo
Release of virus via exocytic pathway and cell necrosis
By lysis of cells, leaks vesicular fluid b/t dermis and epidermis to create the vesicle and
        facilitate spread to other hosts
Infection with HSV-1 is universal by age of 5
Spread via contact with lesions, saliva, genital secretions (HSV 1 often shed from
asymptomatic kids, HSV 2 spread by sexual contact-likelihood of infection increases
with number of partners)
No animal vector, no seasonal patterns
Can be spread by inapparent reactivation
History and presence of vesicles (pathognomonic)
CPE (cytopathic effect) produced in tissue culture
No serology due to universal nature
In encephalitis, PCR of CSF used
Prevention and Treatment
No vaccine for either form
       2 forms of mutations: acyclovir resistant HSV (mutations in viral TK or in viral
                DNA pol (fewer))
       These mutants are avirulent
New trial vaccine: composed of HSV2 envelope glycoprotein D – only affective in
       females, can never have been exposed to HSV-1 or HSV-2)
To prevent spread: codoms, cesarean section for shedding pregnant mom, isolation of
       hospital staff shedding virus

dG analog (not phosphorylated)
host enzymes do not phosphorylate ACV very well, but viral TK (an early enzyme) does
        why? b/c the virus wants to incr. the size of pool for precursors of DNA synthesis
So, in viral infected cells, you get both dGMP and ACVMP
Once in ACVMP form, host enzymes convert it to triphosphate form
Host DNA Pol does not used ACVTP, but viral DNA pol does—second portion of
selectivity to viral infected cells.
ACVTP has no 3’ OH – a chain terminator
Complications: crystallizes in the kidney tubule
The oral prodrug formulation: valacyclovir
Very similar to acyclovir (dG analog)—a derivative
The oral prodrug formulation: famciclovir
Ganciclovir—more toxic, used for CMV (dG analog) in the Immunocompromised/bone
marrow transplant patients b/c CMV does not encode thymidine kinase, but instead a
protein kinase that will not phophorylate ACV, but will phosphorylate GCV; more likely
to be incorporated by viral polymerase
Side effects: reversible neutropenia, thrombocytopenia
A pyrophosphate analog, in principal can bind to all polymerases, so rather toxic (side
effects include reversible nephrotoxicity, seizures)
In practice binds more actively to viral (herpes, HIV-but minimal) polymerases
Esp. used for CMV when resistant to GCV

Systemic Viral Infections-Varicella Zoster, Human Cytomegalovirus, Poxviruses
Varicella Zoster-Herpesviridae family
Large, ds DNA
Transcription, replication, assembly occur in nucleus (this is one way you can tell it apart
from smallpox)
Uses host DNA dep RNA Pol, viral DNA dep DNA pol
Maturation and acquisition of envelope occurs in cytoplasm
Icosahedral capsid, surrounded by the tegument
Envelope (but rapid replication, ease of trans. makes it difficult to exploit this weakness)
Clinical Features
Two distinct clinical entities
        Varicella = chickpox (systemic, disseminated)
        Zoster = shingles (in a dermatome), can infect the eye
Mild, febrile illness of childhood
Causes a disseminated vesicular rash of clear, fluid filled blisters with irregular red
margins: macules – papules – vesicles – pustules – scabs (usually no scars remain)
Can see all stages at once
Also: headache and malaise – pruritic rash – low grade fever and irritability
Resolves in a few weeks—self limiting (few fatalities/year however)
Complications: secondary infection of the varicella lesion (septicemia)
                 Post infectious encephalomyelitis (good prognosis if immunocompetent)
                 Fluminant infections (pneumonia)
                 Varicella pneumonia (more in adults), can spread cell to cell via fusion
                 Reye’s syndrome
A reactivation of latent VZV, in conjunction with immunosuppression (likelihood
        increases with age, stress, test for HIV if in a surprisingly young patient)
Vesicles coalesce into larger lesions, lesions often within one dermatome
Can be very painful during and after vesicular stage
Complications: post herpetic neuralgia – hypersensitive to touch and temp extremes
                                          -- can persist for months, either episodic or
These complications can be prevented by treating early on with acyclovir
Inhalation – nonspecific binding to target cells in nasopharynx – initial replication in
respiratory epi, fibroblasts, forms a syncitium – spreads to lymph nodes – viremia –
spleen and liver – secondary viremia (mediated by PBMCs) – Cutaneous epi (rash),
respiratory mucosal sites (spread to other hosts) – latency in sensory nerve ganglia via
hematogenous and neural spread
Spread asymptomatically throughout life whenever activated
Universal childhood infection before vaccine arrival
Spread via respiratory droplets before symptoms—hard to control
Maternal protection for first 6 months
Immunity for chickenpox is cell mediated-infection provides lifelong immunity
Immunity for shingles-reactivation protects against further episodes
Above 80, risk is 50% for shingles
Primary: presentation, history of exposure, lab results including fluorescent Ab of virus in
lesion, Tzanck smear from vescicles (syncytia, intranuclear inclusion bodies), culture for
definitive diagnosis (but this is difficult to do successfully)
For shingles, do not mistake for slipped disc and pinched nerve!
Vaccine for children over 12 mo. (live, attenuated—induces humoral and cell mediated)
Acyclovir – must be prompt; will terminate viremia, reduce shedding, lessen severity
Zoster immune globulin (for at risk non immune exposees)
Trial in progress for using booster vaccine for those over 60 to prevent shingles

Cytomegalovirus-Herpesviridae family (HHV-5)
Large, ds DNA—largest genome of human herpes viruses
Transcription, replication, assembly occur in nucleus
Uses host DNA dep RNA Pol, viral DNA dep DNA pol
Maturation and acquisition of envelope occurs in cytoplasm
Icosahedral capsid, surrounded by the tegument
Envelope-sensitive to heat, low pH, lipid solvents
Clinical Features
If in immunocompetent individuals:
Typically unremarkable
        Adults—due to contact with urine, saliva, feces, or intimate contact; mild
                pharyngitis, EBV like mononucleosis, mild hepatitis
after primary infection, symptoms cease, shedding decreases but can continue for years
and may recur, goes latent in lymphocytes, heart, kidneys (myloid progenitors)
If congenital:
Occurs if pregnant woman is infected for the first time, most common viral cause of
        congenital malformations (if 2ndary infection, baby will also get antibodies, will
        retard infection until child can make its own IgG, IgM
During first trimester: severe birth defects (enlarged liver, microcephaly)
Later in pregnancy: no abnormalities
Children may appear normal at birth but will have progressive damage, esp. to hearing
If immunosuppressed:
Severe disease, either primary or reactivated
Can include: interstitial pneumonia, retinitis, enteritis, meningitis, myelitis, hepatitis,
        leucopenia, disseminated disease
Connection to AIDS: may be a co-factor in infection, incr. the severity OR just an
opportunistic infection; high % actively shed virus and 50% will have infection
Post transplantation: CMV is primary infection in many hospitals, esp. for bone marrow
        CMV could be in transplanted organ/blood or could be latent in patient
Outcome determined by host
Primary infection in salivary gland
Has a fusion protein so can cause infection of healthy neighboring cells—characterized
by giant cells and inclusion bodies (all herpes viruses can induce cell-cell fusion)
Can cross placenta
Limited host range, ubiquitous in humans, but more prevalent in areas with close contact
Found in all body fluids, common in transfused blood
         Significant sources: infected children – daycare worker
         Immunocompromised patient
         Seropositive mother’s breast milk
In general:
b/c it is ubiquitous, it is hard to diagnose as cause of specific problem
often mistaken for EBV (if EBV is -, then it is probably the cause for mono)
the CMV Ag in WBCs by immunoflourescence (the antigenemia assay)
appearance of cytomegalic cells with intranuclear inclusion bodies
shell vial assay can detect gene expression within 24 hours
for immunocompetent: serology for IgM and IgG
for congenital: culture mother’s urine and saliva for virus
for immunocompromised: culture biopsy
HCMV does not encode a viral TK—so no acyclovir or penciclovir
Ganciclovir works b/c HCMV does encode a protein kinase
         This drug has a much higher toxicity and is more expensive than ACV or PCV
         Also a dG analog
Foscarnet – if resistant to Ganciclovir

Poxviruses-Poxviridae family
Includes the viruses: variola major and minor (smallpox)
                       Monkey pox
                       Molluscum contagiosum- a minor member
                       Zoonotic poxviruses
Large, ds DNA
Transcription, replication, synthesis occur in cytoplasm
Contain DNA dep. RNA AND DNA pol in the nucleocapsid-also has own 5’ CAPing
enzyme, polyAtail enzyme, thymidine kinase (but will not phosphorylate ACV, GCV)
Brick shaped virions (dumbbell forms), complex structure
Complex viral envelope; largest of all virions, can be seen by dark field microscopy
Clinical Features
Smallpox- classic case = joseph stalin (survived childhood disease)
Eradicated in 1977 (due to WHO eradication program, a few escapes from labs)
Major has mortality of 10-30% (partly due to mass starvation due to disruption of
       society); Minor is a less virulent form
Iceland had huge mortality—18K deaths/50K population in 1707
Rash: macules – papules – vesicles – pustules – crusts – loss of scab leads to scarring
All cases are symptomatic
Virus shed before rash appears, found in skin lesion, covers body and oropharynx
Endemic in certain African primates, transmissible to humans, identical to smallpox
Less virulent than variola and used as a prophylaxis against it
        Following subcutaneous inoculation, a papule appears at site, follows pattern until
        it forms a scar (a vaccination scar)
Rarely, sequelae such as auto inoculation of the cornea, or systemic vaccinia could occur
        if immunocompromised
Molluscum contagiosum
Self limiting infection of the skin – small umbilicated nodules with small white cores
Sexually transmitted
Lasts for years then spontaneously resolves
More severe in AIDS, more frequent in genital infections
Zoonotic poxviruses
Animals to humans by direct contact—an occupational hazard
A self limiting lesion on hands or face
Ex:     orf virus of sheep or goats
        Bovine pustular stomatitis
        Pseudocowpox of cattle
Inhalation, Direct contact – initial replication in upper and lower respiratory tract –
infections of macrophages – migration to lymph nodes – viral replication – primary cell
associated viremia (still asymptomatic, non infectious) – replication in spleen and bone
marrow – secondary viremia – replication in the small vessels of the dermis – migration
to epidermis (rash) and oropharyngeal epi (spread)
Immunity is humoral!! (important for recovery and protection from re-infection, lifetime)
Virus only shed during acute infection—VERY CONTAGIOUS
Age of host: if in rural area, then all ages
                 If in urban area, then childhood
Monkey pox only seen in a few small villages in Africa, primates
        Much less transmissible (human to human is rare)
Vaccinia vaccination only recommended for lab workers working with Vaccinia, cowpox
or monkey pox (no more research on variola)
History of vaccine used:
First: variolation – scarfication with virulent variola virus (exposure in non natural site)
Second: vaccination with cowpox (Jenner)
Third: vaccination with Vaccinia—a live virus vaccine (vaccinia probably arose due to a
recombination formed by injecting cowpox into rodents); can disseminate if
Eradication of Smallpox due to: (shows why other eradications are so much more
One serotype
Human reservoir
100% symptomatic
Physical mark for vaccination or former infection
Vaccine was stable

Gastrointestinal Viruses
In General:
The most commonly acquired disease in the world
Three main Virus Groups:
        Calicivirus (Norwalk agent)
        Enteric Adenoviruses type 40 and 41
Rotaviruses-Reovirus Family
11 pieces of Segemented ds RNA – high rate of reassortment during dual infection
        Only can occur w/i groups
        Purified segments not infectious, each codes for at least one protein
Replication occurs in cytoplasm
Contains all enzymes necessary for mRNA production
Triple layered icosahedral capsid with spikes extending from the surface
Resistant to inactivation, frequent nosocomial infection
Clinical Features
Range from subclinical to severe
        <6 mo are asymptomatic
        6-24 mo are the most severe
        25+ mo are mild or asymptomatic, unless immunocompromised
Incubation (48 hours) – lots of viral shedding – Vomiting (3 days), then diarrhea and
fever for 7-10 days – shedding can continue for days after symptoms end

Ingested via fecal oral route, aerosol spread, fomites, replicates in columnar epi of
intestines – villi lose the surface epi cells – malabsorption of fluids AND virus protein
(glycoprotein 4) is an enterotoxin – diarrhea
Cytocidal virus, rapidly kills permissive cells, released by lysis of cell
Proteases required to cleave outer capsid spike protein
Forms inclusion bodies
Unique morphogenesis involves transient enveloped particles
Morbidity due to dehydration
No residual damage to intestinal cells
Major cause of severe diarrhea in developed and less developed countries
        In developed countries, seen more in cooler months
         In US, goes from southwest to northeast
Requires as few as 10 viral particles
Three groups (A, B, C) found in humans, numerous serotypes within each
         A found in US
Targets those 6-24 months old
Very contagious
Not an important factor in HIV associated diarrhea
Once infected, rare to get another infection that is not subclinical, unless exposed to A
LOT of viruses
Serologically, groups share cross reactive antigens
Must detect rotavirus or viral Ag
In stools, electron microscopy used
ELISA, PCR also used
Vaccine should be designed for prevention during first 2 years of life, so far the only one
failed. (it was a tetravalent, live vaccine, led to serious bowel disorders—intussusception
= intestinal tract telescopes up. Made by combining 4 serotypes of major Ags. Rheus
monkey strain was engineered such that it had sequence coding for all 4. it was able to
replicate at colder temps (UTR vs. GI))

Calicivirus = Norwalk Agent
+ ss RNA
No envelope
Fastidious growth requirements, replicate poorly, if at all, in cell culture
Villi of small intestines broaden and become blunted (epi mucosa remains intact) – leads
to malabsorption and thus diarrhea
Clinical Features
24 hour incubation period -- Vomiting, nausea (due to affected gastric motor function)
and epidemic diarrhea for 24-48 hours
For kids: more vomiting
For adults: more diarrhea
Often the cause of outbreaks in which:
        No other agents involved
        >50% of patients are vomiting
        Epidemic fashion, follows a point-source exposure by 24-48 hours
        Seen in schools, institutions, camps, families
        Due to shellfish
Older children and adults
No animal host/model has been found
NOT a specific problem for AIDS patients or in Infantile Diarrhea
No protection gained from previous exposure
Often seen on cruise ships

Clinical Features:
Acute respiratory syndromes
Outbreaks of epidemic keratoconjunctivitis
Two of the dozens of serotypes associated with gastroenteritis
Not a major cause of severe diarrhea
Cause of nosocomial diarrhea in children


The Virus-Retroviruses
Two variants: HIV 1 and HIV 2, with HIV 1 being more pathogenic, HIV 2 is clustered
in W. Africa, India
Enveloped, spherical with icosahedral nucleocapsid
Major capsid protein is p24 and can be measured in serum to detect early infection
Envelope glycoproteins gp120 and gp41, held in place by matrix proteins (MA)
       Gp120 = head, gp41 = stalk, together = gp160, bind CD4 receptor
RNA: two identical ss RNAs associated with NC proteins
       LTRs flank entire genome (have sticky ends, promoter/enhancer function)
       Gag sequences code for the proteins w/I the envelope: NC, CA (capsid), MA
                These are the most antigenic proteins
       Pol encodes the viral protease, integrase and RTase
       Env codes for envelope proteins
       Regulatory proteins (tat, rev, nef) NOTE nef deficient viruses have been shown to
                not cause AIDS
Several virion-associated enzymes (RT, RNaseH, integrase, protease)
Clinical Features
Acute: level of virus within first 6 months of infection predicts clinical course
       Initial immune insult cannot be rectified by subsequent control of viral replication
       Like mononucleosis, develops 1 mo after exposure, high viral load, spread to
                lymph nodes and macrophages
       Immune response lowers viremia; replication continues in lymph nodes and
                peripheral blood
Clinical Latency: median of 8 years—not true latency b/c virus continues to replicate, kill
       CD4’s, causes lymphadenophathy, susceptibility to bacterial infection rises
Chronic: high rates of ongoing viral replication and immune clearance
          More rapid disease is a result of use of a different cellular co-receptor
AIDS = CD4+ count below 200 cells/mm3
Opportunistic Infections:
        Candida – oral candidiasis, may extend to esophagus
        Pneumocystis carinii – pneumonia – PCP
        Cryptococcus neoformans – meningitis
        Histoplasma capsulatum – pneumonia or disseminated
        Cytosporidium – gastroenteritis
        Toxoplasma gondii – encephalitis
        Mycobacterium tuberculosis – pneumonia and/or disseminated
        Mycobacterium avium complex – MAC, disseminated infection, fever
        Higher susceptibility to bacterial infections in general
        Cytomegalovirus – retinitis, pneumonitis, esophagitis (minor)
        Herpes simplex virus – mucocutaneous lesions
        Epstein-Barr virus – oral hairy leukoplakia, lymphomas
        Varicella-zoster – shingles
        Other cancers (Kaposi’s sarcoma—HHV8 and CNS lymphoma—EBV)
Blood borne pathogen, found (significantly) in blood, semen, vaginal secretions, breast
Chance of transmission thru sex is 0.3 to 3 %, increased with concurrent STD infection
                          thru childbirth is 15-30% (in utero, perinatal, or breast feeding)
                                chance reduced by 2/3 with AZT
                          thru direct blood infusion is 90%
                          thru organ transplants is ??%
In US, most spread is via IV drug use and homosexual relationships
In developing countries, spread is via heterosexual relationships
Binds via gp160 to CD4 protein as receptor and a member of the chemokine receptor
        family as a co-receptor (fusin on T lymphs CKR5 on macrophages – fusion of
                viral and cell membranes)
        These receptors primarily found on CD4+ T helper cells. Also found on
                macrophages, monocytes, CNS dendritic cells
Replication strategy:
1) RNA – DNA via RT + RNaseH found in virion
2) DNA is transported to nucleus
3) integrase inserts viral DNA into host chromosome
4) viral DNA is expressed by host enzymes once T cell is activated
5) DNA is transcribed into RNA for both translation and packaging into virion
5) large precursor proteins used to assemble the particle
6) precursors are cleaved by viral proteases (gag from pol)
7) virion buds out through cell membrane, kills cell
Results in:     progressive loss of CD4+ helper cells – state of immunodeficiency – death
due to opportunistic infections (endogenous and exogenous)
                Hypergammaglobulinemia (p. 198)
                Macrophages and monocytes not destroyed – serve as reservoirs, can
migrate across the blood brain barrier
                Level of viral load varies dramatically
Survival with quality treatment at least until CD4+ count is 50, very variable
1-2 % in NC area STD clinics
750,000 to 1 million in US
        30-50,000 more each year
        Most in homosexual men, IV drug users, now more women and their children
36 million worldwide
        5.3 million more each year
        3 million deaths each year
Hot spots: Thailand and India, cities of third world countries (IV drugs, commercial sex)
Five settings:
1) AIDS defining illness in otherwise healthy individual, confirmed with western blot
        Begin treatment immediately
2) Positive test for anti-HIV 1 Ab, confirm test, and clinical assessment (CD4+ cell
count, level of plasma viral RNA)
3) Flu-like symptoms as a result of acute HIV 1 infection; check for viral RNA level,
realize Ab may not yet be present.
        Treatment began early may reduce the extensive seeding of lymphoid organs
4) Following a known exposure, risk is small
5) Following birth of a baby to an HIV infected mother, should be monitored for anti-
HIV 1 Ab or plasma HIV viral RNA for 6 mo.
        Treatment is sometimes begun to attempt to eradicate the transmitted virus
Simple test, with + = active infection

CD4 vs. viral load:
CD4 = where train is in relation to cliff
Viral load = how fast it is going
Current targets of antivirals: RT and protease
Three classes of inhibitors:--once resistance develops to one drug in a class, often all
drugs in that class are useless
1) Nucleoside analogs—chain terminators incorporated by RTase
        AZT, 3TC, ddI, ddC
        AZT: (zidovudine) reduces mortality, opportunistic infection, delays AIDS,
                reduces vertical transmission, adverse side effects, resistance arises when
                used alone
        ddI (didanosine), ddC, d4T, 3TC (lamivudine): reduces resistance to AZT
               when used in combo, reduces viral load, incr. CD4 count, delays AIDS.
               3TC + AZT is considered a first line drug (combo called Combivir)
               3TC in particular—also used for HBV in combo with interferons, no
               limiting toxic effects
               ddI in particular—unstable in acid environment (GI), formulated with
               antacid, can cause pancreatitis
               ddC in particular—GI not a problem, well absorbed, though a few ulcers
               have been reported
               the d’s—can give you peripheral neuropathies
2) Non-nucleoside RT inhibitors—bind to a hydrophobic pocket on RT, inactivate it
        High rate of resistance, only one mutation needed, occurs w/i a month
3) Protease inhibitors—bind to viral protease, block processing; particles made with non-
processed proteins are not infectious
        More mutations needed, take longer to develop resistance, often mutation found
               in target (the protease)
        Indivair—absorbed quickly in the fasting state (opposite of saquinavir), causes
               GI complications, kidney stones

Alternative Therapy: IL2 to stimulate CD4+ T cell production; no change seen in viral
                     bone marrow transplants

Three standards:
       Strength of antiviral affect
       Ease of resistance—drugs must be used in a such a way as to avoid this
              (combinations used, low viral levels (<50) w/o virus replication usually do
              not progress or develop resistance, Ex: AZT, 3TC, and indinavir)
       Tolerance by patient

For opportunistic infections:
For most—treat symptomatically
For Pneumocystis pneumonia, Toxoplasma encephalitis, Mycobacterium avium – treat
prophylatically when CD4+ count drops to 200/mm3, 100mm3, and 50/mm3 respectively
For CMV, prophylactic treatments being developed

Decrease number of sex partners
Wear a condom
Screen blood (**not all virus containing blood has anti HIV 1 or anti HIV 2 Ab)
Heat treat factor 8 and 9 clotting factors to inactivate virus
Immediate AZT treatment after exposure (an unknown)
        Difficult due to: variability of HIV sequence; hypervariable regions lie within the
                env gene
        Strategy may be to block initial infection by attaining sufficiently high levels of

In retroviruses = oncogenes
In humans = proto oncogenes if inactive
                Oncogenes when active
Oncogenes cause cancer
Cancer is a loss of contact inhibition, control of cell growth via growth receptors, etc.
        Receptor bound by growth factor – intracellular phosphorylation of tyrosine –
phosphotyrosine acts as an intracellular growth messenger

Oncogene examples: src, erb-B

Retroviruses cause: sarcoma OR leukemia (so called leukemia sarcoma viruses)
       Can integrate a viral oncogene (acute transforming) with sticky ends and integrase
               Rous sarcoma virus (has rsc gene) – not defective
               Were created by ―capturing‖ a host protooncogene into its genome and
                      activates it; often due to the length of the oncogene, viruses lose
                      their own RNA necessary for replication = defective acute
                      transforming viruses (require a co-infecting virus to cause cancer)
       Can activate a host protooncogene by integrating into key regulatory area

Human Retroviruses
Retroviruses seen in many animals; began to look for them in humans
Human T cell leukemia virus (HTLV 1) – linked to paralytic disease in tropics (tropical
spastic paraparesis); isolated from patient with adult T cell leukemia virus
HTLV II – not linked to disease
AIDS epidemic
        Linked to retroviruses due to: in the blood, too small to be filtred
                                       Delayed onset (common for retroviruses)
                                       Immunodeficiency seen in animal retroviruses
                                       Destruction of T helper lymphocytes (HTLV I, II
                                               was T cell trophic)
        found DNA and RNA in T cell culture growth
        identified virus as HIV (strains 1 and 2 have been found)
SIV (simian immunodeficiency virus) shares close homology to 2, causes AIDS like
        disease in primates

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