Viral Infections & Structure

Viral Infections and Structure

• Viruses infect humans through attachment (adsorption), sometimes binding to ACE-2 receptors
• Beijerinick discovered acellular, filterable, infectious agents
• Louis Pasteur coined the term "virus," meaning "poison"
• Viruses aren't cells; they are obligate intracellular parasites needing a host cell to fulfill life characteristics
• Viruses have a protein shell (capsid) covering the nucleic acid core and are ubiquitous
• Viruses contain either DNA or RNA
• Consisting of a protein capsid and nucleic acid, viruses may include:
  • Capsid and envelope, though the envelope isn't always present
• A virus central core contains
  • DNA or RNA
  • Matrix protein enzymes, though not always present
• A virion is a complete virus particle
• Nonenveloped viruses are also known as naked viruses
• Enveloped viruses contain an envelope external to the capsid
• Viral spikes are
  • Proteins projecting from the envelope or capsid surface involved in viral attachment to a host cell and are used for virus identification
• Genome = sum total of all genetic information carried by an organism
• All viruses have at least a capsid and RNA or DNA

Types of Viral Genomes

• DNA viruses include:
  • Double-stranded DNA (dsDNA)
  • Single-stranded DNA (ssDNA)
• RNA viruses include:
  • Double-stranded RNA (dsRNA)
  • Single-stranded RNA (ssRNA); these can be segmented where each gene exists on a separate RNA piece (e.g., influenza, HIV)

Animal Virus Multiplication Cycle and Tropism

• The six stages animal virus multiplication = adsorption, penetration, uncoating, synthesis, assembly, and release
• Adsorption for animal viruses = specific attachment to host cell receptors via spikes/capsid proteins, receptor determines host range/preference
• Viruses typically infect only a specific tissue or cell type i.e. tropism
• Cellular tropism exists when a virus only infects a specific cell type, for example HIV infects macrophages and not neurons
• Tissue tropism exists when a virus only infects a specific tissue, for example influenza infects lung tissue and not brain tissue
• Host range example: Ebola affects primates but not fruit bats and pigs, indicating primates are Ebola's host range

Animal Virus Penetration, Uncoating, and Synthesis

• Animal viruses penetrate/uncoat in two ways:
  • Penetration by endocytosis: specific attachment engulfs the virus into a vesicle the vesicle, envelope, and capsid break down to free DNA or RNA
  • Penetration by fusion with the host cell membrane (enveloped viruses only): irreversible attachment forms membrane fusion entry of nucleocapsid, which uncoats the nucleic capsid to free DNA or RNA
• Synthesis and assembly of ssRNA viruses happens in the cytoplasm
• Synthesis and assembly of DNA viruses happens in the nucleus
• Retroviruses are RNA viruses
  • Their viral DNA incorporates into host DNA and is passed to cell progeny becoming a provirus

Viral Enzymes, Transcription, and Release

• Preformed enzymes: some viruses carry these inside the virion
• Transcription involves translating DNA to RNA
• Reverse transcription (RT) involves translating RNA to DNA
• Virion release happens in two ways:
  • Nonenveloped viruses lyse the host cell
  • Enveloped viruses release through budding or exocytosis

Viral Species, Infections, and Cancer

• The species determines the host range of a virus
• Persistent viral infections can be triggered to reactivate due to stresses, chemicals, UV light, pregnancy, etc.
• Carcinogenesis is a complex, multi-step process turning normal cells into cancer cells

Bacteriophages and Viruses

• Bacteriophages (phages) are viruses infecting bacteria
• Every bacteria species can be parasitized by a phage
• Viruses infecting bacteria lack the ability to enter DNA and operate two ways:
  • Lytic/virulent phage = one reproductive choice where it enters, multiplies, and lyses the host in a lytic cycle only
  • Temperate phage = two reproductive options
    • Reproduce utilizing lytic cycle
    • Remain in the host cell without destroying it to cause latent infection, integrating their genome into the host genome, and becoming a prophage
• Lysogenic conversion occurs when a bacterial cell gains a new trait from the prophage

Viral Culturing and Pathogenesis

• Culturing viruses requires inoculation into a suitable living host
• In vivo experiments are performed in a living body
• Prion pathogenesis = no nucleic acids present, and prions cause spongiform encephalopathies

Good Viruses and Plasmids

• Good viruses encompass Tulip mosaic virus, the evolution of life, gene therapy, and bacteriophage therapy
• Plasmids are in some bacteria and are dsDNA and circular
• Chromosomes are in all bacteria and are dsDNA and circular

Endosymbiosis and Eukaryotic Microbes

• Mitochondrial evidence supports endosymbiosis as shown through:
  • Independent division (binary fission)
  • Circular chromosome
  • DNA sequences resembling bacterial DNA
  • Prokaryotic ribosomes
  • being similarly inhibited by drugs
  • double membrane
• Eukaryotic microbes include:
  • Fungi
  • Protozoa
  • Algae
  • Helminths (some life stages)

Microscopic Fungi and Saprobes

• Microscopic fungi exist as either yeasts (round/oval shapes) or molds (long filaments with spores that are easy to kill)
• Saprobes feed on dead and decaying matter and are decomposers

Fungal Infections and Nutrition

• Mycoses are fungal infections
• The majority of fungi are harmless saprobes
• Fungi thrive in high salt/sugar, low water environments and cause opportunistic infections in patients with AIDS, cancer, or diabetes

Adverse and Beneficial Impacts of Fungi

• Adverse impacts of fungi include mycoses, allergies, toxin production, and destruction of crops and food storages
• Beneficial impacts of fungi include decomposition of dead plants and animals, serving as a source of antibiotics and some chemicals, biotechnology, and mycorrhizae

Mycorrhizae and Algae

• Mycorrhizae are symbiotic fungi aiding most plants in absorbing nutrients and water
• Algae exhibit:
  • Free-living plankton
  • The basis of the food web
  • Production of atmospheric oxygen
• Algae blooms bad because thickening prevents oxygen from entering the water, causing fish to die because bacteria consumes all available oxygen

Paralytic Shellfish Poisoning and Toxoplasma gondii

• Paralytic shellfish poisoning = life-threatening syndrome with neurological symptoms
  • Severe cases = respiratory arrest within 24 hours of eating the toxic shellfish, with no cure or antitoxin available
• Toxoplasma gondii = protozoan parasite
  • Mild infection for healthy individuals
  • Congenital infections can cause severe abnormalities later in life or stillbirth

Microbial Colonies and Binary Fission

• Microbial colonies aren't everywhere because they are not always in the right conditions with respect to temperature, nutrients, and access to water
• Binary fission is the most common way bacteria reproduce

Doubling Time and Logarithmic Representation

• Doubling time (generation time) defines amount of time it takes for one bacterium to grow and divide into two bacteria
  • Example: 2 cells + 1 generation = exponential value of 2^1
• Logarithmic scale helps accommodate huge numbers of bacteria and accurately shows change in growth at early stages through Log scales
  • 1=10
  • 2=100
  • 3=1,000
• Log phase = most metabolically active and cannot be shortened
  • Shows growth represented by 2^n where n represents the number of generations
  • Growth curve displays trend of population growth

Lag and Exponential Growth

• Lag phase involves microbes adjusting to new environment in medium prior to resuming growth, synthesizing enzymes to use nutrients present, and repairing damage from previous environments
  • Time in lag depends on the change in environment
• Log phase (exponential growth phase) happens when microbes divide at maximal rate at a regular interval
• Stationary phase exists when cells are not dividing but are metabolically active

Death Phase and Viable But Non-Culturable (VBNC) State

• Death phase means deaths far exceed new cell growth.
• Cells are too damaged to repair themselves and will not reproduce even in ideal conditions
• Viable but non-culturable (VBNC) = alive but can't culture - Temporarily unable to grow on media means this state can be a problem for public health and medicine because most diagnoses rely on growth

Digestion and Chemical Composition

• Walled cell as a barrier transports enzymes outside the wall enzyme hydrolysis of the bonds on nutrients allows smaller molecules to transport across the wall into the cytoplasm
• Digestive method shows how bacteria can "eat" a carrot even without a digestive system
• E. coli and microbial nutrition chemical composition = 70% water, CHONPS at 96% of cell
  • Bacteria cannot replicate in pure water because it only has H and O and bacteria needs C, N, P, S

Nutrients and Growth Factors

• Nutrients = chemical substances acquired from the environment and used in cellular activities
• Macronutrients = needed in large quantities in a cell to play roles in cell structure/metabolism i.e. CHONPS
• Micronutrients (trace elements) = needed in smaller quantities in a cell for enzyme function and protein structure i.e. Ca, Cl, Fe, etc. Growth factors = essential compounds not synthesized by body and required for growth i.e. amino acids, vitamins

Microbial Growth Requirements

• A microbe needs CHONPS for growth
• Physical requirements temperature ranges:
  • Psychrophile grows in freezing conditions
  • Psychrotolerant grows at room temperature
  • Mesophile grows in human infections at body temperature
  • Thermophile grows in hot temperature; and,
  • Extreme thermophile grows above boiling

Chemical Requirements for Oxygen

• Chemical requirements oxygen includes Reactive Oxygen Species (ROS)
  • Toxic derivatives of atmospheric oxygen (O2) occur
    • Produced during normal metabolism in an oxygenated environment where they cause extreme damage (nucleic acids, proteins, lipids) if not converted to less harmful substance
  • No enzymes = death
  • Need enzymes to grow in oxygen
• An aerobe utilizes oxygen and detoxifies, obligate aerobe cannot grow without oxygen
  • Microaerophilic requires small amount of oxygen (less than 20%) and cannot grow in full atmospheric oxygen
• Anaerobe does not utilize oxygen
  • Facultative anaerobe utilizes oxygen (certainly preferred) but can also grow without it
    • Able to use oxygen but doesn't need it
  • Obligate anaerobe lacks the enzymes to detoxify oxygen so cannot survive in an oxygen environment
  • Aerotolerant anaerobes can grow equally well with or without oxygen

Endospores & Antibiotics

• Endospores form in stationary phase when nutrient amount starts to decline
• Most antibiotics targeting cell call synthesis require actively dividing cells
  • Exponential phase is when bacteria should be most effectively targeted

Viral DNA, Host Cells, and Viral Cycles

• 40-80% of human DNA is thought to consist of viral DNA sequences
• Host receptors determine which cells viruses can infect
• The general steps in a viral multiplication cycle are adsorption, penetration, synthesis, assembly, and release
• Phage nucleic acid is incorporated into the nucleic acid of its host cell when the host DNA is replicated occurs during the lysogenic cycle
• A virus that undergoes lysogeny is a temperate phage
  • Clear patches in cell cultures, indicating sites of virus infection = plaques

Mitochondria, Yeasts, and Fungi

• Mitochondria likely originated from bacteria
• Yeasts are unicellular
• Fungi and molds are filamentous
• Fungi produce spores as structures for reproduction and multiplication

Bacterial Hypertonicity and Pathogens

• Most bacteria increase their numbers through binary fission
• A cell exposed to a hypertonic environment loses water by osmosis
• A pathogen would most accurately be described as a parasite
• In a viable count, each colony represents a CFU from the same population

pH Levels

• Neutral pH range for most bacteria is 7, or neutrophiles
• Acid-loving microbes are acidophiles
• Alkaline-loving microbes are alkaliphiles
• Low pH = Highly acidic
• High pH = Basic/alkaline
• Cytoplasm is always maintained at neutral pH to prevent denaturation of proteins/enzymes and disruption of PM

Cranberry Juice and Salt Microbes

• Doctors suggest patients drink cranberry juice when fighting a UTI because cranberry juice can slightly alter pH and make it more acidic, slowing the growth of microbes if drinking is done in big amounts
• Obligate halophiles require high salt for growth above 30%
• Facultative halophiles don't require salt, but prefer salt for growth

Microbial Environments and Quantification

• Hypotonic environments are more frequently encountered by microbes
• Quantifying bacteria by count by filtration provides advantages as one can quantify low numbers in a liquid
• Quantifying bacteria via direct counting using cytometer and stain provides advantages as you know the number right away, don't need incubation, and one can get the total number of microbes
• "turbid" by eyes suggests 1 million cells/ml
• "turbid" by spectrophotometer = 10-100 million cells/ml

Explore viral infections, attachment mechanisms like ACE-2 receptors, and the historical context from Beijerinick to Pasteur. Understand viruses as obligate intracellular parasites with a capsid and nucleic acid core of DNA or RNA. Learn about virions, enveloped vs. naked viruses, and the role of viral spikes.