Virology Exam 1: Chapter 1-4

What are the recent viral epidemics?

zika, ebola, coronavirus

characteristics of viruses

- Smaller than bacteria
- Dependent on host cell to reproduce
- Genome consists of one type of nucleic acid, DNA, or RNA• - Receptor-binding protein

what is the smallest virus out there?

rhinovirus

what virus was recently discovered that challenged traditional norms?

Mimivirus recently discovered

What are some algae viruses?

Mimi, Pandora, Pitho

own tRNA

Mimivirus and Large Viral Groups have components to produce these

receptor binding protein

Physically attach to a ligand of a cell that it is going to infect
- lock and key mechanism

HIV attaches to

CD4 protein of CD4-positive protein

Plant viruses attach by:

they do not have receptor binding protein interaction: Stalk transfer, mechanical ripped cells through rubbing together like wheat
- Insects feed on one plant and then goes and acts on another plant
- Nematodes: Worms in the soil through the roots

Protein coat (capsid)

The capsid of certain particles is wrapped by an additional membrane stolen from host

Viruses cannot change their shape

Hot Stones in Yellowstones: Archaea - Extremophiles still have viruses that infect them
May have protrusions that extend out: Viruses that affect Archaea

How were bacteriophages discovered?

first isolated in human sewage
- Replicate by introducing their genetic material into host cell

Bacteriophage plaque assays

holes in bacteria on bacterial plate/lawn that indicate viruses present: count the holes and multiply back through the dilution factor

Electron Microscopy in 1931: Very complicated to use

- White background and black film indication of present organisms
- Must take hundreds of photographs to get real shape due to focal point focus: very small window of visualization

1930

2 vaccines to prevent Smallpox and Rabies - Predict Viral attachment proteins

1931

Ernest Goodpasture and Eugene and Alice Woodruff produce fowlpox

1948

Enders, Weller, and Robbins show poliovirus can be grown in non-nervous tissue
- Viruses are very hard to cultivate

The Hershey-Chase Blender Experiment

DNA is the genetic information
1 flask: E.coli infected with phosphate found in nucleic acid 32-P
2 flask: E.coli infected with sulfur (amino acid) 35-S
- Differences in energy
- 32-P was passed down in Virus not 35-S - radioactivity enters cell and is in pellet and not supernatant
- Viruses were used to understand translation, replication, everything except tRNA codon association

HSV-1

highest genetic diversity in Africa and go along with human migration

Panspermia Hypothesis

viruses and other microorganisms are raining down from outer space upon the Earth

LUCA

- Evolved generally from RNA
- Some RNA molecules that can cut themselves 800 + 200 nucleotide strand through ribosine and cleavage sites

Hydrothermal Origin Hypothesis

Deep from ocean vents
- Bacteria virus probably came first

Class 1 viruses are

Viral genes that have closely related homologs in cellular organisms (hosts and given viruses)

Class 2 viruses are...

Viral genes that are conserved within a major group that have distantly related cellular homologs

class 3 viruses are...

No detectable cellular homologs. ORFans

class 4 viruses:

Virus-specific genes that are conserved in a broad group but have no detectable homologs in cellular life forms

class 5 viruses...

Genes shared by many diverse groups of viruses with only distantly related homologs in cellular organisms. VIRAL HALLMARK GENES - related to everything

Parasitoid Wasps and Polydnaviruses

- Wasps deposit eggs and polydnavirus particles into caterpillars
Polydnavirus expresses only wasps genes that paralyze caterpillar
- wasp eggs develop into larvae: need virus for development/survival of wasp egg in caterpillar
- Provirus: Obligatory Mutualism

Plant-Cryptic Virus Collaborations

- Cryptic Viruses: Persistent viruses that form lifelong associations with host without causing disease
- Bioinsecticides: Cryptic viruses can protect plants from insecticides

Bacteriophage "BAM Velcro"

- BAM: Bacteriophage Adhering to host Mucus - head gets stuck in mucus membranes and their tails stick out to infect flowing bacteria and kills them that can possibly infect you.
- Bacteriophage protect metazoan host from invading bacteria

Herpesvirus "protection"

- Latency: Dormant
- Not all bad: latent viruses from immunity against bacterial pathogens

Viruses on human skin

- Microbiome: Total of all Microbiota that live on or inside the human body
- Human Microbiome Project: (The HMP has characterized the microbial communities found at several different sites on the human body: nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract.)
- Metagenomics: study of genetic material recovered directly from environmental or clinical samples by a method called sequencing.

Aquatic Viromes

Influence ecology and diversity, evolution, and health of all aquatic organisms

Bacteriophage therapy

As a weapon against bacterial superbugs - Treatment of bacterial biofilms

Gene therapy

Delivery of functional copies of dysfunctional genes via retroviruses and adenoviruses

Vaccine development

- Edward Jenner's work with cowpox vaccination
- Robert Koch and Koch's postulates

Cancer-causing viruses and virotherapy

- Viral infections linked to approx 12% of all cancers - Example: HPV and cervical cancer - Virotherapy: Oncolytic viruses used to kill cancer cell

Smallpox

the only virus that was broken at the transmission cycle and vaccinated against.

Virus entry route

1. Virus
2. Reservoir (source of Virus)
3. Transmission
4. Portal of Entry
5. Portal of Exit

Indirect spread

Fomites, Aerosols, Blood, Water: Any material separating

What virus is the most contagious?

Measles: just need 1 particle

1880s

Koch formalized germ theory of disease

Why does the Spanish Flu kill so many people?

Attacked healthy individuals - the better your immune system, the better it kills you through a cytokine storm

Influenza is judged based on the previous system from Australia: Viruses are easily synthesized

1918 Pandemic
Killed 20-50 million people: Spanish Fly
Very rare strain: lottery ticket
A unique viral pneumonia

HIV unit 1

about 100 particles need to be exposed
1980s
Retrovirus human immunodeficiency virus (HIV)
No vaccine available to prevent HIV
Take antiviral for 66 years everyday to eradicate HIV

Poliomyelitis: 1916 and 1940s and 1950s

- Mode of transmission: Human feces which was unknown at the time
- FDR was the most famous adult who suffered from polio
- The March of Dimes began in 1938 to raise money for polio treatment and research

Influenza A (H1N1) 2009

First influenza pandemic of the 2000s
Mexico was the epicenter
Outbreak results in various public health initiatives
In U.S 30,000 people die of Flu.

Severe Acute Respiratory Syndrome (SARS)

2002-2003
Emerged in China in the late 2002: Spread rapidly in healthcare setting
Super-spreading: Droplets and it has a longer incubation time than other viral diseases; people traveled without symptoms.

Middle East Respiratory Syndrome-Coronavirus (MERS-CoV): 2012-present

Exact origin unk.
Dromedary Camels studied as a possible animal reservoir

Hantavirus: 1993 (U.S. Four Corners Region) and 2012 Yosemite

Resulting new or emerging infectious disease named hantavirus pulmonary syndrome (HPS)
Isolated from the deer mice - first infected people were Native Americans
Not contagious human-to-human

Schmallenberg Virus in Europe: 2011-2013

Disease of livestock spread via biting midges
Congenital defects in calves and lamb
Major impact on farmers, meat industry, and the food supply

Ebola Virus

Bats thought to be reservoir
Spready rapidly through healthcare and travel
The WHO and United Nations Mission for Ebola Response: 70-70-60 plan: 70% of burials are done safely and 70% of suspected cases are isolated within 60 days
People are more rapidly affected in Africa because people bring sick people home instead of leaving them in the hospital.
40% or more death rate

Coronavirus

3 known strains
Kills 100 people a year

Measles

Once eliminated in the 2000s
Resulting from unvaccinated U.S residents contracting disease traveling to/from affected origins
Andrew Wakefield: published fraudulent report linking MMR Vaccine to Autism
Report lowered confidence in vaccination
Recent outbreaks underscore the importance of viral immunity control through vaccination.

Human Papillomavirus (HPV)

Took 45 years to grow Human Papillomavirus in lab
5 layers deep
Complex and life cycle involves replication in multiple cell types
Produce STEM proteins in basal cells in the skin and get to the last layer of the skin before assembling virus

Discovery of Emerging Viruses in the 21st Century

Size of a typical virus in nm range• Discovery of new viruses increasing rapidly- Metagenomics- Next generation sequencing- Bioinformatics

Viruses and Disease in Humans

Approximately 220 disease-causing viruses
Zoonoses
Contributing factors:
Trafficking of bushmeat
Bioterrorism
Climate change

Swine Flu

Have protrusions that stick out to attach particular swine cells: this is why it does not affect humans because the protein attachments do not match to human proteins
Mutations possible

HIV - unit 2

HIV has 2 attachment proteins: GP120 - Glycoprotein 120 molecular weight Protein & GP30
Both of these proteins have to attach to CD4 on T-Cells and CCR5 - Chemokine Receptor in order to get into body
20% of white male population have a mutation in CCR5 so they are immune
Steals the Golgi Apparatus membrane for envelope

Yellow virus

Self-assembling

West Nile Virus

Pores in structure: expand and contract
Susceptible to clorox and things that lyse it: denature proteins

Polio

Receptors made up of 3 triangles in a chain

Influenza virus

Filamentous virus
Enveloped virus: Get from host - tend not to lyse the cell
Buds from the membrane

Smallpox Unit 2

"Brick"
Family of the most complex virus: 200 proteins w/ 40 enzymes w/ functional DNA polymerase
Replication in the cytoplasm because it can make its own mRNA but Herpes cannot so it needs to replicate in the host's nucleus

Dengue virus

+ssRNA, causes hemorrhagic fever. Mosquito bite causes viremia, fever, rash. Confirm with serology, no vaccines or anti-virals. Increased severity infection if previously infected by another serotypeb

Coronavirus (SARS)

Nomenclature: Looks like it has a crown around it.

Properties of Viruses

Why are particles formed?
- Protection against environment
- Viral attachment protein
- Self-Assembly

Slelf-Assembly

- Folding of polymer chains in packed cubic states
- T=1 Virus, how many viral particles it takes up to make up a virus: simple Virus: 3 proteins
Come together precisely the same way:
Fidelity: Use the same proteins
Smaller genomes for economic purposes: Make giant protein and use a protease to cut it up from small genome

Adenovirus splicing

Splicing discovered in Adenovirus: makes about 30 RNA from genome from splicing

Viral Structure and Morphology

- Capsid and nucleic acid required
- Icosahedral: 20 triangles: stuff the nucleic acid inside the structure before completion
- 1.3-1.6x can hold than actually can but not 2x
Extremely stable
Some have a motor that causes the virus to turn and integrate the double helix DNA to instill the DNA inside the virus particle
- Helical: Synthesis nucleic acid and coat it with protein

Naked vs. Enveloped Viruses

Naked: no envelope
Enveloped viruses: Lipid bilayer stolen from host cell
Spherical and helical types
ALL MAMMALIAN VIRUSES: helical (-) RNA viruses has an envelope

Virus Envelopes

Specific packaging signals direct incorporation of viral genomes into virions
Core proteins: may accompany the viral genome inside the capsid

Non-structural viral proteins

Found in virus infected cells not in the viral particle itself
Regulatory proteins, interactions with the host protein, made by the virus

CORE/Structural proteins:

Binding proteins, etc. INCLUDING all the enzymes that the virus carries. Physical composed of the particle.

envelope formation

Formation of viral envelopes by budding is driven by interactions between viral proteins.

Envelope viruses do not lyse the cell; they just keep secreting viruses until the cell is out of energy

how come mammalian cells dont lyse?

NO MAMMALIAN viruses have protein creation that lyse the cell
- If it does lyse, it is due to our cells
- When you lyse a cell, you alert the immune system: virulence does not want to lyse: bacteria does not have an immune system and can lyse
- Viruses that do lyse in humans replicate fast
- Generally not lytic, slow and have envelope

Viral Genomes consist of either

Single-Stranded or Double-Stranded
- SS viral genomes have length advantage
-- If DNA
- Single strand
- Double strand
If DNA strand is (+) it is equivalent to the mRNA
dsDNA: transcribed into mRNAs by a DNA-dependent RNA polymerase

RNA genome

SS RNA: (+) or (-) sense strange
(+) Sense makes more than 50% of virus proteins in vitro translation system (mRNA equivalent)
(-) Sense makes less than 50% of virus proteins in vitro translation system: every (-) sense strand has a RNA polymerase that makes (+) sense strand

RNA polymerase

enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template

does not need primer like DNA polymerase does but DNA polymerase are more progressive and more accurate (proofreading)

ambisense RNA

SINGLE STRANDED (-) RNA VIRUSES: Each segment has a region that is positive sense and a region that is negative sense - possessing two ORFs but in opposite directions! Separated by intergenic region

Retrovirus genome technique

has (+) sense that never gets translated: Uses reverse transcriptase to replicate (-) DNA and from that (+) DNA then integrated to host genome changing it:

retroviral DNA is referred to provirus.

The host cell treated the viral DNA as part of its genome and transcribes and translates the viral genes along with the cell's own genes producing the proteins required to assemble new copies of the virus.

Viral genomes can be

linear or circular
monopartite: nonsegmented
multipartite: segmented
- RNA Virus are usually segmented
- Coronavirus is SS RNA virus it has the most significant single stranded RNA genome known: 30,000 nucleotides long
- Influenza A has 8 segments

What are some viruses that challenge the definition of a virus?

Giruses: GIANT DNA-containing viruses
Mimivirus
Mamavirus
Virophages: subviral particles within the other big viruses (satellite viruses)
-------- Sputnik: depends on other virus
Small, DS DNA viral lagged that require the co-infection of another virus

Taxonomy

firstly based on size but now named after
- disease
- morphology
- places
- discoverers
- acronyms

Baltimore classification

a classification scheme that groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus
1. dsDNA
2. ssDNA
3. dsRNA
4. ssRNA (+)
5. ssRNA (-)
6. ssRNA RT (+)
7. dsDNA RT

The International Committee on Taxonomy of Viruses (ICTV)

Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species

Additional Lower Hierarchical Levels

Species: Polythetic class viruses that constitute a replicating lineage and occupy a particular ecological niche. Having many, but not all properties in common.

Strain: Different isolates of the same virus
Variant: Differs from original wild-type strain

Syndrome

Set of physical signs and symptoms that occur together

Capsid information

- Capsid protects nucleic acid genome of virus from nucleases
- Nucleocapsid: Capsid + Genome
----- May or may not have this

Can have 2 capsids

Outer envelopes

Cell membranes: made up of a variety of cell particles

Infectious dose (ID)

the minimum number of microbes necessary to cause an infection to proceed

Different membranes for viruses

- any part of the cell
Herpes uses nuclear membrane\
-- Influenza always uses outer cell membrane

Genes code for

- capsid protein / viral attachment protein

virus genome length

ssRNA: 2300 to less than 31000
dsRNA always segmented (135)
- Smallest: 3
- Largest: 13
Giruses 300 kb and up to 1200 kb. Can encode up to 900 proteins

Replication, Transcription, Translation

are localized processed in eukaryotic cells - central dogma

Translation of processed mRNAs in cytoplasm

5' to 3' directionality of nucleic acid synthesis

DNA replication and RNA transcription within nucleus

Herpes do not have enzymes for mRNA but can make its own tRNA

Pox Virus can replicate in cytoplasm w/ leading and lagging strands

Central Dogma of Molecular Biology

our DNA is used to create RNA then used to make protein

Introns vs. Exons: Introns are removed

some viruses do make small RNA for what?

regulation of replication

some viruses have promotors and enhancers

Enhancers: Increase level of transcription

Distal control regions: Bends/folds to meet promotor

Most viruses (small ones) do leading strands

Most RNA viruses have own RNA polymerase and ...

replicate in the cytoplasm making everything needed like mRNA

Do not have introns or exons: no way to get them out