ssRNA Single-Stranded RNA

Either top-strand (plus strand) or bottom strand (negative strand).

Human RNA uses plus strand RNA, so any negative strand has to be duplicated into it's sister, plus strand, using specific enzymes in order to be read by the host cell's ribosomes.

dsDNA Double-Stranded DNA

Like human DNA.

Viruses Are Diverse

Genes are highly diverse.

Genomes are generally very small.

Have multiple strains: rapid mutations/evolution.

Examples of Viruses

Influenza, Coronavirus, HIV, Herpes, Bacteriophages, Mimivirus.

Symptoms/Diseases Associated with Viruses

Polio, Smallpox, Chickenpox, Rabies, Tobacco Mosaic Virus, Zikavirus, Tulip Breaking Virus.

Structure of Viruses

Capsid

Outer protein coats surrounding nucleic acids.

Enveloped Virus

These have a capsid inside the lipid membrane.

Has a lipid membrane outer coating that is taken off of the host cell.

• Susceptible to detergents.

• Required for infectivity, spike proteins exist on the lipid membrane.

• "Hides" virions from the immune system.

Non-Enveloped Virus

Outer-capsid only.

"Naked"

More hearty.

Resistant to detergents.

Spike proteins exist on the outer capsid.

Types of Viruses

ssRNA Viruses

Influenza

• Has 8 -ssRNAs.
• mRNAs re-assort in the host cell creating genetic diversity.
• Needs viral RdRp (rna-dependent RNA polymerase).
  • Converts the negative virus RNA into positive RNA that the host can read and replicate.
• Many types of H and N proteins define virulence.

  • H1N1, H2N3, H7N9

  • H stands for Hemaglutinin, helps infect.
  • N stands for Neuraminidate, helps escape (spread).

Strains

A

B

C

D

Different types of in the same cell may mix and match genes when they re-package themselves.

Viruses can swap genes!

Coronavirus

• Single +ssRNA

dsRNA Viruses

• Two non-enveloped capsids. An inner capsid and an outer capsid.
• Replicates inside the inner capsid to evade defenses.
• Needs RdRp to make RNAs.

dsDNA Bacteriophages Infect Prokaryotes

• Non-enveloped, protein capsid head.
• Phages kill bacteria, as bacteria evolve more resistance to antibiotics, phages also evolve and can kill them.
• Turns to circular DNA in host cell
  • Rolling circle replication.

dsDNA HSV

_Herpes Simplex Virus

• Doesn't integrate into the host genome.

dsDNA HPV

_Human Papilloma Virus

• Can integrate into the host cell's genome.
  • Causes cervical cancer, degrades tumor-suppressing proteins.

Giant dsDNA Viruses

• Have very large genomes comparatively.

Retroviruses

• Has viral Reverse Transcriptase (RT).
• Integrates into the host genome.
• Difficult to get rid of (HIV).

Vaccines

mRNA Vaccines

Teaches cells to build the spike proteins used by viruses that your immune system can then recognize before encountering the real virus.

Does your immune system kill your cells that made the spike protein that your immune system doesn't recognize?

Question

Study Guide

• What types of cells can be infected by viruses?
  • Prokaryotes, archaea, and eukaryotes.
• Why is it difficult to create a viral phylogenetic tree?
  • Because they mutate rapidly and there are so many different varieties.
• Why do you think one vaccination may not perfectly protect against different strains: why do we need boosters, or why do we need a new flu vaccine every year?
  • Because viruses mutate rapidly.
• Name some viruses that affect human health, animal health, plant health?
  • Tulip Breaking Virus affects plants, HIV affects humans, Influenza A affects pigs.
• What are the differences in viral coatings, how does that affect infection biology? Spike proteins exist on the lipid membrane in enveloped viruses, they exist on the capsid in non-enveloped viruses.
• Are viruses alive?
  • That's debatable, they replicate, but they don't replicate themselves.
• What types of genomes can they have? What is -ssRNA versus +ssRNA, how differ?
  • -ssRNA is negative single-strand RNA, +ssRNA is positive single-strand RNA.
  • -ssRNA must be converted into +ssRNA for our host ribosomes to read and replicate it.
• Know example of each type of virus
  • -ssRNA
    • Influenza
  • +ssRNA
    • Coronavirus
  • dsDNA phage
    • Bacteriophages
  • dsDNA linear
    • HSP
  • dsDNA circular
    • HPV
  • a Retrovirus
    • HIV
  • dsRNA virus
    • Rotavirus
• Influenza:
  • What influenza causes most season flu (and global pandemics) - what are its hosts?
    • Influenza A, humans, pigs, birds, and other mammals.
  • How many strands of RNA make up its genome?
    • 8, it's a small one.
  • How is diversity generated in these viruses - how do new strains get new combinations of H and N genes.
    • If there are multiple different strains in the same cell, they can mix and match rna strands. Also, replication is messy, they don't have checker proteins.
  • What do H and N stand for?
    • Hemaglutinin and Neuraminidate
  • What does the H protein do, what does the N protein do?
    • H is used to infect, N is used to escape.
  • What other viruses have genomes similar to influenza ssRNA?
    • Measles
• Why do we vaccinate against viral diseases when it's possible to do so?
  • To teach our immune system how to recognize and kill the virus before it has a chance to take hold in our bodies.
• Throughout all the slides: what enzymes are specifically viral (not found in host cells)? There are at least two named.
  • RdRP, RT
• Name other viruses related to COVID19/SARS-CoV2.
  • Hepatitis C
• SARS-COV2: what part of virus is commonly used for vaccinations?
  • Spike proteins
• What type of genome do corona viruses have? Why is that helpful for the virus?
  • Single +ssRNA, it's similar to our own mRNA so it can be replicated immediately.
• Why do dsRNA viruses have TWO capsids? What deadly disease can these cause: name it.
  • Rotavirus, to evade the host's immune response.
• Why could phage be better than drugs to kill bacterial infections?
  • Because phages can evolve along with the bacteria and still be able to kill it.
• What is HSP, what does it cause. What is HPV, what does it cause. How are HSP and HPV different?
  • Herpes simplex virus. Causes cold sores.
  • Human papilloma virus. Integrates into the host's genome and degrades tumor-suppressing proteins, causing cancer.
• Why are giant viruses casting inquiry on how prokaryotes arose as first cells to exist?
  • Because they have giant genomes. How would they be the first cells to arise if they need a host to infect.
• What is unique about retroviruses? Name a retrovirus. Why are they difficult to get rid of, once infected?
  • HIV. They reverse transcribe DNA to integrate into the host's genome in order to take control of the host.
• What does RT stand for and what does it do? Is it a virus enzyme or an cell enzyme?
  • Reverse Transcriptase, it's a virus enzyme that transcribes RNA into DNA.
• What cells does HIV target for infection? How was HIV phylogeny used to solve crime?
  • Targets T-cells, a part of your immune system. By using phylogeny.
• Through all the slides, what three types of viruses integrate into the host's genome?
  • Retroviruses, HPV, Bacteriophages
• Through all the slides, which viruses cause sexually transmitted diseases? How does one protect against them?
  • dsDNA, HPV, HSP. By getting vaccines or practicing safe sex.
• For fun: listen to this 16-minute interview of Carl Zimmer, a famous evolutionary biologist, hosted by Ira Flatow o National Public Radio. © https://www.npr.org/2011/05/06/136057352/carl-zimmer-explores-the weird-lives-of-viruses