Alain C.

Juayang, RMT, MSMT, MPH

Key Concepts: Properties of Viruses
• Viruses are small obligate intracellular parasites.
• Mature extracellular virus particles are called virion
(metabolically inert and mediate the transmission of
virus from host to host).
• The virion is consist of a genome (DNA or RNA)
surrounded by a protein coat (capsid).
• Intracellular viral replication requires disassembly of the
virion , viral genome-directed synthesis of virion
components by cellular machinery, and the assembly of
progeny genomes and viral proteins to form new virions.
 Virion Components and Functions
• Virion = genome and protein capsid = nucleocapsid
• Some virions posses a lipid envelope (cell membrane –
derived) that contains glycoproteins.
• Capsids and envelopes served to protect the viral genome
in its extracellular state.
• Capsids contain binding site for attachment to cell
receptors and mediate entry of the virion.
• Some virion contains enzymes (polymerases) or other viral
proteins necessary for efficient viral reproduction.
 Virion Components and Functions
• The viral nucleic acid may be “ss or ds”, linear
or circular.
• DNA virus genomes may be “ss or ds”, linear
or circular.
• RNA virus genomes may be may be “ss” or
“ds”, linear or circular, segmented or
nonsegmented.
• The ss viral RNA can either be (+) RNA or (-)
RNA
Virion Structure
• Viral nucleocapsid have 2 types of symmetry:
helical & icosahedral.
• Capsid symmetry is based on the arrangement
of morphologic subunits called capsomers
(composed of multiple copies of 1 or several
different polypeptides that form the capsid).
• Helical nucleocapsid is composed of protein
subunits bound to the viral RNA in the form of
helix.
Virion STructure
• Icosahedral nucleocapsids have protein subunits
arranged in the form of an icosahedron with 20
triangular faces and 12 vertices.
• Construction of viruses with icosahedral and helical
symmetries is the most efficient and economical
means for assembling a virion with limited coding
capacity.
• Some viruses have neither helical nor icosahedral
symmetry and are designed structurally as complex.
Sizes of Medically Important Viruses
(+) Strand RNA Viruses Genome Size Envelope Capsid Symmetry
(kb)
Picornaviridae 7.2 – 8.4 No Icosahedral
Calciviridae 8 No Icosahedral
Togaviridae 12 Yes Icosahedral
Flaviviridae 10 Yes Icosahedral
Coronaviridae 16-21 Yes Helical

(-) Strand RNA Viruses Genome Size Envelope Capsid Symmetry

(kb)
Rhabdoviridae 13 - 16 Yes Helical
Filoviridae 13 Yes Helical
Paramyxoviridae 16-20 Yes Helical
Sizes of Medically Important Viruses
Segmented Genome Size Envelope Capsid Symmetry
(-) Strand RNA Viruses (kb)
Orthomyxoviridae 14 Yes Helical
Bunyaviruses 13 – 21 Yes Helical
Arena 10 – 14 Yes Helical
Reoviridae (double strand) 16 - 27 No Icosahedral

Retroviruses Genome Size Envelope Capsid Symmetry

(kb)
Retroviridae 3-9 Yes Icosahedral
Sizes of Medically Important Viruses

DNA Viruses Genome Size Envelope Capsid Symmetry

(kb)
Parvoviridae 5 No Icosahedral
Papovaviridae 5–9 No Icosahedral
Adenoviridae 36 – 38 No Icosahedral
Herpesviridae 100 - 250 Yes Icosahedral
Pox 240 Yes Complex
Virus Classification
• Are classified by nature of nucleic acid, symmetry of
capsid, presence of envelope and the size of the
virion.
Taxonomy Examples
Family: viridae Picornaviridae, Rhabdoviridae

Subfamily: virinae
Genus: virus Enterovirus, Lyssavirus
Species: virus Polio virus, Rabies virus
Viral Replication
Virus Cell Interaction

Steps in Viral Replication 1. Lytic Infection

2. Abortive Infections
3. Persistent Infection
• Attachment
1. Chronic Infectious
• Penetration and uncoating
2. Latent Infections
• Gene expression and
genome replication 3. Transforming Infections
• Virion Assembly and 4. Integration of viral DNA
Release and continuous
expression of specific
viral genes
4. Slow Infectious
Viral Genetics

• Viral Mutations
– Spontaneous
• results in altered virus phenotype
• Acquires phenotype (antigenic drift) or resistance
– Induced
• Generated in the laboratory using chemical mutagens.
Genetic Interactions
• Intramolecular homologous recombination between 2 strains
of the same DNA virus.
• Random reassortment of gene segments that is common in
RNA viruses with segmented genome.
– When cell is co-infected with 2 viral strains, gene segments
are exchanged and progeny virus are produced with RNA
segments from either parenteral virus.
– Reassortment of RNA segments occurring during infection
of a cell with a human and animal influenza that results in
major antigenic changes (antigenic shift).
– Complementation
Just so you know…
Influenza A Virus
• 1918, The Spanish Flu pandemic killed >20
million people world wide.
• Influenza A has a genome composed of
multiple RNA segments.
• The virus can infect humans, pigs and birds
and can exchange with human influenza A by
genetic reassortment.
 Classification of Influenza Virus

• Influenzavirus A, infects birds and humans

• Influenzavirus B, exclusively infects humans
• Influenzavirus C, humans, dogs and pigs
The serotypes that have been confirmed in humans, ordered by
the number of known human pandemic deaths

• H1N1, which caused Spanish Flu in 1918, and Swine Flu in 2009
• H2N2, which caused Asian Flu in 1957
• H3N2, which caused Hong Kong Flu in 1968
• H5N1, which caused Bird Flu in 2004
• H7N7, which has unusual zoonotic potential
• H1N2, endemic in humans, pigs and birds
• H9N2
• H7N2
• H7N3
• H10N7
• H7N9
• H6N1, which only infected one person, who recovered
Viral Pathogenesis
Key Concepts:
• Viral Pathogenesis is between a delicate and dynamic
balance between virus offense and host defense.
• Pathogenesis is a multifactoral process by which
viruses cause disease.
• Most virus infections are subclinical or inaparent.
• Viral pathogenesis is an unintended consequence of
the way the virus has chosen to reproduce, spread and
evade host defense.
• Virulence is the capacity of the virus to cause disease.
Mechanism of Virus Spread
• Some virus infections remain localized to site
of entry.
• Virus spread beyond the primary site of entry
to multiple organs (systemic infection).
– Physical and immune barriers are breached
– Virus spreads via blood stream
– Virus may invade the CNS by axonal transport
along neurons.
Determinants of Tissue Tropism
• Cell Receptors
– Viruses attach to and enter via cell receptor
• Viruses use VAP to attach and adsorb to cell
receptors.
– Examples include the hemagglutinin of measles
and influenza virus
• Other cellular proteins
– Includes cell protease
Virus Immune Evasion Strategies
• Antigenic Variation
• Establish an immunologically silent latent phase
• Hide in immunologically privilege sites.
• Infect immune cells and suppress their functions
• Inhibit viral antigen presentation
• Express extracellular immunomodulatory
proteins
• Counteract the antiviral action of interferons
 Are you aware?

• HCV infects 170M people worldwide frequently leading to

cirrhosis and liver cancer
• It has an error-prone RNA polymerase to produce mutant
viruses causing lifelong infections.
• Chronic infection by HCV is a cycle of immune killing of virus
and infected liver cells, and HCV escape by high rate mutation.
LABORATORY DIAGNOSIS
Non Culture
Methods
• Cytology – inclusion bodies
• Electron Microscopy –
detection of viral particles
and morphology
• Immunofluorescence and
EIA – tagging of
fluorescent molecules and
serology
• Detection of viral nucleic
Acid – DNA Probes like PCR
Cell Culture Methods
• Cytopathic Viruses –
Produces CPE
(microscopic changes in
cells
• Noncytopathic Viruses –
can be detected by
assays that measures
viral antigen expression.
 Serologic Methods
1. Detection of antiviral antibody
– A rise greater than four fold between acute and
convalescent phase of infection.
– Detection of virus specific IgM antibody by serology
– Serologic Assays like immunoblot
2. Detection of viral antigens
– For viruses that cannot be detected in other way.
– HBsAg and HIV p24
Antiviral Therapy
• Approaches to Specific Control
• Immunologic Control - vaccines
• Chemotherapy – antiviral drugs
• IFN Therapy – relative short term effects
• Rationale of Antiviral Therapy
• Under development for prophylaxis
• Some virus undergo antigenic variations thus requires annual
vaccination
• Use for immunocompromised patients that unable to mount
immune response
• Antiviral Drug Targets
• Attachment and Entry
• Translation and Replication
• Virus Assembly and Release
DNA VIRUSES
Key Concepts:
• Most DNA Viruses contain ds DNA genomes except
Parvoviridae
• All DNA except posvirus have icosahedral nucleocapsid
symmetry
• Medically important DNA comprise 7 virus families (Parvo,
Polyoma, Papilloma, Adeno, Herpes, Pox and Hepadna) that
shares similar properties of nucleic acid composition (all
double segmented except parvo), shape (all are icosahedral
except pox) and site of replication (all in nucleus except pox).
Parvoviridae
Parvoviruses:
• Small (parvo), naked, linear ss DNA
• 2 genera infects humans: Dependovirus & Erythrovirus
• Members of Dependovirus include adeno-associated virus
that require helper adenovirus for replication.
• AAVs are used for gene therapy
Parvo Virus B19

• Replicates autonomously and only human pathogen under

Erythrovirus genus
• Causes erythema infectiosum (5th disease / slapped cheek
appearance)
• Infects erythroid precursors in patients with hemolytic anemia
or sickle disease that can lead to aplastic crisis.
• B19 infecting a pregnant women = fetal anemia or congestive
heart failure (hydrops fetalis)
• Transmission: Respiratory or Transplacental
• No virulence Factor, Confers long term protection after
recovery.
Parvovirus B19

• Laboratory Diagnosis:
Serology and PCR
• Treatment: Immune
globulin / No definite
treatment.
• Prevention: No known
vaccine
Polyomaviridae
Polyoma viruses
• Poly = many; oma = tumor
• Icosahedral, naked, circular
dsDNA
• Causes oncogenic
transformations in
laboratory animals
• Associated with human
tumors but still
controversial
• BK and JC Virus are the
polyoma viruses that infects
humans.
JC and BK Virus
• Clinical Manifestation:
• JC causes Progressive multifocal leukoencephalopathy
(PML)
• BKV causes UTI and hemorrhagic cystitis especially in
immunocompromised patients.
• Most infections are subclinical
• Transmission: Respiratory / Ubiquitous
• Pathogenesis: initial infxn in Respiratory Tract then viremia
then to kidney or CNS as latent asymptomatic infections.
• Virulence Factor: establish latent infections and reactivate in
the immunodeficient host.
JC and BK Virus
• Lab Diagnosis: PCR and DNA
hybridization
• Treatment: No specific
Treatment
• Prevention: No vaccines
Papilloma viridae
Papilloma virus:
• Icosahedral, naked, circular
ds DNA
• Causes warts in mammalian
species and are specific.
• Are epitheliotropic and
different types induce
hyperplastic epithelial
lesions of the skin and
mucus membrane.
Human papilloma Virus
• Clinical Manifestation:
– Common Warts on Hands and Feet (Types 1, 2, &4)
– Anogenital warts or Condyloma acuminata (type 6 & 11)
– Genital HPV (type 6 & 11)
– Epidermodysplasia verruciformis is common in patients
with cell-mediated immune deficiency.
– EV and skin warts may progress to skin carcinoma
– HPV types 16 & 18 are highly oncogenic strongly
associated with anogenital, head and neck cancers.
– HPV infections are clinically unapparent
Human papilloma Virus
• Transmission: Direct physical contact with infected
individual or fomites.
• Virulence Factors: capacity to establish latent infection
and high risk HPV types integrates into the
chromosomal DNA.
• Laboratory Diagnosis: Pap Smear, PCR, in-situ or liquid
hybridization.
• Treatment: Removal or warts by surgery or chemical
agents (podophyllin, trichloroacetic acid, imiquimod
(interferon and cytokine inducer) and cidofovir.
• Prevention:
 Comparison of Low Risk and High Risk HPV Types

Property HPV 6 & 11 HPV 16 & 18

Clinical Association Benign Wart Cervical Cancer

Risk of Malignant Progression Low High

Immortalization of Keratinocytes No Yes

Integration into cellular DNA No Yes

Affinity of E7 protein to bind Rb tumor Low High

suppressor protein

E6 Protein binds to & degrades tumor suppressor No Yes

protein p53
Adenoviridae
Adenovirus
• Are icosahedral. Naked,
linear ds DNA
• Originally isolated from
the adenoids
• About 50 different
serotypes
• Oncogenic on some
rodent host but not
associated with human
tumors
Adenovirus
• Clinical Manifestation: Types 1-7 causes common cold,
tonsillitis, pharyngitis, characterized by coryza, fever, cough,
and lymphadenopathy.
o Causes pneumonia characterized by bronchitis and
bronchiolitis
o Acute Respiratory Disease
o Pharyngoconjunctival Fever
o Keratoconjunctivitis
o Enteric adenovirus types 40-41 causes acute
gastroenteritis.
o Type 11 causes hemorrhagic cystitis
• Transmission: Respiratory, fecal-oral and direct contact
Adenovirus
• Pathogenesis: infects epithelial cells of the respiratory,
intestinal and cause direct cytotoxic change.
• Virulence Factor: have the capacity to establish latent
infections. Has specific RNA that interferes with interferon.
– Protein E3-19K prevents antigen presentation and
recognition by cytotoxic T cells.
• Laboratory Diagnosis: Virus Isolation, PCR, Serology and
Antigen Detection
• Treatment and Prevention: No vaccine, Sanitation
HERPESVIRIDAE
• Icosahedral, enveloped linear ds DNA
• Have the ability to establish latent infections that persist for
life that can be reactivated.
• Reactivation of the latent virus can be triggered by a lot of
factors.
• The 8 medically important herpes:
o Alpha – HSV 1 &2 and VZV
o Beta- CMV and HHV 6 and HHV7
o Gamma – EBV, KSHV (HHSV8)
Pathogenesis:
Herpes Simplex
• Transmission: Direct contact of
virus containing secretions and
body fluids
• Virulence Factor: HSV evades
immune system and establish
latent infections in neurons.
HSV encoded protein (ICP47)
down regulates MHC
• Clinical Manifestation:
– HSV 1 (facial)
• Gingivostomatitis
• Herpetic
keratoconjunctivitis
– HSV 2 (genital)
• Herpes genitalis
• Merpes meningitis
• Laboratory Diagnosis:
Tzanck Smear, PCR,
Virus Isolation, Serology
• Treatment: Acyclovir,
Valacyclovir and
Famciclover. Acyclovir
resistant are treated
with Foscarnet
• Prevention: Barrier
contraceptives and
SAFE SEX
• What is the similarity of “TRUE LOVE” and “HERPES”?
Both lasts forever
• If you love something, set it free, but don’t be surprised
if it comes back with Herpes. – Chuck Palahniuk
• Sex can lead to nasty things like herpes, gonorrhoea and
something called relationship. – Sacha Cohem
• Insecurity is like Herpes, It’s not going anywhere.
May as well learn to laugh at it – Daov Davidoff

• Bag-o ka magpakagaga kag magtilaw,

inspeksyona! Dyutay bala deperenxa sang
tanga kag hangag! – Alain Juayang
Poxviridae
• Pox Virus
– Are large, brick shaped
with complex symmetry,
enveloped, ds DNA.
– 2 Genera: Orthopoxvirus
(Variola and Monkeypox)
and Molluscipox
(molluscum contagiosum)
– Naturally occuring
smallpox was eradicated
from the world in 1977.
– Potential Bioterrorist
weapon.
Variola and Monkey Pox
• Clinical Manifestation: small pox with fatality rate
of 30% in unvaccinated persons.
o Incubation of 10-14 days
o Begins as a macular and progresses to papular,
vesicular, and pustular before encrusting and
sloughing off, sometimes leaving pocklike scars on
survivors.
o Death results from overwhelming toxemia and
systemic shock.
• Transmission: Respiratory droplets and thru
fomites, no animal reservoir
Pathogenesis of Variola
• Virulence Factor: has anti-immune proteins,
expresses secreted cytokine mimics, or soluble
cytokine receptors that inhibit host defense.
• Laboratory Diagnosis: PCR, electron
microscopy, histopathology and culture
(biosafety level 4 laboratories only)
• Treatment: live attenuated vaccinia from
vaccinia, isolation of infected individual.
Biosafety Level 4

• Dangerous and Exotic agents that pose a high risk of

aerosol-transmitted laboratory infections & life threatening
disease.
• Same of level 3 but with isolated zone or separate building.
Has dedicated supply and exhaust, vacuum and
decontamination system. No windows.
Molluscum Contagiosum
• Clinical Manifestation: causes benign nodular lesions that appear as
pearly, flesh-colored, raise umbilicated nodules without systemic
symptoms. The lesions are painless and resolves overtime. MCV is
an opportunistic pathogen in immunosuppressed patients, resulting
in widespread and recurrent lesions.
• Transmission: Direct bodily contact with skin lesion.
• Pathogenesis: Infects the epidermal cells to form a localized, fleshy
umbilicated lesions. Because of its epidermal localization, MCV
provokes minimal inflammatory immune response.
• Treatment: No specific Treatment, no vaccine so far.
• Lab Diagnosis: Biopsy (molluscum bodies) and electron microscopy
Hepadnaviridae
Hepatitis B virus
• Hepatotropic, icosahedral, enveloped, ds DNA
• Has a reverse transcriptase DNA plymerase
• Only medical important member is the Hepatitis B virus
• Clinical Manifestation
– Variable clinical outcomes, mild, self-limited, severe
and chronic
– Assymptomatic, Acute hepatitis, Extrahepatic
manifestations such as arthralgia and rashes
– Fulminant hepatitis and death is uncommon
– Chronic hepatitis leads to cirrhosis, liver failure and
hepatocarcinoma
• Transmission:
• Pathogenesis
• Virulence Factor:
overproduction of HBsAg acts
as a decoy, binding
neutralizing antibodies and
evading the immune system.
• Laboratory Diagnosis: Enzyme
immunoassay, PCR
• Treatment: no specific
treatment – interferon alpha,
lamivudine, or adefovir
• Prevention: Immunization
POSITIVE RNA VIRUSES
 Key Concepts: (+) RNA Viruses
• They have single strand RNA that functions as mRNA (naked)
– Naked RNA is infectious
• All (+) RNA virus encodes and RNA dependent RNA
polymerase used in genome replication.
• Medically important encompasses 6 virus families (Picorna,
Calci, Astro, Toga, Flavi and Corona).
• Have similar features in terms of nucleic acid composition,
lack of virion polymerase and site of replication.
 Properties of positive-strand RNA Viruses
Family Virion Shape Envelope Site of Species Included
Polymerase Replication
Picornaviridae No Icosahedral No Cytoplasm Polioviros
Coxsackivierus
Echovirus
Rhinovirus
Hepatitis A
Calciviridae No Icosahedral No Cytoplasm Norovirus
Hepatitis E
Astroviridae No Icosahedral No Cytoplasm Astrovirus
Togaviridae No Icosahedral Yes Cytoplasm Alphaviruses
Rubells
Flaviviridae No Icosahedral Yes Cytoplasm Yellow, Dengue , JE,
MVE, SLE, WN, Hepa
C & Hepa G
Coronaviridae No Helical Yes Cytoplasm Coronavirus
Picornaviridae
• Pico-small, naked, icosahedral
• Enteroviruses, Rhinoviruses & Hepatoviruses are
representative genera
• Members of the Enterovirus genus infect the
gastrointestinal tract and include polioviruses,
Coxsackieviruses and echoviruses.
• Enteroviruses are acid stable and resistant to the low
pH of the stomach.
• Rhinoviruses are acid labile and replicate optimally at
about 33°C, at a temperature maintained in the
nasopharynx.
Polioviridae
• Clinical Manifestation: poliomyelitis
– Abortive poliomyelitis (flu-like)
– -1% of poliovirus infections result in either non
paralytic or paralytic poliomyelitis.
– Nonparalytic polimyelitis recognized by symptoms of
meningitis.
– Paralytic poliomyelitis is characterized by flaccid
paralysis.
– Has three serotypes: 1 - 3
• Transmission: fecal-oral route
POLIOVIRUS
• Virulence Factor: stable in acid conditions, and
encodes the protein that interferes with the
antiviral action of interferon.
• Laboratory Diagnosis: Cell Culture, Serology
and PCR
• Treatment: No specific Treatment
• Prevention: Sabin or Salk vaccine.
Coxsackie Virus (Group A & B) and Echovirus

• Clinical Manifestation:
– Causes aseptic meningitis, enteric disease is
uncommon.
– Respiratory infections (flu-like), foot and mouth
– Cardiovascular Syndromes: myocarditis, pericarditis
• Transmission/Epidemiology:
– Fecal oral and less respiratory, distributed worldwide
– Named after Coxsackie, New York
– ECHO (enteric cytopathic human orphan)
– Most patient recover within a week or 2 without CNS
sequelae.
Pathogenesis: Coxsakie and Echo
 Coxsackie and EchoVirus
• Virulence Factor: No virulence factor
• Laboratory Diagnosis: Serology, PCR and Viral
Isolation
• Treatment and Prevention: No specific
treatment and Vaccine
Rhinoviruses
• Clinical Manifestations:
• causes the common cold
• Incubation period 2-3 days
• Rhinorrhea, nasal congestion, sneezing, headache,
mild sore throat, cough, little or no fever
• Symptoms resolve in a week without complications.
• Transmission and Epidemiology:
• Hand to nose, hand to eye, respiratory secretions
• Distributed worldwide
• Seasonal that peaks in fall and spring
• More than 100 serotypes are known
• Virulence Factor: No
virulence have been
identified
• Laboratory Diagnosis: Self
Diagnosis
• Treatment and
Prevention: anti-
inflammatory treatments
provide symptomatic
relief. No vaccine, hand
washing is effective
Hepatitis A
• Clinical Manifestation:
• Infectious hepatitis
• incubation period of 15 – 50 days
• with fever, anorexia, vomiting, dark urine and jaundice
• self limiting (3-4 weeks recovery)
• Fulminant hepatitis leading to liver failure and death is
uncommon
• Transmission/Epidemiology:
• Fecal –oral route
• Food borne or water borne
• Poor sanitary conditions and poor hygiene
• Infections in children are clinically unapparent, Symptomatic
infections increase with age.
• Laboratory Diagnosis: Serology and PCR
• Treatment: No specific Anti viral therapy
• Prevention: Vaccine that confers long term
protection, passive immunization and hand
washing.
Caliciviridae
• Caliciviruses
– Small, naked icosahedral
symmetry
– Has cuplike depression
when viewed under
electron microscope.
– Acid resistant
– 2 genera under
calicivirus: Norwalk and
Sapporo-like.
Norovirus (NorwlkVirus)
• Clinical Manifestation:
– Gastroenteritis with diarrhea with no mucus or blood
– Indistinguishable with rotavirus, bacterial or parasitic agents.
– Incubation period is within 24 hours and illness last only 1-2
days.
• Transmission:
– Fecal oral route
– Most common cause of gastroenteritis in the US
– Has a worldwide distribution
– Outbreaks in camps, cruise ships, restaurants and families.
– Transmitted via food and water person to person.
Noroviruses
• Virulence Factor: none
• Laboratory Diagnosis:
RT-PCR, enzyme
immunoassays
• Treatment: No specific
treatment
Norovirus (Norwalk virus)
Hepatitis E Virus

• Enteric ally
transmitted
waterborne
epidemics
• Most are subclinical
• Self limiting 1%
mortality rate in
general population.
• Fulminant hepatitis is
a major complication
• 40% mortality rate
for pregnant women.
• Transmission: fecal-oral route. Usually by
contaminated water. Endemic in poor
developing countries.
• Virulence Factor: none
• Laboratory Diagnosis: Enzyme immunoassay
• Treatment: no specific Treatment
• Prevention: no vaccines. Improve sanitary
conditions
Astroviridae
• Astroviruses
– Small, naked,
icosahedral symmetry
– 5-6 point star virion
surface
– Transmitted by fecal oral
route
– Common in winter
months
– Second to rotavirus for
causing diarrhea.
Human Astrovirus 1
Clinical Manifestation:
• Acute gastroenteritis, mostly in infants and young children,
characterized by vomiting, abdominal pain, fever and watery diarrhea
that is self limiting.

Transmission and Epidemiology

• Transmitted by fecal-oral route, usually by person to person contact or
by contaminated food or water
• Astroviruses are distributed worldwide with peak incidence of
infections reported in the winter months in temperate climates.
• Astroviruses is second only to rotavirus as the cause of diarrhea in
children.
Human Astrovirus 1
Pathogenesis:
• Astrovirus infects intestinal epithelial cells and directly damages
enterocytes. Viral clearance and protective immunity are correlated
with serum IgG antibody.

Virulence Factors: None

Laboratory Diagnosis:
• Can be detected by EIA for viral antigen and RT-PCR

Treatment: No specific antiviral therapy

Prevention: No vaccine. Good hygienic practices
Togaviridae family
Togaviruses

• Are enveloped (+) RNA virus with icosahedral symmetry

• Named for the cloak that denotes the virion envelope
• Consists of 2 genera: alpha virus and Rubivirus
• Major human pathogens are with the alpha virus are eastern
and equine encephalitis and Venezuelan equine encephalitis.
• Rubella is the only member in the Rubivirus.
Togaviridae family
Rubella
Clinical Manifestation:
• Causes mild illness called german measles in children and adults
characterized by an incubation period of 14-21 days followed by
general maculopapular rash, low grade fever and lymphadenopathy.
• Rubella virus infection in women in the 1st trimester of pregnancy
causes congenital rubella syndrome in the child which is characterized
by cataracts, cardiac abnormalities, deafness and mental retardation.

Virulence Factors: None

Laboratory Diagnosis: Virus specific IgM and IgG
Treatment: No specific antiviral treatment
Prevention: Live atenuated vaccine (MMR)
Flaviviridae Family
Yellow Fever
Clinical Manifestation:
• Yellow fever virus causes hemorrhagic fever, which is characterized by
jaundice, fever headache, myalgia, black vomit, other hemorrhagesand
shock. The mortality rate is 20-50%.

Transmission and Epidemiology:

• Transmitted by mosquito bite, endemic in Africa and South America
• In the jungle cycle, mosquitoes acquire the virus from viremic monkeys
that acts as permanent reservoir. Humans encroaching the jungle are
accidental hosts.
• In the urban cycle, infected viremic humans acts as a reservoir for
mosquitoes that then transmit the virus to other humans.
Togaviridae family
Rubella
Clinical Manifestation:
• In post natal infections, rubella virus enters through the respiratory
tract and spreads to local lymph nodes, coinciding with
lymphadenopathy.
• The virus spreads to spleen and regional lymph nodes and
disseminates by viremia to skin, kidney, joints and respiratory tract.
• Antibody response limits viral spread, but cell-mediated immunity is
required to resolve infection.

Transmission and Epidemiology

• Rubella virus is recognized as one of the most potent infectious
tetratogenic agents.
Togaviridae family
Rubella
Transmission and Epidemiology
• Rubella virus is recognized as one of the most potent infectious
tetratogenic agents.
• Congenital infections occur by transplacental transmission from
infected mother to fetus.
• Risk of congenital rubella syndrome is greatest during the first
trimester of pregnancy but can occur throughout pregnancy.
• Infants with congenital rubella syndrome excrete virus for many
months and are capable of transmitting the virus to susceptible
individuals.
• The rubella vaccine was licensed to protect against future fetal
infections and birth defects.
Togaviridae family
Rubella
Transmission and Epidemiology
• Rubella virus is transmitted postnatally by respiratory droplets
of infected inviduals.
• Rubella outbreaks in the US are rare, and the source is usually
Traced to infected individuals from countries where rubella
vaccination is not routine, undervaccinated populations in
the US or religious communities that shun vaccination
programs.
• Rubella remains endemic in some developing countries.
Flaviviridae Family
Flavivirus
• Flaviviruses are enveloped, (+) RNA viruses with icosahedral symmetry.
• The flaviviridae family has 2 genera with several human pathogens:
Flavivirus = more than 70 antigenic members
Hepacivirus = 2 members (HCV and HGV)
• Major pathogens in the flavivirus genus are arbovirus that includes:
yellow fever, dengue virus, St. Louis encephalitis virus, Japanese
encephalitis virus, Murray Valley encephalitis and West Nile virus.
• Medically important members of the Flavivirus genus are associated
with several clinical syndromes, including febrile illness with rash,
hemorrhagic fever and encephalitis.
Flaviviridae Family
Yellow Fever
Clinical Manifestation:
• Yellow fever virus causes hemorrhagic fever, which is characterized by
jaundice, fever headache, myalgia, black vomit, other hemorrhagesand
shock. The mortality rate is 20-50%.

Transmission and Epidemiology:

• Transmitted by mosquito bite, endemic in Africa and South America
• In the jungle cycle, mosquitoes acquire the virus from viremic monkeys
that acts as permanent reservoir. Humans encroaching the jungle are
accidental hosts.
• In the urban cycle, infected viremic humans acts as a reservoir for
mosquitoes that then transmit the virus to other humans.
Flaviviridae Family
Yellow Fever
Pathogenesis:
• Yellow fever virus infects mosquitoes and establishes a persistent infection.
• The virus is inoculated directly into the blood stream of the host by the biting
mosquito.
• It spreads via the blood to cells of the monocyte-macrophage lineage with the
liver as target organ.
• Antibody and cell mediated immunity are important in controlling infection.

Virulence Factors: None

Laboratory Diagnosis: Virus specific IgM
Treatment: No specific antiviral treatment
Prevention: Live attenuated vaccine (yellow fever) for urban yellow fever and
mosquito vector control.
Flaviviridae Family
Dengue Virus
Clinical Manifestation:
• Dengue Virus causes dengue fever, an acute febrile disease with
headache, retroocular pain, rash myalgia, and deep bone pain.
• Dengue fever may be mild or severe but rarely fatal.
• Causes dengue hemorrhagic fever or dengue shock syndrome
characterized by symptoms of dengue fever that progress to
prostration, GIT and skin hemorrhages, shock, coma and death up to
10% of the victims.

Transmission and Epidemiology:

• Transmitted by mosquito bite, endemic in Southeast asia, central and
south America and Caribbean Islands. Transmitted primarily in urban
environments where humans serves both as host and reservoir.
Flaviviridae Family
Dengue Virus
Pathogenesis:
• Similar to the yellow fever with vasculature as the target organ.
• Serum antibody and cell-mediated immune responses limit the outcome and
severity of dengue infection and confer long term protection.
• Dengue hemorrhagic fever shock syndrome has an immumopathologic basis
characterized by dengue virus antibody mediated enhancement of monocyte-
macrophage infection and activation of dengue virus specific lymphocytes
with release of cytokines, activation of complement and subsequent tissue
damage.

Virulence Factors: None

Laboratory Diagnosis: Virus specific IgM, RT PCR, NS-1
Treatment: No specific antiviral treatment
Prevention: Mosquito control.
Flaviviridae Family
Japanese Encephalitis Virus and Related Disease
Clinical Manifestation:
• Japanese encephalitis and related viruses causes clinical illness ranging from non
specific flulike febrile illness to encephalitis.
• Symptoms in more severe infection include headache nausea, high fever, malaise,
myalgia, backache, neck stiffness, and disorientation.
• Japanese encephalitis and related viruses cause significant mortality ranging from
10-40% with young children and elderly are at high risk.

Pathogenesis:
• Japanese encephalitis virus and related virus infects mosquitoes and establish a
persistent infection.
• The virus is inoculated directly into the blood stream of the host by the infected
mosquito.
• Virus spreads to the blood to the cells of the monocyte macrophage lineage with
the brain as target organ; it spreads to the CNS via capillary endothelial cells or the
choroid plexus.
• Antibody and cell-mediated immunity are important in controlling infections.
Flaviviridae Family
Dengue Virus
Transmission:
• Transmitted by bite of mosquitoes.
• West Nile can also be transmitted by blood and organ transfusion, breast milk
and transplacentally.
• Japaenese encephalitis (through out asia), Murray Valley encephalitis
(Australia), St Louis encephalitis (North America), West Nile (Africa, Europe,
Middle east, India, Australia and US)
• All virus are maintained in mosquito-bird-mosquito cycle.
• Domestic pigs also act as reservoir for Japanese encephalitis.
• Humans are considered dead end host for JE and related virus.
• JE usually occurs in summer and early fall.

Laboratory Diagnosis: Virus specific IgM in serum, CSF

Treatment: No specific antiviral treatment
Prevention: Mosquito control.
Flaviviridae Family
Hepatitis C and Hepatitis G
Clinical Manifestation:
• HCV cause acute and chronic hepatitis and infection with HCV predisposes
development of hepatocellular carcinoma.
• Primary HCV infections are asymptomatic or results in mild illness with non specific
symptoms and rare jaundice.
• Chronic hepatitis develops in 75% of HCV infections.
• Half of patients with chronic hepatitis are asymptomatic for 20-30 years. The other
half experience fatigue and elevated liver enzymes.
• Approximately 25% of patients have moderate to sever chronic hepatitis that
progress to liver cirrhosis and increased risk of hepatocellular carcinoma.
• HGV is related to HCV, not a major cause of cancer or uncertain clinical
significance.

Pathogenesis:
• HCV infects hepatocytes, causing acute and chronic hepatitis
• Liver injuries is mediated by cytotoxic T cells that both contribute to inflammation
and clearance.
• Hepatocellular Carcinoma linked to HCV is indirect.
Flaviviridae Family
Hepatitis C and Hepatitis G
Transmission:
• HCV Transmission is parentally by blood and blood products.
– Intravenous drug users and organ transplant.
– Sexual and maternal routes are less common
– Worldwide distribution
• HGV is distributed worldwide like HCV
– Coinfection with HCV is common

Laboratory Diagnosis: EIA and RT-PCR

Treatment: Interferon alpha and ribavirin
Prevention: None
Flaviviridae Family
Hepatitis C and Hepatitis G
Clinical Manifestation:
• HCV cause acute and chronic hepatitis and infection with HCV predisposes
development of hepatocellular carcinoma.
• Primary HCV infections are asymptomatic or results in mild illness with non specific
symptoms and rare jaundice.
• Chronic hepatitis develops in 75% of HCV infections.
• Half of patients with chronic hepatitis are asymptomatic for 20-30 years. The other
half experience fatigue and elevated liver enzymes.
• Approximately 25% of patients have moderate to sever chronic hepatitis that
progress to liver cirrhosis and increased risk of hepatocellular carcinoma.
• HGV is related to HCV, not a major cause of cancer or uncertain clinical
significance.

Pathogenesis:
• HCV infects hepatocytes, causing acute and chronic hepatitis
• Liver injuries is mediated by cytotoxic T cells that both contribute to inflammation
and clearance.
• Hepatocellular Carcinoma linked to HCV is indirect.
Coronaviridae Family
Coronaviruses
Transmission:
• Are enveloped (+) RNA virus with helical symmetry
• Largest known RNA genome.
• The error prone, RNA dependent RNA ppolymerase of corona virus
results in a high frequency of recombination and the generation of
mutant progeny viruses.
• Corona virus consists of four serologically unrelated groups and cause
disease in a range of birds, mammals including humans.
Coronaviridae Family
Human Coronaviruses
Clinical Manifestation:
• A novel coronavirus causes severe acutes respiratory syndrome, an
infections with high morbidity and moratlity rate of 10%.
• Previously known coronavirus cause about 30% cases of the common cold.
• SARS is characterized by an incubation period of 2-7 days followed by the
onset of high fever, usually accompanied by headache, generalized
discomfort, body aches and diarrhea in 10-20% of cases.
• 2-7 days later, patient experience a dry, non productive cough, hypoxia
requiring mechanical ventilation and pneumonia.
• Virulence Factors: the capacity of corona virus to undergo high-frequency
recombination provides an immune evasion strategy.
Laboratory diagnosis: Viral Isolation, RT-PCR, EIA
Treatment: No specific antiviral treatment
Prevention: Patient isolation, good hygiene
Coronaviridae Family
Human Coronaviruses
Transmission/Epidemiology:
• Transmitted by respiratory droplets.
• Contaminated fomites by fecal oral route
• Reported in HK in 2003 within months it was spread to North &
South America, Europe and Asia with 8000 cases and 800 deaths.
• An infectious disease that jumped from animal reservoir to humans.
Pathogenesis:
• Lymphopenia and low grade disseminated intravascular coagulation
are seen.
• Patients who died are observed to have diffuse alveolar damage.
• Severe pulmonary damage may be due to the virus directly or may
represent secondary effects of cytokines or other host factors
induced by coronavirus infections.
Finish
Alain C. Juayang, RMT, MSc
Medical Technologist
Alain C. Juayang, RMT, MSc
Medical Technologist
Only the
curious will
learn.

Curiosity
kills the
cat.
§ Are the smallest known form of infectious
disease – causing agents.
§ Size
§ They are _______ the size of bacteria or
__________ size of eukaryotic cells
§ Structure:
§ Composed of nucleic acid: either _____ or
_____
§ Nucleic acid is surrounded by a protein
matrix referred to as
_______________________.
§ The nucleocapsid is being surrounded by
capsid and composed of structural units
called _____________________.
§ Virus can also be naked or enveloped
§ Symmetry: helical, icosahedral or complex
1. ____________________ – adsorption occurs
when it comes in contact with a suitable cell.
2. ____________________ – occurs when it passes
thru the plasma membrane
3. ____________________ – is typically mediated
by cellular protease and results in the
separation of the capsid from viral genome.
4. ____________________– genome replication
and development of structural component
5. ____________________ – packaging of new
copies of genome nucleic acids into capsid
6. ____________________ – egress of the progeny
virus.
§ Isolation of Virus § Infectivity Assays
§ Centrifugation § Quantitative assays
§ Differential Centrifugation § Quantal Assays
§ Density Gradient Centrifugation § One step growth curve

§ Structural Investigation § Virus Genetics

§ Light Microscopy § Genome sequencing
§ Electron Microscopy § Genome Manipulation
§ X-ray Crystallography § Investigation of gene function and
expression
§ Electrophoretic Techniques
§ Investigation of protein – protein
§ Detection of Viruses and Components interactions
§ Detection of Virions
§ Detection of Infectivity using cell cultures
§ Detection of viral antigens
§ Detection if viral nucleic acids
1. Time of collection
2. Viral Culture
1. None Sterile 2. Sterile
i. Conjunctival 1. Autopsy
ii. Skin 2. Biopsy
iii. Vesicular 3. CSF
iv. Nasal 4. Fine – needle Biopsy
v. Throat 5. Blood
vi. Sputum 6. Bronchial alveolar
vii. Urine 7. Pleural Fluid and the like
viii. Genital
ix. Stool / Rectal Swab
1. Specimens are collected with ____________________
swabs and must not dry out during transport.
2. The swabs can be placed on a
____________________ ____________________ and
transport to the laboratory.
3. Nonsterile specimens that are not liquid like non-
blood should be collected on a viral transport
medium like the ____________________.
4. Urine for viral culture should not be collected on
containers with preservatives.
5. Blood for viral culture should be collected in
____________________ ____________________
6. Stool should be collected in sterile container.
• All specimens for viral recovery
regardless of source should be
transported at refrigerated
temperature
(____________________)

• In tissue culture, if the inoculation

of the specimen will exceed 5
days, the specimen should be
quickly frozen at
____________________.
§ Cells that are derived directly from the donor are known as primary cultures.
§ Primary Rabbit Kidney – ____________________
§ Primary Monkey Kidney – ____________________ ____________________
§ Primary Human Embryonic Kidney – ____________________ ____________________
____________________ ____________________ ____________________ ____________________
§ Cell lines – primary cultures that have been subcultured
§ Diploid
§ Heteroploid

§ A549 – derived from human lung carcinoma - ____________________

§ Hep-2 cells – derived from human laryngeal carcinoma - ____________________
§ HeLa cells – derived from human cervical adenocarcinoma –
____________________ ____________________
§ Order of Inoculation: (1) diploid then (2)
heteroploid then (3) primary cells
§ Viral adsorption – time point that the virus
comes in contact with the tissue culture cell.
§ ____________________– incubating the
cells + virus for 30 – 60 min at 35 ℃
§ ____________________– refers to the
gentle rotation of the culture tubes to enhance
adsorption.
§ ____________________– requires shell
vials to be centrifuged at 750 – 1000 x gram
for 30 to 40 min at 25 ℃.
§ Viral detection – can be detected by observing
the cytopathogenic effect such as swelling or
inclusions
§ ____________________– uses fixed or fresh Negri Body Owl’s Eyes
specimens incubated with chemically labeled
fluorescein or enzymatically labeled antibodies
to detect viral antigens.
§ ____________________ - detects viral DNA or
RNA sequence in nucleic acid extracted from
specimens
§ Polymerase Chain Reaction
§ Western Blot – employs single stranded Cowdry Bodies
complimentary nucleic acid probes for detection of
HIV in blood of seronegative individuals.
§ Solid Phase Immunoassay – use antibodies and
radioimmunoassay or enzyme-linked
immunosorbent assay to detect viral antigens.

Western Blot
Immunocomb
§ Largest DNA Virus = Poxviridae § Largest RNA Virus = Paramyxoviridae
§ Smallest DNA Virus = Parvoviridae § Smallest DNA Virus = Picornaviridae

RNA Virus of Medical Importance DNA Virus of Medical Importance

1. Picornaviridae 1. Adeniviridae
2. Togaviridae 2. Herpesviridae
3. Reoviridae
3. Poxviridae
4. Myxoviridae
4. Papovaviridae
5. Pseudomyxoviridae
6. Rhabdoviridae 5. Hepatitis B Virus
7. Paramyxoviridae
§ Naked DNA Viruses with Icosahedral symmetry
§ Parvovirus – B19, erythema infectiosum (5th
disease/rash), spread by close contact
§ Papilloma Virus – papovavirus & Papilloma virus,
Papilloma causes warts
§ Polyomaviridae – JCV and BKV, histologically diverse
tumors in various body parts
§ Adenoviridae – 47 serotypes, causes respiratory, eye
and intestinal illness.
§ Hepadnaviridae – has tropism for infection of the liver,
HBV.
§ Enveloped DNA with Icosahedral Symmetry ____________________
§ Alphaherpesviridae – HSV 1 & 2, Varicella zoster virus; uHSV 1 is usually on eyes and
lips; HSV 2 affects lips and genital area; Varicella zoster (primary disease chicken pox,
recurrent disease shingles).
§ Betaherpesviridae – CMV or the inapparent disease of childhood and can cause fetal
death or infant death.
§ Gammaherpesviridae – EBV causes infectious mononucleosis and associated with
Burkitt’s lymphoma.
§ Naked DNA with Complex Symmetry ___________________
§ Vaccinia - variant of variola, used as immunogen for small pox vaccination.
§ Variola – agent of small pox
§ Molluscum contagiosum – small wart-like lesions on face, arms, buttocks and genitals
that mimics genital herpes.
§ Enveloped RNA with helical symmetry:
§ Orthomyxoviruses – has hemagglutinin, neuramidase and matrix protein
§ Influenza viruses
§ Has types A, B and C
§ Reye’s Syndrome is associated with Flu type B
§ Can be diagnosed by viral isolation or hemagglutination assays
§ Antigenic Drift and Antigenic Shift
§ Paramyxoviridae – paramyxovirus, morbillivirus and pneumovirus
§ Associated with parainfluenza and mumps virus.
§ Parainfluenza causes croup on infants.
§ Pneumovirus: RSV
§ Arenaviridae
§ Hemorrhagic fevers: Machupo, Junin and Lassa
§ Lymphocytic choriomeningitis virus
§ Enveloped RNA with helical symmetry:
§ Rhabdoviruses – bullet shaped virus associated with rabies and bovine stomatitis virus
§ Passive immunization with human rabies immunoglobulin
§ Diagnosis is made by biopsies on skin, cornea impressions or port mortem
examination of the brain tissue
§ VSV – mild disease associated with cattle.
§ Coronaviruses – most common of cold and infant gastroenteritis.
§ Members of Bunyaviridae: Hanta, LaCrosse and California Virus
§ Hanta – life threatening respiratory tract infection in SW United State
§ Transmission is by deer mice droppings
§ Thrombocytopenia, Left shift to myelocytes or earlier stages, blastic forms of
lymphocytes are present and proteinuria.
§ California and LaCrosse viruses – produces encephalitis via infected mosquito bite.
§ Enveloped RNA viruses with Icosahedral Symmetry: Togaviridae,
Flaviviridae and Retroviridae.
§ Medically important in togaviridae: alpha and rubivirus.
§ Alpha virus = arboviruses with mosquito or animal vectors
§ Eastern equine encephalitis
§ Western equine encephalitis
§ Venezuelan equine encephalitis
§ Rubivirus – rubella or german measles
§ The flaviridae include dengue, hepatitis, St. Louis encephalitis,
yellow fever and west nile.
§ Enveloped RNA viruses with Icosahedral Symmetry: Togaviridae,
Flaviviridae and Retroviridae.
§ Retroviridae – contains reverse transcriptase enzyme
§ 3 genera: lentivirus, spumaviruses and oncoviruses
§ Lentiviruses: HIV 1 and HIV 2
§ Transmission: sexual and blood products, transplacental
§ Full-blown AIDS = opportunistic infections
§ Tests: EIA, ELISA, Western Blot
§ Human T-cell leukemia virus 1 – type C oncoviruses
§ Transmission: same as HIV
§ Long Term effects = include debilitation and paralysis
§ Naked RNA viruses with icosahedral symmetry: picornaviridae and Reoviridae
§ Picornaviridae: enterovirus and rhinoviruses
§ Enteroviruses:
§ Polio – aseptic meningitis or poliomyelitis
§ Coxsackie virus – type A (HFMD) type B (herpangina, viral heart disease, Bornholm disease)
§ Echovirus - common cold to meningitis to hemorrhagic conjunctivitis
§ Enterovirus – respiratory, CNS and hemorrhagic conjunctivitis
§ Hepatitis A virus – infectious hepatitis
§ Rhinoviruses =. Causative agent of common cold
§ Reovirus = Rotavirus = acute infantile diarrhea
Virus Type Viral Characteristics Virus Disease
Poxviruses Large brick shape with Variola Small pox
envelope DNA Vaccinia Cow Pox
Polyoma-Pappiloma dsDNA polyhedral Papillomavirus Warts
Polyomavirus Some tumors, some cancer
Herpesvirus Polyhedral with envelope HSV 1 Cold sores or fever blisters
dsDNA HSV 2 Genital herpes
Herpes Zoster Shingles
Varicella Chicken Pox
Adenovirus dsDNA, icosahedral with Respiratory Infections, pneumonia,
enveloped conjunctivitis, some tumors
Picornavirus dsDNA, icosahedral with Rhinovirus Colds
enveloped Poliovirus Poliomyelitis
Hepatitis A Hepatitis
Coxsackievirus Respiratory Infections, meningitis
Virus Type Viral Characteristics Virus Disease
Reoviruses dsRNA, icosahedral with Enterovirus Intestinal Infections
envelope
Myxoviruses RNA, helical with envelope Orthomyxovirus (A&B) Influenza
Myxovirus parotids Mumps
Paramyxovirues Measles
Rhabdovirus Rabies
Arboviruses Arthropodborne RNA, cubic Mosquitoborne type B Yellow fever
Mosquitoborne type A Encephalitis
Tickborne, coronavirus Colorado Tick Fever
Retroviruses dsRNA, helical with envelope RNA tumor virus Tumors
HTLV Leukemia
HIV AIDS
Viral Infections Antiviral Agents
HSV Acyclovir, cidofovir, famciclovir, fomivirsen, foscarnet, ganciclovir,
penciclovir, valacyclovir, vidarabine
Respiratory Viruses Amantadine (flu A), Oseltamivir (Flu A & B), Ribavirin (RSV, Flu A
and B, parainfluenzavirus), Rimantadine (Flu A), Zanamivir (Flu A
and B)
HIV Abacavir, Didanosine, Lamivudine, Stavudine, Tenofovir,
Zalcitabine, Zidovudine (AZT, ZDV)
Delavirdine, Efavirenz, nevirapine
Amprenavir, Indinavir, Lopinavir, Nelfinavir, ritonavir, Saquinavir
 RNA FAMILIES

A A B C C F F O P P
R R R T

A O
A P
B P
C R
C R
F R
F T
 RNA FAMILIES

Friends, Punta Tayo sa MOA Arena Para

Flaviviridae. Picornavirus Togaviridae Arenaviruses. Paramyxo

mag Bunyi. Nanalo Ang Filipinas!

Bunyaviridae Astroviridae Filoviridae

Nauwi ni Catriona ang Corona

Calciviridae Coronaviridae

OR - RHAyT!!!
Orthomyxoviridae Rhabdoviridae
 All RNA viruses are single
stranded except REOviruses
 DNA FAMILIES

PA – PA – AD – PO – HE – HE
Papova Parvovirus Adenovirus Pox Hepadna Herpes
 Agent Incubation Period Agent Incubation Period
Influenza 18 – 72 hours Hepatitis B 1 - 6 months
Yellow Fever 2 – 6 days Herpes Simplex 5 – 8 days
Polio 4 – 33 days Mumps 16 – 20 days
Measles 10 – 14 days Rubella 16 – 20 days
Japanese Encephalitis 1 – 15 days Cholera 1 – 2 days
Rabies 20 – 60 days Diptheria 2 - 6 days
Hepatitis A 15 – 45 days Typhoid 10 – 14 days
Tetanus 6 – 10 days
HHV1 Herpes Simplex 1 Simple
HHV2 Herpes Simplex 2 Simple
HHV3 Varicella zoster Very
HHV4 Epstein Barr Easy
HHV5 Cytomegalovirus Chicken
HHV6
Roseola infantum Roasting
HHV7
HHV8 Kaposi Sarcoma (in) Kenny
Alain C. Juayang, RMT, MSc
Medical Technologist
§ Eukaryotic, non-motile, lack chlorophyl.
• Have definitive cell walls and they absorb nutrients.
• Reproduction: Sexual (fusion of 2 haploids nuclei) and Asexual (division of haploid
nucleus and budding production of conidia.
• Growth
• Diverse – bacteria like to yeast to mush rooms
• Hyphae – septate / aseptate; racquet / favic chandeliers / pectinate / nodular / spiral;
Mycelium (vegetative or aerial)
• Pseudohyphae – elongated budding yeast.
• Fruiting Bodies - Asexual / Sexual
• Mycelial structures – stolons and rhizoids
§ Classification:
§ Zygomycotina – ribbon-like- aseptate hyphae: sexual and asexual
§ Ascomycotina – septate sexual and asexual; produces asci
§ Basidiomycotina – aseptate; sexual and asexual; club looking fungi.
1. Things to remember for collection:
a. Sterile technique / aseptic technique
b. Adequate amount
i. Blood –
ii. Bone marrow -
iii. CSF –
iv. Urine –
v. Respiratory –
vi. Wound and abscess -
c. Sample from area most likely affected
§ Things to Remember During Transportation
§ 10% KOH Preparation Fungal Culture:
§ Lactophenol Cotton Blue 1. Optimum Temperature:
§ India Ink for moulds;
§ Calcoflour white 2. Hold for __________for moulds,
_________ for yeast
§ Primary growth agars
§ 3. Use screw cap tubes or tape plates
§ to avoid accidental opening or
drying.
§ Specialty growth media
§ Bird Seed Agar 4. Work under biosafety cabinet
§ Corn Meal Agar
5. Always wear proper PPE.
§ Rice Infusion Oxgall Tween 80
 Media
Brain Heart Infusion Agar
BHIA with antibiotics
BHI biphasic blood culture bottles
Dermatophyte Test Medium
Inhibitory Mold Agar
Potato flake agar
Mycosel
SABHI Agar
Yeast extract phosphate Agar
Indications for
Saprobic and Pathogenic Fungi
Pathogenic fungi exclusive of dermatophytes
Fungi in blood
Recovery of dermatophytes (screening only)
Pathogenic fungi exclusive of dermatophytes
Saprobic and Pathogenic Fungi
Dermatophytes
Saprobic and Pathogenic Fungi
Pathogenic fungi exclusive of dermatophytes
 Media Indications for
Ascospore Agar Detection of ascospores from ascoporogenous yeast
Corn Meal Agar with Tween 80 and Chlamydospore production of C. albicans
tryphan blue
Cotton seed conversion Agar Conversion of spores of dimorphic fungus from mold to yeast
Czapek’s Agar Identification of Aspergillus species
Niger Seed Agar Identification of C. neoformans
Nitrate Reduction Medium Nitrate reduction to confirm C. neoformans
Potato Dextrose Agar Pigment production of T. rubrum and sporulation of dermatophytes
Rice Medium Identification of M. audouinii
Trichophyton Agars Identification of Trichophyton genus
Urea Agar Detection of Cryptococcus, differentiation of Trichophyton
Yeast Fermentation Broth Identification of yeast by fermentation
Yeast Nitrogen Agar Base Determination of Carbohydrate Assimilation
Stain Use Remarks
Acid fast Stain Mycobacteria and Nocardia Some isolates of Blastomyces can be stained
Calcofluor White Detection of Fungi Detects fungi rapidly because of
fluorescence
Gram Stain Dectection of bacteria and fungi Weak on Cryptococcus
India Ink C. neoformans Diagnostic of fungal meningitis
KOH Fungal elements Dissolves cells to clear specimens
Fungi in histologic sections Best stain to detect fungal elements
Malignant Cells It can stain fungal elements
Fungi Stains fungal elements well
Wright Stain Blood and bone marrow H. Capsulatum and C. neoformans
VITEK 2 COMPACT

VITEK 2 is a fully automated

system that performs bacterial
identification and antibiotic
susceptibility testing. User
interface screen for immediate
notification of system status to
increase productivity. Unique
vacuum filler provides both safety
and the highest level of
automation.
BD PHOENIX
The BD Phoenix™ automated identification
and susceptibility testing system provides
rapid, accurate and reliable detection of
known and emerging antimicrobial
resistance. It also enables workflow
efficiency by utilizing automated
nephelometry, which results in a
standardized isolate inoculum and a
reduction in potential technologist error.
Additionally, state-of-the-art data
management monitors, analyzes and
communicates actionable results directly to
laboratories and clinicians.
MALDI-TOF MS
(Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry)
§ is an analytical technique in which particles are
ionized, separated according to their mass-to-
charge ratio, and measured by determining the time
it takes for the ions to travel to a detector at the end
of a time-of-flight tube. The resulting spectrum, with
mass-to-charge values along the x-axis and
intensity along the y-axis, is compared to a
database of spectra from known organisms.
§ It relies on measuring microbial proteins that are
typically well conserved within a species leading to
more reliable means of discriminating one species
from another.
BIOFIRE FILM ARRAY SYNDROMIC TESTING

§ PCR based Multiplex Testing

§ Syndromic Testing
§ Fungal Pathogens:
• Candida albicans
• Candida auris
• Candida glabrata
• Candida krusei
• Candida parapsilosis
• Candida tropicalis
• Cryptococcus (C. neoformans/C. gattii)
GeneXpert (MVP)

§ The Xpert Xpress MVP (MVP;

Cepheid) test is designed to be an
automated, qualitative in vitro
diagnostic PCR test for the
detection of DNA targets from
anaerobic bacteria associated with
BV, Candida species associated
with VVC, and Trichomonas
vaginalis (TV).
CANDIDA CHROMOGENIC AGAR

§ is a selective chromogenic culture

medium intended for use in the
qualitative direct detection,
differentiation and presumptive
identification of Candida species.
CANDIDA ALBICANS GERM TUBE ANTIBODY (CAGTA) ASSAY

§ available in IFA IgG is a commercially available

indirect immunofluorescence kit that detects
antibodies against antigens in the cell wall
surface of the mycelium of C. albicans, in human
serum or plasma.
§ CAGTA assay despite being easy handling, with a
fast performance at low cost, this assay is one of
the few antibody-based that falls short in terms
of sensitivity and specificity for invasive
candidiasis diagnosis, which ends up being a
huge drawback
CRYPTOCOCCAL ANTIGEN LATEX AGGLUTINATION SYSTEM (CALAS)

• The Cryptococcal Antigen Latex Agglutination System

is a qualitative and semi-quantitative test system for
the detection of capsular polysaccharide antigens of
Cryptococcus neoformans.
• Latex agglutination test has both diagnostic and
prognostic value since progressive disease is usually
accompanied by increasing antigen titers. Declining
titers are usually associated with clinical improvement,
with or without therapy. Inadequate therapy is
indicated by stationary or rising titers on subsequent,
sequential specimens. Cryptococcal antigen in the
body fluids of the untreated patient indicates active
infection. However, in some treated patients, titers
remain positive at low levels for extended periods
during which the organism can no longer be
demonstrated
MANNAN AND ANTIMANNAN ANTIBODY

§ Mannan is one of the major

components of the Candida cell wall
that has been used as a diagnostic
biomarker of invasive candidiasis.
§ 25 Mannan, a cell-wall glycoprotein of
fungi, not only inhibits the proliferation of
keratinocytes, but, most importantly, has
been demonstrated to inhibit the
development of cell-mediated immunity
against the infecting dermatophyte.
GALACTOMANNAN TEST

§ Galactomannan (GM) is a component of

the Aspergillus species cell wall and is released into the
surrounding environment during fungal growth or tissue
invasion. A serum GM antigen test has been widely used to
diagnose invasive pulmonary aspergillosis.
Galactomannan antigen levels may be useful in the
assessment of therapeutic response. Antigen levels decline
in response to antimicrobial therapy.
§ Galactomannan antigen levels may be useful in the
assessment of therapeutic response. Antigen levels decline
in response to antimicrobial therapy.
§ Reference value: <0.5 index.
Β-(1,3)-D-GLUCAN ASSAY

§ This assay measures the presence of (1→3)-β-D-

Glucan in serum and CSF. Studies have shown
that glucan levels become elevated in fungal
infection in advance of conventional clinical signs
and symptoms. The assay therefore has utility as
an aid in the presumptive diagnosis of invasive
fungal disease in at risk patients. Serum is the
only specimen type cleared by the FDA for this
assay.
• Interpretation of Results
• Negative: <60 pg/mL
• Indeterminate: 60 pg/mL – 79 pg/mL
• Positive: 80 pg/mL – >500 pg/mL
§ SUPERFICIAL MYCOSES § CUTANEOUS MYCOSES /
DERMATOPHYTES
§ Ptyriasis versicolor
§ Piedraia hortae § Microsporum
§ Trichosporon beigelii / § Epidermophyton
asahii
§ Trichophyton
§ Phaeoannelomyces
werneckii § Epidermophyton
 M. furfur P. werneckii P. hortae T. beigelii
Disease P. versicolor T. nigra Black Piedra White Piedra
Microscopic Spaghetti and Annelids Ectothrix Endothrix;
characteristics Meatball arthroconidia and
appearance blastoconidia
Site Body and Trunk Palm and Soles Scalp Hair Beard, Axilla Hair,
Pubic Hair
§ Keratinolytic
§ Tinea = ringworm
§ Septate hyphae; micro and
macroconidia
§ Can cause tinea capitis
§ Endothrix
§ Ectothrix

§ Wood’s lamp
§ Treatment – miconazole, clotrimazole,
griseofulvin
Condition Organism Body Area Remarks

Tinea capitis M. audouinii Scalp Gray Patch = ectothrix

T. tonsurans Eyebrows Hair breaks off above scalp
T. violaceum Eyelashes Hair is grey and lusterless
T. mentagrophytes
T. verrucosum Black-dot = endothrix
Hair breaks off at follicle
Tinea favosa T. schoenleinii Scalp; glabrous skin Scutula
Extensive alopecia, scarring
Mousy odor
Infection can last a lifetime

Tinea corporis T. Mentagrophytes Glabrous skin Fungal metabolites acts as toxins

T. Rubrum or allergens
T. tonsurans
M. canis
M. audouinii
Tinea cruris Epidermophyton Skin of groin Raised red border and scaling
T. Rubrum
T. mentagrophytes
§a severe and chronic inflammatory
dermatophyte infection,
§ Favus'had been used, at the
beginning of the nineteenth century,
to characterize the honey-like
exudate in some scalp infections.
§ Favus is essentially a chronic
disease and can last from 10 to 20
years.
Condition Organism Body Area Remarks

Tinea unguium Trichophyton Invasion of nail plates White patches on surface or

Epidermophyton invasive infection beneath nail
plates.
onchomycosis C. albicans Nail infection caused Yeast in nail and tissue
C. parapsilosis by non-dermatophytic Fungi in grooves of nail
Trichosporon fungi and yeast
Geotrichum
Scopulariopsis
Aspergillus
Tinea barbae T. mentagrophytes Bearded areas of face Mild superficial type or severe
M. canis and neck deep pusticular folliculitis
T. verrucosum
T. rubrum
T. violaceum
Condition Organism Body Area Remarks

Tinea manuum T. Rubrum Hands hyperkeratotic

Tinea T. Mentagrophytes In between fingers
interdigitalis Epidermophyton
Tinea
interdigitalis
Tinea pedis Epidermophyton Feet Intertriginous
T. rubrum Toes Hyperkeratotic
T. mentagrophytes soles Vesicular
Ulcerative
 M. audouinii M. canis M. gypseum M. ferrugineum
Distinguishing Terminal Macroconidia May macroconidia No conidia, only
characteristics chlamydoconidia abundant with 4 – with 3-5 septa and chlamydospores
8 septa, knoblike echinulate surface
and echinulate (not knobby)
Hyphae Usually sterile Thick walls Thin walls Bamboo hyphae
Days to grow 10 – 21 days 4 – 5 days 6 – 10 days 7 - days
Colonies Reddish – brown Yellow color on Orange to brown Cream to buff color
color on reverse the reverse side of color on reverse on top, no reverse
side of colonies colony side of the colonies pigment
location Hair (fluoresce) Ectothrix Ectothrix Hair
Disease caused Epidemic tinea Dog and cat ring hair Juvenile tinea capitis
capitis worm
 T. mentagrophytes T. rubrum T. tonsurans T. schoenleinii T. violaceum
Microconidia Numerous with Tear shaped Numerous, Favic chandeliers Hyphae and
spiral and nodular and disperse clavate varying with chlamydoconidia
bodies along hyphae in size (balloons chlamydoconidia in chains
and matchsticks)
Colony Rose – brown color Cherry red Yellow red color No pigmentation Purple Colony
on reverse side color on reverse on reverse side on reverse side
side
Location Endothrix Ectothrix Endothrix Endothrix Scalp and body
Remarks Urease 2- 3 days Urease Black dot ring Severe tinea
Negative worm capitis (favus)
Epidermophyton floccosum

§ Commonly infects nails and skin

(feet, hands and groin).
§ Macroconidia is large, club-shaped
that are found in singles or clusters at
the end of the hyphae, has 2-4 septa.
§ No microconidia
§ Olive-green or khaki background.
 Sporothricosis Chromoblastomycosis Mycetoma
Organism S. schenkii Phialophora Pseudallescheria
Cladosporium Scedosporium
Distinguishing Yeast = cigar Cladosporium – conidia Conidia borne on
characteristics bodies in branched chains conidiosphores.
Mycelial = rosette Phialophora = phialides
Lesions Pyogenic and Scaly and wart-like Draining sinuses;
granulomatous purplish
discoloration and
tumor-like
deformities
 B. dermatitidis C. immitis H. capsulatum P. brasiliensis P. marneffei
Distinguishing Broad based Spherule Pyriform/ Mariner’s wheel 4-5 metulae
Characteristics yeast Arthroconidia tuberculate with 4-6
microconidia phialides.
Source of Soil Soil Bird and Bat Soil (semi-arid) Bamboo rats
Infection droppings
Disease Caused Gilchrist’s Valley Fever Darling’s South American Talaromycosis
Disease Disease blastomycosis
Primary Focus Pulmonary, Skin Pulmonary Pulmonary Pulmonary (may Skin (skin
have cutaneous bumps)
or
mucocutaneous)
§ Group of fungi that act as a
decomposer feeding on dead
or decaying wood, leaves,
litter and other organic
matter.
§ Produces or secretes an
enzyme to break organic
matter.
§ Most common type of fungi.
• Any candida sp is a potential pathogen for
patients with tissue transplant/ taking § Causes acute to Chronic fungal infection.
immunosuppressants or
immunocompromised. § Naturally occurring fungus that lives on the body.
• Saprophytic in oral cavity, GIT and vaginal § Commonly found on throat, mouth, gut and vagina.
tract. § Infections: skin, mucosa, blood stream, kidney, brain,
• Most frequently encountered opportunistic
fungal infections or even heart.
§ Changes in conditions may encourage its
proliferation.
Most common species:
§ Hormones
1. Candida albicans
§ Medicines
2. Candida glabrata
3. Candida tropicalis § Changes in the immune system
4. Candida parapsilosis § Comorbidities (on chemotherapy, diabetes, on
5. Candida krusei steroids).
§ Sometimes called Monilla albicans
§ Kills 200,000 people; health care cost of
$2B per year
§ 75% of all Candida infections
§ Premiere cause of yeast infection in the
world
§ Has become the 4th most common
cause of bloodborne infection in the
United States
§ Presumptive identification germ tube
(germ cells)
§ Candida _________
§ Can cause severe illness and spreads easily
among patients in healthcare facilities
§ it is often resistant to antifungal treatments,

§ Candida __________
§ 2nd most common Candida species to incite
disease
§ Infections are aggressive and difficult to
treat with traditional anti-fungal therapy
§ Has different sugar assimilation patterns
from Candida albicans
§ Candida ______________
§ Has high resistance to some antifungal
medications
§ 3rd most common Candida isolated
§ Candida _______________
§ Major cause of hospital outbreaks of nosocomial
infections
§ Refractory to traditional anti-fungal therapy.
§ spider or sagebrush” colonies away from agar
streak
§ Candida _______________
§ Now known as Candida kefyr
§ “Logs in a stream” microscopic description
§ The most commonly encountered
genus of fungi in the clinical
laboratory
§ Causes aspergillosis
§ Grows rapidly, producing aerial § Virulence Factors:
hyphae that bear characteristics
1. Elastase – serine protease
conidial structures: long
2. Elastine-metaloprotease
conidiophores with terminal vesicles
on which phiallides produce 3. Aspartic Acid Proteinase
basipteral chains of conidia. 4. Aflatoxin
5. Catalase
6. Lysine biosynthesis
7. P-aminobenzoic acid synthesis
§ 2 subspecies:
§ C. neoformans var neoformans
§ C. neoformans var gatti
§ The most common causes of
meningitis and pulmonary disease
(major manifestation is not
pneumonia but meningoencephalitis)
§ With capsule (polysaccharide) which
produces a mucoid colonial
appearance non dimorphic.
§ No. 2 cause of death among HIV
patients
§ The fungus is found in nature,
especially in pigeon droppings and
eucalyptus tree.
§ Diagnosis:
§ Mucicarmine
§ Negative Staining
§ Latex Agglutination
§ Causes geotrichosis
§ Grows only on 25°C (rapid-yeast-like
growth) but not on 37 °C
§ Microscopically: wide septate hyphae,
segmented into rectangular arthrocoidia,
___________ germ tubes project from
one corner of arthroconidia.
§ Clinical manifestation:
§ Oral geotrichosis may resemble thrush
§ Pulmonary geotrichosis may resemble
tuberculosis
§ Saprophyte on skin, sputum or stool.
§ Fusarium is a large genus of
filamentous fungi, part of a group
often referred to as hyphomycetes,
widely distributed in soil and
associated with plants.
§ cause a broad spectrum of infections
in humans, including superficial,
locally invasive, and disseminated § Macroconidia are hyaline, two to
infections. Most common mycotic several-celled, fusiform to sickle-
keratitis and onchomycosis. shaped, mostly with an elongated
§ Risk factors: T cell deficiency apical cell and pedicellate basal cell.
§ Most common agents: Rhizopus and
Mucor
§ Broad (50 µm wide), non septate,
twisting ribbon like hyphae.
§ Primary cutaneous or mucus
membrane, wound contaminated by
soil, then progresses to cellulitis.
§ Progressive pneumonia in patients
with immunocompromised status.
§ Can cause rhinocerebral disease
§ Causes PCP pneumonia
§ Pneumocystis jirovecii
§ Common on HIV/AIDS patients
§ Diagnosis:
§ Chest X-Ray
§ Stained Respiratory Specimen
§ NAAT
§ Common Symptoms:
§ Fever
§ Cough
§ Difficulty of Breathing
§ Chest pain
§ Fatigue § Treatment is with antibiotics:
§ trimethoprim/sulfamethoxazole or dapsone p
lus trimethoprim, clindamycin/primaquine, ato
vaquone, or pentamidine
Organism Characteristics Notes Images

Candida albicans Numerous blastoconidia Germ tube – positive in

along pseudohyphae, 2 hours
germ tube Urease Negative
chlamydoconidia

Candida tropicalis No Chlamydoconidia Germ Tube Negative

Sparser blastoconidia

Geotrichum Arthroconidia Hockey Stick

Appearance
Organism Characteristics Notes Images
Trichosporon Arthroconidia and Budding from both
blastoconidia corners of Arthoconidia
Urease positive

Candida glabrata No pseudohyphae Assimilates glucose and

trehalose

Cryptococcus No pseudohyphae, Urease positive; brown

neoformans encapsulated colonies on Bird seed
agar
Organism Characteristics Images
Penicillium Green or Blue-Green Colonies: Branching
or Penicillus Head

Acremonium Delicate Hyphae: Elliptical Conidia with

appearance of brain surface

Fusarium Colonies are lavender to purple – banana

shaped macroconidia

Aspergillus Conidiophore ends in swelling

Fumigatus: Green conidia
Flavus: Yellow Conidia
Niger: Black conidia
Organism Characteristics Notes Images
Curvularia Macroconidia: 4-6 Saprobe
cells; Center cell
larger

Altenaria Microconidia have Saprobe

transverse and
longitudinal septa in
chains
Bipolaris Slightly protruding Germ Tube forms
squared off Hilum along the conidia axis

Aureobasidium Produces white yeast Large segmented

like and black yeast hyphae, forms like oreo
like colonies cookies
Organism Characteristics Notes Images
Cladosporium Branching Shield Cells
conidiospores with
chains of ‘Tree-like
conidia

Phialophora Flask-shaped Vase of flowers

verrucosa Phiallides with
adistinct collarette at
the apex

Fonsecaea pedrosoi Short chains of 3 types of sporulation

conidia from sides (Rhinocladiella,
(rabbit ears) Acrotheca and
Phialophora)
Organism Characteristics Notes Images
Exophiala Black yeast cells but Does not grow at 40 C
jeanselmei eventually forms
hyphae

Wangiella Black yeast cells but Can grow at 40 C

dermatitidis eventually forms
hyphae

Pseudallescheria Lollipop forms Can be confused with

boydii Blastomyces
Organism Characteristics Images
Rhizopus Nodal Rhizoids

Mucor No Rhizoids

Absidia Internodal Rhizoids

Drug Fungal Disease
Amphotericin B Aspergillus, Blastomyces, Invasive candidiasis, coccidioidomycosis,
cryptococcosis, fusariosis, histoplasmosis, mucormycosis,
paracoccidioidosis, penicillosis, systemic sporotrichosis
Atovaquone Pneumocystis pneumonia
Echinocandins Aspergillosis, Candidiasis
Fluconazole Blastomycosis (oropharyngeal or esophageal), invasive candidiasis,
coccidioidomycosis, cryptococcosis, fusariosis, histoplasmosis,
sporotrichosis
Flucytosine Candidiasis, chromoblastomycosis, cryptococcosis
Griseofuvin Dermatomycosis
Drug Fungal Disease
Itraconazole Aspergillus, Blastomyces, Invasive candidiasis,
coccidioidomycosis, cryptococcosis, fusariosis,
histoplasmosis, mucormycosis, paracoccidioidosis,
penicillosis, systemic sporotrichosis
Ketoconazole Blastomycosis, Coccidioidomycosis, histoplasmosis,
paracoccidioidomycosis
Terbinafine Dermatomycosis
Trimethoprim-Sulfamethoxazole Pneumocystis pneumonia
Voriconazole Aspergillosis, invasive candidiasis, scedosporiasis