Comprehensive notes on Influenza, Coronaviruses, and Virus Biology

What Is the Flu?

• The flu goes by many different names (examples on slides): Bird flu, swine flu, H1N1, Spanish flu. All are caused by a type of virus known as the influenza virus.

What Is a Virus?

• Viruses are basically parasites of our cells. The purpose of a virus is to find a host cell and hijack its metabolic machinery to produce more copies of itself.
• Viruses need a host cell in order to replicate.
• Viruses vary in their shape and the types of cells they infect.
• They are very small—smaller than a bacteria cell.
• General virus structure:
  • Genetic material: DNA or RNA that contains a relatively small number of genes.
  • Capsid: a protein coat that surrounds the genetic material.
  • May have proteins attached to it (tail fibers or spikes) that help the virus attach to a target host cell.

What Is a Virus? (Influenza specifics)

• The influenza virus possesses:
  • RNA
  • A capsid
  • An envelope
• The envelope is the remnants of the plasma membrane of the host cell and assists in attachment and entry of the virus into a host cell.

How Are Flu Viruses Named?

• Flu forms: Influenza A, B, C, D.
  • Influenza A and B are the two most prevalent forms that infect humans.
  • Influenza C infects pigs and rarely humans.
  • Influenza D infects pigs and cattle.
• WHO naming convention uses:
  • Host (if not human)
  • Type (A or B)
  • Strain
  • Year of isolation
• For Influenza A, nomenclature includes spikes on the surface: the H and N glycoprotein spikes (e.g., H1N1).
• Influenza B viruses have a lineage designation: B/Yamagata or B/Victoria.

Flu Vaccine Strains (an example)

• For the 2017–2018 flu season, the vaccine protected against:
  • A/Michigan/45/2015 (H1N1)pdm09-like virus
  • A/Hong Kong/4801/2014 (H3N2)-like virus
  • B/Brisbane/60/2008-like (B/Victoria lineage) virus
• Using A/Michigan/45/2015 (H1N1)pdm09-like virus as an example:
  • Type: Influenza A isolated in Michigan
  • Strain: 45
  • Year: 2015
  • What about the “H1N1”?: The nomenclature includes the surface spikes (H and N) that define subtypes such as H1N1.

Surface Spikes on Influenza A

• On the surface of an influenza A virus are two different types of spikes.
  • These spikes are glycoproteins (a protein with a sugar attached).
  • They assist the virus in identifying and entering its host cell.
• The two spikes are collectively referred to as $H ext{ and } N$ (eg, $H<em>1 ext{N}</em>1$).

What Is a Coronavirus?

• Coronavirus names come from their crown-like spike proteins.
• They infect a variety of species (bats, camels, birds, livestock, humans).
• There are $7$ types known to infect humans (as of the slides).
• Timeline references on the slides include years such as 2002, 2019, 2012 (context: emergence events for different coronaviruses).

A Look at COVID-19

• The World Health Organization (WHO) named the novel coronavirus that causes the disease COVID-19 as severe acute respiratory syndrome coronavirus 2 ($ext{SARS-CoV-2}$) in January 2020.
• The disease is named from a contraction of the term coronavirus disease 2019 ($ext{COVID-19}$).
• The disease was first observed in humans in Wuhan, China in December 2019.
• The WHO named COVID-19 a global pandemic.

History and Zoonotic Transmission

• Three coronaviruses have crossed the species barrier (zoonotic transmission) cases:
  • SARS-CoV and SARS-CoV-2 likely originated from bats, with small mammals as intermediate hosts between bat and human.
  • MERS-CoV originated from a camel with direct transfer to humans.

COVID Virus Characteristics

• SARS-CoV-2 is an envelope virus with an RNA genome.
• Genetic material consists of a small number of genes (4 main structural proteins and 16 nonstructural proteins).
• The four main structural proteins are:
  • $S$: spike glycoproteins (protrudes from the viral surface and aids in binding the envelope of the virus to host cells)
  • $E$: envelope glycoproteins (production and maturation of the virus)
  • $M$: membrane glycoproteins (determines the shape of the virus envelope)
  • $N$: nucleocapsid proteins (involved in viral replication)

Structure and Appearance

• SARS-CoV-2 particles are spherical with $S$ proteins (spikes) protruding from the surface; spikes give the virus its crown or corona appearance.
• Spikes assist the virus in identifying and entering host cells.

Are Viruses Alive?

• Biologists use five characteristics to determine if something is alive:
  • The ability to process energy and materials
  • The ability to maintain an internal environment
  • The ability to respond to stimuli from the environment
  • The ability to reproduce
  • The ability to adapt to changing environmental conditions
• Viruses are not capable of processing energy or materials on their own; they rely on a host cell for those processes.
• Viruses do not have scientific names (they are not named as organisms in the traditional sense by binomial nomenclature).
• Historically, biologists have not classified viruses as living organisms.
• This view is challenged by discoveries of new groups of viruses (e.g., giant viruses) that blur the line between living and non-living.
• Note: The slide mentions the term "giant viruses" as a factor in the discussion about whether viruses can process their own proteins.