BIOL 3340 Lecture Notes - Chapters 25 & 26

Overview of Viruses

• Small, obligate intracellular parasites.
• Contain either an RNA or DNA genome surrounded by a protective coat.
• Dependent on a host cell; many viruses target specific cells in a host.
• A virion is a virus particle that delivers its RNA or DNA genome into a host cell.
• The particle is transcribed and translated by the host cell.
• Viral genome contained inside a protein capsid (outer protein shell).
• A nucleoprotein and the genome form the nucleocapsid.
• Enveloped viruses have a phospholipid bilayer surrounding the nucleocapsid. The lipid bilayer is modified from the host cell membrane and contains an outer layer of virus envelope glycoproteins.
• Most complex capsids are found in bacteriophages.

Baltimore System of Classification

• Classification based on the genetic material present in the virion.
• Group I: DNA (+/-)
• Group II: DNA (+)
• Group III: RNA (+/-)
• Group IV: RNA (+)
• Group V: RNA (-)
• Group VI: RNA (+)
  • DNA (+/-) via reverse transcription.
• Group VII: DNA (+/-)
  • Reverse transcription.
• mRNA is produced, which then leads to proteins.

Size and Morphology of Viruses

• Morphology is based on size and shape, chemical composition, and structure of the genome (RNA/DNA, SS, DS) & mode of replication.
• Helical: Seen in nucleocapsids where capsid proteins are wrapped around nucleic acid.
• Icosahedral: Nucleocapsids of spherical viruses.
• Polyhedral.
• Complex: Head and tail structures (e.g., bacteriophages).

Viral Structure

• Examples:
  • Tobacco mosaic virus: Helical capsid surrounding a single helical RNA molecule, rigid rod shape (18 x 250 nm).
  • Adenoviruses: Icosahedral capsid with a protein spike at each vertex, containing double-stranded DNA (70-90 nm diameter).
  • Influenza viruses: Outer envelope studded with glycoprotein spikes, containing eight double-helical RNA-protein complexes, each associated with a viral polymerase (80-200 nm diameter).
  • Bacteriophage T4: Complex capsid consisting of an icosahedral head and a tail apparatus; double-stranded DNA enclosed in the head (80 x 225 nm).

Virus Composition

• Chemical composition and configuration of nucleic acid play a role.
• Genomic RNA strand of single-stranded (SS) RNA viruses is called a sense.
  • Positive Sense (+sense): Viral RNA is identical to viral mRNA and is immediately translated into protein by the host cell.
  • Negative Sense (antisense): Complementary to mRNA and must be converted to (+)sense RNA by RNA polymerase before translation.

Viral Multiplication/Replication

• Mechanism depends on viral structure and genome.
• 7 Steps:
  • Attachment/Adsorption to host cell.
  • Entry into cell.
  • Uncoating of genome.
  • Replication/Synthesis.
  • Assembly.
  • Maturation.
  • Release.

Infection & Pathogenicity

• Infection: A microbe growing and multiplying on or within a host.
  • May or may not result in overt infectious disease.
• Infectious Disease: Any change from a state of health.
  • Part or all of the host is incapable of carrying on normal functions due to the presence of a pathogen or its products.
• Pathogenicity: Ability of a pathogen to cause disease.
• Virulence: Degree of harm (pathogenicity) inflicted on the host.

Extracellular vs. Intracellular Pathogens

• A pathogen must contact a host AND survive within it to cause a disease.
• Extracellular pathogens:
  • Grow outside host cells in tissues and fluids.
• Intracellular pathogens:
  • Grow and multiply within host cells.
  • Facultative intracellular pathogens: Reside within the cells of the host or in the environment but can also be grown in pure culture without host cell support.
  • Obligate intracellular pathogens: Only grow when inside host cells.

Course of Infectious Disease

• Incubation period: Period after pathogen entry, before signs and symptoms.
• Prodromal stage: Onset of signs and symptoms, not clear enough for diagnosis.
• Illness period: Disease is most severe, displays signs and symptoms.
• Convalescence: Signs and symptoms begin to disappear; recovery.

Course of Infectious Disease—Important Terms

• Signs: Objective changes in the body that can be directly observed (e.g., fever, rash).
• Symptoms: Subjective changes experienced by the patient (e.g., pain, loss of appetite).
• Disease syndrome: Set of characteristic signs and symptoms for a disease.

Sources of Pathogens

• Animate Sources:
  • Other humans or animals.
  • Infections passed from animal to human are termed zoonoses.
• Inanimate Sources:
  • Water, food.
• Reservoir: Natural environmental location in which the pathogen normally resides and multiplies.
• Vector: Organism that spreads disease from one host to another (e.g., mosquitoes, ticks, fleas, mites, or biting flies).

Transmission & Virulence

• Occurs either directly or indirectly.
• Four main routes:
  • Airborne.
  • Contact.
  • Vehicle.
  • Vector-borne.
• Pregnant women can also pass a pathogen to their unborn child via vertical transmission.
• Transmission alone is not enough for infection to occur.

Airborne Transmission

• Droplets—direct transmission:
  • Up to 2 mm in diameter.
  • Produced when liquids are placed under force (e.g., sneezing, coughing).
  • Can travel less than 1 m.
• Droplet nuclei—indirect transmission:
  • $1$ to $5 μm$ in diameter.
  • Result from evaporation of the larger droplets.
  • May remain airborne for hours or days and travel long distances.
• Dust particles—indirect transmission:
  • Microorganisms adhere to dust particles.
  • Can survive long periods outside host.

Contact Transmission

• Coming together or touching of source/reservoir and host.
• Direct contact (person-to-person):
  • Physical interaction between source/reservoir and host (e.g., kissing, touching, and sexual contact).
• Indirect contact:
  • Involves an inanimate object (fomite) (e.g., eating utensils, bedding).

Vehicle Transmission

• Vehicles: Inanimate materials that transmit pathogens (e.g., food, water, biological materials (fluids and tissues), air).
• Vehicle transmission: Single vehicle spreads pathogen to multiple hosts.

Vector-Borne Transmission

• Vector: Direct living transmitter of a pathogen.
  • Most are arthropods (e.g., insects, ticks, mites, fleas) or vertebrates (e.g., dogs, cats, skunks, bats).
• Pathogens transmitted by arthropods are often highly virulent.
  • Cause diseases such as malaria, typhus, and sleeping sickness.
• Important that pathogens do not harm their vectors.

Vertical Transmission

• Occurs when the unborn child acquires a pathogen from an infected mother.
• Not as common as horizontal transmission.
• Babies born with an infectious disease are said to have a congenital infection.
• Examples include:
  • Gonorrhea.
  • Syphilis.
  • Herpes.
  • German measles.
  • Toxoplasmosis.

Infectious Dose versus Lethal Dose

• Infectious dose 50 ($ID_{50}$):
  • Number of pathogens that will infect 50% of inoculated hosts.
  • Varies with pathogen.
• Lethal dose 50 ($LD_{50}$):
  • Dose that kills 50% of experimental animals within a specified period.

Adherence and Colonization

• First steps in disease are entry and attachment.
• Portal of entry:
  • Skin, respiratory, gastrointestinal, urogenital systems, or conjunctiva of eye.
• Adherence:
  • Mediated by special molecules called adhesins.
• Colonization:
  • Establishing a site of microbial replication on or within host.
  • Does not necessarily result in tissue invasion or damage.

Invasion Disseminates Pathogens

• Infectivity: Ability to create a discrete point of infection.
• Invasiveness: Ability to spread to adjacent tissues.
• Penetration can be active or passive:
  • Active: Occurs through lytic substances that alter host tissue by:
    • Attacking the extracellular matrix and basement membranes of integuments and intestinal linings.
    • Degrading carbohydrate-protein complexes between cells or on the cell surface.
    • Disrupting the host cell surface.
  • Passive: Not related to the pathogen itself (e.g., skin lesions, insect bites, wounds).
• Successful pathogens overcome the competition and elude initial host responses as well as the adaptive immune system.

Invasion—Specific Examples

• Once in circulatory system, bacteria have access to all organs and systems.
• Bacteremia: Presence of viable bacteria in the blood.
• Septicemia: Bacterial or fungal toxins in the blood.
• Varies among pathogens:
  • Clostridium tetani (tetanus) produces a number of virulence factors but is noninvasive.
  • Bacillus anthracis (anthrax) and Yersinia pestis (plague) also produce many virulence factors and are highly invasive.

Strategies to Evade Host Immune Response

• Production of decoy proteins to bind available neutralizing antibodies.
• Change cell surface proteins by mutation or recombination or downregulate the level of expression of cell surface proteins.
• Produce capsules that resemble host tissue components.
• Phage variation to alter pili protein sequence and expression.
• Produce proteases that degrade host proteins.
• Produce special proteins that interfere with the host’s ability to detect and remove them.
• Cause host cell fusion.
• Infect cells of the immune system and diminish their function while ensuring their own survival.
• Eliminate O-antigen on lipopolysaccharide to diminish immune response and clearance.

Exotoxins & Types of Exotoxins

• Soluble, heat-labile proteins.
• Among the most lethal substances known.
• Types:
  • AB toxins: Composed of two subunits: A subunit (responsible for toxic effect) and B subunit (binds to specific target cell).
  • Specific host site exotoxins.
  • Membrane-disrupting exotoxins.
  • Superantigens.

Endotoxin—Lipopolysaccharide

• Lipopolysaccharide (LPS) in Gram-negative cell wall can be toxic to specific hosts.
  • Called endotoxin because it is endogenous, bound to the bacterium and released when the microorganism lyses.
  • Toxic component is the lipid portion, lipid A.
• Heat stable.
• Toxic (nanogram amounts).
• Weakly immunogenic.

Coagulation Cascade

• Intrinsic Pathway: Surface contact activates Factor XII to Factor XIIa, which activates Factor XI to Factor XIa, which activates Factor IX to Factor IXa.
• Extrinsic Pathway: Tissue damage activates Factor VII to Factor VIIa.
• Common Pathway: Factor IXa activates Factor X to Factor Xa, which converts prothrombin to thrombin, which converts fibrinogen to fibrin. Factor XIII is activated to Factor XIIla to stabilize the fibrin clot.

Exotoxin vs. Endotoxin

Mycotoxins

• Toxins produced by fungi.
• Common contaminants of food crops.
  • For example, Aspergillus flavus and A. parasiticus produce aflatoxins, cause chronic and acute liver disease and liver cancer.
• Contaminate water-damaged buildings.
  • For example, Stachybotrys produce satratoxins, potent inhibitors of DNA, RNA, and protein synthesis; induce inflammation, disrupt surfactant phospholipids in the lungs, and may lead to pathological changes in tissues.

What Is Epidemiology?

• Science that evaluates occurrence, determinants, distribution, and control of health and disease in a defined human population.
• Epidemiologist: One who practices epidemiology.

Epidemiology Terminology

• Sporadic disease: Occurs occasionally and at irregular intervals.
• Endemic disease: Maintains a relatively steady low-level frequency at a moderately regular interval.
• Hyperendemic diseases: Gradually increase in frequency above endemic level but not to epidemic level.
• Outbreak: Sudden, unexpected occurrence of disease/Usually focal or in a limited segment of population.
• Epidemic: Outbreak affecting many people at once.
  • Sudden increase in occurrence above expected number.
  • Index case—first case in an epidemic.
• Pandemic: Increase in disease occurrence within a large population over at least two countries around the world.

Measuring Infectious Disease Frequency

• To determine if an outbreak, epidemic, or pandemic is occurring, epidemiologists measure disease frequency at single time points and over time.
• Statistics: Mathematics dealing with collection, organization, and interpretation of numerical data.
• Three important statistical measures of disease frequency:
  • Prevalence = $\frac{total \ number \ of \ cases \ in \ population}{total \ population}$
  • Morbidity rate = $\frac{number \ of \ new \ cases \ during \ a \ specific \ period}{number \ of \ individuals \ in \ population}$
  • Mortality rate = $\frac{number \ of \ deaths \ due \ to \ given \ disease}{total \ number \ of \ cases \ of \ the \ disease}$

Patterns of Infectious Disease in a Population

• Infectious disease: Disease resulting from an infection by microbial agents.
• Communicable disease: Can be transmitted from one host to another.
• Two types of epidemics:
  • Common source epidemic: Single common contaminated source (food or water).
  • Propagated epidemic: One infected individual into a susceptible group, infection propagated to others.

Study of Infectious Disease

• Epidemiologist is concerned with:
  • Causative agent.
  • Source and/or reservoir of disease agent.
  • Mechanism of transmission.
  • Host and environmental factors that facilitate development of disease within a defined population.
  • Best control measures.
• Patterns of Infectious Disease in a Population—Surveillance:
  • To recognize and measure an infectious disease in a population, various surveillance methods are used.
  • Gathering information on development and occurrence of a disease.
  • Collating and analyzing the data.
  • Summarizing the findings.
  • Selecting control methods.

Herd Immunity

• Herd immunity: Resistance of a population to infection and pathogen spread because of immunity of a large percentage of the population.
  • Level can be altered by introduction of new susceptible individuals into population.
  • Level can be altered by changes in pathogen.
• Recommended that 80% and 95% of the population be immunized against common infectious diseases, providing the herd immunity necessary for protection of those who are not immunized.

Systematic Epidemiology

• Focuses on ecological and social factors that influence development and spread of emerging and reemerging diseases.
• Numerous factors have been identified.

Increases in Emerging and Reemerging Infectious Diseases

• Reasons include:
  • World population growth, urbanization.
  • Inadequate public infrastructures.
  • Increased international travel, mass migrations.
  • Climate change.
  • Habitat disruption.
  • Microbial evolution and development of resistance.

Nosocomial Infections

• Healthcare-acquired infections.
  • From pathogens within a hospital or other clinical care facility, acquired by patients in the facility.
• $5$ to $10$% of all hospital patients acquire a nosocomial infection.
• Often caused by bacteria that are members of normal microbiota.
• Many hospital strains are antibiotic-resistant.

Healthcare-Associated Infections (HAIs)

• Examples:
  • Ventilator-Associated Pneumonia.
  • Bloodstream infections.
  • Intestinal Tract and Liver infections.
  • Urinary Tract infections.
  • Surgical Site Infections.

Sources of Healthcare-Associated Infections

• Endogenous pathogen:
  • Brought into hospital by patient.
  • Patient is colonized after admission.
• Exogenous pathogen:
  • Microbiota other than the patient’s.
  • May come from hospital staff, other patients and visitors, food, plants and flowers, computer keyboards, intravenous and respiratory therapy equipment, and water systems.

Control, Prevention, and Surveillance of Nosocomial Infections

• Nosocomial infections:
  • Prolong hospital stays by $4$ to $14$ days.
  • Result in additional $28$ to $33$ billion per year to direct healthcare costs.
  • Result in approximately 99,000 deaths annually.
• Proper training of personnel in basic infection control measures:
  • For example, handling of surgical wounds and hand washing.
• Monitoring of patient for signs and symptoms of nosocomial infection.

Two Types of Control Measures

1. Reduce or eliminate source or reservoir of infection
   • Quarantine and isolation of cases and carriers.
   • Destruction of animal or arthropod reservoir.
   • Treatment of water and sewage.
   • Therapy that reduces or eliminates infectivity of the individual.
2. Reduce the number of susceptible individuals and raise the general level of herd immunity.
   • Immunization and prophylactic treatment to prevent infection.

Vaccines and Immunization Protection

• Vaccine: Preparation of microbial antigens used to induce protective immunity.
  • May consist of killed, living, weakened (attenuated) microbes or inactivated bacterial toxins (toxoids), purified cell material, recombinant vectors, or DNA.
• Immunization: Result obtained when vaccine stimulates immunity.
• Vaccines attempt to induce antibodies and activated T cells to protect host from future infection.
• Adjuvants: Are mixed with antigens in vaccines to enhance the rate and degree of immunization.
  • Can be any nontoxic material that prolongs antigen interaction with immune cells and stimulates the immune response to the antigens.
  • Several types are available.

Acellular or Subunit Vaccines

• Use of purified molecules from microbes avoids some of the risks of whole-cell vaccines.
• Forms of subunit vaccines:
  • Capsular polysaccharides.
    • Example: Haemophilus influenzae type b.
  • Recombinant surface antigens.
    • Example: Hepatitis B virus.
  • Inactivated exotoxins (toxoids).
    • Example: Corynebacterium diphtheriae toxin, Clostridium tetani toxin

Other Types of Vaccines

• Recombinant-Vector vaccines
  • Pathogen genes that encode major antigens inserted into nonvirulent viruses or bacteria which serve as vectors and express the inserted gene.
  • Released gene products (antigens) can elicit cellular and humoral immunity.
• DNA vaccines
  • DNA directly introduced into host cell DNA taken into nucleus and pathogen’s DNA fragment is expressed.
  • Host immune system responds to foreign proteins produced. Many DNA vaccine trials are currently under way.