Ch 6: Acellular Pathogens

acellular pathogens

• don’t have a membrane (not membrane bound)

• can’t replicate on their own → rely on host for resources

• have enough genetic material available that if/when they infect a host, they are able to replicate

characteristics of viruses

• infectious, acellular pathogens

• obligate intracellular parasite with host & cell-type specificity

• DNA or RNA (never both)

• genome is surrounded by a protein capsid

  • in some cases, a phospholipid membrane stuffed with viral glycoproteins (spike proteins)

• lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce

virus size

small relative to the size of most bacterial & eukaryotic cells and their organelles

• need to use transmission electron microscope to see viruses

viron

a complete virus particle

nucleocapsid

genome + capsid

non-enveloped virus

capsid only → just the capsid surrounds the genome

• made up of capsid + nucleic acid (RNA or DNA)

• can tolerate drying & some detergents

enveloped vius

maintain capsid & envelope

• envelope (membrane that is stolen from the host on their way out) + spike (glycoproteins → help virus attach to next host cell) + capsid + nucleic acid

• much more sensitive to soaps & drying out due to membrane and lipids

  • reason why handwashing is so effective

• envelopes help them fuse with host membranes

capsid

composed of protein subunits — capsomeres

envelope

phospholipid membrane from host cell membrane

spikes

glycoprotein extension of the capsid or envelope

viral shapes: helical

cylindrical or rod

• genome fitting inside the length of the capsid

viral shapes: polyhedral

3D, 20-sided structure with 12 vertices

viral shapes: complex

features both polyhedral & helical viruses

• mix of features

bacteriophage

viruses that infect bacteria

bacteriophage shape

complex viral shape

• polyhedral head & sheath connects the head to the tail fibers & tail pins that help the virus attach to receptors on the host cell’s surface

classifications of viruses

• dsDNA, enveloped

• dsDNA, naked

• ssDNA, naked

• dsRNA, naked

• +ssRNA, naked

• +ssRNA, enveloped

• -ssRNA, enveloped

viral life cycle

all viruses depend on cells for reproduction & metabolic processes

• commandeer cellular machinery to produce more viral particles

viral replication in prokaryotic cells

bacteriophages replicate only in the cytoplasm

viral replication in eukaryotic cells

most DNA viruses replicate inside the nucleus

• exception: large DNA viruses — replicate in the cytoplasm

life cycle of viruses with prokaryote hosts

• the lytic cycle

• the lysogenic cycle

the lytic cycle

1. attachment - the phage attaches to the surface of the host

2. penetration - the viral DNA enters the host cell (through the membrane of the bacteria & into the cytosol of the bacteria)

3. biosynthesis - phage DNA replicates & phage proteins are made

4. maturation - new phage particles are assembled → DNA packaging is last stage

5. lysis - cell lyses releasing newly made phages

virulent bacteriophage

enter the lytic cycle → phage replicate & lyses the host cell at the end of replication & goes on to infect neighboring cells

lysogenic cycle

1. phage infects the cell

2. phage DNA becomes incorporated into the host genome → stays dormant

3. cell divides & the prophage DNA is passed onto daughter cells

4. under stressful conditions the prophase DNA is excised from the bacterial chromosome & enters the lytic cycle

   • once activated, prophage cuts itself out of chromosomal DNA & enters lytic cycle

5. phage DNA replicates & phage proteins are made

6. new phage particles are assembled

7. cell lyses releasing newly made phages

temperate bacteriophage

becomes part of the host cell chromosome → don’t jump into lysing their cell right away

lysogenic cycle: prophage

the integrated phage genome

lysogenic cycle: lysogen

the bacterial host with a prophage in its genome

lysogenic cycle: lysogeny

the process in which a bacterium is infected by a temperate phage

• during lysogeny, the prophage persists in the host chromosome until induction → results in the excision of the viral genome from the host chromosome

lysogenic conversion/phage conversion

change that occurs when prophage alter the phenotype of the bacterium (the DNA they become part of)

transduction

transfer of genetic material through bacteriophage

• phage transfer bacterial DNA from one bacterium to another

steps of transduction

1. viral attachment & penetration - phage infects cell

2. integration - the phage DNA becomes incorporated into the host genome

3. excision - the phage is exercised from the bacterial chromosome along with a short piece of bacterial DNA → DNA os then packed into newly formed capsids

4. infection - phage containing both viral & bacterial DNA infect a new host cell

5. recombination - the phage DNA, along with the attached bacterial DNA are incorporated into the new cell

generalized transduction

a random piece of bacterial chromosomal DNA is transferred by the phage during the lytic cycle

specialized transduction

occurs at the end of the lysogenic cycle, when prophase excised itself out of the bacterial chromosome it occasionally removes some bacterial DNA near the site of viral infection

• NOT RANDOM — is the piece of DNA next to the prophage when it was on the chromosome

phage therapy

use certain bacteriophage in precision medicine to target specific bacteria

viruses with animal hosts

• require different mechanisms of penetration, biosynthesis, & release

• host specific - only infect a certain type of host

• tissue specific - infect certain types of cells that have the specific receptor (tissue tropism)

  • ex. poliovirus → tropism for brain & spinal cord cells (neurotropism)

  • ex. influenza→ primary tropism for respiratory tract (epithelial cells)

life cycle of viruses with animal hosts (influenza ex)

1. flu virus becomes attached to a target epithelial ell

2. the cell engulfs the virus by endocytosis

3. fusion & uncoating: viral RNA release

4. viral RNA enters the nucleus where its replicated by the viral RNA polymerase

5. viral mRNA used to make viral proteins

6. new viral particles are made & released into the extracellular fluid

   • the cell which isn’t filled in the process continues to make new virus

viruses with animal hosts: genetic information

animal viruses don’t always express either genes using the normal flow of genetic information from DNA to RNA to protein

• ssDNA → dsDNA → replicated, transcribed, & translated similar to host DNA

• +ssRNA can be directly read by host ribosome

• -ssRNA has to be replicated into +ssRNA by RdRP

• RdRP is brought in by the virus

RdRP

viral RNA-dependent RNA polymerase

retroviruses

reverse the flow

• convert ssRNA into dsDNA using reverse transcriptase

• dsDNA integrates into host cell genome becoming a permentant part of the host & serves as template for mRNA synthesis & genome syntheses

  • integrated viral genome = provirus

  • unlike prophage, provirus doesn’t undergo excision after slicing into the genome

human immunodeficiency virus (HIV)

• cause of acquired immunodeficiency syndrome (AIDS)

• globally important pandemic

• member of genus Lentivirus

  • HIV-1 (most common cause in US), HIV-2 (common in Africa)

HIV-1

• enveloped virus (has a membrane)

• two copies of RNA genome

• reverse transcriptase & integrase

how HIV works

1. HIV fuses to host-cell surface

2. HIV RNA, reverse transcriptase, integrase, & other viral proteins enter the host cell

3. viral DNA is formed by reverse transcription

4. viral DNA is transported across the nucleus & integrates into the host DNA

5. new viral RNA is used as genomic RNA and to make viral proteins

6. new viral RNA & proteins move to the cell surface and a new, immature HIV forms

7. the virus matters when protease releases the proteins that form the mature HIV

more on HIV

• gp120 binds CD4+ T cells, macrophages, dendritic cells, & monocytes

  • virus enters by receptor-mediated endocytosis

  • coreceptor also requires to gain entry to cell

• reverse transcriptase is:

  • RNA dependent DNA polymerase

  • DNA dependent DNA polymerase

  • error prone, has no proofreading capability

types of infections

• acute

• persistant

  • latent

  • chronic

acute infections

symptoms worsen over short period followed by the elimination of the virus & recovery

persistant infections

virus stays in certain tissues or organs of infected person

latent infections 

virus stays hidden or dormant inside the cells 

• ex. chicken pox, shingles, herpes 

chronic infections

disease with symptoms that can be recurrent over a long time

• ex. HIV

isolation of viruses

• growth of viruses require living host cell

• infected host cells (eukaryotic or prokaryotic) can be cultured & grown

• filtration is used to separate visions related in the liquid medium from the host cells

size of different cells

• animal: >10 microns

• bacterial: 1-5 microns

• virus: <5 microns

cultivation of viruses

number of viruses (viral titer)

• culture flasks for infected human cells (animal virus)

why cultivate animal viruses?

1. identification & diagnosis of viruses in clinical specimens 

2. production of vaccines 

3. basic research studies 

viral vector vaccine (ex. covid-19 virus) 

1. genetic material inserted into inactive (harmless) virus

2. viral vector vaccine 

3. harmless virus enters cell 

4. covid-19 virus spike protein created 

5. spike proteins recognized by immune system, specific antibodies agains virus produced 

6. if you are infected with covid-19 virus, antibodies bind to virus & stop it from replicating 

cultivation of viruses in tissue cells

cell cultures can be prepared of be used for viral infections

• individual cells isolated from tissue → primary cell culture → contact inhibition - → some cells transferred to new medium (secondary culture)

  • transformed cells or individual cells isolated from tumor → continuous cell line

1st immortal research cell line

HeLa cells

detection of virus 

observing infected cells under microscope 

• CFEs: 

  • loss of adherence to the surface of container 

  • changes in cell shape 

  • shrinkage of nucleus 

  • vacuoles in cytoplasm 

  • fusion of cytoplasmic membranes 

  • formation of multinucliated syncytia 

  • incision bodies in the nucleus or cytoplasm

  • complete cell lysis 

cytopathic effects (CPEs)

distinct observable cell abnormalities caused by viral infection 

hemagglutinin

present in spikes protruding from some viruses

detection by hemagglutination assay 

serological assay to detect the presence of some viruses in patient serum 

hemagglutination 

agglutination (clumping) together of erythrocytes (RBCs) 

detection by enzyme immunoassay 

• rely on antibodies that detect & attach to specific biomolecules called antigens 

• the antibody is linked to an enzyme that can interact with a colorless substrate, leading to the production of a colored end product 

• this assay is used as preliminary screen for presence of viral antigens 

prions

proteinaceous infectious particles

• misfolded rouge form - PrPsc of a normal protein PrPc

• caused by a genetic mutation or occur spontaneously

• can be infectious, stimulating other normal proteins to become misfolded

• no cure, disease progresses rapidly

• cause transmissible spongiform encephalopathy in humans & animals