VIROLOGY

WHAT THE HELL IS IT?

• Study of viruses (I don’t want to add the super long definition; please have mercy on yourselves—)
o “Virus” è Latin word meaning “slime” or “poison”

WHERE DO THEY COME FROM?
• Completely UNKNOWN D:
o Retroviruses may have arisen from transposable elements
§ Transposable elements (TE)/Transposons/Jumping Genes
• Main components of eukaryotic genomes
• DNA sequences that can change its position (jump) within a genome, sometimes
creating/reversing mutations and altering the cell’
o Some may have arisen from eukaryotic parasites that lost most of their genomes

NOT SO BRIEF HISTORY
• 1800s
o Jacob Henle
§ hypothesized the existence of infectious agents that were too small to be seen with light microscopy
o Louis Pasteur & Robert Koch
§ developed methods for sterile culture & bacterial culture
o Adolf Mayer
§ described a non-bacterial, non-fungal cause of tobacco mosaic disease
§ Proved that it wasn’t caused by any toxins via limiting dilution
§ Filtered the infected plant through a Chamberland filter (unglazed porcelain)
• 1901
o Walter Reed
§ Discovered the first filterable infectious agent in Cuba– Yellow Fever Virus
o Many new viruses were discovered along with bacteriophages
§ Bacteriophages – viruses that infect bacteria
• Similarity between Genes and Bacteriophages
o They both initiate replicative events causing the production of several progenies
o Electron microscopy was developed and was helpful in conclusively showing the existence of viruses
o Early Concepts about Viruses:
§ They are parasites
§ They are mobile genetic elements
§ They are filterable agents
• Modern Period of Virology (1965 – PRESENT)
o Virology led to the basic discoveries in basic biology
§ Revolutionized molecular biology
§ Understanding of gene regulation, genetic recombination & cancer
o Thousands of new viruses were isolated and identified
o Recombinant DNA was used to produce vaccines for unsafe vaccines
o Reverse genetics was developed to produce infectious DNA clones of RNA viruses

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PROPERTIES OF VIRUSES
• Complex macromolecules
o In terms of its massive chemical structure and its
macromolecular structures
o Diameters usually range from 20-300 nm
• Smallest biological entity (refer to Figure 1)
• Obligate intracellular parasites
• Metabolically inert
o They are NOT alive
o Therefore, you cannot kill them L
o You can only inactivate them
• Either have DNA or RNA genomes; NEVER BOTH Figure 1. Size of Bacteria vs. Some Viruses
• Inanimate in nature
o Their effects on the body are seen
o But the virus itself cannot be seen
• Cannot be cultivated in a cell-free medium
• All species are susceptible to viruses

BASIC STRUCTURE OF VIRUSES
• Virion
o Refers to the complete viral particle
o Composed of 2-3 parts:
§ Nucleic acid core/Genome
• DNA or RNA
• NEVER BOTH
• Contain only one copy of the genome Figure 2. Basic Parts of the Virion
• Maybe double-stranded or single-stranded
o If single stranded RNA, it may be in a positive or negative sense
• Maybe be linear or circular
§ Capsid/Shell/Protein Coat
• Composed of capsomeres
o Capsomere
§ Morphologic unit of capsid
§ cluster of polypeptides
• Encloses the nucleic acid and protects it from denaturation
• If the virus is NAKED, it is the component responsible for attachment
• Determines specific viral antigenicity
§ Envelope (only for some viruses)
• Phospholipid bilayer membrane
• Surrounds the capsid
• Acquired during viral maturation via budding
• Other Structures present on the envelope
o Peplomer/Spike proteins
§ Spike-like projections
§ Mediate cellular entry
o Matrix

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§ Other parts:
• Enzymes
• Hemagglutinin
• Tegument
§ Other terms to remember:
• Protein Subunit
o Single polypeptide
• Structural unit
o 2 or more bound non-identical subunits
forming a larger building block Figure 3. Naked vs. Enveloped Virus
• Assembly Unit
o Multiple structural units
• Viruses may be either…
o Enveloped
§ Either labile or ether-sensitive
§ More sensitive compared to naked viruses ( ͡° ͜ʖ ͡°)
§ Factors that can damage the envelope:
• High and very low temperatures
• pH less than 6 or above 8
• Disinfectants (e.g. Hydrogen peroxide, phenol)
o Naked ( ͡° ͜ʖ ͡°)
• Chemical composition of viruses
o Proteins
§ All viruses have structural proteins
§ Some have enzymes
§ Viral proteins are principal targets of the immune response
o Nucleic Acids
o Lipids
§ Some viruses have lipid envelopes acquired from the cell in which the virus was produced
o Glycoproteins
§ Some viral proteins, particularly those that protrude outward, have carbohydrate groups
§ Those carbohydrate groups often mediate viral attachment to susceptible cells


CLASSIFICATION OF VIRUSES
• formulated by the International Committee for the Taxonomy of Viruses (ICTV)
• Universal System of Virus Taxonomy
o “–viridae” for family
Ex. Flaviviridae

o “–virus” for genus
Ex. Flavivirus

o Species name
§ based on the geographic region of discovery
§ No italicizing!!
Ex. West Nile virus – discovered in Uganda

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o Strain
§ Different wild isolates of the same virus
Ex. WNV-NY – New York isolate of the West Nile Virus
o Type
§ Distinct strains of the same virus based upon known genetic differences
Ex. HIV Type 1 vs. HIV Type 2
o Variant
§ Virus that behaves differently than the wild-type in the laboratory for
unknown reasons

• Baltimore Classification Figure 4. Helical Virus
o Based on genome, strandedness, sense, and method of replication
Group No. Category Examples
I dsDNa Adenoviridae, Herpesviridae,
Poxviridae, Papovaviridae
II ssDNA Parvoviridae
III dsRNA Reoviridae
IV (+) sense ssRNA Picornaviridae, Caliciviridae,
Togaviridae, Flaviviridae,
Coronaviridae, Herpeviridae
V (-) sense ssRNA Orthomyxoviridae,
Arenaviridae, Figure 5. Icosahedral Virus
Paramyxoviridae,
Bunyaviridae, Rhabdoviridae,
Filoviridae
VI Reverse transcribing RNA Retroviridae
VII Reverse transcribing DNA Hepadnaviridae

• Basis of Classification
A. Morphology (usually via EM)
B. Physiochemical properties
C. Genome
D. Macromolecules
E. Antigenic properties (via serology)
F. Biological Properties (e.g. host range, mode of transmission, etc.)

A. MORPHOLOGY OF VIRUSES
• Helical (as seen in Figure 4)
o Shaped like a hollow protein cylinder
o May be either rigid or flexible
o Nucleic acid and protein are closely associated
Ex. Tobacco Mosaic Virus
Ebola Virus
• Icosahedral (as seen In Figure 5) Figure 6. Some examples
o Polyhedrons (geometric shape with 20 sides) of complex viruses
o Assemble in a cubic manner
o Appear spherical when viewed under LPO in EM

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o Can be crystallized and viewed using radiocrystallography
Ex. Adenovirus
• Complex (as seen in Figure 6)
o Not purely icosahedral or helical
o May possess tails and other structures (ex. Bacteriophages)
o May also possibly have complex, multilayered walls surrounding the nucleic acid (ex. Vaccinia virus)

B. PHYSICOCHEMICAL PROPERTIES: Reactions of Virus to Physical & Chemical Agents
• Heat and Cold
o Heat inactivates some viruses
o Cold preserves them
• Stabilization by Salts
o … unknown…
o … this bullet is honestly a waste of space—
• pH
o some viruses are resistant to any drastic changes in pH
• Radiation
o Damages nucleic acids by cross-linking the viral proteins
• Photodynamic inactivation
o Renders some viruses susceptible to visible light
• Ether susceptibility
o Damages the envelope/membranes of viruses
• Detergents
o Amphipathic
o They solubilize the membranes and dissociate the noncovalent bonds between viral proteins
• Formaldehyde
o Cross-links nucleic acids and proteins

GENETICS OF VIRUSES
• In nature, viruses are under extreme selective pressure from the host response
• DNA viruses use high fidelity (10-9) DNA polymerases for genome replication
• RNA viruses, on the other hand, use low fidelity polymerases with spontaneous mutation rate as high as 10-4
o The occurrence of viral quasispecies within an individual is common among RNA viruses
§ Viral quasispecies
• Group of viruses with similar mutation(s) competing within a highly mutagenic environment
• Mutations can result in viruses with new phenotypes that can alter infectivity. With that, they could…
o Have increased virulence
o Better evade the host’s immune response
• Propagation of wild-type viruses in cell culture or eggs often lead to the formation of mutant viruses
o Mutant/Attenuated viruses:
§ Have little selective pressure
§ Have high replicative capacity
§ Have low virulence
§ Can be used for vaccine production
• Defective viruses
o Mutant viruses that are unable to infect as wild-type viruses
o Can occur due to:

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§ Deletion of genetic information
§ Mutation
§ Encapsidation of host DNA instead of the viral DNA
• Interaction among viruses
o Recombination
§ acquisition of genes from other viruses
o Complementation
§ Defective viruses can regain their infectious capacity if another virus helps infects the cell and provides the
molecule
o Phenotypic mixing
§ Two different species of virus coinfect a cell and their genes are packaged with the other
o Interference
§ A virus alter’s the cell’s physiology so that no other virus is able to infect it
o Reassortment
§ Viruses of the same genus can exchange
gene segments with each other

VIRAL GROWTH CURVE
• Linear representation of the process of viral
replication (as seen in Figure 7)
1. Virus Entering the Cell
2. Eclipse Period
3. Latent Period
4. Extracellular Release of Viruses
Figure 7. Typical viral growth curve

VIRAL REPLICATION IN DETAIL
Let’s get to making babies— ( ͡° ͜ʖ ͡°)
I found this very fun to make tbh-

1. Attachment/Adsorption
• Virus will attach to the susceptible cells and
interact with specific molecules on the cell’s
surface
• Boy (virus) and girl (cell) meet—

2. Penetration
• Viruses have their own distinct method of
penetration:
o HIV gp120 interacts with a cell’s chemokine Figure 8. Overview of the process of viral replication
receptor in such a way that it would induce
membrane infusion between its own viral envelope and the cell’s plasma membrane
§ This kind of guy (virus) will entice the girl (cell) in such a way that they’d let them get into their
pants—
o Other viruses would exploit receptor-mediated endocytoses to gain access to the cell’s cytoplasm
§ This guy (virus) ain’t—

3. Uncoating
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• Once it’s inside the cell, the virus uncoats its capsid and releases its viral nucleic acids and enzymes into the
cytosol
o I’m honestly getting weird ideas from this—
o You know what happens ( ͡° ͜ʖ ͡°)

4. Macromolecular Synthesis (Transcription & Translation)
• Once its insides are roaming free within the target cell (oml), the virus will make polypeptides and replicate
its genome
o DNA viruses replicate in the nucleus
§ Uses DNA-dependent RNA polymerase to synthesize mRNA
o RNA viruses replicate in the cytoplasm
§ (+) sense – use the host’s RNA polymerase to synthesize mRNA
§ (-) sense – uses their own RNA polymerase to synthesize mRNA
§ Double-stranded RNA – carries its own RNA polymerase
§ Retrovirus
• ssRNA is transcribed into dsDNA via reverse transcriptase (RNA-dependent DNA polymerase)
• dsDNA copy is then turned into mRNA by the host’s RNA polymerase
• Early transcription and translation è results to polypeptide synthesis using the cell’s polypeptide synthesis
mechanism to gain control (mmhmm. They totally taking control— ( ͡° ͜ʖ ͡°) )
• Viruses have highly economic genomes
o Some genes encode polypeptides that are cleaved into two or more functional proteins
o Some genes encode mRNA that are overlapping or going in both directions
• DNA synthesis, late transcription, and late translation è this is for producing the bab— new
macromolecules for new progeny virions

5. Morphogenesis/Viral Maturation
• Condensation è the viral macromolecules formed will accumulate in compartments and assemble in the
cytoplasm as a nucleocapsid

6. Release
• Viruses will exit the cell either by…
o Lysis – when the cell dies, the progeny virus will move into the extracellular department
o Budding – assembled nucleocapsids push through a membrane, taking a part of it so that it acts as the
virus’ envelope
o Exocytosis
• So it’s either the girly dies while giving birth or not oml this is one hell of a fucked up story—

ECOLOGY OF VIRUSES
• They persist in a host long enough to allow transmission to a new susceptible host
• They infect without causing pathology or eliciting an immune response
• Portals of Entry:
o Mucosa of respiratory and GI tract
o Mechanical inoculation
o Skin
o Intimate contact
• Transmission mechanisms:
o Communicable (person to person)

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o Incidental transmission of animal virus to humans (spill-over)
o Arthropod-borne (Arboviruses)


• Emerging & Re-emerging Viral Diseases
o Principal Causes:
§ Human encroachment upon uninhabited areas
§ Climate Changes
§ Changes in societal structure/behavior
o Recently Emergent Viruses
§ SARS CoV § H5N1 Avian Influenza
§ Hendra Virus § West Nile Virus
§ Nipah Virus

PATHOGENESIS OF VIRAL DISEASES
1. Viral infection
• Expression of the viral replicative cycle in a host cell
• Clinical presentations:
o Acute
o Latent
§ Viral integration into the cell
§ No replication; may resume several weeks/years after
§ No disease manifestation
§ Host cells aren’t damaged
§ Seen in cases of HSV1, HSV2, VSV, CMV, EBV, measles
o Chronic/Persistent
2. Viremia
• Occurs after local viral infection
• Release mediators of immune cell functions
• Secondary viremia occurs in skin, salivary glands, kidneys, and brain tissues
o Symptoms manifest
• Disease is resolved once viral replication is prevented
3. Tissue Damage
• Cell lysis
• Immunopathologic mechanisms
4. Latency of virus in host tissues
5. Autoimmune Pathogenesis
6. Oncogenesis

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SPECIMEN COLLECTION & HANDLING
• Should be collected in the early stages of the infection (at least 3-4 days after the onset of signs and symptoms)
o Exceptions:
§ Diagnosis for adenovirus, enterovirus, and CMV – prolonged viral shedding in stool & CMV respectively
• All specimens are to be submitted to the microbiology lab to be processed immediately
• Best to get the sample at the infected site directly
• Swabs:
o Should be made of dacron, cotton or rayon
o NEVER use calcium alginate, charcoal, or swabs with wooden shafts
• Transport Media
o Specimens requiring transport media: respiratory, swabs, and tissue samples
o Saline/Trypticase Soy Broth
o Commercial viral transport media:
§ Hank’s balanced salt solution § Eagle’s tissue culture
§ Veal infusion broth § Viral culturettes
§ Leibovitz Emory medium § Virocult
§ Stuart’s Medium § Universal transport medium
§ Amie’s medium
• Storage:
o 4˚C for no more than five days if there is a delay in specimen processing
o Further delay = -70˚C for 6 or more days

PURIFICATION OF VIRUSES
• Precipitation with Polyethylene Glycol at 4C overnight
• Once it’s precipitated, wash it with a buffer to remove the PEG

LABORATORY DIAGNOSIS
A. DIRECT DETECTION
• Light/Electron Microscopy
o Detection of virions
o Useful for non-culturable viruses
o Detection of
Cytopathic/Cytopathogenic Effects
(CPE)
§ Structural changes in host cells
caused by viral invasions leading
to necrosi
§ Examples:
• Cell degeneration
• Cell death (necrosis)
• Plaque formation Figure 9. Microscopically viewed CPEs
• Syncytia formation
o Syncytia – giant
multinucleated cells formed from the fusion of cell membranes
• Inclusion body formation
• Microscopically visible aggregation of viral proteins in the cells
• Viral Antigen Detection

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o Direct Fluorescence Antibody Testing
o Antigen Capture Techniques
o Latex Agglutination
o Enzyme Immunoassay
o RIA
o Immunoperoxidase
o ELVIS

B. NUCLEIC ACID BASED DETECTION
• Molecular methods
o Quicker release of results
o More sensitive
o Quantitative
o Detects unculturable viruses
o Can detect multiple viruses
o COSTLY; needs more specialized training
• Methods: Figure 10. Sample PCR Graph
o Real-time PCR
§ Relies on the fluorescence of DNA
§ Requires known nucleic acid sequence of for the virus and gene-specific DNA primers
• In RNA viruses, the RNA should be copied into cDNA using reverse transcriptase
§ Procedure:
1. Extract DNA or RNA from a virally-infected tissue
NOTE!!
If RNA is used, copy the RNA into cDNA using reverse transcriptase
2. Add DNA, forward & reverse primers, and real-time PCR mixture
PCR Mixture Components:
ü Taq Polymerase
ü dNTPs
ü SYBR Green I dye
o Fluorescent dye that binds ONLY to double-stranded DNA
3. Conduct PCR for 50 cycles
4. After collecting the 50 data points from each cycle, a graph of DNA abundance is generated
(refer to Figure 10)
Cycle Threshold (Ct)
• Cycle at which the fluorescence crosses the orange line
• The smaller the Ct, the greater the amount of DNA template in the tube
§ Determining the copy number:
• In separate tubes, there are plasmid standards mixed with the viral gene in known
copy numbers
§ The known copy numbers can be used to generate a standard curve, which
can be used to quantify the copy number in test samples using statistical
algorithms
o Nucleic Acid Probes
o Hybridization Tests

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C. BIOLOGICAL ASSAYS
• Ability of the virus to induce CPE in cell culture or eggs
• Viruses can be classified based on how difficult they are to cultivate:
o Simple – viruses of this type can be grown using…
§ Cell Culture
• Use of cell lines/tissue cultures
• Host cells grow confluent (grow into a monolayer) on the sides of
glass/plastic test tubes
• Growth Medium
o Prepared with Eagle’s minimum essential medium in Hank’s or
Earle’s balanced salt solution
§ Antimicrobials are sometimes added
o Serum rich medium (10%)
• Maintenance Medium
o Similar to growth medium
o Only has 0-2% serum
• Incubated in Roller drums tilted by 5-7˚ (33 ˚ for respiratory
viruses)while being rotated at a speed of 0.5-1 rpm
Figure 11. Roller
o Incubation lasts for 1-4 weeks (usually ends at around 2 weeks)
Bottles where the
• To maintain the cells at a physiologic pH (7.2), a bicarbonate
specimens are
buffering system is added
incubated
• pH indicators like phenol red are added to monitor any adverse changes
§ Cell Lines
• Cell cultures become cell lines have been “passed”/subcultured in vitro
• Categories:
o Primary
§ Passed only 1-2x
§ Uses:
• Sensitive to influenza viruses, parainfluenza viruses, mumps, enteroviruses,
and adenoviruses
§ Examples:
• Human • Primary monkey kidney
embryonic • Rhesus monkey kidney
kidney • African green monkey kidney
• Rabbit kidney
o Diploid/Low Passage/Finite
§ Diploid cell lines must have at least 75% of cells with the same karyotype as the
normal cells of the tissue
§ Remain viable to viruses from 20-50 passages
§ With increasing passage, these cells become more insensitive to viral infection
§ Ex.
• Human diploid fibroblasts
o Continuous/Heteroploid/Immortal
§ Capable of infinite passage
§ Less than 75% normal cells; more than 25% of the cells have an abnormal
karyotype
§ Obtained from malignant tissues

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§ Uses:
• Sensitive to HSV, VSV, CMV, Adenovirus, and rhinovirus
§ Examples:
• HeLa
• Hep-2
• KB
• A-549
• Vera

Cultures are examined for CPEs

• To be observed under the inverted light/phase contrast microscope under LPO
• May be seen as…
o Formation of inclusion bodies
o Rounding
o Clumping
o Granulation
o Untypical CPES:
§ Syncytia – in Parainfluenza 1 & 2
§ Hemadsorption
§ Hemagglutination
• Quantitation:
Grade Interpretation
Negative Uninfected monolayer
Equivocal Atypical alteration of monolayer involving a few cells
1+ 1-25% of monolayer exhibit CPE
2+ 25-50% of monolayer exhibit CPE
3+ 50-75% of monolayer exhibit CPE
4+ 76-100% of monolayer exhibit CPE

§ Shell Vial
• Rapid modification of conventional cell culture
• Cells are grown on a round coverslip in a shell vial which is incubated, centrifuged, and
incubated again for 1-5 days
• It will be stained and a fluorescein-labelled monoclonal/polyclonal antibody specific for viral
antigens are added
• Fluorescence microscope is used
§ Specific Pathogen-Free (SPF) Embryonated Chicken Eggs
• Involves the inoculation of chorioallantoic membrane (CAM) or the yolk
o Difficult – viruses of this type can be grown using…
§ Whole animal
• After the virus replicates in the animal, the target organ must be collected, pureed, and
centrifuged to collect the virus homogenate
• Cannot be used for vaccines
o Except for the Vaccinia virus (smallpox)
o Impossible (Don’t even think about it; if it’s impossible, it’s impossible. Don’t even fucking try—)
• Uses limiting dilution to determine virus numbers
• Tissue Culture Infectious Dose – 50 (TCID50)

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o The dilution showing the virus infecting/killing 50% of the cells
o Eggs = EID50
o Animals = ID50 or LD50
o Calculation:
§ Reed-Muench Method (1938)
• Calculation of TCID50
• Procedure:
1. Make a log10 dilution series of a virus preparation
2. Add 100 µL of dilutions in 5 replicates in a 96-well plate containing confluent susceptible
cells
3. Incubate the cells until the CPE is complete
4. Check if there is any infection occurring in any of the wells
5. Identify the two adjacent dilutions where more than 50% of the wells are infected, and less
than 50% are infected
6. Determine the TCID using the formula
% $#/&%&0* 12#0* 50% − 50%
!"#$#"%&#' &')*+%*, =
%$#/&%&0* 12#0* 50% − %$#/&%&0* 2*6#7 50%

1
89:;<= = + !"#$#"%&#' &')*+%*,
(% $#/&%&0* 12#0* 50%)

§ Plaque Assay Method
• Counting plaque forming units (pfu) as a quantitative
measure of infectious virus
• Basic Procedure
1. Allow susceptible cells to confluent on 12- or 6-
well plates
2. Add 1 mL of log10 dilutions of virus to the cells
in duplicate
3. Incubate for 1 hour to allow the virus to adsorb
to the cells
4. Replace the liquid media with a semi-solid
media (e.g. agarose, methylcellulose) Figure 12. Sample plate used in
This will restrict viral infection from plaque assay method that has been
spreading to other cells besides the stained with formaldehyde containing
adjacent cells crystal violet
5. Allow the infection to proceed for a few days
6. Stain the cells with formaldehyde containing crystal violet (as seen in Figure 5)
7. Select the dilution with 10-100 plaques and count
Calculate the mean of the counted plaques
Calculate the titer based on log dilution and the number of plaques
8&%*" = B#C ;&6D%&#' E (F*1' $61GD* +#D'%)

D. SEROLOGY
• Tests:
o Complement fixation
o ELISA
o Western Blot

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o Indirect Immunofluorescence
o Hemagglutination/Hemagglutination inhibition Assays
• Uses:
o For diagnosis of non-culturable viruses
o Determination of immune status in rubella, VZV, HAV, and HBV
o Monitoring of immunosuppressive or transplant patients
o Epidemiologic or prevalence studies

LABORATORY SAFETY
• Guys, ilang beses na ung lab safety??
• Kailangan pa ba??
• Essential when dealing with viruses… duh.
• Levels of Practice that Ensure Containment
o Proper Technique
o Proper Equipment
o Prevention & Containment Break Policies and Procedures
• Aerosols & punctures are the principal threats
o Ingestion and splashes are less common—
§ Who exactly has the guts to put anything that deadly in their mouth—
• Biosafety Practices
o Training in aseptic technique
o No mouth pipetting
o No eating, drinking, smoking, or applying make-up or lip balm in the laboratory
o Use PPE
o Sterilize infectious wastes
o Use biosafety cabinets
o Immunize yourselves if necessary

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DNA VIRUSES
Herewegonosebleednathiiiiiiiis—

Generalities:
• All are linear except for Papovaviridae & Hepadnaviridae
• All are doublestranded except Parvoviridae
• All are naked except Herpesviridae, Hepadnaviridae, and Poxviridae
• All are icosahedral except Poxviridae
• All replicate in the nucleus except Poxviridae
• DNA Tumor viruses:
o Human Papilloma virus
o EBV
o HBV
o Polyomavirus
o SV40
• Smallest DNA Virus = Parvoviridae
• Largest DNA Virus = Poxviridae

• Alpha Group
- HHV1 Original 6
- HHV2 Exanthematous Disease
- HHV3 1. Measles
2. Scarlet Fever
• Beta Group 3. Rubella
- HHV5 4. Dukes
- HHV6
5. Erythema
- HHV7

Infectiosum
• Gamma Group
6. Erythema
- HHV4 Subitum
- HHV8

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HERPESVIRIDAE
Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV1 Simplexvirus HSV1 Mucoepithelial Neuron (trigeminal Close contact; oral • Children • Oral Herpes
- Very common ganglion) • Sexually active - Appear as intraoral mucosal vesicle/ulceration
- Most pxs are individuals on the buccal mucosa, posterior pharynx,
asymptomatic • Medical professionals gingival & palatal mucosa (refer to Fig. 1)
- Reactivation may coming in contact • Others:
occur during with oral & genital o Keratojunctivitis
periods of stress secretions o Encephalitis – necrotic lesion in one temporal
- Life-long • Immunocompromised lobe
infection • Infants o Herpetic Whitlow
o Herpetic gladiatorum
o Disseminated Infections
-

HHV2 HSV2 Neuron (sacral Close contact; sexual • Genital Herpes (Herpes Genitalis)
ganglion) contact - Painful vesicular lesions on the genitalia (refer to
Fig. 4)
• Neonatal Herpes
- Acquired from infected mothers during utero,
birth, or after birth (refer to Fig. 5)
- Erythema multiforme
- Bull’s eye/Target lesion/rash on the trunk,
hands & feet (refer to Fig. 6)

Diagnosis: Treatment

• Direct Microscopic Exam • Serology Acyclovir

o Tzanck smear to visualize CPE) o EIA
o Presence of Giant Multinucleated Cells & Cowdry’s Type A inclusion Bodies o ICT
• Cell Culture • Molecular Methods
o Gold Standard o DNA detection via PCR
o CPE can be seen within 1-2 days • NAT

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Fig 1. HSV 1 – Primary herpes gingivostomatitis

Most common in children

Fig 5. HSV 2 – Neonatal

Fig 4. HSV 2 – Herpes genitalis Herpes

Fig 3. HSV 1 – Herpetic

Whitlow
Fig 2. HSV 1 – Herpes Labialis
(Recurrent HSV infection)

Fig 6. Erythema multiforme –

bull’s eye/target lesions

Fig 7. Tzanck smear showing a giant multinucleated cell

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Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV3 Varicellovirus VZV Mucoepithelial Neuron (dorsal root Close contact & • Occurs in epidemics • Chickenpox
- ganglion) respiratory • Mostly occurs in - Incubation period: 2-3 wks
childhood - S/S: fever, malaise, pruritic rash & vesicular
lesions on head, trunk, then limbs
- Rash: papules>vesicles>pustules &crusts
- Lesions dry, crust over & heal in 1-2 wks
- “dewdrop on a rosepetal” appearance
- Complications:
- Teens & adults
- Immunocompromised
- Reye’s Syndrome
- Immunity to chickenpox is lifelong
• Shingles
- Reactivated chickenpox found among the
elderly and immune suppressed
- Rashes followed by vesicular lesions in a
unilateral dermatome pattern
- Postzoster/Postherpetic neuralgia:
- Prolonged disabling pain that can remain
for months even if the lesions disappear
Diagnosis: Treatment

• Direct Microscopic Exam • Antigen detection

o Tzanck smear to visualize CPE (as seen in Fig. _) o Addition of specific fluorescent-labelled antibodies
o Presence of Giant Multinucleated Cells • Molecular Methods
• Cell Culture
o Definitive diagnosis
o Small ovoid cells in fibroid cells (MRC-5, HF, A549)

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Figure 8. Chickenpox/Varicella Figure 9. Tzanck stain with Varicella vesicle
 VIROLOGY


Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV4 Lymphocryptovirus EBV B cells & B cells Close Oral Contact • Young adults • Infectious Mononucleosis (Mono/Kissing
epithelia - Infected B cells are (Kissing) • Children Disease/Pfeiffer’s Disease/Glandular Fever)
destroyed by T cells - Virus is in saliva (asymptomatic/ have - S/S: fever, chills, sweats, headache, very
but some EBV hide in and infects the mild symptoms) painful pharyngitis, lymphadenopathy may
the B cells (latency) oral epithelial occur
- Can be reactivated cells before - Malignancy:
once the body is spreading to the - Uncontrolled growth of B-cells leading to
immunocompromised B cells, which in Burkitt’s Lymphoma
turn, transforms - Nasopharyngeal carcinoma
to produce
copies of the
EBV DNA

Diagnosis: Treatment

• Antigen detection • Direct Microscopic Exam --

o Presence of EBV nuclear antigen (EBNA Test) o Blood picture: lymphocytosis with Downey cells
o Presence of Heterophil antibody against EBV (atypical lymphocytes)
§ Monospot Test (presumptive test) • Cell Culture
§ Paul Bunnel Heterophil Test (screening) o Using B-cells
§ Davidsohn’s Differential Test (specific)

o Antibodies Produced
§ Anti-VCA (Viral Capsid Antigen) (IgM) –early course of
infection; current infection
§ Anti-VCA (IgG) – acute stages; persists for life
§ Anti-EA/D (Early Antigen/Diffuse) – acute stage;
current/recent infection
§ Anti-EA/R (Early Antigen/Restricted) – acute stage; can persist
up to 2 years
§ Anti-EBNA –1 month after infection; can peak in 6-12 months
after infection; can peak in 6-12 months
Anti-EBNA - appear 1 month

©MANALO.2017 19
Figure 10. Hairy leukoplasia caused by EBV Figure 11. Downey Cells/Atypical
Lymphocytes
 VIROLOGY


Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV5 Cytomegalovirus CMV Lymphocytes, Monocytes, T cells, • Orally • Infants • Most of the cases are asymptomatic infections
- Can cross epithelial cells macrophages • Sexually • Sexually active - 80% of adults are infected
placenta • Blood individuals - No apparent symptoms
- transfusions • AIDS patients • Cytomegalic Inclusion disease
• Tissue Transplant • Immunosuppressed - CMV cossing the placenta will lead to…
• In utero • organ transplant - Petechiae
• At birth patients - Hepatosplenomegaly
• By nursing - Mental retardation
- Microcephaly
(Saliva, Urine, - Deafness
Breastmilk) - Seizures
And other birth defects
- Presence of purpuric papules & nodules
- Can occur if pregnant mother becomes infected
• Cytomegalic Mononucleosis
- Mono-like symptoms + Hepatitis
• Reactivation
• Among AIDS patients
- Intractable colitis with diarrhea
- retinitis
• Among Iorgan transplant patients
- Can cause pneumonia, pneumonitis,
hepatitis
Diagnosis: Treatment

• Serology (IgM or IgG) • Cell Culture Ganciclovir

• Antigen detection (ex. Detection of pp65) o CPE: Owl’s eye inclusions Preventive Measures
• Fluorescent Antibody Techniques o Urine/Respiratory secretions
• Molecular Methods o Shell vial technique (72 hrs) • No vaccine
• Antiviral drugs for AIDS patients
• Refrain from sexual contact
• Screening blood and organ donors

©MANALO.2017 20
Figure 13. Owl’s eye inclusion

Figure 12. Congenital Cytomegalovirus

 VIROLOGY


Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV6 Roseolovirus Herpes Lymphotropic B & T cells T cells, B cells. • Inhalation of • Variant A - • Roseola infantum/Exanthem subitum
Virus - Viral monocytes aerosols immunocompromised - Characterized by a febrile illness with
• Variant A – causes receptor: • Close Contact • Variant B - Children (6 mild constitutional symptoms lasting 3-
disease in CD46 - Viral shedding months to 2 years) 5 days
immunocompromised in saliva causes - After rapid defervescence, a pink
• Variant B – causes - Causes Roseola (macro)papular rash appears on the
disease (Roseola infantum or trunk lasting for hours to days
infantum, exanthema exanthema • Associated with the development of
subitum, sixth subitum progressive multifocal
disease) leukoencephalopathy & multiple sclerosis
• • Reactivation of latent infection occurs
among the immunocompromised
- Can lead to pneumonia

HHV7 Pityriasis Rosea T cells and ???* T cells • Children older than 6 • Also causes Roseola infantum but less
- Viral usually become common
receptor: seropositive • Latency may also occur
CD4

* They know
they infect
something other
than the T cells.
They just don’t
know which
specific one.
Diagnosis: Treatment

• Cell Culture
o Use of Lymphocyte
• Serology
• PCR & Viral Load Testing
• Clinical Diagnosis

©MANALO.2017 21

Figure 14. Roseola infantum
 VIROLOGY


Type Genus Virus Target Cell Site of Latency MOT People Affected Clinical Manifestations
HHV8 Rhadinovirus • Karposi’s Sarcoma B cells B cells • Transplantation • HIV-infected patients • Karposi’s Sarcoma
Associated Herpes - Viral • Close Contact • MSMs are more - Malignancy common among AIDS
Virus receptor: (Sexual) prone to infection patients
CD46 • - Viral shedding - Virus inactivates the retinoblastoma
in saliva causes tumor suppressor protein
- Causes Roseola - Affects vascular endothelium
infantum or - Systemic disease with cutaneous
exanthema lesions (patches) on the lining of the
subitum nose, mouth, or throat

Diagnosis: Treatment

• Cannot be cultured
• Immunohistochemistry
• PCR
• In-situ hybridization

Figure 15. Karposi’s Sarcoma

Cutanious Lesions

©MANALO.2017 22

 VIROLOGY


HEPADNAVIRIDAE
Genus Generalities MOT At Risk Diagnosis Clinical Manifestations Treatment
Hepatitis B Virus (HBV) - HepaB is specifically • Parenteral • Hepatits B/Serum Hepatitis
caused by “Dane Route • Median incubation period: 3
Particle” - Blood months
- Structure: - Intimate • Clinical Syndromes:
Ø Enveloped, contact o Acute Hepatitis
icosahedral - Needles o Fulminant Hepatitis –
capsid Perinatal severe acute hepatitis
Ø dsDNA with rapid destruction of
liver
o Chronic hepatitis
o Primary hepatocellular
carcinoma
ADENOVIRIDAE
Genus Generalities MOT At risk Diagnosis Clinical Manifestations Treatment
Mastadenovirus - 52 serotypes • Aerosols • Day care centers • EIA • Associated diseases
- Species: A to G • Fomites • Military training • IFA o Respiratory tract
- Structure: • Oral-fecal personnel • Antigen infections (pneumonia)
Ø Linear, dsDNA • Personal • Camps, swimming clubs detection kits o Gastroenteritis
Ø “orbiting contact • Culture o ARD
satellite” • Shell Vial Ø Caused by serotypes 4
appearance; • Serology & 7 among military
§ protruding • CPE recruits
fibers from - Grape-like o Epidemic
each of the appearance keratoconjunctivitis
12 vertices of • Vaccine Ø Caused by serotypes 8
the capsid & 19
- Formerly
Ø presence of available for o Pharyngoconjunctival
hexons & serotypes 4 & fever
pentons 7 for the • Latency period
military

What the fuck is so grapey about this anyway???

©MANALO.2017 23

Figure 16. Epidemic keratoconjunctivitis
Figure 17. Grape-like appearance of CPE
 VIROLOGY


POXVIRIDAE
Generally…
- Replicates in the host cell’s cytoplasm - Structure:
- Assembled in the Guarneri bodies Ø Linear, dsDNA
- Has DNA-dependent RNA polymerase Ø Enveloped
Ø Brick-shaped complex with a disk/dumb bell-shaped core
Ø Multi-layered

Virus Description MOT At Risk Diagnosis Clinical Manifestations Treatment
Small Pox Virus • Inhalation • Cell culture • Smallpox/Variola Vaccination
of aerosol • Growing of virus in - Acute contagious disease of administered
droplets chick embyo the reticuloendothelial, intradermally
• Face to face • Viral antigen vascular endothelial, and
contact detection via IF epithelial cells
• Direct - Synchronous progressive
contact rash with fever
• Fomites - Due to viral replication in
skin and damage from the
cytotoxic T cells attacking the
infected cells
- Categories:
Ø Variola major
§ Severe form; can
cause disfiguring
Ø Variola minor/”Alastrim”
§ Milder form
- Now eradicated
Ø Disease was exclusive to
humans
Ø Only 1 serotype
Ø Always present with
visible pustules
Ø Vaccines were available
Ø Scar indicates successful
vaccination
Vaccinia Virus - Used to vaccinate • Sexually • Lesions are larger than
against smallpox transmitted smallpox with necrotic
st
- 1 reservoir host • Skin contact centers
Molluscum Contagiosum Virus - • Direct skin • Children & young adults • Molluscum Removal of lesion
contact Contagiosum/Water Warts

©MANALO.2017 24

 VIROLOGY


• Intimate • Immunocompromised - “Cup-shaped crater”; small
contact patients papules on the skin/mucus
• Indirect • AIDS patients membrane
contact

PAPILLOMAVIRIDAE
Genus Description MOT At Risk Diagnosis Clinical Manifestations Treatment
Papilomavirus - Species: Human • Sexual • Indication: • Clinical Picture • Usually subclinical; no apparent • Prevent via
Papilloma virus contact Females 9-26 years • Cytology sections symptoms Vaccination
- More than 100 • Use of old • PCR • Warts/Veruccae/Papilloma o “Gardasil”
serotypes; some are shared • Immunosuppressed • Pap’s smear o Cutaneous – against
oncogenic object patients - Presence of koilocytes - Mostly caused by HPV 1-4 serotypes
- Have a predilection • prenatal (hallmark of infection) - Types: 6, 11, 16,
to infect only certain § Verrucae Vulgaris and 18
parts of the body (Common Wart);
- Target Cells: serotypes 2 or 4
Cutaneous/Mucosal § Plantar Wart; serotype
epithelia 1
- Site of Latency: § Verrucae Planae (Flat

Epithelia Warts); skin, forehead,
arms, face
§ Butcher’s Warts
(occupational);
Serotype 7
o Genital/Venereal Warts
(Condyloma Acuminata)
- Flat keratotic warts
- Commonly caused by
serotypes 6 & 11
• Carcinomas of Cervix, Penis, Anus,
Oropharyx
- Serotypes 16 & 18
- Specifically caused by E6 & E7
genes that inactivate
retinoblastoma proteins

©MANALO.2017 25

 VIROLOGY


PARVOVIRIDAE
- Structure:
Ø Smallest DNA virus
Ø ssDNA
Ø naked & icosahedral
Ø spherical under EM
- Target Cells: Erythryoid progenitor cells, adult bone marrow, fetal liver cells
- Site of Latency: Epithelia
- Requires growing cells (B19) or another virus (dependovirus) for replication
o Erythrovirus – virus that doesn’t need the help of another virus or helper cells to replicate (it’s a damn strong virus mmhmm— very strong very independent haha—)
Genus Description MOT At Risk Diagnosis Clinical Manifestations Treatment
th
Parvovirus B19 - Only • Respiratory & • Children with • Enzyme Immunoassay (IgG & • The 5 Disease/Erythema Infectiosum
medically oral secretions chronic anemia IgM) - Biphasic illness
important • Infants • PCR (blood or amniotic fluid) - Phases:
genera • Women o Initial
- Erythovirus • HIV patients - Marked fever
• Chemotherapy - Malaise
patients - Myalgia
• Transplant - Chills
Patients o Second
- Maculopapular rash
§ “slapped cheek appearance”
§ due to immune complex
deposition in skin capillaries
- Arthralgia
- Arthritis
• Aplastic Anemia
- Blood picture shows pancytopenia
• Hydrops Fetalis
- Fetal infection
- Virus crosses the placenta and infects the
fetus
• Arthritis
- Seen among women
- Small joints of feet and hand are affected
bilaterally
• Chronic B19 Infection
- Immunocompromised patients
- Characterized by chronic anemia,
leukopenia, thrombocytopenia

©MANALO.2017 26

 VIROLOGY

POLYOMAVIRIDAE
- Structure:
Ø Small
Ø dsDNA
Ø icosahedral, naked
- Site of Latency: Kidney & B cells
Genus MOT At Risk Clinical Manifestations
JC Virus Direct contact with • During childhood • Progressive Multifocal Leukoencephalopathy
respiratory secretions - Demyelinating disease

BK Virus • BM transplant patients • Heymorrhagic cystitis

• Immunocompromised renal transplant
patients
MC Virus • During childhood • Merkel Cell Carcinoma
SV40 (Simian Polyomavirus 40) • During childhood • Tumors in animals and humans

©MANALO.2017 27