Microbiology Exam #2 - Virus Chapter

Nonliving infections particles include

• Viruses

• Virophages

• Viroids

• Prions 

Are viruses cells?

• NO, they are not cells, they are obligate intracellular parasites/pathogens 

• cannot reproduce outside their host cell

The Novel Properties of Viruses

• Inert macromolecules outside of a cell but become active inside a cell

• DO NOT divide and grow = need host cell

• Acellular (A = not)

• Contain EITHER DNA OR RNA (not both), with a few exceptions

• Genome can be dsDNA, ssDNA, dsRNA, or ssRNA

• Usually ultramicroscopic in size, ranging from 10nm to 500nm = need an electron microscope to see

• Have a proteinaceous capsid around genome; some have an envelope around the capsid

• Replicate in an assembly line manner using the enzymes and organelles of a host cell

• NO ribosomes = no protein synthesis

• No ATP-generating mechanism

• Are infectious! Many viruses are medically important

Herpes

• Huge family of viruses

• Chicken pox, cold sores, STI

• Icosahedral shape!

HPV

• Human Papilloma Virus

• Can show no symptoms, not necessarily sexual

• Icosahedral shape

General Structure of Viruses: Capsids

• ALL viruses have capsids!

• Protein coats that enclose and protect their nucleic acid 

  • Constructed from identical protein subunits called capsomeres

  • The capsid together with the nucleic acid form the nucleocapsid

• NOTE: Our immune system DOES NOT like repeating units = the capsomeres

• A good example would be the Rhinovirus - common cold

Capsid Structure types: Helical 

• Continuous helix of capsomers forming a cylindrical nucleocapsid 

Capsid Structure types: Polyhedral (Icosahedral)

• 20 sided with 12 corners

• Vary in number of capsomers

• Each capsomer may be made of 1 or several proteins

• Some are enveloped = membrane EXTERNAL to capsid (outer) 

What shape is the rabies virus?

• It is bullet shaped

The viral envelope (how it’s derived)

• The viral envelope is derived from the host cell membrane

• Some animal viruses - *NOT on bacteriophages b/c bacteria have cell walls

  • Meaning bacteria can pierce bacterial cell walls while animal cells need that envelope to help fuse into the membrane(we don’t have cell walls)

• acquired when virus leaves or buds through the host cell

• exposed proteins on the outside envelope, called spikes/peplomers are essential for: binding to receptor and infectivity of the host cell

• Those without an envelope = Naked viruses ‘

• NOTE: Proteins on nucleocapsid or envelope interact with complementary host cell receptors!

Envelope: Functions

• NOTE: is REQUIRED for enveloped viruses 

• Protects the nucleic acid when the virion is OUTSIDE the host cell 

• Is used to: bind to receptor and infect the host cell 

• If there is no envelope = Naked virus (capsid binds to host cell) 

Advantages of the Envelope

• Is similar to host membranes so helps the virus evade host immune response for a time

  • Molecular mimicry = virus looks like host cell

• Required for infectivity: fuses with host cell membrane = no envelope = no infectivity

  • True for enveloped viruses!

• Enveloped viruses are easier to kill on surfaces BUT harder for the body to detect

  • Opposite for naked viruses

Disadvantages of Virus envelope 

• Anything that damages a cell membrane will damage the viral envelope = like soap!!

• So = damaged by environmental conditions 

  •  Temp, pH, pressure, toxins, detergents, etc

  • Damages to viral envelope = no infectivity!

• So, naked viruses are → More resistant to damaging environmental factors

Why is resistance to environmental conditions important?

• Naked virus can persist! → While enveloped viruses cannot 

• Viruses with a damaged/destroyed cell envelope cannot interact with (complementary) molecule/host receptor 

Growing Viruses (obligate intracellular pathogens)

• Viruses must be grown on living cells 

  • Animal viruses may be grown in living animals or in embryonated eggs or in cell structures (tissue culture)

    • Continuous cell lines

  • Bacteriophages form plaques on a lawn of bacteria

• For infection: All viruses must interact with host cell receptor

1. Host receptor is complementary to molecule on virus (spike protein (peplomer))

2. Viruses are nonmotile

3. Chemical attraction involved = sense presence of host cell

Viral Replication of animal viruses 

• Replication of Animal Viruses 

  • Must attach to host cell first

  • Entry and uncoating of animal viruses

    • At least three different mechanisms by which animal viruses enter a cell!

What are the three mechanisms that an animal virus uses to enter a cell? 

• Direct penetration: only nucleic acid enters host cell

  • For naked viruses ONLY

• Membrane fusion: only nucleocapsid enters

  • For enveloped viruses ONLY

• Endocytosis: entire enveloped OR naked virus enters the cell

  • Specific to animal cells!

• Viruses that enter cell with capsid intact are uncoated inside the cell → the genetic information is floating around (nucleic acid)

  • Genome/Nucleic Acid has to be released into the cytoplasm for viral replication = enzymes needed

Release of animal viruses 

• Assembled animal viruses leave host cell in one of two ways!

1. Budding/blebbing: exocytosis; nucleocapsid binds to membrane which pinches off and sheds the viruses gradually (typically by enveloped viruses)

2. Lysis: virus released when cell dies and ruptures (typically for naked viruses)

• Number of viruses released during lysis is variable

  • Poxvirus 3,000-4,000 released

  • Poliovirus >100,000 released

The process of budding in enveloped viruses & molecular mimicry 

• Molecular mimicry = enveloped virus looks like host cell due to presence of host cell membrane = but immune response will eventually recognize viral components 

• Virus budding will eventually kill host cell 

Complex structure of viruses

• Some bacteriophages have a polyhedral nucleocapsid along with a helical tail and attachment fibers

Multiplication Cycle in Bacteriophages

• Multiplication goes through similar stages as animal viruses!

• Only the nucleic acid enters (through direct penetration) the cytoplasm

• Release due to cell lysis = lytic cycle

Background - Bacteriophages: bacterial viruses (phages)

• Most widely studied are those that infect Escherichia coli

Virus Host Range 

• Host cell infection → Due to affinity of viral surface proteins for complementary proteins (receptor) on host cell surface means:

  • Host cell must possess a receptor that interacts with viral surface → no host receptor = no binding/ no infectivity

• SO host range is determined by the presence of the receptor/complementary molecule

  • Examples of host range: Rabies = mammals, T4 bacteriophage = one strain of E. coli (narrow)

  • Small number of people cannot catch HIV

5 Steps in Phage Replication (basic viral lifecycle) 

• True for ALL viruses 

1. Absorption/Attachment: binding of virus to specific molecule/receptor on host cell

2. Penetration (entry): genome/nucleic acid enters host cell 

3. Biosynthesis: viral components produced

   1. All viruses use host ribosomes! (Protein synthesis and translation (RNA → proteins)

4. Maturation (spontaneous): Assembly and completion of viral formation

5. Release (exit): viruses leave cell via lysis to infect other cells

• Burst time: time from attachment to lysis

• Burst size: # of viral particles released

• T4 Bacteriophage infects E. Coli = releases ~ 200 virions

Bacteriophage T4 (dsDNA) infecting Escherichia coli (gram neg. rod) 

• T4 produces lysozyme = weakens E. coli’s cell wall to allow viral tail penetration 

• LPS is a receptor for T4 on E.coli (gram negative) 

Lytic vs. Lysogenic → Lifecycle Stages

• Lytic Phase: makes progeny and lysis open the host cell → Happens under BAD environmental conditions

• Lysogenic Phase: DNA of the virus enters host cell genome. Every time the host cell divides and copies its genome, the viral genome is copied too

The Lytic Replication Cycle in Bacteriophages

• Maturation = spontaneous reaction but always in the same order!

Lysogeny: The Silent Virus Infection (LYSOGENIC CYCLE)

• Some DNA phages, called lysogeny or temperate phages, undergo adsorption and penetration but don’t replicate (only first 2 of lytic cycle)

• The viral DNA inserts into bacterial genome and becomes an inactive prophage

• The prophage is retained and copied during normal cell division resulting in the transfer of temperate phage genome to ALL HOST CELL PROGENY (Lysogenic cycle)

• Induction: activation of lysogenic prophage followed by viral replication and cell lysis

  • Causes = UV light/Chemicals/environmental cues

*Note: Lysogeny is longer than lytic = virus will stay in this cycle longer

The lysogenic cycle of bacteriophage in λ in E. coli

1. Absorption/attachment (both): Phage attaches to the host cell and injects DNA

2. Penetration (entry): Phage DNA circularizes and enters lytic cycle or lysogenic cycle (happens for both)

Step 3 is where we split off

• 3A: Biosynthesis/maturation: New phage DNA and proteins are synthesized and assembled into virions

• 3B: Integration: Phage DNA integrates within the bacterial chromosome by recombination, becoming a prophage

• 4A: Release: cell lyses, releasing phage virions 

• 4B: Lysogenic bacterium reproduces normally 

  • GOOD CONDITIONS: keeps dividing!

  • BAD CONDITIONS: Induction occurs (activation of lysogenic prophage followed by viral replication and cell lysis)

• 5B: Occasionally, the prophage may excise from the bacterial chromosome by another recombination event, initiating a lytic cycle

  • Temperatphage = do BOTH LIFECYCLES 

Lysogeny and its impact 

• Results in the spread of the virus without killing the host cell

  • LESS DEADLY form of parasitism

• IMPACT:

  • Phages can serve as transporters of bacterial genes from one bacterium to another = transduction

  • (2nd Mechanism) Allows bacteria to acquire new genes (transduction) = new proteins → New properties/new activities 

  • HGT = Conjugation, Transduction, Transformation 

Transduction by a bacteriophage

1. A phage infects the donor bacterial cell

2. Phage DNA and proteins are made, and the bacterial chromosome is broken into pieces

3. Occasionally during phage assembly, pieces of bacterial DNA are packaged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA

4. A phage carrying bacterial DNA infects a new host cell, the recipient cell

5. Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells

• Movement of genes from one bacteria to another by a virus → The amount of material is limited by the size of the capsid 

Examples of viruses that MMR vaccines protect against

• Measles: deadly, neurological effects, weakened immune system

• Mumps: Keeping men from having children

• Rubella (German Measles): Kills children in the womb, miscarriage, birth defects

Different types of Vaccines

• Getting the virus:

  • Getting infected

  • Virus can replicate

  • All the protein all the genome (RNA/DNA)

• Killed Vaccine

  • Grow the virus in tissue culture or eggs

  • Purify it → Kill it

  • All the protein all the genome

• Attenuated Vaccine

  • Grow virus

  • Purify it → DON’T kill it

  • Damage it or take some genes (People with suppressed immune system don’t take it)

  • Almost all proteins almost all genome

• mRNA Vaccine

  • Scientists gets sequence of viral genome

  • Make the mRNA to the spike protein

    • Lipid around mRNA → Ribosome to make spike proteins → Control the Poly A tail length

Coronavirus

• World Health Organization (WHO) names coronavirus “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2)

• Virus can be transmitted from animal to human (direct contact) and human to human (droplet) 

• Human-to-human transmission of virus is primarily through droplets that may travel up to 6-10ft from person to person!

  • Coughing, sneezing, or talking

• Virus can become aerosolized (airborne) and remain viable for up to 3 hours in the air

• Enveloped = easier to get rid of on surfaces!

Coronavirus Transmission

• Indirect transmission via a fomite (anything that you touch)  can occur since virus remain viable on surfaces ~3 days 

• Viral particles have been found in fecal samples but there is no evidence for fecal-oral transmission 

• Outdoors was safer = enveloped, RNA virus 

Positive ssRNA Viruses vs. Negative ssRNA Viruses

• NOTE: DNA viruses use ALL of the host cell stuff!

  • And all viruses use host ribosome for translation

• Positive ssRNA: Can go straight to the ribosome

  • Genome looks like mRNA

• Negative ssRNA: Must make complementary copy to make mRNA

  • Complementary to mRNA 

• BOTH negative and positive ssRNA use an RNA polymerase, which makes more mistakes than DNA polymerase = Viruses have a high mutation rate!

  • Genetic Drift: recombination of viruses from different species 

• 5’ methyl Gaumine Cap: lets ribosome recognize it as mRNA

  • Poly A Tail: longer it is, more stable the mRNA is  

Virus Characteristics (Spike (S))

• There are four main structural proteins, BUT the most important one is spike (S) glycoproteins 

• S proteins protrude from the viral surface resembling a crown, or corona! 

• The genome also codes for 16 nonstructural proteins that are involved in viral replication, maturation, and release 

NOTE: this slide has to do with SARS-CoV-2

• Belongs to genus β-coronavirus, family Coronaviridae 

• It is an enveloped virus with an unsegmented single stranded postive-sense mRNA (+ssmRNA) 

Entry into the host

• Portals of entry include

  • Nasal and oral passages

  • Conjunctiva of the eyes

• S-proteins on the viral envelope bind to angiotensin-converting enzyme (ACE2) on host cells. Which triggers either viral endocytosis, or membrane fusion and mRNA entry.

• ACE2: proteins present in many tissues (including lungs, kidneys, heart, arteries, and the gastrointestinal tract)

  • Functions: lower blood pressure, control fluid balance, and regulating the inflammatory response

Disease Manifestations (SARS-CoV-2)

• STAGE 1: Asymptomatic State: Incubation time (the time from exposure to first symptoms) median to 5 days, range 2 to 14 days

  • Virus can be detected and is shed by the host in droplets

  • Virus propagates, mild immune response initiated

• Up to 80% of COVID-19 cases are asymptomatic, but about 60% of COVID cases are transmitted from asymptomatic individuals

• ~18% of Covid infections are symptomatic and progress to stage 2

• STAGE 2: Upper Airway Response: Robust immune system - symptoms appear, which include cough, fever, shortness of breath, chills, muscle pain, loss of taste and/or smell, sore throat, nausea, diarrhea

• STAGE 3: Hypoxia (decrease of O2 to the body): progression to acute respiratory distress syndrome (ARDS)

  • Critical care/hospitalization

  • Pneumonia: difficulty breathing, persistent chest pain/pressure, confusion, inability to stay awake, bluish lips or skin 

  • Cytokine storm: leads to dramatic decrease in blood pressure, leaky blood vessels, formation of blood clots, organ failure

Disease Manifestation 

How mRNA COVID-19 Vaccines work

Coronaviruses, including the one that causes COVID-19, are named for crown-like spike proteins on their surface, which are key targets for vaccines.

mRNA is genetic material that tells your body HOW to make proteins

The vaccine is made of mRNA wrapped in a coating that makes delivery easy and keeps the body from damaging it

• Does not contain ANY virus

• Does not change your DNA

How does it work? The mRNA vaccine teaches cells to make spike proteins. Later, if exposed to the real virus, the body recognizes it and fights it off

Virophage

• Small virus that INFECTS VIRUSES

• Mamavirus when infected: Deformed and sickened/less infective

Mamavirus (2008) - infected by a virophage = sputnik

• Found in an amoeba in a water cooling tower

Prions

• Discovered by Stanley Prusiner

• Proteinaceous infections particle = slow/persistent/deadly neurological diseases

• Inherited and transmissible by ingestion, transplant, and surgical instruments

  • Transmissible spongiform encephalopathies: sheep scrapie’s, Creutzfeldt-Jakob disease, Kuru, fatal familial insomnia, mad cow disease

• BSE - bovine spongiform encephalopathy

Prions: PrP^c and PrP^Sc

• PrP^c :normal cellular prion protein, in brain and CNS

  • Fxn: Involved in regulation of cell death and cell differentiation

• PrP^Sc: scrapie protein (folded wrong); accumulates in brain cells, forming plaques/fibrils - serves as template = cause refolding of the normal PrPC proteins

  • Misfolds and makes everything else misfold

What is the difference between the normal protein vs. the prion?

• Conformational change = folded differently no longer functional

• VERY resistant to enzymes! = will stick around (major problem) 

• OUTCOME: neuronal damage in brain/CNS = DEATH OF THESE TISSUES 

Human SE - KURU

• Recognized in cannabalistic tribes in New Guinea

• Progressive, Fatal neurological disease

• Affects the CNS = mental derangement and loss of motor function

• If tribe member died the women prepared body for burial: women would eat the brain, and children ate the feet

Human SE - Creutzfeldt-Jakob Disease (CJD)

• Slow progressive dieases’s 

• Extremely rare disease (runs in families) 

• Usually person > 50 years old (unknowingly passes it on!) 

Other ways CJD is acquired (vCJD) 

• Corneal transplant, growth hormones, surgical instruments (electrodes in brain), and ingestion of prion contaminated beef (all contamination) 

Bovine (cattle) Spongiform (hole in brain = sponge) Encephalopathy (issues with brain) (BSE)

• Also known as Mad Cow Disease!

• First reported in Britain (1986) and linked to supplementing cattle food with bone meal and tissues of sheep!

• In 1981 (slow acting process) = change in manufacturing process of cattle feed.

• Eliminated treatment of feed with organic solvents = eliminated the important step that inactivated/destroyed prions

Prions resistant to and sensitive to

• FIRSTLY prions are transferred during corneal implants, by growth hormones from cadaver pituitaries, surgical instruments, or ingestion of contaminated beef

•  They are resistant to: formaldehyde, ethanol, proteases (enzymes), ionizing radiation, cooking to 662ºF!

• They are sensitive to: bleach, phenol, strong detergents, autoclaving (heat + pressure), organic solvents

• Dairy is fine because there is no nervous tissue present and gelatin is made from cattle products BUT is fully processed 

Plant Viruses and Viroids

• Enters through wounds or via insects! (clean saws b/n cutting plants)

• Viroids: infectious, circular ssRNA (not a virus)

  • Ex: potato spindle tuber disease or Avocado sunbloch viroid

• Very small piece of naked RNA

• ONLY associated with plant disease

Chronic Wasting Disease in Deer and Elk 

CWD is a fatal, neurodegenerative disease that affects deer, elk, and moose in North America. It is caused by a misfolded protein called a prion. 

Transmission: 

CWD is spread through direct contact with infected animals or their bodily fluids, such as saliva, urine, or feces. It can also be transmitted through contaminated soil or vegetation. (Deer hunters eating meat from elk/deer 

Comparisons of Viruses, Viroids, and Prions to Bacterial Cells

Filamentous Helical (Virus Shape)

• Rigid Helical: Tubalovirus

• Flexible Helical: Ebola

  • Only a couple pics because not a lot of people want to work with it

Icosahedral (Virus Shape)

• Icosahedral: Adenovirus

  • Spike proteins (pleplomere)

Enveloped 

• Enveloped = Herpes and smallpox 

• The envelope is taken from the host cell! 

Head and Tail (complex)

• Complex = Bacteriophage

  • Viruses that only infect bacteria

  • T4 phage

  • lamba phage

Enveloped Viruses - Bacteria and Animal Cells

• Bacteria, plants, fungi and protists cannot have enveloped viruses!

  • This is due to their cell walls!!

• Animal cells can have enveloped viruses due to only having cell membranes and no cell walls