Basic virus structure
Capsid protein
NucleocapsidNaked
capsid virus
DNA
RNA
or =+
NucleocapsidLipid membrane,
glycoproteinsEnveloped virus+
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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
Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5www.freelivedoctor.com
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
Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA , Box 6-4www.freelivedoctor.com
Classification of Human Viruses
"Group" Family Genome Genome size (kb) Capsid EnvelopedsDNA
Poxviridae dsDNA, linear 130 to 375 Ovoid YesHerpesviridae dsDNA, linear 125 to 240 Icosahedral YesAdenoviridae dsDNA, linear 26 to 45 Icosahedral NoPolyomaviridae dsDNA, circular 5 Icosahedral NoPapillomaviridae dsDNA, circular 7 to 8 Icosahedral No
ssDNAAnellovirus ssDNA circular 3 to 4 Isometric NoParvoviradae ssDNA, linear, (- or +/-) 5 Icosahedral No
RetroHepadnaviridae dsDNA (partial), circular 3 to 4 Icosahedral YesRetroviridae ssRNA (+), diploid 7 to 13 Spherical, rod or cone shaped Yes
dsRNAReoviridae dsRNA, segmented 19 to 32 Icosahedral No
ssRNA (-)Rhabdoviridae ssRNA (-) 11 to 15 Helical YesFiloviridae ssRNA (-) 19 Helical YesParamyxoviridae ssRNA (-) 10 to 15 Helical YesOrthomyxoviridae ssRNA (-), segmented 10 to 13.6 Helical YesBunyaviridae ssRNA (-, ambi), segmented 11 to 19 Helical YesArenaviridae ssRNA (-, ambi), segmented 11 Circular, nucleosomal YesDeltavirus ssRNA (-) circular 2 Spherical Yes
ssRNA (+)Picornaviridae ssRNA (+) 7 to 9 Icosahedral NoCalciviridae ssRNA (+) 7 to 8 Icosahedral NoHepevirus ssRNA (+) 7 Icosahedral NoAstroviridae ssRNA (+) 6 to 7 Isometric NoCoronaviridae ssRNA (+) 28 to 31 Helical YesFlaviviridae ssRNA (+) 10 to 12 Spherical YesTogaviridae ssRNA (+) 11 to 12 Icosahedral Yes
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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
Secondary sites
Spread
Entry Shedding
Shedding
LocalLymphaticNeuronalBlood (viremia)
Primary site
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Time course of infection; host response
0 2 4 6 8 10 12
time (days)
infection without spread:
infection with spread:
host response:
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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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ParamyxovirusesStructure
•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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RabiesStructure
•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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RotavirusStructure
•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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EnterovirusesStructure
•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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ArbovirusesStructure
•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
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Rubella virusStructure
•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 VirusesStructure•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 carcinomaLiver 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
Flavi ///////////hepe
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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
From Murray et. al., Medical Microbiology 5th edition, 2005, Chapter 66, published by Mosby Philadelphia,,
A) Acute B) Chronic
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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
CCR5
CD4
CXCR4
Reverse Transcription Integration
Uncoating
Assembly
Budding
Attachment
Maturation
ReverseTranscriptase
Integrase
Protease
Beth D. Jamieson, Ph.D.
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Natural Course of HIV-1 Infection
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HerpesvirusesHerpes 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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Virus Subfamily Disease Site of Latency
Herpes Simplex Virus I Orofacial lesions Sensory Nerve Ganglia
Herpes Simplex Virus II Genital lesions Sensory Nerve Ganglia
Varicella Zoster Virus Chicken Pox Sensory Nerve Ganglia Recurs as Shingles
Cytomegalovirus Microcephaly/Mono Lymphocytes
Human Herpesvirus 6 Roseola Infantum CD4 T cells
Human Herpesvirus 7 Roseola Infantum CD4T cells
Epstein-Barr Virus Infectious Mono B lymphocytes, salivary
Human Herpesvirus 8 Kaposi’s Sarcoma Kaposi’s Sarcoma Tissue
Human Herpesviruses
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A study of HSV-2 recurrence in women
010
20
30
40
50
6070
80
90
100
1 5 9 13
17
21
25
29
33
37
PCR
HSV
lesions
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O
N
N N
HN
N 2 H
O HO
Herpesvirus Thymidine
Kinase
O
N
N N
HN
N 2 H
O P O
O
N
N N
HN
N 2 H
O P O P P cellular
enzymes
DNA DNA
replication
XTP's
1) Blocks Viral DNA Polymerase2) Chain Terminates
O
N
N N
HN
N 2 H
O HO
OH
Deoxyguanosine
Acyclovir
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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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