Basic virus structure
DNA
or
+
Capsid
protein
Nucleocapsid
=
Naked
capsid virus
RNA
Nucleocapsid
+
Lipid membrane,
glycoproteins
Enveloped virus
Properties of enveloped viruses
• Envelope is sensitive to
–
–
–
–
Drying
Heat
Detergents
Acid
• Consequences
–
–
–
–
–
Must stay wet during transmission
Transmission in large droplets and secretions
Cannot survive in the gastrointestinal tract
Do not need to kill cells in order to spread
May require both a humoral and a cellular immune
response
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Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5
Properties of naked capsid viruses
• Capsid is resistant to
–
–
–
–
–
Drying
Heat
Detergents
Acids
Proteases
• Consequences
–
–
–
–
–
–
Can survive in the gastrointestinal tract
Retain infectivity on drying
Survive well on environmental surfaces
Spread easily via fomites
Must kill host cells for release of mature virus particles
Humoral antibody response may be sufficient to neutralize
infection
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Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A.
(2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA , Box 6-4
Classification of Human Viruses
"Group"
dsDNA
Family
Genome
Genome size (kb)
Capsid
Envelope
Poxviridae
Herpesviridae
Adenoviridae
Polyomaviridae
Papillomaviridae
dsDNA,
dsDNA,
dsDNA,
dsDNA,
dsDNA,
130 to 375
125 to 240
26 to 45
5
7 to 8
Ovoid
Icosahedral
Icosahedral
Icosahedral
Icosahedral
Yes
Yes
No
No
No
Anellovirus
Parvoviradae
ssDNA circular
ssDNA, linear, (- or +/-)
3 to 4
5
Isometric
Icosahedral
No
No
Hepadnaviridae
Retroviridae
dsDNA (partial), circular
ssRNA (+), diploid
3 to 4
7 to 13
Icosahedral
Spherical, rod or cone shaped
Yes
Yes
Reoviridae
dsRNA, segmented
19 to 32
Icosahedral
No
Rhabdoviridae
Filoviridae
Paramyxoviridae
Orthomyxoviridae
Bunyaviridae
Arenaviridae
Deltavirus
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
(-)
(-)
(-)
(-), segmented
(-, ambi), segmented
(-, ambi), segmented
(-) circular
11
19
10
10
11
11
2
Helical
Helical
Helical
Helical
Helical
Circular, nucleosomal
Spherical
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Picornaviridae
Calciviridae
Hepevirus
Astroviridae
Coronaviridae
Flaviviridae
Togaviridae
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
ssRNA
(+)
(+)
(+)
(+)
(+)
(+)
(+)
7 to 9
7 to 8
7
6 to 7
28 to 31
10 to 12
11 to 12
Icosahedral
Icosahedral
Icosahedral
Isometric
Helical
Spherical
Icosahedral
No
No
No
No
Yes
Yes
Yes
linear
linear
linear
circular
circular
ssDNA
Retro
dsRNA
ssRNA (-)
to 15
to 15
to 13.6
to 19
ssRNA (+)
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Variations on the replication theme
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Summary: structure,
classification & replication
• Structure
– Nucleic acid in a protein shell, +/- lipid envelope
– Structure impacts on biological properties
• Classification
– Many virus families, organized by structure and
biology
• Replication
– Generic scheme
– Varying strategies depending on nucleic acid
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Summary: laboratory virology
• 4 main clinical diagnostic techniques
– Culture, serology, antigen detection, nucleic acid
detection
• Virus culture
– Cultured cell types
– Cytopathic effect
– Not all viruses can be cultured
• Virus quantitation
– Biological
– Physical
• Basic serological techniques
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Cycle of infection
Entry
Primary site
Spread
Shedding
Local
Lymphatic
Neuronal
Blood (viremia)
Secondary sites
Shedding
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Time course of infection; host response
infection without spread:
prodrome
symptoms at
primary site
healing
infection with spread:
symptoms at
secondary sites
prodrome
host response:
innate immunity:
interferon
0
2
adaptive immunity:
cellular, antibody
4
6
time (days)
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inflammatory;
immunopathogenesis
8
10
12
Patterns of disease
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Summary:
Pathogenesis & Genetics
• Cycle of infection
• Effects on cells
– Abortive, lytic, persistent, latent, transforming
infections
• Effects on the organism
• Genetics
– Mutation, genotype, phenotype, reversion,
recombination
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For each virus, know:
• Structure (cheat sheet)
• Pathogenesis
–
–
–
–
–
transmission/entry/shedding
replication
spread
immune response/counter response
damage/disease mechanism
• Diagnosis
• Treatment/prevention
– drugs
– vaccines
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Human papillomavirus
•
Structure
– Small (8 kb) circular dsDNA genome, naked capsid
•
Pathogenesis
– transmission by direct contact or sexual; skin, mucosa
– replication in nucleus of basal cells of epithelium; very host dependent; coupled
to epithelial differentiation
– no spread
– primarily cellular immune response
– transforming infection; warts are tumors; cervical carcinoma
•
Diagnosis
– cytology (PAP smear; koilocytosis)
– immunohistochemistry
– nucleic acid
•
Prevention/treatment
– recombinant subunit (VLP) vaccine
– PAP smear
– surgery
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Parvovirus
• Structure
– Small (5 kb) linear ssDNA genome, naked capsid
• Pathogenesis
– respiratory transmission
– replication in nucleus, very host dependent, needs S phase cells
or helper virus
– viremia
– antibody important in immunity
– targets erythroid lineage cells; fifth disease (symptoms
immunological); transient aplastic crisis; hydrops fetalis
• Diagnosis
– serology, viral nucleic acid
• Treatment/prevention
– none
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Polyomavirus
• Structure
– Small (5 kb) circular dsDNA genome, naked capsid
• Pathogenesis
–
–
–
–
–
respiratory transmission
replication in nucleus; very host dependent
viremia
persistence in kidneys; reactivation with immune compromise
inapparent infection; hemorrhagic cystitis; PML
• Diagnosis
– viral nucleic acid
• Treatment/prevention
– cidofovir ?
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Adenovirus
• Structure
– Medium sized (36 kb) dsDNA genome, naked capsid
• Pathogenesis
–
–
–
–
respiratory or fecal oral transmission
replication in nucleus; moderately host dependent
local spread; viremia
cellular and humoral immunity important; virus encodes
countermeasures against MHC I expression and apoptosis
– direct cell damage from replication; respiratory illness,
conjunctivitis, gastroenteritis, cystitis
• Diagnosis
– culture, viral antigen detection
• Treatment/prevention
– live military vaccine
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Influenza
• Structure
– Negative sense segmented ssRNA genome, helical nucleocapsid,
enveloped
• Pathogenesis
–
–
–
–
–
respiratory transmission
replication in nucleus; budding
no spread (usually)
innate and antibody response important; antigenic shift and drift
local symptoms from cell killing; systemic symptoms from immune
response; exaggerated disease in young and elderly; viral and bacterial
pneumonia complications
• Diagnosis
– culture, hemadsorbtion, viral antigen detection
• Treatment/prevention
– amantidine and rimantidine target matrix; zanamivir and oseltamivir
target NA
– killed and live vaccines need constant updating
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Paramyxoviruses
• Structure
– Negative sense ssRNA genome, helical nucleocapsid, envelope with
attachment protein and F protein
• Pathogenesis
– Transmission in respiratory droplets and fusion of virus envelope via F
protein with plasma membrane of cells in the respiratory tract
– Replication in cytoplasm, budding
– Viremia except for RSV and PIV
– Innate and antibody response important; many symptoms from immune
response: rash in measles and swelling in mumps; PIV bronchitis and
croup; RSV bronchiolitis and pneumonia in infants
– Sequelae in CNS for measles and mumps
• Diagnosis
– Serology or nucleic acid
– Measles: Koplik spots; mumps: swelling of parotid gland
• Treatment/prevention
– MMR live attenuated viral vaccine for measles and mumps, none for
RSV or PIV
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Rabies
• Structure
– Negative sense ssRNA, helical nucleocapsid, envelope
• Pathogenesis
–
–
–
–
–
Transmitted by bite of rabid animal
Replication in cytoplasm; budding
Spread by axonal transport to brain; long incubation period
Fever, nausea, hydrophobia, coma
Almost always fatal
• Diagnosis
– Viral antigen or nucleic acid, Negri bodies
• Treatment/prevention
– Inactivated viral vaccine for humans after exposure, live
virus vaccine for animals
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Rotavirus
• Structure
– Naked double shell capsid
– 11 segment double stranded RNA genome
• Pathogenesis
–
–
–
–
–
Fecal oral transmission
Replication in cytoplasm
Fever, vomiting, diarrhea in infants and young children
Incubation period less than 48 hr, highly infectious
Infection of intestinal epithelium causes loss of electrolytes and
prevents readsorption of water
– Long term immunity; asymptomatic infection in adults
• Diagnosis
– viral antigen detection
• Treatment/prevention
– RotaTeq live, oral vaccine
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Summary
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Paramyxoviruses
Structure
•Negative sense ssRNA genome, helical nucleocapsid, envelope
with attachment protein and F protein
Pathogenesis
•Transmission in respiratory droplets and fusion of virus envelope
via F protein with plasma membrane of cells in the respiratory tract
•Replication in cytoplasm, budding
•Viremia except for RSV and PIV
•innate and antibody response important; many symptoms from
immune response: rash in measles and swelling in mumps; PIV
bronchitis and croup; RSV bronchiolitis and pneumonia in infants
•Sequelae in CNS for measles and mumps
Diagnosis – serology or nucleic acid
•Measles Koplik spots; mumps swelling of parotid gland
Treatment/prevention
•MMR live attenuated viral vaccine for measles and mumps, none
for RSV or PIV
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Rabies
Structure
•Negative sense ssRNA, helical nucleocapsid, envelope
Pathogenesis
•Transmitted by bite of rabid animal
•replication in cytoplasm; budding
•Spread by axonal transport to brain; long incubation period
•Fever, nausea, hydrophobia, coma
•Almost always fatal
Diagnosis
•Viral antigen or nucleic acid, Negri bodies
Treatment/prevention
•Inactivated viral vaccine for humans after exposure, live virus vaccine for
animals
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Time course of Rabies infections
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Rotavirus
Structure
•Double stranded, 11 segment RNA genome, two protein coats
Pathogenesis
•Fecal oral transmission
•replication in cytoplasm
•Epidemic diarrhea in infants and young children- fever,
vomiting, diarrhea
•Incubation period less than 48 hr, highly infectious
•Infection of intestinal epithelium causes loss of electrolytes
and prevents re-adsorption of water
Diagnosis
•culture, viral antigen detection
Treatment/prevention
•RotaTeq live, oral vaccine
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Enteroviruses
Structure
•Positive sense ssRNA genome, protein coat
Pathogenesis
•Fecal oral transmission
•replication in cytoplasm
•Viremia to diverse target tissues. Viruses very cytopathic, killing cells
they infect
•Infections often asymptomatic; polio causes paralytic poliomyelitis;
rhinoviruses restricted to upper respiratory tract, common cold;
caliciviruses diarrhea
Diagnosis
•Serology and nucleic acid
Treatment/prevention
•Only polio vaccines, Salk and Sabin
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Arboviruses
Structure
•Positive sense ssRNA genome, icosahedral nucleocapsid, enveloped
Pathogenesis
•Transmitted by bite of insect from host species; sylvan and urban
cycles
•replication in cytoplasm; budding
•Viremia to target tissue
•Influenza-like initial symptoms; different viruses cause encephalitis,
hemorrhagic fever, hepatitis, rash, arthritis
Diagnosis
•Serology and nucleic acid
Treatment/prevention
•No human vaccines, except yellow fever virus live attenuated
vaccine, control of insect population
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Arboviruses: Vectors, Hosts, and Diseases
Rubella virus
Structure
•Positive sense ssRNA genome, helical nucleocapsid, enveloped
Pathogenesis
•respiratory transmission
•replication in cytoplasm; budding
•Viremia
•Mild rash in adults; congenital rubella syndrome (CRS) after
infection in first trimester when virus passes the placenta and
infects fetus
•CRS- deafness, blindness, mental retardation
Diagnosis
•Nucleic acid, viral antigen detection
Treatment/prevention
•MMR live attenuated virus vaccine
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RNA Hepatitis Viruses
Structure
•Various different families for HAV, HCV, HEV, HGV all positive sense ssRNA
Pathogenesis
•HAV and HEV fecal oral then viremia; others sexual and blood borne, viremia
•Liver is target organ; most infections are subclinical, acute infections differ in
onset and severity.
•HAV and HEV cause hepatitis with no carrier state; others cause hepatitis
with chronic infection and possible carcinoma
Liver damage due to cell mediated immune response
Diagnosis
• viral antigen detection, nucleic acid
Treatment/prevention
• HAV killed virus vaccine; HCV alpha-interferon effective for some serotypes
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HGV
///////////hepe
Flavi
Hepatitis B Virus
• Structure
– Small (3.2 kb) circular partially dsDNA genome, envel. capsid
• Pathogenesis
–
–
–
–
–
Sexual, parenteral, and perinatal transmission
Replication via an RNA intermediate (reverse transcriptase)
Tropism for liver
Acute vs. chronic infections occur: highly age dependent
Chronic infections are a major cause of PHC
• Diagnosis
– Multiple serological components (viral proteins and anti-bodies)
• Treatment/prevention
– Subunit vaccine (based on HBsAg)
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Hepatitis B virus
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Immunological events of acute vs. chronic HBV
infection
A) Acute
B) Chronic
From Murray et. al., Medical Microbiology 5th edition, 2005, Chapter 66, published by Mosby Philadelphia,,
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Clinical interpretation of the Hepatitis B
antigen panel
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Hepatitis D Virus
• Structure
– Very Small (1.7 kb) circular ssRNA genome, envel. capsid
• Pathogenesis
–
–
–
–
–
Sexual, parenteral, and perinatal transmission
Replication by RNA-directed RNA Pol (Host RNA Pol II)
Requires concurrent HBV infection (needs it for HBsAg)
HDV greatly exacerbates liver damage caused by HDV
Chronic infections are a major cause of PHC
• Diagnosis
– Serologically for HDV delta antigen
• Treatment/prevention
– Subunit vaccine for HBV prevents productive infection
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HIV
• Structure
– 9.0 kb diploid ssRNA genome, envel. capsid
• Pathogenesis
–
–
–
–
Sexual, parenteral, and perinatal transmission
Replication by cDNA intermediate (reverse transcriptase)
Replication cycle requires the DNA intermediate to integrate
HIV establishes a persistent infection that ultimately reduces CD4
helper T cell population
– During course of infection, tropism shift from M-tropic to T-tropic
• Diagnosis
– Serologically for antibodies against HIV antigens (gp120)
• Treatment/prevention
– Antivirals (HAART)
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HIV-1 Replication Cycle
Reverse
Transcription
Integration
Assembly
Integrase
Attachment
CD4
Reverse
Transcriptase
Uncoating
Budding
CCR5
Maturation
Protease
CXCR4
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Beth D. Jamieson, Ph.D.
Natural Course of HIV-1 Infection
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Herpesviruses
Herpes simplex I & II (cold sores, genital herpes)
Varicella zoster (chicken pox, shingles)
Cytomegalovirus (microcephaly, infectious mono)
Epstein-Barr virus (mononucleosis, Burkitt’s lymphoma)
Human herpesvirus 6 & 7 (Roseola)
Human herpesvirus 8 (Kaposi’s sarcoma)
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Human Herpesviruses
Virus
Subfamily
Disease
Site of Latency
Herpes Simplex Virus I
a
Orofacial lesions
Sensory Nerve Ganglia
Herpes Simplex Virus II
a
Genital lesions
Sensory Nerve Ganglia
Varicella Zoster Virus
a
Chicken Pox
Recurs as Shingles
Sensory Nerve Ganglia
Cytomegalovirus
b
Microcephaly/Mono
Lymphocytes
Human Herpesvirus 6
b
Roseola Infantum
CD4 T cells
Human Herpesvirus 7
b
Roseola Infantum
CD4T cells
Epstein-Barr Virus
g
Infectious Mono
B lymphocytes, salivary
Human Herpesvirus 8
g
Kaposi’s Sarcoma
Kaposi’s Sarcoma Tissue
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A study of HSV-2 recurrence in
women
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37
33
29
25
21
17
13
9
5
PCR
HSV
lesions
1
100
90
80
70
60
50
40
30
20
10
0
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Vaccines – live or killed?
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FDA approved antiviral drugs
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Non-equilibrium human virus
1. Virus has a stable relationship with an animal
host.
2. Virus can be strikingly lethal since it hasn’t
evolved to coexist with humans.
3. Virus will be in genetic flux until it reaches
equilibrium or human infection chain is broken.
4. HIV, Ebola virus, Hantavirus and Influenza virus
are examples
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