Harifaroosh - intro to viruses

virus

• the name comes from Latin and means poison

• they contain a single nucleic acid: DNA or RNA

• they are obligate intracellular parasites

  • replicate inside the cell; inactive outside of the

• they do NOT change in size or shape or divide by binary fission

• they LACK genetic information for energy metabolism, ribosomes, etc

human vs bacterial cells:

• human cells

• has nuclei

• 80S ribosomes (found in eukaryotes)

• NO cell walls

• human enzymes

• aerobic (need oxygen)

human vs bacterial cells:

• E. coli cells

• NO nuclei

• 70S ribosomes (found in prokaryotes)

• cell walls

• bacterial enzymes

• aerobic, anaerobic, and microaerophilic

human cells vs herpes viruses

human cell:

• has membranes

• 80S ribosomes

• requires human enzymes

• requires humans for replication

herpes viruses:

• carries an envelope

  • NOT ALL viruses have envelopes

• uses 80S ribosomes

• requires some human enzymes

• requires humans for replication

why viral infections are hard to treat

• viruses are eukaryotic

  • not really, but they use host cell enzymes

  • viruses are obligate intracellular parasites

• viruses are biologically highly diverse and rapidly mutate

  • makes developing vaccinations difficult

• infections are typically advanced before they are clinically detected

• vaccinations are NOT useful after infection occurs

variations in viruses

• size

• shape

• structure

• genomic content

positive sense

genome used is similar to mRNA

negative sense

complimentary to positive sense so it has to be translated to positive sense by RNA replicase

virus structure

virus stability

• stability of the viron affects mode of transmission

• naked capsids are generally more stable outside the human body

naked capsid virus structure

nucleocapsid:

1. DNA or RNA

2. + structural proteins

3. ± enzymes and nucleic acid binding proteins

nucleocapsid = naked capsid virus

enveloped virus

1. nucelocapsid

   • DNA or RNA

   • + structural proteins

   • ± enzymes and nucleic acid binding proteins

2. + glycoproteins and membranes

viral classification (old)

based on disease

this practice was abandoned (mostly) because many diverse viruses cause similar diseases

viral classifications (old)

hierarchical and based on structure:

• nucleic acid: DNA or RNA

• symmetry of structure: cuboidal, helical, or asymmetric

• presence of envelope

RNA viruses:

• singled stranded positive sense

• enveloped

• icosahedral

• flaviviridae

• togaviridae

• retroviridae

  • retroviruses use DNA as intermediate

  • very high mutation rates due to no error checking by reverse transcriptase

RNA viruses:

• singled stranded positive sense

• enveloped

• helical

coronaviridae

RNA viruses:

• singled stranded positive sense

• nonenveloped

• icosahedral

• picornaviridae

• caliciviridae

RNA viruses:

• singled stranded negative sense

• enveloped

• helical

• orthomyxoviridae

  • influenza belongs to the orthomyxoviridae family

• paramyxoviridae

• rhabdoviridae

• filoviridae

• bunyaviridae

• arenaviridae

RNA viruses:

• double stranded (directly encode viral proteins)

• nonenveloped

• icosahedral

reoviridae

DNA viruses:

• double stranded

  • (must enter cell nucleus and use host cell polymerase. highly dependent on host cell cycle)

• enveloped

double stranded = must enter cell nucleus and use host cell polymerase. highly dependent on host cell cycle

• herpesviridae

• hepadnaviridae

DNA viruses:

• double stranded

• non-enveloped

• circular

double stranded = must enter cell nucleus and use host cell polymerase. highly dependent on host cell cycle

• papillomaviridae

• polyomaviridae (formerly grouped together as the papovaviridae)

DNA viruses:

• double stranded

• non-enveloped

• linear

double stranded = must enter cell nucleus and use host cell polymerase. highly dependent on host cell cycle

• adenoviridae

DNA viruses:

• single stranded non-enveloped

single stranded non-enveloped = mostly circular genomes, so can make many copies quickly

• parvoviridae

DNA viruses:

• complex enveloped

poxviridae

how many genes can viral genomes contain?

5 to > 200 genes

generic viral life cycle

viruses: initiation of infection

1. virus attach to a receptor on the cell surface

2. penetrate into the cell following receptor engagement

3. the nucleic acid of the virus must be release from the virus

to replicate, a virus must express genes that encode proteins which:

• alter cellular metabolism in order to:

  • provide the precursors for the synthesis of virion components

  • preclude host response to infection

  • alter the physiologic state of the cell to facilitate assembly

  • enable virus egress from the infected cell

• take over the cell’s synthetic machinery to replicate the viral genome and produce viral proteins

• package the newly synthesized genomes in virions

viral macromolecular synthesis: DNA viruses

viral macromolecular synthesis: RNA viruses

viral capsid assembly

viral replication

viral egress

the process can involve one or more of the following:

• lysing the cell

• fusing cells (syncytia)

• acquiring an envelope with viral glycoproteins

• budding out of the infected cell

antigenic drift

generation of point mutations

• many viral polymerases (esp RNA polymerases) have poor fidelity and lack proofreading

• rapid viral life cycle and large burst size create accelerated evolution

antigenic shift

exchange of large segments of genetic material

why are the processes of antigenic drift and antigenic shift major obstacles in therapeutics?

• drug resistance

• resistance to immune response

• ineffective vaccination

why is a new flu shot made each year?

Influenza A mutates its coat proteins (viral genetic mutation), avoiding host immunity

• CDC collaborates with organizations in UK, Australia, Japan, and China via the WHO

• year-round surveillance of circulating influenza

• experts meet in February each year to determine composition of vaccine for the northern hemisphere (they meet again in Sept. for the southern hemisphere flu season)

• each country then makes its own vaccine

cause of major pandemics

• viral genetic exchange

• exchange of genetic material allows jumping from species to species

• large changes subvert any immunity in the host

viral pathogenesis

the process by which a virus causes disease

virulence

capacity of a virus to cause disease

viral disease

sum of the effects of:

• the virus replication and direct damage to cells (cytopathogenesis)

• the immune response on the host (immunopathogenesis)

cytopathogenesis

abortive infections

viruses do NOT complete the replication cycle

• mutations

• interfering particles

• action of interferons

productive infections:

• cytolytic infections

• viruses replicate & produce progeny

• cell death & cytopathic effects (CPE)

productive infections:

• non-cytolytic infections

• viruses replicate & produce progeny

• viruses released by cell budding & little or NO CPE

cytopathic effects (CPE)

CPE can take several forms:

• cell lysis

• cell rounding

• syncytium formation

• inclusion bodies formation

non-productive infection:

• latent infections

• viruses infect cells that either restrict expression of viral genes or lack the machinery for transcribing viral genes

• viral genome either integrates into cell DNA or is a circular episome, or both

• persistent, non-productive infection

• limited expression of viral genes

• infected cell retains its normal properties

• examples include Herpes Simplex Virus

non-productive infection:

• transformation

• causes cancer!

• virus stimulates uncontrolled cell growth

• alters the expression of cell cycle checkpoint genes

• virus infects then leaves behind viral genes in the host genome

• no viral replication

• examples: Epstein-Barr, Human Papilloma viruses

pathogenesis at the host level

1. transmission of the viruses & its entry into the host

2. replication of the virus & damage to cells

3. viral shedding

4. virus remains localized or spreads to other organs

5. the immune response: host defense immunopathogenesis

horizontal transmission

• skin contact

• blood

• respiratory route

• fecal - oral route

• genital contact

• animal-human

vertical transmission

maternal-child

common routes of human infection by viruses

local infections

• example — rhinovirus

• site of pathology — portal of entry

• duration — relatively short

• viremia — absent

• duration of immunity — variable (may be short)

systemic infections

• example — measles

• site of pathology — distant site

• duration — relatively long

• viremia — present

• duration of immunity — usually, life long

macrophages

• antigen presenting cell

• phagocytosis

• cytokine production

cytokines

• interferons (IFN)

  • 𝜶, β-IFN — inhibit the viral and the host cell mRNA translation

  • ɣ-IFN — stimulates phagocytosis and killing by macrophage & NK cells

• interleukins (IL)

  • stimulate Ab production

  • activate T cells & cell-mediated immunity

  • suppress the immune response

immune response to virus

natural killer (NK) cells lyse viral infected cells

the stages of a typical viral infection

• the incubation period

  • no symptoms

• prodromal period

  • minimal symptoms

• the specific-illness period

  • the signs & symptoms of viral diseases are the result of:

    • cell killing by inhibition of cellular macromolecular synthesis

    • immunologic attack (immunopathogenesis)

    • cytotoxic T cells (e.g., hepatitis virus infections)

• the recovery period

stages of viral infection and illness

1. asymptomatic infection

2. acute infection

3. persistent infection

   • late complication of acute infection

   • latent infection

   • chronic infection

factors influencing viral disease

• primary tissue infected

  • many viral infections are restricted to specific cell types

    • mode of transmission (respiratory, blood, STD, fecal/oral)

    • cell-specific receptor expression

    • presence of cell-specific replication factors

    • absence of antiviral proteins/RNAs

• effect of infection on host cell

  • cytopathic effect

  • cellular transformation

• spread of virus

  • secondary sites of infection

• immune response to viral infection

  • immune destruction of infected cells

  • generalized inflammatory response (cytokines, etc)

  • “inappropriate” immune response (autoimmunity)

target tissues of HSV

• brain

  • HSV-1 — encephalitis

  • HSV-2 — meningitis

• mouth

• skin and mucous membranes

• eyes

• throat (pharyngitis)

• urogenital tract

influenza A

• negative-stranded RNA genome

• genome divided into 8 gene segments that encode 10 proteins

• spiked envelope

  • H-spike — hemagglutinin (subtypes H1-H18)

    • mediates attachment

  • N-spikes — neuraminidase (subtypes N1-N11)

    • cleaves H protein to allow fusion of viral and cellular membranes (i.e., entry into the cell)

    • requires cellular enzyme trypsin to facilitate infection

influenza A viral life cycle

the HA and NA polypeptides

• HA encodes hemagglutinin spike protein

  • binds to any cellular protein with a 𝜶2,6-sialic acid group

  • mediates penetration of viral core and RNA into target cell

  • it is the major target of neutralizing antibodies for vaccines and successful immune responses

• NA encodes neuraminidase protein

  • this enzymes cleaves the HA protein upon cell binding and facilitates penetration of the viral core

• together they mediate cell infection

• influenza A viruses are named by their HA and NA subtypes (e.g., H5N1)

coronavirus structure

• spike protein

  • recognizes and binds to host cell surface protein

• nucleocapsid

  • binds the viral RNA to protect and stabilize it

• membrane

  • outer protective layer of lipid, hold spike proteins in place

• envelope

  • proteins that form and stabilize the outer protective layer of the virus particle

• RNA viral genome

  • contains the genetic code of the virus

SARS-CoV-2 replication

HIV

• a retrovirus that infects and destroys helper T cells of the immune system

• HIV is a lentivirus

  • genus of the Retroviridae family

  • produce multi-organ diseases

  • characterized by long incubation periods and persistent infection

HIV life cycle

• ssRNA + strand (2 copies)

• RNA gets reverse transcribed to DNA by HIV reverse transcriptase

• DNA gets integrated into host genome by HIV DNA integrase

• viral RNA and proteins made by host machinery

• HIV proteases process proteins to assemble mature virons

hepatitis

these are different classes of viruses, but still are named after the disease (old classification)

• hepatitis A (HAV) infectious hepatitis

• hepatitis B (HBV) blood bourne

• hepatitis C (HCV) non A, non B

• hepatitis D (HDV) delta virus

• hepatits E (HEV) similar to HAV

hepatitis A

• picornaviridae family

• 27-29 nm icosahedral structure

• ssRNA

• only one serotype

• oral-fecal transmission

  • water

  • infected food handlers

hepatitis B

• hepadnaviridae family

• 42 nm icosahedral structure

• enveloped, circular dsDNA, 3200 nucleotides

• forms Dane particles

  • small pleomorphic particles 20-22 nm

  • excess viral capsids released into blood stream

• blood-blood, sexual, perinatal transmission

hepatitis C

• Flavivridae family

• 6 genotypes

• 60 nm icosahedral structure

• ssRNA

• blood borne

  • transfusions

  • nocosomial transmission

herpes simplex

• herpesviridae family

• 2 genotypes, HSV-1 and HSV-2

• icosahedral structure

• dsDNA, 74 genes

• persistent infection via latent virus neural ganglia

• spread by intimate contact

  • HSV-1 cold sores

  • HSV-2 genital herpes

human papilloma virus

• papillomaviridae family

• over 170 genotypes

• icosahedral structure, 60 nm

• dsDNA, non-enveloped

• most transmission via sexual intercourse

• causes warts and linked to cancer of many organs (cervix, vulva, vagina, penis, anus, mouth, throat)

• vaccines (Gardasil) effective against most common forms of HPV