Virology exam 1

How can viruses be harmful

Cause disease in humans, animals, plants (e.g., influenza, HIV, rabies, crop failures). Can trigger pandemics and major economic losses. Sometimes lead to cancer (oncogenic viruses like HPV, EBV)

how can viruses be benefical

Used in gene therapy (vectors to deliver healthy genes).Basis for vaccines (attenuated or viral vector–based). Used in phage therapy to kill antibiotic-resistant bacteria. Contribute to ecological balance by regulating populations of microorganisms.

Define Zoonoses

diseases naturally transmitted from animals to humans (e.g., rabies, influenza, SARS-CoV, Ebola).

Variolation

deliberate exposure to material from smallpox sores (usually scabs or pus) to induce a mild infection and immunity

History of variolation

Practiced in China, India, and the Middle East centuries ago.
Introduced into England in the early 1700s by Lady Mary Wortley Montagu.
Risky: could cause severe disease or spread smallpox.
Replaced by Edward Jenner’s vaccination with cowpox (1796), which was safer.

Attenuation

 process of weakening a pathogen so it loses ability to cause severe disease but can still stimulate immunity.Achieved by repeated passage in non-human hosts or cell culture.Basis for live attenuated vaccines (e.g., MMR, Sabin polio).

list koch postulates

1. The microorganism must be found in all cases of the disease.
   
   

2. It must be isolated and grown in pure culture.
   
   

3. The cultured organism must cause disease when introduced into a healthy host.
   
   

4. The same microorganism must be re-isolated from the experimentally infected host.
   
   

(Note: strict postulates don’t always apply to viruses since they require host cells.)

definite properties of viruses

Obligate intracellular parasites, Contain DNA or RNA, but never both., Genome is surrounded by a protein capsid (sometimes with a lipid envelope).Lack metabolic machinery (no ribosomes, no energy generation).Multiply only inside living cells by taking over host machinery.Produce progeny virions that can infect new cells.

method of hershey chase experiment

Used bacteriophages (viruses infecting bacteria).
Labeled DNA with ³²P (phosphorus isotope).
Labeled protein coat with ³⁵S (sulfur isotope).
Allowed phages to infect bacteria.
Used blender + centrifuge to separate viral coats from infected cells.

results and conclusions of hershey chase

 Radioactive DNA entered bacterial cells; protein did not. So DNA not protein is genetic material

characteristics of classification system for classificatipn

• Based on observable virus properties (before molecular methods):
  Nature of the host (animal, plant, bacteria).Type of disease caused.Viral morphology (size, shape, presence of envelope).
  Physical/chemical properties (stability, sensitivity).Mode of transmission.

Baltimore classification

Classifies viruses by genome type and replication strategy (how mRNA is made).

the 7 Baltimore classes

dsDNA, ssDNA, dsRNA, +ssRNA (directly used as mRNA), –ssRNA (must make +RNA first), ssRNA-RT (retroviruses; RNA → DNA via reverse transcriptase), dsDNA-RT (e.g., Hepatitis B; DNA with RNA intermediate)

properties of viral propogation

• Require living host cells for replication.

• Exhibit host specificity (infect certain species or cell types).

• Involve an eclipse phase (no infectious virus detectable inside cell).

• Produce large numbers of progeny rapidly.

• Spread via cell lysis, budding, or cell-to-cell transmission.

 steps of the infectious cycle

1. Attachment and entry
   
   

2. Production of viral mRNA
   
   

3. mRNA translation by host ribosomes
   
   

4. Genome replication
   
   

5. Assembly and release of virus particle

Describe the process of viral attachment

Virus collides with a cell by Brownian motion (chance)., Susceptible cells have the correct receptor that allows binding.
,Binding is the first step before entry and infection

Susceptible cell:

 has receptors for viral attachment

Permissive cell:

allows viral replication once the virus has entered.

viral pathogenesis

the process by which viruses cause disease.Depends on virus-cell interactions, host defense responses, and spread to other hosts.

Primary cell lines:

Limited lifespan (5–20 passages).Retain differentiated state. Used for vaccines to avoid oncogenes.

Transformed cell lines

Propagate indefinitely. Derived from tumors or transformed by tumor virus/mutagen. Less differentiated, often aneuploid. Lose contact inhibition.

Define CPE and examples

changes in cells due to viral infection such as:Cell rounding, detachment, lysis. Swelling of nuclei. Formation of syncytia (fused cells). Inclusion bodies

3 methods for viral propagation (cultivation)

cell culture, embryonic eggs, live animals

cell culture

common shows CPE

embryonic eggs

influenza vaccine production

live animals

historical use now mainly for resarch

infectious particles

capable of initiation infections

Non-infectious particles

Present physically, but damaged mutated or incomplete so cannot establish infection

Viral tirer

Concentration of a virus and sample this is determined via serial dilution plus infection assays (plaque focus transformation and point dilution)

Describe the steps of plaque assay

1.viral dilutions incubated with mono layer cells 2.virus absorbs inoculum removed 3. cells are covered with gel restricts the viral spread for overtime infected cells dies4. clear zones are Plaques fix and stain

Calculate pfu/ml of 50 plaques from 10^-6 with 0.1 ml plated

50\(10^-6×0.1)

Describe a transformation essay

Some retrovirus do not form plaques instead infected cells lose contact, inhibition, and grow into foci. viral concentration is measured as a focus forming units per millimeter

Describe an endpoint essay and how to calculate TCID 50

Youth for viruses that do not form plaque serial dilution are inoculated into replicate cell cultures, eggs, and animals infection detected by CPE the end point dilution at which 50% of test units are infected and they reported as TCID 50

Explain particle/PFU ratio

Ratio of total viral particles measured physically to infectious particles PFU not all particles are infectious due to damage mutation or inefficiency ratio varies by virus important and experiments

Physical methods for detecting, viral particles and component

Electron microscopy live cell imaging hemagglutination detection of viral enzymes, immunological methods nucleic acid detection

Biological method for detecting, viral particles, and components

Measure infectious particles, plaque, essay, and point dilution, and transformation essay

Burst concept

Refers to the viral replication strategy. It is a two phase process. The first part is makes spiral components the second part assembles into a giant viral particle, then burst from the cell and then the cell capacity limitations depend on metabolic resources number of replication site regulation of viral release and host defense.

Typical burst size of a bacterial phase of bacterial cell

150 viral particles for sale

Viral infection of a eukaryotic cell burst size

10^ 3–10 ^4 particles for sale

One step growth cycle

Synchronous affection it adds virus rapidly growing cells allows, absorption that dilute to prevent further absorption as a single replication cycle, which is measured over time shows lips and latent periods, clearly used to timing of the viral replication effects

Two step growth cycle

Low MOY multiple cycles of viral replication occur shows exponential increases new progeny in fact, remaining cells. Multiple rounds of infection and replication demonstrates how virus spreads through population.

Eclipse period

Complete loss of ineffective for 10 to 15 minutes after initial virus edition reason viral nucleic acid is uncoded and no infectious virus can be detected inside the cells. This represents the time when the Geneo is being replicated with the particles are assembled.

Latent period

No extra cellular virus can be detected. It takes time to replicate the symbol and release new virus particles before license and it’s longer than the eclipse.

MOI or multiplicity of infection

Ratio viral particles to cells

How to calculate for MOI

Number of viral particles over a number of cells

MOI follows what kind of distribution

Poison statistic to a random collision of viral particles with cells

Nucleic acid types

DNA or RNADNA with short segments of RNA or DNA and RNA with covalently attach proteins

Strand types, m

the positive strand, the negative strand and the ambience strand and then you also have double strands

Physical forms of viral genomes

Linear or circular it can be segmented or non-segmented and gapped, which is partially double stranded

Ambience

A single strand of RNA that contains both positive and negative strain information, different regions of the same RNA molecule service templates for different genes. It requires viral RNA dependent, viral RNA to transcribe both orientations for example, some negative strand RNA viruses have an ambience segment.

Class one Baltimore

Double-stranded DNA or dsDNA has 32 families of linear or circular and uses a host or viral DNA dependent DNA polymerase

Class two of Baltimore

Single stranded DNA or ssDNA must convert dsDNA before transcription uses host DNA polymerase

Baltimore class three

Double-stranded RNA or DSRNA segmented gnomes cannot translate dsRNA directly uses viral RNA dependent RNA polymerase

Class 4 Baltimore

Positive single-stranded RNA most abundant type can be translated directly by host ribosomes genome serves mRNA

Class five Baltimore

Negative single strand RNA must first copy positive mRNA requires viral RNA dependent RNA polymer can be segmented or non-segmented

Class six Baltimore

Positive single stranded RNA with DNA intermediate retroviruses uses reverse transcript to make DNA intermediate

Class seven Baltimore

Gap DNA partially double stranded uses reverse transcripts must repair graphs before transcription

Reassortment

Genetic combination, mechanism and segmented viruses were two different viral strains con infect the same cell genome segments mixed during replication/assembly progeny viruses contain segments from both parents creates new combinations of genetic material important for influenza virus evolution and pandemic emergence for example, influenza has gone a Gino segment that we can re-sort

Two ways to manipulate viruses

Original method or modern method

Original method

Viral stock plus Mugen plaque, isolation, which you pick out individual plaque and study mutants and then random mutant Genesis, where you create various types of mutations

Modern method

Molecular biology techniques to engineer specific mutations types of mutations, deletion insertion substitution nonsense manipulation can add/remove entire jeans and then you have targeted approach precise control for changes

Transfection

Introduction of the viral DNA or RNA into cells with the goal of obtaining viral reproduction it rescues infectious virus from clone, genetic material and challenges for RNA viruses which are less stable and harder to introduce in DNA. You can apply this to study. Gene function, create mutant, viruses and resurrect historical viruses like 1918 influenza and often uses multiple plasma containing different genome segments for segmented viruses.

Structural proteins

Capsid envelope, glycoproteins, or specialized proteins

Captured proteins

For the protein shell that protects the viral genome

Envelope Glycoproteins

Ectodomain functions attachment to host cells antigenic sites and membrane fusion we also have internal domain functions which is virus assembly form all the metric spikes on the viral service

Specialized proteins

Proteins with specific rolls in large complex capsules like adenovirus fibers assembly proteins that help organize viral particle construction

Metastisible

Refers to the unique energy state of virus particles that have not attained a minimum free energy confirmation existing higher energy states that requires surrounding unfavorable energy, barrier energy stored in the virus particle during assembly. The stored for potential energy can be used for disassembly with the cell provides proper signals and must be stable enough to protect the genome yet unstable enough to become a partnering infection.

Methods for examining viral structure

Electron microscopy, x-ray crystallography electron microscopy nuclear magnetic resonance apectrscopy

Electron micro

1940s uses negative staining with electron dense materials (Italy’s acetate) and the resolution is 50 to 75 angstorms, limited, detailed structural interpretation

X-ray crystallography

Requires crystallization of milligram amounts of virus produces defraction patterns analyzed by computer

Cryo-electron microscopy

Freeze samples and equate solution, preserves native structure, better than traditional EM

Symmetry rules for self assembly

1. each sub has identical bonding contracts with its neighbors

2. The bonding contracts are usually non-covalent that allow for assembly, and that is reversible enables every free assembly process and permits disassembly when needed for infection

VLP‘s

Many capsid did proteins can self assemble into VLP without containing viral, genetic material HPV vaccines made from VLP is produced yeast HPV vaccines from VLP technology and maintain the structure and antigenic properties needed to simulate enemy response without the risk of an actual infection

Helical symmetry

The shape is rod shaped assembly code, protein, molecules, engage identical, equivalent interaction to each other in the viral genome the structure forms, large stable structures from single protein, subunits genome interactions between capsule proteins, and burrow genomes animal viruses with helical symmetry are always developed and influence of viral Neuro Capi

icosehedr symmetry

Spherical/round viruses based on ice Cohron proteins, arranged as hexamers and pentamer and are always in multiples of 60 can form close shelves with minimum of 60 identical subunits less direct interaction between the cap and the genome and Aidan associate

Key difference between helical and Icosehedral

Chemical symmetry creates rod shaped structures with direct protein genome interaction while the other creates vehicles structures with a defined amount of subunits, arranged, mathematically precise

Steps of viral attachment, and entry

1. Adhere to the soul surface via electrostatic interaction

2. Attached the specific receptor on the cell surface to more than one receptor may be involved initial reaction maybe with the extra cellular matrix

3. Transfer Jena to wholesale entry mechanism is very virus type

Where is non-developed viruses bind to cells

Attachment via surface features (canyons plateau loops) to attachment via protruding (adenovirus fibers), Attachment via glycolipids(polygons)

Receptor that fits into the groove of Icosahedral capsids

Polio virus binding CD 155 receptor

Receptors binding n platue of icosahedral capsid

Human rhinovirus type 2 binding ldl receptor at 5 fold axis of symmetry

Protruding fiber attachment of icosahedral capsid

Adenovirus knob(turner) binding CAR receptor

How enveloped viruses bind to cells

Transmembrane glycoproteins: protrude from viral envelope, specific bounding domains for cellular receptor, often require multiple receptor interactions, may undergrad conformational changes

Hemagglutin

Protein bines cyclic acid residues on integral membrane, glycoproteins, low affinity individual interactions, but many interactions create high overall

Nia Mendes

Clefs psychic acid linkages to facilitate virus release and spread

HIV

Initial heparin sulfate proteoglycans primary receptor CD4 induces the confirmational change cover receptor CCR5 binding results in membrane fusion

SARS CoV-2

Spike protein binds to ACE2 receptor

Viral entry movement in cells

Ours are too large to diffuse they use cellular transport machinery can, and proteins entry can occur with plasma membrane, or after endocytosis

Transport mechanisms of virus entry and movement and cells

Active transport along side of cytoskeleton, preceptor meeting, endocytosis and the direction fusion of the plasma membrane

General fusion process

1. Virus and cell membrane brought into close contact be glycoprotein, receptors, and interaction

2. Removal of water from the membrane surfac

3. Water removal occurs during the viral glycoprotein hair pending?

4. Formation of fusion poor allowing mature exchange

Class one fusion Proteins

Structure of a helicis formed trim as perpendicular to the membrane probably protein precursor to create fusion peptide. It’s often acidic and combined hairband structure formation found in Ebola.

Class 2 fusion protien

Beta sheets form, dimers, parallel to the membrane low pH catalyzed Flaviviruses

Fusion reg

Must occur the correct location various triggers are the neutral pH secondary receptor interaction, low pH and pro cleavage