Classification Of Virus[Summary]

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


Variations on the replication theme


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


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


Cycle of infection

Secondary sites

Spread

Entry Shedding

Shedding

LocalLymphaticNeuronalBlood (viremia)

Primary site


Time course of infection; host response

0 2 4 6 8 10 12

time (days)

infection without spread:

infection with spread:

host response:


Patterns of disease


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


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


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


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


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 ?


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


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


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


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


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


Summary


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


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


Time course of Rabies infections


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


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



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


Arboviruses: Vectors, Hosts, and Diseases


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


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


HGV

Flavi ///////////hepe


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)


Hepatitis B virus


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


Clinical interpretation of the Hepatitis B antigen panel


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


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)


HIV-1 Replication Cycle

CCR5

CD4

CXCR4

Reverse Transcription Integration

Uncoating

Assembly

Budding

Attachment

Maturation

ReverseTranscriptase

Integrase

Protease

Beth D. Jamieson, Ph.D.


Natural Course of HIV-1 Infection


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)


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


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


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


Vaccines – live or killed?


FDA approved antiviral drugs


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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Classification Of Virus[Summary]