Chapter 21: Viruses

virus

* parasitic
* doesn't fit into any domain of life
* infects ANY organism
* non-cellular
* no metabolism
* no growth
* no cell division
* copies/replicates itself only WITHIN host

capsid

outer protein coat

nucleic acid genome

single/double-stranded DNA or RNA

envelope

membrane covering capsid (not all viruses)

detection of viruses

polymerase chain reaction (PCR) or immunoassays

Chamberland-Pasteur filter

* how viruses were first discovered
* a porcelain filter that could remove all bacteria visible in the microscope from any liquid sample

Adolph Meyer

demonstrated that a disease of tobacco plants (tobacco mosaic disease) could be transferred from a diseased plant to a healthy one via liquid plant extracts

Dmitri Ivanowski

showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract

* meant something else was infecting the tobacco plants that wasn't bacteria

electron microscopy

* developed in 1930s
* had first view of views
* TVM was first to be seen and described

evolution of viruses

3 hypotheses

* H1: Regressive
* H2: Progressive or Escapist
* H3: Self-replicating

Regressive

viruses evolved from free-living cells or from intracellular prokaryotic parasites

Progressive or Escapist

viruses originated from pieces of RNA and DNA that escaped from a host cell and gained the ability to move between cells

Self-replicating

viruses may have originated from self-replicating entities similar to transposons or other mobile genetic elements

virus size

extremely small; a single particle (virion) is 20-250 nm in diameter

noncellular

lack almost all cell components (e.g. organelles, ribosomes, and membranes)

virus make up

made of nucleic acid core, capsid, and sometimes outer envelope

filamentous

long, thin, worm-like shape

isometric/icosahedral

spherical-shape

enveloped

have membranes that surrounding the capsids

complex/head and tail

infect bacteria and have a head that is similar to icosahedral viruses and a tail shaped like helical viruses

virus core

* contains nucleic acid
* DNA or RNA (never both)
* single-stranded or double-stranded
* circular or linear
* in one piece or in multiple segments

genome

total genetic content of the virus

* viral genomes = very small
* contain only genes that encode proteins that virus cannot get from host cells
* DNA directs host cell to make new virus copies
* RNA viruses uses enzymes that make more errors
* RNA viruses mutate more frequently

DNA viruses

* double-stranded (rarely single-stranded)
* replication in nucleus
* few have DNA polymerases and can replicate in host cell's cytoplasm
* ex: smallpox virus

RNA viruses

* single-stranded (rarely double-stranded)
* replication in cytoplasm
* mutation rate is very high bc RNA polymerase does not have proofreading capabilities
* ex: influenza viruses, coronaviruses

ways to classify viruses

1. according to nucleic acid type and function
2. according to capsid structure
3. enveloped/non-enveloped
4. genome structure

group I

* double-stranded DNA
* mRNA is transcribed directly from the DNA template
* ex: herpes simplex (herpesvirus)

group II

* single-stranded DNA
* DNA is converted to double-stranded form before RNA is transcribed
* ex: Canine parvovirus (parvovirus)

group III

* double-stranded RNA
* mRNA is transcribed from the RNA genome
* childhood gastroenteritis (rotavirus)

group IV

* single stranded RNA (+)
* genome functions as mRNA
* common cold (picornavirus)

group V

* single stranded RNA (-)
* mRNA is transcribed from the RNA genome
* rabies (rhabdovirus)

group VI

* single stranded RNA viruses with reverse transcriptase
* reverse transcriptase makes DNA from the RNA genome; DNA is then incorporated in the host genome; mRNA is transcribed from the incorporated DNA
* human immunodeficiency virus (HIV)

group VII

* double stranded DNA viruses with reverse transcriptase
* the viral genome is double-stranded DNA, but viral DNA is replicated through an RNA intermediate; the RNA may serve directly as mRNA or as a template to make mRNA
* hepatitis B virus (hepadnavirus)

reverse transcriptase

* enzyme found in Baltimore groups VI and VII that converts single-stranded RNA into double-stranded DNA
* never occurs in uninfected host cells —> only derived from the expression of the viral genes within the infected host cells

steps of viral infection

1. attachment
2. entry
3. replication and assembly
4. egress (release)

attachment

* receptors on surface of the host cell bind to virus capsid proteins or virus envelop glycoproteins
* virus can attach only to cells that have right receptor molecules
* viruses can be very specific about what species or cell type they infect

entry

viruses may enter eukaryotic cells by endocytosis or, if enveloped, by fusion with the cell's membrane

replication and assembly

depends on the viral genome

* DNA viruses: usually use host-cell proteins and enzymes to replicate the viral DNA and to transcribe viral mRNA, which is then used to direct viral protein synthesis
* RNA viruses: usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. the viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins and assemble of new viruses
* RNA retroviruses: have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome DNA directs synthesis and assembly of new viruses

egress (release)

* may involve lysis and death of the host cell
* may involve budding, which does not directly kill the host cell

bacteriophages

* aka phage or bacterial virus
* group of viruses that infect bacteria
* are double stranded DNA viruses (use host enzymes for DNA replication and RNA transcription)
* many have central shaft and leg-like appendages
* legs attach to bacteria and genetic material is injected through the shaft into host cell cytoplasm, where it replicates and reassembles into progeny

lytic phages

lyse the host cell after replication of the virion and phage progeny are then released to find new hosts

lysogenic phages

do not immediately lyse the host cell

known as temperate phages

lytic cycle

1. the phage infects a cell
2. the phage DNA circularizes, remaining separate from the host DNA
3. phage DNA replicates and phage proteins are made. new phage particles are assembled
4. the cell lyses, releasing phage

lysogenic cycle

1. phage infects a cell
2. the phage DNA becomes incorporated into the host genome
3. the cell divided, and prophage DNA is passed on to daughter cells
4. under stressful conditions, the phage DNA is excised from the bacterial chromosome and enters the lytic cycle
5. phage DNA replicates and phage proteins are made; new phage particles are assembled
6. the cell lyses, releasing phage

horizontal transmission

* virus typically enters by way of damaged plant tissue
* may come from pollen, another plant, or vectors such as insect bites

vertical transmission

* virus is transmitted from the parent plant
* may cause hypoplasia (decreased growth and vigor)
* may cause hyperplasia (uncontrolled cell growth —> tumors)
* may cause necrosis (death of plant cells) of plant or plant tissue

plant viruses

* most are single stranded RNA viruses
* virus needs mechanism for entry (damage from weather, insects, animals, etc) due to host's cell wall
* causes devastating crop loss

animal viruses

* don't need to penetrate a cell wall to gain access to host cell
* associated with a variety of human diseases

acute disease

symptoms get increasingly worse for a short period followed by the elimination of the virus from the body by the immune system and eventual recovery from the infection

* ex: the common cold and influenza

chronic infections

long-term viral infections

* ex: the virus causing hepatitis C

oncogenic viruses

have the ability to cause cancer

* ex: the hepatitis C virus (liver cancer), HPV (cervical cancer)

intermittent symptoms

stays in a state of latency

* herpes simplex virus

asymptomatic infection

cause productive infections without causing any symptoms at all in the host

* ex: human herpesviruses 6 and 7

vaccines

* primary method of controlling viral disease
* designed to boost immunity to a virus to prevent infection
* may be prepared by live viruses, killed viruses, or molecular subunits of the virus
* live vaccines usually made by attenuating (weakening) the disease-causing virus
* prime immune system to react when body exposed to virus
* few can work during early stages of viral infection (ex: rabies vaccine)
* if virus is stable and doesn't mutate frequently, it can work for years w/o update (ex: measles, mumps, etc)
* may need frequent re-design (ex: annual flu vax)
* may be difficult to design at all (ex: vax against HIV)

antiviral drugs

inhibit the virus by blocking the actions of one or more proteins

* the proteins must only be encoded by viral genes, not any present in a healthy host cell
* ex: Tamiflu

Tamiflu

* can reduce the duration of "flu" symptoms by one or two days, but the drug doesn't prevent symptoms entirely
* works by inhibiting Neuraminidase (NA) (a viral enzyme in influenza) and prevents virions from exiting the cell

prions

proteinaceous infections particles

* very small (< virus)
* no nucleic acids (no DNA or RNA)
* causes fatal neurodegenerative diseases
* ex: mad cow disease, Creutzfeldt-Jakob disease (humans), Kuru (humans cannibalism), Scraple (sheep), chronic wasting disease (deer)
* not destroyed by cooking

PrP^c

normal prion protein

PrP^sc

infectious form of a prion protein

viroids

* small circles of RNA
* only infect plants
* can reproduce only in host cell
* do not manufacture any proteins
* cause crop failures