Week 7 Class 15: How virus spread and cause disease (MICRO)

virus

• is a noncellular particle with a genome contained by a capsid (protein coat).

the term virus refers

• to the particles and their replication cycle

The term virion refers

specifically to the structure of the virus particle

virus and reproduce ability

• he virus takes over a cell to manufacture progeny (offspring). 

  • Viruses require a host cell to reproduce. 

cells vs virus

• nlike cells, some viruses (such as HCV) have a genome of RNA. Other viruses (such as herpes) have DNA genomes.

  • RNA viruses have high error rates during replication and therefore high rates of mutation

• They are not considered to be prokaryotic or eukaryotic because they are acellular

• Every kind of cellular organism known (including bacteria) can become infected by viruses!

In general, viruses evolve at different levels.

within a host community

within a virus species pop.

within a indivisual organism

Within a host community: virus evolve

• Evolve to infect different species

• Example: equine herpes in horses vs. murine herpes in mice

Within a viral species population: viruses evolve

• Strains evolve that vary in infectivity and virulence.

• Closely related viruses may cause diseases that are similar (herpes simplex viruses 1 and 2) or different (varicella-zoster vs. cytomegalovirus).

Within an individual organism: viruses evolve

• Viruses evolve variants that resist therapeutic agents. 

• Example: Hepatitis C and HIV evolve into diverse strains that infect different tissues within the host.

How do viruses find their host cell, subvert its defenses, and take over its metabolism?

Contain diverse mechanisms for infection and replication

All viral replication cycles must achieve the following:

Host recognition and attachment

Genome entry

Assembly of progeny virions

Exit and transmission

Host recognition and attachment

• Contact and adhere 

  • host cell must have the virus’s specific binding protein surface receptors

Genome entry

• Viral genome must enter host cell and gain access to cell’s machinery for gene expression

• injection of genome or total engulfment then uncoating to reveal genome

Assembly of progeny virions

• Expression and virion assembly

  • These components usually “self-assemble”

Exit and transmission

• Budding or cell lysis

  • Following lysis or budding they must reach new host cells to infect

  • Eventually spread from one host to another through transmission

Binding is Important For Viral Replication!

• A virus needs to contact and attach to the surface of an appropriate host cell

  • Virus will have evolved to take over specific host cells

Viruses specifically bind to a

surface receptor

surface receptor

• are proteins on a host cell surface that is specific to the host species and binds to a specific viral part

  • Example: The tail fibers of Bacteriophage T4 specifically bind to the bacterial cell-surface lipopolysaccharide (LPS)

    • Can it bind to Gram-positive cells?

      • No, they lack LPS on their cell surface

• Often the surface proteins on host cells that viral surface receptors bind to are proteins that are important for other purposes in the cell

Bacteriophages

• interact with bacteria in all ecosystems and help:

  • Decrease population density

  • Increase host density

  • Transfer genes amongst diverse bacteria

what do phages do

• Inject their genome through the cell envelope in bacteria into the cytoplasm, avoiding the cell wall
  
  

• Following injection, the sheath of the phage neck tube contracts, bringing the head near the surface to insert its DNA
  
  

• The pressure of the spooled DNA is released, expelling the DNA into the cell
  
  

• After inserting its genome, the phage capsid remains outside, attached to the cell surface

Lytic infection

lysis (rupture) of host cell following the assembly of new phage particles

Lysogeny

• Rather than break out of the cell some bacteriophages want to become part of their host cell’s genome

  • Phage genome integrates in host cell

Prophage

•  bacteriophage genome that has been integrated into the DNA of a bacterial cell, essentially becoming part of the bacterial chromosome

• Whether the bacteriophage undergoes the lytic or lysogenic cycle can depend on the proteins that bind DNA and repress the transcription of genes needed for virus reproduction

Virulent phage:

bacteriophages that reproduce entirely via the lytic cycle

Temperate phage

phage that can undergo lysogeny

Viruses must be cultured in

a host cell

Any virus culture system must be a double culture of host cells plus viruses

bacteriophages are grown in

batch culture

batch culture

• Culture in an enclosed vessel of liquid medium that enables growth of a large population of viruses for study

• A phage sample is usually inoculated into a growing culture of bacteria that is sampled over time and assayed for phage particles

Culturing viruses: one-step growth curve

• Complex

  • Need host cells, phage, and high-powered microscopes

• Multiplicity of infection must be reached

  • MOI = every host cell infection

Eclipse period

• Undetectable in medium while phages are replicating in host cells

• Rise period

  • Phage particles start to appear.

  • visible using electron microscopy

burst size

can measure to determine rough concentration of phage particles

• divide concentration of progeny phages by the original concentration of the host cells

Culturing viruses: plaque assay

• Plaques are clear areas on a plate inoculate with host bacteria and bacteriophages capable of lysing their surrounding host cells
  
  

• The number of phages produced per infected host cell is called the burst size

Immortalized cell lines

• contain cells that can divide indefinitely (often due to a cancer-driven mutation) and be cultured for extended periods of time outside of the body

To culture animal viruses these cells are inoculated with virus suspension

• Viruses adhere to cells.

• Culture fluid is removed.

• Fluid is replaced by a gelatin medium that halts the dispersal of viruses from infected cells.

• When host cells die, plaques are observed.

Unique Medical Viruses

• Human papillomavirus (HPV)

• Influenza A Virus

• SARS-CoV-2 (Coronavirus or COVID-19)

• Human Immunodeficiency Virus (HIV)

Case History: Genital Warts from a Virus

1. HPV infects basal cells, where it remains dormant

2. karatinocytes differeniate vorus replcation is activated

3. shedding cellls release hpv virons

4. hpyv intergation into host genome may transform cells into cancer

Papillomavirus: DNA Genome: human papillomavirus (HPV)

• In the United States, HPV infects 80% of adults

  • Cervical cancer HPV link

    • Harald zur Hausen – Nobel Prize in Physiology 2008

  • Also linked to cancers of the penis and anus

HPV strains are highly infectious

• Sexual contact, including oral contact leading to throat cancers

• normally symptomless, not regularly tested for

• symptoms include genital warts that are contagious 

Human papillomavirus (HPV): pervention

• Condoms – partial

• Gardasil – vaccine, greater protection

  • Only effective before first exposure to HPV

  • Girls and boys ages 11–12

  • Protection against four prevalent strains linked to cervical cancer

Human papillomavirus (HPV): treatment

• exist to help with symptoms but aren’t able to clear the virus

• low risk strains may be cleared by the immune system naturally over time

Papillomavirus: DNA Genome: Narrow tissue tropism

Strains infect specifically the skin or the mucous membranes depending on the cell surface protein receptors

Some HPV strains use

• heparan sulfate proteoglycans (HSPGs) as their cell-surface receptor 

HPV gains access to the actively dividing cells of

• the basal layer (deepest layer of the epidermis) usually because of tiny wounds in the tissue

  • Virions are then endocytosed by basal cells 

  • Once inside, HPV does not replicate until basal cells start to differentiate into keratinocytes

  • As these keratinocytes reach the surface of the skin and slough off, progeny virions are shed

In other infected cells, HPV virions become latent and persist in the cell for months to years

• Potentially causes abnormal growths like warts and cancers

• Specific strains cause skin warts, genital warts, or cancer
  
  

Papillomavirus: DNA Genome: small icosahedral voruses

• Symmetrical

• Circular, ds DNA 

  • 8,000 base pairs

    • Encoding eight genes

• Overlapping reading frames

reading frames

• represent the three different ways that an RNA sequence can be read to define triplet codons

• Allows partial overlap of gene information and maximizes the efficiency of the information content in the shortest possible genome

• Often eliminated by the immune system

  • No known drug therapies to date

Papillomavirus Replication Cycle

1. The virion binds to cell-surface receptors and becomes endocytosed by the cell

2. The virion docks onto the nuclear membrane

3. Genome is uncoated

4. The viral DNA uses host polymerases for transcription

5. Translation takes place into the cytoplasm

6. Translated capsid proteins return to the nucleus for assembly into progeny virions

7. Shedding of epithelial cells release virions

   • If HPV instead remains infected in basal cells, they can transform host cells into cancer cells

Virus with an RNA-based genome have

• High mutation rates because their RNA-dependent RNA polymerases lack proofreading!

• Their (+) genome can be translated directly by ribosomes to make proteins

  • Unlike influenzas which must be copied to complementary strand RNA before synthesizing proteins as they are (-) strand

• Known to cause respiratory infections of humans

  • Certain strains can cause an epidemic of more severe disease

What is SARS-CoV-2?

• Very commonly spread in congregate living facilities

  • To avoid the spread of COVID-19 originally these congregate facilities (nursing homes, schools, in-person businesses) closed or limited the amount of people allowed in the facility

  • Social distancing!
    
    

• While the pandemic caused by SARS-CoV-2 is “technically” over, this virus (which causes COVID-19) still spreads in our communities and is an endemic seasonal disease
  
  

• Just like it is recommended to get a yearly flu shot, it is recommended to receive a yearly COVID-19 booster

  • Like the flu, the stains of SARS-CoV-2 causing COVID-19 change per year/season

COVID-19 Statistics

• Since the start of the pandemic in 2020, in the United States there has been:

  • Over 100 million confirmed cases

    • Likely more- why do you think that is?

  • Over 1 million deaths

Considered to be a primary pathogen

• Both direct and indirect transmission

• Treated using antiviral medications like Paxlovid 

covid 19 symptoms

• Fever or chills, cough, shortness of breath, sore throat, loss of smell or taste, fatigue, muscle aches

• Serious infections include respiratory distress, chest pressure, confusion, pale/blue skin

SARS-CoV-2 Coronavirus Structure  

• +) strand RNA

  • genome can be directly used as mRNA to make viral proteins

• Contains core particle of RNA packaged in proteins (nucleoprotein complexes linked by RNA) with a surrounding envelope and spike proteins.

• "Crown" of spike proteins inspired the name corona (Latin for crown).

  • Spike proteins are a target of the COVID-19 vaccines and boosters

SARS-CoV-2 Replication Cycle

1. Spike protein attaches to ACE2 receptor found on cell surface

2. Enters cell and uncoats to reveal strand of genomic (+) RNA

3. RNA genome translation makes polyprotein (Paxlovid inhibits this step)

4. Protease cleaves polyprotein, making the enzyme RNA replicase

5. “Viral factory” is made from endoplasmic reticulum

6. 6.RNA replicase-transcriptase makes (-) strand RNA

   
   
   

   7.  RNA replicase-transcriptase makes viral mRNAs and progeny (+) genomic RNAs, which then become capped mRNAs via enzymes

   
   
   

   8. mRNA translation to viral proteins occurs

   
   
   

   9. New virions are assembled then secreted out of the cell via the Golgi apparatus and exocytosis

   
   
   

Influenza Virus Traits

• Orthomyxovirus family

  • Virus that consists of three types (species): A, B, and C

  • Virus that causes influenza

• One of the most common life-threatening viruses in the United States

influenza virus effects

• Infects cells of the upper respiratory mucosa

  • Causes fever, sore throat, headache, and other symptoms

  • Influenza A infects roughly 10% of the US population yearly causing about 36,000 deaths annually

  • Elderly people are most susceptible but epidemic years allow mortality to rise in younger people

• Influenza strains have envelope proteins that continually mutate, evading the host immune system

• New strains emerge annually – “seasonal flu”

• Vaccines only good for 1 year because of this

• Can sometimes mutate to become a pandemic

  •  1918 last time this occurred

Influenza Virion Structure: reassortment

• between human and avian strains causes antigenic shift

  • Reassortment is the process by which genome segments come together from different influenza strains infecting the same host cell 

Antigenic shift-

• genes reassort from two or more different influenza viruses

  • Essentially creates new strains of influenza virus

  • Can cause pandemics

Antigenic drift

• he occurrence of small mutations that continually generate slightly different forms of a particular virus

Influenza Virion Structure 

• Segments from different strains reassort by coinfection of a host cell.

• No fixed capsid
  
  

• Genome

  • (–) sense RNA

  • Eight chromosome segments that each contain a different essential gene

  • These RNA segments can undergo reassortment

    • Can easily change host type because of this

    • Less than 1% of influenza particles are capable of causing infection

• Enveloped by viral proteins

  • Hemagglutinin (HA)

  • Neuraminidase (NA)

  • Influenza A strains classified by subtypes due to composition of HA and NA on the viral surface

  • Example: H1N1
    
    

• RNA-dependent RNA polymerase

  • Brings to host cell to start transcription

  • Used for synthesis

Influenza Replication Cycle

1. An influenza A virion attaches to a cell by its HA envelope protein binding to a host protein

2. Virion uptake and lysosome fusion occurs

3. (-) RNA and RNA-dependent RNA polymerase are released and enter the nucleus

4. Transcription is primed by caped host mRNA

5. (+) mRNA translation occurs

6. (+) mRNA translation: envelope proteins enter ER and Golgi for transfer to cell membrane

7. NP packaging proteins return to nucleus

8. From (+) RNA, make (-) RNA genomes to package into virions

9. Viral RNA genome segments bind NP packaging proteins and exit nucleus

10. Virion assembles, including matrix and envelope

11. Neuraminidase (NA) cleaves host receptor, releasing virion to bud out

Human Immunodeficiency Virus (HIV)

• HIV is the causative agent of acquired immunodeficiency syndrome (AIDS)

• HIV is a lentivirus

• 33 million people globally are estimated to be living with HIV

  • 3 million people die of AIDS annually

• Can be spread through high risk behaviors like unprotected sexual contact and sharing needles

  • Can also be spread through contaminated blood and breast milk

Lentivirus

•  is a retrovirus that causes infections that progress slowly over many years

During initial HIV infection, an immune response is generated that leads to

• a rebound of T cells and a reduction of virion particles. 

  • Immune response does not prevent the next phase of HIV infection, which is the slow and steady loss of T cells until a level is reached at which the immune system fails (shows symptoms of AIDS)

  • Leads to opportunistic infections

• Initial infection often goes unnoticed because they may not have any symptoms or just mild symptoms

HIV Structure

• HIV structure

  • Lentivirus

    • Retrovirus

      • Retroviruses are viruses that use RNA instead of DNA as its genetic material

  • Capsid

    • Conical-icosahedral

      • Unusual shape

  • Enveloped

    • Spike proteins

    • Binding target CD4 and CCR5 cell-surface proteins on T lymphocyte cells 

  • Reverse transcriptase

    • Enzyme

      • RNA template to synthesize DNA

    • High error rate

      • Can cause mutations that lead to resistance to antiretroviral drugs and causes immune system evasion

• While there is no cure or vaccine, it now can be effectively treated by using a combination of different antiretroviral drugs at the same time

HIV Replication Cycle- Part 1

• HIV adheres to T-lymphocytes by attaching to CD4 and CCR5

• The envelope fuses with the cell membrane of the T cell

• HIV core directly released into the cytoplasm without endocytosis

• The two-RNA genome copies are then reverse-transcribed to form double-stranded DNA

• dsDNA copy of the HIV genome enters the nucleus through a nuclear pore where it integrates as a provirus at a random position in a host chromosome

  • This ensures permanent infection in the host

• The entire length of the integrated HIV genome is transcribed to RNA by the host RNA polymerase II

HIV Replication Cycle- Part 2

• Some of the RNA copies exit the nucleus to serve as mRNA translation to proteins
  
  

• Proteins are synthesized to alternative versions and then broken down into to smaller active proteins by viral protease
  
  

• Some full-length RNA transcripts exit the nucleus to be packaged as genomes for progeny virions

• Envelope proteins are made within the endoplasmic reticulum
  
  

• These proteins pass through the Golgi for glycosylation (adding sugar chains) and are exported to the cell membrane
  
  

• As the membrane envelope proteins interact with the core particle as it forms from the RNA dimers and gene peptides
  
  

• Virions bud out from the host cell

HIV Replication Cycle 

HIV titer increase and T-cell decline over time

Antiretroviral drugs target important points in the replication cycle.

Key Characteristics of Viral Pathogenesis

• Viruses “float” in our environment until they encounter a suitable target cell

  • If the host cell has the correct surface receptor the virus can attach then infect the host cell

• Viruses take over host cells to replicate themselves

• Once in a host cell viruses do not need to do the following because the host cell does it for them:

  • Transport nutrients

  • Expel waste

  • Generate energy

• Viruses damage and debilitate host cells

  • Lysing cells to release progeny

rhinovirus.

• The common cold is caused by several different types of viruses, including more than 100 known serotypes of rhinovirus. 

  • Nonenveloped, single-stranded, positive-sense, RNA virus

  • Antibodies that neutralize one strain of rhinovirus will not neutralize a different strain.

  • Cause disease by infecting the respiratory tract and releasing bradykinin and histamine

    • Cause fluid loss from local blood vessels

    • Can alter the ability of immune cells leukocytes to move through blood vessels

Influenza

• Infection proceeds differently from rhinovirus infections. 

  • Targets and kills mucus-secreting, ciliated epithelial cells (destroys primary defense)

  • Can cause the shedding of bronchial and alveolar epithelium in the lungs

    • Compromises oxygen and carbon dioxide exchange making breathing difficult

  • Can trigger the release of molecules from immune cells that cause symptoms like headaches and muscle aches

  • Can cause lung inflammation that leads to respiratory failure

  • Can cause secondary infections

Antigenic variation: rhinovirus vs influenza

• 100 known serotypes of rhinovirus; each virus has a unique capsid protein. Antibodies to one capsid protein are not effective on another.

Antigenic shift: rhinovirus vs influenza

• two strains of influenza virus infect the same cell and the genomes get mixed. This makes a dramatically different virus.

Antigenic drift: rhinovirus vs influenza

random mutations can occur within the cell that a virus infects, creating small changes in virus proteins.

Human Immunodeficiency Virus 

what happens

• HIV binds to CD4 receptor on T helper cells as well as the chemokine receptor CCR-5.

• HIV inhibits apoptosis in T cells and allows the cell to survive longer to make more virus.

Human Papillomavirus 

what does it do

• Infects skin cells causing them to divide excessively

  • Some strains can cause warts

    • Found on the feet, hands, vocal cords, mouth, and genital organs

• Excessive cell division due to self-preservation

  • The more often HPV makes cells divide, the more often HPV particles can be made

• HPV can stimulate host cell division in multiple ways

  • Synthesize protein caused E7 that inactivates a protein in host cells called pRb that limits cell division

Latent Herpesvirus

• Can cause diseases like cold sores, genital herpes, mononucleosis, and some cancers

• Rapid replications in epithelial cells

• Human herpesviruses and latency

  • After a primary infection, human herpesviruses become latent in host cells (nerve cells or white blood cells).

    • DNA circularizes and exists as an episome.

    • DNA integrates into host cell genome.

  • Latent virus can reemerge after years of latency and cause a new active infection. 

  • Small RNA molecules called microRNAs (miRNA) made by herpesvirus interfere with the host cell’s apoptosis program

Infections of the Central Nervous System

• Some viral infections primarily affect the central nervous system (CNS)

• Infections of the nervous system can be devastating due to the importance of the CNS in everyday functions

Central nervous system (CNS)

• Controls and coordinates everything 

• Includes the brain and spinal cord

Peripheral nervous system (PNS)

• Collects and transmits data from the body 

• Includes spinal nerves and neurons

Sensory neurons:

•  send signals from the sensors in the periphery to the CNS

Motor neurons

•  send signals from the CNS to the periphery

How do we diagnose infections found in the CNS?

Lumbar puncture

Overview of CNS diseases

• Pathogens invade other tissues, then travel to the CNS.

  • Bone, eyes, sinus, or ears

• A few directly infect the CNS from the blood.

common s and s w cns disease

• Headache

• Dizziness

• Fatigue

• Determination of pathogen type can be difficult.

cns disease: menigitis

• inflammation of the meninges 

  • Causes severe headache, fever, and confusion

cns disease: encephalitis

• inflammation of the brain 

  • Causes problems with cognitive, sensory, and motor functions

Primary encephalitis: cns disease

microbe directly infects the brain.

cns disease: Secondary encephalitis:

• microbe spreads from an infection of the meninges to the brain tissue.

Viral infections of cns

• Most common pathogen of the CNS 

• Treatment is supportive. 

• Aimed at reducing inflammation

• Bacterial, fungal, and parasitic infections

of cns

• Less common but often more severe

• Antibiotics, antifungals, or other drugs are often used to limit pathogen growth.

• Vaccination is best for prevention but is not available for every disease.

Viral Encephalitis

• Rabies

  • RNA virus, bullet-shaped

  • Zoonotic disease

  • Neurotropic 

    • Prefers to replicate in nerves

Viral Encephalitis: three forms

• Encephalitic 

• Paralytic 

• Atypical 

Viral Encephalitis: treatment

• Immunoglobulin

• Rabies vaccine

Viral Encephalitis: Mosquito-borne encephalitis

• Eastern equine encephalitis (EEE)

• Transmitted from bird to bird by mosquitoes

• Can also be passed to horses and humans

• Rare, but has a high rate of fatality (35%)

Viral Encephalitis:West Nile encephalitis (WNV)

• Transmitted in bird populations 

• Most infected patients do not develop disease.

• Usually causes a flu-like illness, but some develop encephalitis

Viral Meningitis 

• Normally not as severe as bacterial meningitis

• Called aseptic meningitis as CSF fluid is clear

Lymphocytic choriomeningitis virus (LCMV)

• RNA virus

• Household mice are a reservoir.

• Causes elevation of lymphocytes in the CSF

viroids

• are virus-like infectious agents in which an RNA genome is itself the entire infectious particle.

  • There is no protective capsid.

  • Most infect plants.
    Some infectious agents are so limited in content that they can’t even be considered “true” viruses

• Consists of a circular, single-stranded molecule of TNA that doubles back on itself to form base pairs interrupted by short unpaired loops

  • Avoids being broken down by host RNase enzymes

• Prions

• No nucleic acid

• Abnormal form of a brain protein(Prp^c)

  • The prion form of the protein acts by binding to normally folded proteins of the same class and causes them to misfold

  • Prion-caused cell death leads to tissue deterioration and dementia

• Inherited or transmissible

  • Creutzfeldt-Jakob (mad cow disease)

    • Bovine prion so close to a human protein that it caused misfolding of human brain proteins

    • Bovine prion came from consuming tainted beef

  • Scrapie

    • Brain disease of sheep

  • Kuru

    • Caused by eating the brains of dead relatives!