Taxonomy and Classification in Biology

• Viruses: Some images are disturbing

Things to Think About

• Consider whether understanding HIV replication can help prevent or stop the progress of the virus into developing AIDS
• Consider whether to get an HPV or COVID-19 vaccine/booster, and what they entail
• Consider how pandemics can be prevented
• Consider how viruses can be used to treat cancer

Viruses and Life

• Viruses aren't considered living
• Lack cellular structure preventing viruses from being alive
• Cannot metabolize energy.
• Viruses are obligate parasites
• Viruses cannot reproduce on their own
• Their energy is acquired by being parasites
• Viruses depend on a living host organism to be active
• A virus is a non-cellular particle
• Made up of genetic material covered by protein which invades living cells

Composition

• Viral particles range from 10 to 300 nm in size
• Genetic material is surrounded by a protein coat called a capsid
• Some viruses that infect animals possess an envelope
• Envelope surrounds the capsid
• Derived from the membrane of the host animal cell
• Protein spikes may protrude from the viral particle
• Protein spikes are involved in the attachment of the particle to the host cell
• Viruses contain either DNA or RNA

Characteristics

• Virus strains attack specific host organisms
• Specific viruses attack tobacco plants or bacterium
• Tobacco virus attacks the tobacco plant
• Bacteriophage attacks bacterium
• Viruses are classified according to genetic material
• Genetic material determines traits, what protein is manufactured, and what is inherited from parent to offspring

Classification

• Viruses are classified by:
• Genetic material (DNA or RNA)
• Nucleic acid (single-stranded or double-stranded)
• Shape of the protein coat
• Nature of host (plant, animal, or bacteria)
• Presence or absence of an envelope

Viral Shapes

• Cylindrical
• Polyhedral
• Spherical
• Irregular (bacteriophage)

Bacteriophages

• Bacteriophages (phages) are viruses that infect bacteria only
• Bacteriophage structure includes:
  • Capsid (entire top part)
  • Nucleic acid
  • Tail (entire bottom part)
  • Sheath
  • Tail fibres
• Bacteriophages can kill good bacteria in the gut
• Killing good bacteria in the gut can prevent the intestines from being healthy
• Decreased bacteria can cause an irritable bowel, or Crohn's disease

DNA vs. RNA

• Both are types of genetic material
• DNA is deoxyribonucleic acid
• RNA is ribonucleic acid
• DNA, "blueprint," codes for all the proteins that the body needs to function
• Key steps to make a protein: DNA → mRNA → Protein

Examples of Viruses

• Tobacco Mosaic Virus
• Cold Virus
• Flu virus
• Corona Virus Causing SARS
• Bird flu
• Zika Virus
• Transmitted by mosquito bites
• About 1 in 5 of those infected will become ill
• Symptoms normally last 2-7 days
• Mosquitoes that transmit the virus are not present in Canada
• There is no treatment or vaccine available
• Symptoms: fever, rash, joint pain, conjunctivitis(red eyes)
• Illness is usually mild and death is rare

Infectious Cycles

• A virus infects a cell by inserting its nucleic acid (DNA or RNA)
• The viral nucleic acid then enters 1 of 2 cycles

Lysogenic Cycle

• Stages of Lysogenic Virus Cycle
• Attachment & Entry
• Integration
  • Viral nucleic acid becomes a part of the bacterial nucleic acid
• Multiplication of Genome
• Cell Division
• Provirus: a viral section of DNA that integrates and becomes part of the host cell's DNA

Lytic Cycle

• Cycle stages:
• Attachment
• Insertion
• Replication – Host’s metabolism replicates the RNA/DNA
• Assembly
• Lysis & Release
• New viral particles are assembled
• A virus can switch back and forth between cycles
• It can remain lysogenic for many years

RNA Virus

• Genetic material is RNA
• RNA enters a host cell and provides its own instructions and does not interact with DNA.
• RNA viruses only go through the lytic cycle.

Retrovirus

• Genetic material is RNA
• Instructs a host cell to use viral RNA to create viral DNA by using the enzyme reverse transcriptase
• Goes through lysogenic cycle
• A trigger causes the viral genes to become active and make viral protein (lytic cycle)

Human Immunodeficiency Virus (HIV)

• Is a retrovirus
• Has RNA instead of DNA
• Causes AIDS-acquired immunodeficiency syndrome
• Replication of HIV in T Cells includes:
• Fusion of HIV to the host cell surface.
• HIV RNA, reverse transcriptase, integrase, and other viral proteins enter the host cell
• Viral DNA is formed by reverse transcription
• Viral DNA is transported across the nucleus and integrates into the host DNA.
• New viral RNA is used as genomic RNA and to make viral proteins.
• New viral RNA and proteins move to the cell surface; a new, immature HIV forms
• Virus is released.
• The viral protease cleaves new polyproteins to create a mature, infectious virus.
• AIDS affects immune system by weakening it
• T cells, B cells, and antibodies are affected
• Death can occur from infections
• Some people are immune to HIV
• Preventive measures

Human Papiloma Virus (HPV)

• It is the most common STI
• May cause genital warts
• Most of the time it is a silent killer
• Responsible for cervical cancer
• HPV Vaccine can be taken for prevention
• If you are sexually active get a PAP test
• PAP detects abnormal cells which lead to cancer

Questions to Consider

• Consider the advantages and disadvantages of each cycle

• Understand whether do host cells have any defense mechanisms

• Discuss how to manipulate the viral cycle process

• Examining statistics comparing unvaccinated, partially vaccinated, and fully vaccinated people

• Data includes cases for hospitalization and ICU admissions with fully vaccinated people having the highest numbers.

• In hospital but not the ICU

• Unvaccinated cases 522

• Partially vaccinated cases 111

• Fully vaccinated cases 1332

• In ICU

• Unvaccinated cases 161

• Partially vaccinated cases 19

• Fully vaccinated cases 179

• Reviewing age-standardized case showing those who are unvaccinated are far more likely to be hospitalized critically ill, or die

• The vaccine effectiveness of 2 vs 3 doses of mRNA vaccines for Delta and Omicron report:

• Vaccine Effectiveness against ER and Urgent Care Visits: - Delta

  • <6 months after dose 2: 86%

  • 6 months after dose 2: 76%

  • After a 3rd dose: 94% - Omicron
  • <6 months after dose 2: 52%

  • 6 months after dose 2: 38%

  • After a 3rd dose: 82%

Organs of the Immune system

• Tonsils and adenoids
• Thymus
• Lymph nodes
• Lymphatic vessels
• Spleen
• Peyer's patches
• Appendix
• Bone marrow

Immune Response

• Non-specific immune responses:
• Skin
• Mucous
• General white blood cells
• Specific immune responses:
• Cellular immunity
• Antibody (humoral) immunity

Components of Immune System

• Macrophage
• Viral antigen
• B Cell
• Plasma cell
• Antibodies
• Virus
• Cytotoxic T Cell
• Body Cell

Vaccines

• Active immunity stimulates the body to produce antibodies against the disease
• Creates long term immunity
• Passive immunity gives antibodies are given from one individual to the other individual
• Creates temporary immunity
• RNA Vaccine
• First spike exposure from a vaccine teaches the immune system
• Spike proteins on cells create antibodies
• Second spike exposure from a virus creates a prepared immune response
• B cells quickly assemble
• Antibodies inactivate the virus

Explore the basics of taxonomy and biological classification, including species definitions and estimated numbers. Discover the diversity of life, from insects to mammals, and their classification.