World of Viruses: Midterm

5′ cap
A cap on the 5′ end of mRNAs. Discovered by A.J. Shatkin and B. Moss in 1975. Important for translation.
?X174
An ssDNA virus with a circular genome.
A.E. Smith
In 1984, discovered nuclear localization signals.
A.J. Shatkin and B. Moss
In 1975, discovered 5′ caps of mRNAs in reovirus and vaccinia virus.
Achilles
A Spartan who fought in the Trojan wars. He was killed by the brother of Hector, from an arrow to the heel.
Acidianus bottle virus
A virus, 230 nm long, 75 nm wide. Affects archaebacteria hosts.
Acylation
A post-translational protein modification. Addition of lipid components to the polypeptide. Makes a protein hydrophobic.
Adenoviridae
A family of isometric viruses. 80 – 110 nm in size. Includes fowl adenovirus 8.
Adenovirus
A genus of dsDNA viruses with a linear genome. Affect birds. Has isometric symmetry, T = 25. Has twelve pentons, each composed of 5 protomers. Has twelve hexons per triangular face, for a total of 240, each composed of 3 protomers. Has fibres which are receptors for cells. Can be used to make vaccines. Inhibits the immune system response of apoptosis.
Adolf Mayer
In 1886, asked if tobacco mosaic disease was caused by an infectious agent. Used his tumb to transfer the virus from a diseased plant to a healthy plant, causing it to become diseased.
Alex Carrel
Grew organs in rich media. Won a Nobel Prize in 1912. Had problems with contamination; competition between virus and bacterial or fungal contaminations.
Alfred Hershey and Martha Chase
In 1952, proved that DNA was the genetic material for bacteriophage T2. Blended phage T2 to demonstrate that labelled DNA but not labelled protein entered bacteria to initiate virus ifnection.
Alice Woodruff and Ernest Goodpasture
In 1931, grew fowlpox virus on the chorioallantoic membranes of chicken embryos. The poxvirus resulted in thickening of the membrane, resulting in distinct pocks on the membranes; each pock is one viral infection. Allowed for testing of Koch’s postulates for viruses. Studies extended to growth of vaccinia and herpesvirus in chicken embryos or tissues.
Alimentary tract

Gastrointestinal

A portal of entry. The virus is eaten. Poliovirus, norovirus, and diarrhea can infect through this point.

Ambisense
A virus with part of the genome is +RNA, and part of the genome is -RNA.
American Revolutionary War

1775 – 1776

A war between America and Britain. The British army held Quebec from American invasion due to smallpox. False British maps were used to trick Americans into thinking their march would be shorter, and winter weather caused many soldiers to go AWOL or die from harsh conditions.

Amino acid
A type of molecule. There are 20, with functional groups providing chemical characters such as charge and polarity.
Animal viruses
More difficult to work with because animals are expensive, the virus many need specific tissues, there may be other diseases, nutritional problems, or latent infections, as well as ethical issues.
Anthrax
A disease caused by bacteria which affects cattle. Robert Kock discovered their endospores.
Antonie van Leeuwenhoek
A Dutch scientist from 1683 who invented a high resolution light microscope with excellent visual acuity. Described “little animalcules” in water droplets.
Anus
A portal of entry. HPV and HIV can infect through this point.
Apoptosis
A defense mechanism of the cell against the virus, but it can be caused by the virus in order to replicate itself.
Arenavirus
A genus of negative RNA viruses.
Arterivirus
A genus of positive sense RNA viruses.
Arthropod borne
Intravenous vector borne. Yellow fiver virus, West Nile virus, and Eastern equine encephalitis virus can infect through this point.
Arthur Kornberg
In 1967, generated the ?X174 genome with purified enzymes and viral DNA template.
Asfarivirus
A genus of dsDNA viruses.
Assembly
The fifth sequelae of virus replication. There is self-assembly of viral nucleic acids and proteins.
Astrovirus
A genus of positive sense RNA viruses.
Attachment
The first sequelae of animal virus infection and virus replication. Common to all viruses. The virus attaches to a cell receptor. Receptors can be highly specific or highly generalized. Viruses can infect cells with the receptor, and cannot infect cells lacking the receptor. Viruses cannot infect cell in which the virus was removed, or treated with antibodies of the receptor. Viruses can infect cells into which the receptor was introduced by transformation. The more the amount of virus, the more likely that attachment will occur.
Autism
It is not correlated with vaccines.
Avian influenza virus
A virus. During attachment, it recognizes ?2, 3 linkage between sialic acid and galactose.
Axial rise (p)

The raise in height between each subunit.

P = ? ? p

Bacterial virus
Research is cheap, and they are easy to grow and handle.
Bacteriophage
A virus with a tail structure; it is a combination of helical and spherical structure.
Bacteriophage lytic cycle
Cell receptor and phage interaction is very specific, sometimes strain specific.
Bacteriophage replication

Has three stages: eclipse phase, maturation, and latent phase.

1. Attachment to host cell receptor

2. Localized lysis with viral lysozymes, and penetration and injection of virus DNA into the cell

3. Early mRNA is transcribed and viral enzymes are syntehsized

4. Nucleic acid replication

5. Late mRNA syntehsis

6. Late protein synthesis

7. Formation of empty precapsids

8. Assembly and DNA packaging of precapsids

9. Lysis of cell wall with viral lysozymes

10. Release of viral particles through the rent in the wall

11. Infection of adjacent cells, repeating the lytic cycle

Baculoviurses
Viruses that affect insects.
Baltimore classification
Classification of viruses based on nature of their genomes and mRNA synthesis.
Bangalali Youngi
An Ebola survivor from Liberia in 2016; this marked Ebola transmission as no longer a global health risk.
Baozhong Meng
A professor at University of Guelph doing research on grapevine stem pitting disease virus.
Beet curly top virus
A virus in the family Geminiviridae. Affects beets and tomatoes.
Beluga whale coronavirus
A positive sense ssRNA virus in the family Coronaviridae. Genome is 31.7 kb.
Binomial nomenclature
The species and genus of a living organism.
Biosynthesis
The fourth sequelae of virus replication. Viral nucleic acids and proteins are synthesized. Includes transcription, translation, and replication.
Birnavirus
A genus of dsRNA viruses with a linear, segmented genome.
Bornavirus
A genus of negative sense RNA viruses.
Bronchiolitis
Inflammation of the small airways. Can be caused by RSV.
Budding
The method of release of enveloped viruses. The virus buds through the endoplasmic reticulum, Golgi body, or plasma membrane. The cell membrane becomes the viral membrane surrounding the nucleocapsid.
Bunyavirus
A genus of negative sense RNA viruses with a linear, segmented genome.
Calicivirus
A genus of positive sense RNA viruses.
Camelpox virus
A virus that affects pigs and camels.
Capillary

Drug injetion

A portal of entry. HIV, rabies, and flaviviruses can infect through this point.

Capsid

“Box”

A component of the nucleocapsid. A hollow protective protein shell surrounding the core. Composed of capsomeres which self-crystallize into the capsid’s final shape and size. The nucleocapsid morphology and symmetry is based on the nature of capsid protein interactions. Its structural integrity depends on the environment. Helps assemble the genome. Protects the genome outside of the cell, and dissociates inside the cell to release the genome. In naked viruses it is needed for attachment to cell receptors, indicating host specificity.

Capsid protein (C)
A component of the Zika virus virion. Forms the icosahedral capsid.
Capsomere
The protein structural unit of a virus capsid. Visible with an electron microscope. Consists of protomers. Includes hexons and pentons.
Carbohydrate
A component of a virion. Associated with protein and/or lipids. Includes glycoproteins and glycolipids.
Carlos Finlay
A Cuban who suggested in 1881 that mosquitoes could transmit yellow fever.
Case
An individual who is suspected to have the disease in an outbreak.
Chamberland filter
Invented by Edoard Chamberland in 1884. A filter used to sterilize water, using an unglazed ceramic powder. Effective in removing large bactiera, protozoa, and fungi from water, making it safe to drink. Cannot filter out viruses.
Chicken embryo
Found in fertilized chicken eggs. Susceptible to many viruses, making them good hosts for culturing viruses.
Chicken sarcoma virus
A disease discovered by Peyton Rouse in 1910. Symptoms include avian muscle cancer. The first virus found to cause cancer.
Chickenpox
A childhood illness that used to be common, but is now preventable through a varicella vaccine. Caused by varicella zoser virus. Symptoms are itchy spots. It can cause dangerous complications in newborns, adults, and pregnant women. Before the development of the vaccine, it caused hospitalization in 11,000 Americans every year.
Cholera
A disease. The person has diarrhea and can die from dehydration, but can be saved by forced rehydration. Every year, 100,000 people die from cholera. It is spread by contaminated water.
Circoviridae
A family of viruses. Includes coconut foliar decay virus.
Circovirus
A genus of isometric ssDNA viruses with a circular genome. 17 nm in diameter.
Classification
Grouping of species according to shared physical properties. Includes Baltimore classification.
Closed structure
Lenth of the nucleic acid dependson the structure. Isometric viruses have closed structure. There is a maxmum amount of nucleic acids which can fit in the capsid.
Closteroviridae
A family of helical viruses. 12 x 2200 nm in size. Affects plant hosts.
Coconut foliar decay virus
A DNA virus in the family Circoviridae. Has complete genome, 1.3 kb.
Coconut virus
An ssDNA virus in the family Nanoviridae. Genome is 1.3 kb, with 3 open reading frames.
Colony
A group of bacteria growing on an agar plate large enough that you can see it. Millions of bacterial cells can arise from one cell.
Communicable disease
In ancient times, it was thought they were caused by divine intervention, imbalances of elements, miasmas, vapours, or spirits.
Complex
A shape of virion. Has limit or no symmetry. A mixture of isometric and helical symmetry. Includes pox virus, rabies virus, T4 phage, pandornavirus, flowpox virus, and enterobacteria phage.
Conjunctiva

Eyes

A portal of entry. Some herpesviruses and adenoviruses can infect through this point.

Constantin Levaditi
In 1906 used chicken embryos to grow microorgnaisms. In 1909 showed that the poliomyelitis agent was a virus using tissue explants. Opened a small hole in the chicken egg to insert the virus. This method is used to make influenza vaccines.
Contagion
A movie abotu a disease, based on a virus.
Core
A component of the nucleocapsid. The DNA or RNA genome, and core nucleoproteins. The viral chromosome encodes all viral proteins, structural, and non-structural.
Coronaviridae
A family of viruses. Includes beluga whale coronavirus and murine hepatitis JHM.
Coronavirus
A genus of positive sense RNA viruses.
Coupled transcription
Translation occurs at the same time as translation, with the ribosome attaching to mRNA while it is still being transcribed. Occurs in prokaryotes.
Coxsackievirus A 16
A virus in the family Picornaviridae. Causes hand-foot-and-mouth disease.
Craig Venter
In 2003, chemically synthesized ?X174 ssDNA genome in vitro from oligonucleotides. This was the first time DNA was synthesized.
Croup
A childhood illness most common in children under the age of 5. Caused by parainfluenzavirus. Symptoms are a tight cough that sounds like a barking seal, caused by inflammation of the upper airways. If breathing becomes severely impaired, hospitalizaton may be required. Most children recover in about a week.
Cytopathology

“Cell illness”

A criterion for demarcation of viruses into species. Cellular symptoms of a disease. Includes lysis, or occlusion bodies. Can be seen with microscopy.

Dead-end host
A host which can contract a virus, but cannot transmit it. Horses are a dead-end virus for West Nile virus; horses can be affected by the virus, but a mosquito cannot acquire the virus from a horse.
Delta agent
Has a subviral genome.
Demarcation criteria
Things you can look at to determine taxonomy. Decided by the ICTV. Includes cytopathology, physiochemical, genome, proteome, and morphology.
Dmitri Ivanovsky
In 1892, demonstrated that tobacco mosiac disease is caused by a filterable virus. In his experiments he filtered matter from an infected plant, and found that the fluid was still able to infect healthy plants. A healthy plant was infected with the fluid from another healthy plant as a control. Concluded that the disease is caused by something very small.
Direct release
The method of release in naked viruses. The cell lysis, or there is apoptosis.
Disease
A nomenclature system for viruses. Viruses are named for the disease they cause. Example: encephalitis virus, sarcoma virus.
DNA
A compnent for DNA replication and transcription. Used as the template.
DNA binding protein
A component for DNA replication.
DNA-dependent RNA polymerase (DrRp)
Needed by DNA viruses for transcription of mRNA.
DNA helicase
A component for DNA replication.
DNA polymerase
A component for DNA replication.
DNA virus
Includes ssDNA and dsDNA viruses, which can have linear or circular genomes. Genome size is 1.3 – 1200 kb. Needs DdRP to transcribe mRNA. Needs DNA polymerase (host or viral) to replicate the genome. The 5′ cap is added to mRNA in the nucleus.
dNTP
A type of molecule, a component of DNA. Includes dA, dG, dT, and dC.
Double stranded DNA (dsDNA)
A type of DNA virus. Can have more variation in structure than ssDNA viruses. The dsDNA is transcribed into mRNA. The dsDNA is replicated into dsDNA for genome replication.
Double stranded RNA (dsRNA)
A type of RNA virus. Genome is always segmented. The dsRNA is transcribed into mRNA. The dsRNA is transcribed into dsRNA for genome replication.
E. Volkin and L. Astrachan
In 1956, indirectly discovered mRNA while studying T2 phage.
Early protein
Proteins produced early in viral infection. Enzymes that interact with host defenses. May prevent apoptosis.
Ebola restin
A virus that affects monkeys, and not people.
Ebola virus (EBOV)
A simple, helical negative-sense ssRNA virus in the genus Ebolaviurs, family Filoviridae. Has a complete genome, 18.9 kb. The name of this virus comes from the Ebola River in the Congo, where it was first isolated. There are several species, including Zaire, Sudan, Tai Forest, Bundibugya, and Reston. The virion is long and filamentous, 90 nm in diameter and 1000 nm in length. It has an envelop with GP protein surface projections. Transcription begins at the 3′ end, and can halt or continue at each point between reading frames, causing polypeptides near the 3′ end to be most numerous than polypeptides near the 5′ end. Protein components in the virion, in order of most to least translated are: NP, VP35, VP40, GP, sGP, VP30, VP24, and L. The virus can be detected in blood serum, even in people who are not sick. It can be transmitted by fruit bats, especially when eaten. It can last for 565 days in human semen.
Ebola virus outbreak
Occured in Sierra Leone in 2013 – 2016. Caused 28,646 cases and 11,323 deaths. The virus peaked in November 2014, and the last case was in March 2016.
Ebolavirus
A genus of viruses. Includes Ebola virus.
Eclipse phase
The first phase of bacteriophage replication. There is no infectious virus produced. Virus is not detectable in this phase.
Edouard Chamberland
Invented the Chamberland filter in 1884.
Egyptian priest
Images of a priest were found, made in 1403 – 1365. Shows evidence of an injured leg from polio virus.
Emile Ouamouno
The index case of Ebola; he contracted the disease in December 2013. He was a bat hunter, and may have contracted the disease from eating bats.
Emiliania huxleyi
An organism affected by phycodnavirus.
Endemic
When a disease is present in a local area.
Enterovirus
A genus of RNA viruses.
Entomopoxvirus
A genus of complex brick shaped viruses. 450 x 250 x 250 nm in size. Affects insect hosts.
Envelope
Present in enveloped viruses. A lipid and protein membrane which surrounds the nucleocapsid. May have peplomers. Provides surface proteins for attachment to cell receptors, dictating host specificity. Does not provide very much protection; it can dry out, killing the virion. Dictates how the virus can enter a cell.
Envelope protein (E)
A component of the Zika virus virion. A dimer.
Enveloped virus
A virus which has an envelope. The nucleocapsid is usually flexible, to prevent shearing. Exit the host cell by budding. Transmission must be quick because the envelope can dry out. Includes herpesvirus and HIV.
Epidemic
When a disease is present worldwide. HIV and influenza are epidemic.
Ernst Ruska and Max Knoll
Invented the electron microscope in 1933. Ernst Ruska is the brother of Helmut Ruska, and won the Nobel Prize in 1986.
Escherichia coli
Genome is 4,600 kb.
Eshmuna Code
Written in 2300 BC. It mentions rabies.
Eukaryotes
Cells have a nuclear membrane, endoplasmic reticulum, and Golgi body. There is nuclear processing including splicing, addition of 5′ cap and 3′ poly-A tails. mRNA has cytoplasmic translation and is monocistronic. Ribosomes are free as well as membrane-bound. No cell wall, plant and yeast cells excepted.
Eukaryotic initiation factor 4G (eIF4G)
A cellular cap binding protein for the 5′ cap of cellular mRNAs in eukaryotes. It is needed for ribosomes to recognize a cellular mRNA for translation. It is cleaved by viral proteases of poliovirus, causing cessation of translation of host mRNAs.
F. Bawden and N. Price
In 1937, crystalized tobacco mosaic virus, and found that it contained protein and nucleic acid.
Family

-viridae

A taxonomic level. There are 103 families of viruses.

Felix d’Herelle
A Quebecois scientist who discovered plaques in Shigella lawns in 1915.
Fifth disease

Slapped cheek disease

A childhood illness that first causes mild cold symptoms, then causes a bright red rash on the face, and may also appear on the torso, arms, or legs. Once rash appears the child is usually no longer contagious, and it lasts for seven to ten days. Caused by human paravirus B19. Very common; up to 60% of people have had it by age of 19.

Filoviridae
A family of viruses. Includes Ebola virus.
Filovirus
A genus of negative sense RNA viurses. Rod-shaped or helical. 80 x 14 ?m in size.
Filterable virus
In the 1880s all infectious agents were called “viruses”, at that time the term “filterable virus” was used for true viruses.
Flaviviridae
A family of isometric viruses. 40 – 60 nm in size, with an envelope. Includes Zika and hepatitis C virus.
Flavivirus
A genus of positive sense RNA viruses with a linear, non-segmented genome. Includes Zika and yellow fever.
Flu
A disease caused by influenza virus. Symptoms are high fever, chills, body aches, extreme fatigue, nausea, and vomiting. Most children recover on their own, but the flue can lead to complications including pneumonia, especially in younger children. Annual flu vaccinations are recommended for children aged 6 months and older.
Fomite
A non-living thing which can transmit a virus, such as blankets, clothes, or linens. Things which are not themselves, corrupt, but can foster the essential seeds of contagion, and cause infection.
Foot and mouth disease virus
A disease of cattle and goats. Discovered by Fred Loeffler and Paul Frosch in 1898.
Forced rehydration
Treatment of plenty of water with disolved sugar and salt. Used to treat hemorrhagic fever and cholera.
Fowl adenovirus 8
A DNA virus in the family Adenoviridae. Has a complete genome, 45.1 kb.
Fowl avian leucosis
A disease discovered by Wilhelm Ellerman and Olaf Bang in 1908. Symptoms include avian cancer.
Fowlpox
A complex virus in the family Poxviridae. 330 x 280 x 200 nm in size. Affects fowl, causing a pox. Each pock is the site of a single viral infection.
Frank McFarlane Burnet
In 1932, develoepd the chicken embryo as a host for some animal viruses, such as canarypoxvirus.
Fred Bawden and Norm Pirie
In 1937 found that tobacco mosaic virus crystals contained 6% RNA.
Fred Loeffler and Paul Frosch
Discovered foot and mouth disease in cattle in 1898.
Fred Twort
Discovered glassey transformation of micrococci in 1915. Noticed that bacteria were being made to lyse.
Frederick Sanger
In 1977, sequenced ?X174 ssDNA genome, which has 5,375 nucleotides.
Fusion
A way that an enveloped virus may penetrate a cell. The envelope fuses with the plasma membrane, releasing the nucleocapsid into the cell. Includes measels virus, herpesvirus, and HIV.
Geminiviridae
A family of viruses. Includes beet curly top virus.
Geminivirus
A genus of ssDNA viruses with a circular genome. It looks like two parts stuck together.
Generalized eukaryotic virus replication

Only a small fraction of virions produced are infectious.

1. Attachment. Viral glycoproteins bind to receptors on the host cell’s membrane

2. Penetration. The viral core enters the cell

3. Uncoating. The viral genome is uncoated and the viral proteins degrade

4. Genome transcription. The viral genome is transcribed into mRNA

5. Translation. Enzymes are produced early on, then later on capsid proteins. The transcripts are translated into new capsid proteins and envelope glycoproteins

6. Genome replication. The viral genome is replicated

7. Transport of glycoproteins to cell membranes (enveloped viruses only). Glycoproteins are transported in vesicles to the host plasma membrane

8. Virus assembly. New virions assemble from replicated genome and capsid proteins. Genome, capsid, proteins, and envelope all assemble

9. Release from the cell.

Genome
A criterion for demarcation of viruses into genera and families. Whether the genome is DNA or RNA, positive, negative, or double stranded. Often the first demarcation criteria to be checked.
Genome replication
A component of biosynthesis. Replication of the viral genome.
Genus

“-virus

A taxonomic level. There are 455 genera of viruses.

Geography
A nomenclature system for viruses. VIruses are named after places. Example: Powassan virus.
Girolamo Fracastoro
An Italian scientist from 1546. Said that epidemic diseases were due to infection with transferable minute bodies. Defined fomites.
Glassey transformation of micrococci
A bacteriophage discovered by Fred Twort.
Glycolipid
A component of a virion. Found in the envelope.
Glycoprotein

“Sugar protein”

A component of a virion. Found in the envelope or the capsid.

Glycoprotein (GP)
An open reading frame in the Ebola virus genome. Encodes a major envelope homotrimer protein, the fourth most numerous polypeptide. A surface protein that latches onto the cell. It is sensed by the immune system, which produces antibodies to cover the glycoprotein. Assists in budding of nucleocapsids from cells.
Glycosylation
A post-translational protein modification. Carbohydrates are added to polypeptide. Only certain amino acids can be glycosylated.
Golgi protease
A peptide that cleaves the Zika virus polyprotein.
Goose hepadnavirus
A dsDNA virus with 3.0 kb, with 4 open reading frames.
Grapevine stem pitting disease virus
Research is being done on this virus by Dr. Baozhong Meng at the University of Guelph.
Great flue pandemic
An outbreak of Spanish flu that occurred in 1918, causing 20 – 70 million deaths, mostly in India.
Greek
A nomenclature system for viruses. Viruses are named with Greek words. Example: rhabdovirus (rod).
Guy Carleton
Commanded the British army in the American Revolutionary War.
H.H. McKinney
In 1926, isolated variants of tobacco mosaic viurs based on lesion morphology.
Haemaglutinin (HA)
A surface protein of influenza virus. Trimeric. Has 16 subtypes. Causes red blood cells to stick together.
Hand-foot-and-mouth disease
A childhood illness that causes fever and blisters on the inside of the mouth, palms of the hands, buttocks, and soles of the feet. Caused by coxsackievirus A 16. Tends to spread among children during summer and early fall. Most children recover in a week to ten days.
Hector
A Trojan protecting Helen from being returned to the Greek King Menelaus. He was described as being very mad, and having foam coming from hist mouth, suggesting that he had rabies! He might have spread the rabies virus to Achilles.
Heinz Fraenkel-Conrat and Beatrice Singer
In 1957, did a classic experiment that proved that RNA was the genetic material in tobacco mosaic virus. At this point in time it was known that DNA was the genetic material in living organisms. Dissociated two different mutants of the virus into protein and RNA, then re-associated the protein with the opposite RNA. Plants infected with tehse new viral agents produced the virus phenotypes of the RNA donor.
Heinz Fraenkel-Conrat and Robley Williams
In 1952 dissociated tobacco mosiac virus agent into protein and RNA fractions, and found that they occurred in a 200:1 ratio. They could re-associated protein and RNA into infectious tobacco mosaic agent.
HeLa cells
An immortalized cell culture collected from the cervical cancer of Henrietta Lacks in 1951. These cells are still alive.
Helical

Rod-shaped

A shape of virion. Has radial symmetry. Capsid proteins wrap around the core in a helical pattern to form a rod. May only use one protomer. Includes tobacco mosaic virus, infuenza virus, and Ebola virus. Have open structure.

Helicase
A component for transcription.
Helmut Ruska
Observed tobacco mosaic virus using an electron microscope in 1939. The brother of Ernst Ruska.
Hemorrhagic fever
Caused by Ebola virus. Blood oozes from pores. Vomiting and diarrhea, and the person can die from dehydration, but they can be saved by forced rehydration.
Henle/Koch’s postulates

Proposed by Robert Koch. Prove that an agent causes a specific disease.

1. Every diseased organism has the agent, and every healthy organism lacks the agent

2. The agent can be grown in a “pure culture”

3. Infection of a healthy organism with the pure culture of the agent should cause the same disease

4. The diseased organism shows evidence of the agent, and the agent can be re-isolated and cultivated and shown to be the same.

Henry Bouquet
A colonel who in his correspondence with Jeffrey Amherst, said he would try to inoculate Native Americans with smallpox using blankets.
Hepadnavirus
A genus of dsDNA retroviruses with a circular genome. Some parts of the genome are double-stranded, and some parts are single-stranded. The DNA enters the nucleus, is repaired to become fully ddDNA, then it is transcribed into +RNA, then into -ssDNA, then transcribed into dsDNA that is transcribed into mRNA. The mRNA is then exported from the nucleus for translation. Pleomorphic; some are long, and some are spherical.
Hepatitis
A disease of the liver. Can be caused by many viruses.
Hepatitis A virus
A virus in the family Picornaviridae.
Hepatitis B virus
A DNA virus.
Hepatitis C virus
An RNA virus in the family Flaviviridae. Has a complete genome, 9.4 kb.
Herpesviridae
A family of isometric viruses. 100 – 110 nm in size. Includes varicella zoser virus and human herpesvirus 2.
Hepevirus
A genus of positive sense RNA viruses. Isometric, T = 16.
Herpesvirus
A genus of dsDNA viruses. 200 nm in diameter. Causes a latent infection, activated by stress hormones; can cause cold sores. Once a person contracts it, they have it for life. A latent virus, stimulated to reproduce by stress hormones. Isometric, with 12 pentons composed of the same protomer as the 150 hexons. Only one gene is needed. Has larger capsomers than adenovirus, and is larger than adenovirus, despite having a smaller T value. Has an envelope with a tegument. Buds through the endoplasmic reticulum or Golgi body when released. During translation there is a scaffold that disintegrates once capsids are formed.
Hexon
A capsomere of any shape found within the 20 triangular faces of an isometric virion. Generally six-sided, and consisting of 6 protomers. If you have only hexons, they make a flat surface.
Host
A nomenclature system for viruses. Viruses are named for their hosts. Example: tobacco mosaic virus, human herpesvirus.
Host range
A phenotype of a virus. A criterion for demarcation of viruses into species. The range of hosts that a virus can infect. The host species, tissue, and cells affected. In tobacco mosaic virus, some mutants can also infect tomato.
Human
Genome is 3.038 billion bp, with 25,000 open reading frames. Humans are susceptible to about 100 viral diseases.
Human enterovirus-D68
A virus related to polio. Children are susceptible to it, because they don’t have immunity. Symptoms can include paralysis and a runny nose. There was an outbreak in BC in September 2016, with 8 confirmed cases.
Human herpesvirus 2 (HSV2)
A DNA virus in the family Herpesviridae. Has a complete genome, 154.7 kb.
Human immunodeficiency virus (HIV)
A complex RNA virus in the family Retroviridae. 110 nm in diameter. Has a complete genome, 9.2 kb. Transmitted sexually; there must be tears in sexual organs for transmission. Capsid consists of two halves of an icosahedron, separated by a tubular layer of hexons. Has an envelope.
Human influenza virus
During attachment, it recognizes ?2, 6 linkage between sialic acid and galactose.
Human papillomavirus (HPV)
A virus that is transmitted sexually. The cause of most cervical cancer. There are 9 differen types.
Human papilloma virus type 52
A DNA virus in the family Papoviridae. Has a complete genome, 7.9 kb. Causes cervical cancer.
Human paravirus B19
A virus in the family Parvoviridae. Causes fifth disease.
Human rhinovirus 16
An RNA virus in the family Picornaviridae. Has a complete genome, 7.1 kb.
Icosahedron
A polyhedron with 12 pentagonal apexes, 20 triangular faces, and 30 edges. Has 5:3:2-fold axes of symmetry. Similar to a geodesic dome, or a soccer ball. Triangular faces may each contain one or more hexagons, depending on the size of the icosahedron and the triangulation number.
Immortalized cell culture

Continuous culure

A kind of tissue culture. Cells are grown on fresh medium. Not all cells are capable of this. Includes HeLa cells.

Inclusion body
Virogenic stroma areas of virus assembly. Clusters of capsids where a virus is replicating in a cell. Visible by light microscopy.
Index case
The first human individual confirmed to have the disease in an outbreak.
Infectious pancreatic necrosis virus (IPNV)
A virus that affects fish.
Influenza virus
An RNA virus is the famliy Orthomyxociridae. Has an ssRNA segmented genome with 8 segments, encoding 8 nucleocapsids. May be transmitted by ducks. Symptoms may be similar to the cold or to the flu. Has a membrane. Can be pleomorphic. Virion has two surface proteins: haemaglutinin and neuraminidase. The receptor for virus attachment is sialic acid. Human and avian influenza viruses can both affect pigs; there can be recombination of viral genes in pig cells infected by both. Buds through the plasma membrane when released. The 5′ cap of the genome is stolen from cellular mRNAs, and the poly-A tail is encoded.
Influenza H5N1
A virus that affects ducks. There was an outbreak recently in St. Catherine’s.
Insect polydnavirus
A dsDNA virus with a circular, polydisperse genome.
Internal ribosome entry site (IRES)
A sequence of poliovirus mRNA that acts like a 5′ cap, allowing the ribosome to recognize it and translate mRNA.
International Committee on Nomenclature of Viruses (ICNV)

1966 – 1973

First meeting was at the Ninth International Microbiology Congress in Moscow. Has accepted rules for viral classification.

International Committee on Taxonomy of Viruses (ICTV)

1973 – present

Tries to classify all viruses. Responsible for updated reports of the ICTV. The most recent is the 9th report, 2011. Define criteria for demarcation of viruses.

Iridoviridae
A gamily of isometric viruses. 170 nm in size.
Iridovirus
A genus of large dsDNA viruses with a linear, circularly permuted genome. Forms iridescence when crystalized. Insect larvae infected have iridescence.
Isometric

Spherical

A shape of a virion. Has icosahedral symmetry. Allows for limited viral genome; the capsid is composed of one or two polypeptides. All have 12 penton capsomers, and hexon capsomers within the 20 triangular faces, number indicating the triangulation value of the virus. Have closed structure. Includes rhinovirus, poliovirus, flavivirus, herpesvirus, Zika virus, and adenovirus.

James Hillier, Albert Prebus, and Eli Franklin Burton
Built the first practical electron microscope prototype in the USA in 1938.
James Kates
In 1970, discovered polyadenylation of mRNAs in vaccinia virus.
Jeffrey Amherst
A British general who in 1763 suggested germ warfare by distributing smallpox-contaminated blankets to the Native American allies of the French. Wrote a letter to Colonel Henry Bouquet discussing it.
Jesse Lazear

1866 – 1900

Worked on mosquito transmission of malaria. Worked on rearing and infecting mosquitoes. Worked with Walter Reed in yellow fever research, and was interested in testing Dr. Finlay’s theory of mosquito transmission. Could not satisfy Koch’s postulates using the suspected bacteria, Bacillus icteroides. Began experiments using infected mosquitoes, allowing them to infect volunteers at different days post infection. Only mosquitoes which had been infected for 12 days or more could transmit the disease. He died from yellow fever himself at age 34.

John Enders
Grew poliovirus in African green monkey kidney cells. Won a Nobel Prize in 1954.
Justin Trudeau
Raised money for HIV, malaria, and tuberculosis research, to find new drugs and treatments.
KDEL
A signal which retains proteins in the endoplasmic reticulum.
Kilbase (kb)
1000 base pairs. About the size of one gene.
L.K. Miller
In 1994, discovered the first inhibitor of apoptosis (IAP) in P38 baculoviruses.
lamB
The bacterial binding protein for maltose, and important energy source. The receptor for lambda phage. Bacteria which lack this receptor are resistant to lamba phage.
Lambda phage
The first virus discovered to attack bacteria. Its receptor is lamB. Causes lysis of bacterial cells.
Late protein
Proteins produced late in a viral infection. Proteins for virus structure and release, produced in greater amounts than early proteins.
Latent phase
The third phase of bacteriophage replication. The period prior to extracellular virus release.
Latin
A nomenclature system for viruses. Viruses are named with Latin words. Example: baculovirus (stick).
Left-handed helix
No screws for carpentry have a left-handed helix, but if they did, if you turned it clockwise, the screw would come out of the wood.
Ligase
A component for DNA replication. Puts together Okazaki fragments.
Limiting dilutions
Can be used to clone a virus for a pure culture. A solution containing a virus is diluted until there is one virion.
Lipid
A type of molecule. Amphipathic with polar and apolar regions. Forms the envelope of enveloped viruses. Naked viruses have no lipids in their virion.
Lipid bilayer
A macromolecule of lipid proteins. Has hydrophobic interactions.
Listeria monocytogenes
A disease that contaminates deli meats, cheese, and mushrooms.
LISTEX
A bacteriophage product that is effective against Listeria monocytogenes.
Lytic infection
After uncoating, the virus multiplies and lysis occurs, releasing new viruses. Viruses produced infect adjacent cells, and move through tissues.
Malaria
A virus transmitted by mosquitoes.
Marcus Terentius Varro
A Roman scholar/philosopher from 100BC. The first microbiologist/epidemiologist/virologist. Suggested that people avoid swamps, which he said bred minute creatures, which could not be seen but which floated in the air, and entered via the mouth and nose to cause diseases. Actually it was mosquitoes breeding in swamps that were spreading disease.
Martinus Beijerinck
A Dutch scientist who in 1898 carried on Dmitri Ivanovsky’s observations, and saw that the filterable agent causing tobacco mosaic virus could not be seen by the highest resolution available at the time, that it spread systemically throughout the plant, it could not be grown in plant sap in a test tube, and it could be continuously passed from infected plants to healthy plants. It had biological properties in terms of its replication. Could not satisfy the Henle/Koch’s postulates. He called it Contagium vivum fluidum: “living contagious fluid”.
Mary and Hugh Maitland
In 1911, used medium for growing tissue cultures. Used Tyrode’s solution, blood serum, and minced tissue. Grew vaccinia virus in chicken kidney cells. Had problems with contamination; competition between virus and bacterial or fungal contaminations.
Matrix
The layer between the nucleocapsid and envelope. Includes tegument.
Matrix protein VP40
An open reading frame in the Ebola virus genome. Encodes viral protein 40 kDa, the third most numerous polypeptide. A major matrix protein between the nucleocapsid and envelope. Assists in budding of the nucleocapsid from cells.
Maturation
The seventh sequelae of virus replication. There is modification of the virus into its infectious form. Most viruses mature right away, but some need time, including picornavirus and poliovirus; they do not cleave their proteins completely in the cell.
Maturation phase (bacteriophage)
The second phase of bacteriophage replication. A few new viruses are assembled inside the cell.
Measles
A childhood illness that is preventable with the MMR vaccine. Infection starts with a fever, runny nose, and cough. As symptoms fade, full-body rash appears. Most children recover in two weeks, but some can develop pneumonia or other problems. Cause by viruses in the family Paramyxoviridae. Outbreaks have been reported among unvaccinated children, and there was an oubreak recently in Ottawa. Virion is enveloped, with helical symmetry. No longer endemic to the Americas, due to vaccines. An RNA virus.
Measlevirus
A genus of RNA viruses.
Megavirus
A genus of viruses discovered in 2011. Isometric shape, 440 nm in diameter. Affects acanthamoeba hosts. Genome is 1,250 kb with 1,120 genes.
Megavirus salinus
A dsDNA virus with 2,472.9 kb, with 2,541 open reading frames. Affects amoeba hosts.
Membrane protein (M)
A component of the Zika virus virion.
Mimiviridae
A family of isometric viruses.
Mimivirus
A genus of dsDNA viruses. Asymmetrical shape. 400 nm in diameter, with 100 nm filaments. Affects amoeba hosts. Genome is 1,181.4 kb, with 911 open reading frames.
Minor matrix protein VP24
An open reading frame in the Ebola virus genome. Encodes viral protein 24 kDa, the second least numerous polypeptide.
Mitovirus 6-Ld
A positive sense ssRNA virus in the family Narnaviridae. Genome is 2.3 kb. Affects mitochondria.
MMR vaccine

Mumps, Measles, Rubella vaccine

Prevents mumps, measles, and rubella. It is usually given to children at the age of 12 months.

Mode of replication
A criterion for demarcation of viruses into genera and families.
Mononegavirales
An order of viruses with a single, negative-sense RNA genome. Includes Ebola virus.
Morphology
A criterion for demarcation of viruses into genera and families. The shape and size of virion, and if it has an envelope. Visualized with electron microscopy and negative staining.
Mouth

Oral

A portal of entry. Human herpes virus 1 and enterovirus D-68 can infect through this point.

mRNA
A component for translation. Used as a template.
Mumps
A childhood illness that was common before the MMR vaccine was developed. Often causes no symptoms, but when it does it causes swollen glands between the jaw, creating the appearance of “chipmunk cheeks”. Caused by viruses in the family Paramyxoviridae. Despite high vaccination rates, recent outbreaks have infected thousands of people in the USA.
Murine hepatitis JHM
An RNA virus in the family Coronaviridae. Has a complete genome, 31.4 kb.
Myoviridae
A family of viruses. Includes T4 phage.
Naked virus
A virus which lacks an envelope. The capsid attaches to cell receptors, dictating host specificity. The nucleocapsid is rigid or flexible. Incldues poliovirus.
Nanoviridae
A family of viruses. Incldues coconut virus.
Narnaviridae
A family of viruses. Includes mitovirus 6-Ld.
Nature of protein
A criterion for demarcation of viruses into genera and families. The size of proteins and enzymes.
Negative sense RNA (-RNA)

Anti-sense-like

Written 3′ to 5′. The genome is complementary to mRNA, and cannot be translated. All negative sense viruses encode for a polymerase for RNA. The -RNA is transcribed into mRNA. The -RNA is transcribed into +RNA, then into -RNA for genome replication.

Negative staining
Adding stain to areas between objects you want to see. The canyon between hexons of a virus might be stained.
Negri bodies
Inclusion bodies of rabies virus.
Neuraminidase (NA)
A surface protein of influenza virus. Tetrameric. Has 9 subtypes.
Nodavirus
A genus of positive sense RNA viruses.
Nomenclature
Assignment of names. Includes binomial nomenclature, and naming a virus by a host or a disease.
Non-segmented ssRNA
An ssRNA virus with the RNA in one piece.
Non-structural protein
Intracellular viral proteins that help the virus replicate.
Non-structural protein (NS 1 – 5)
Components of the Zika virus virion.
NS3 protease
A peptide that cleaves the Zika virus polyprotein. It frees up the NS3 protein. This protein is carried in the virion.
Nuclear export signal (NES)
Tags which localize proteins out of the nucleus. Discovered by U. Fisher et al in 1995. Rich in leucine. Some virus proteins have an NES.
Nuclear localization signal (NLS)
Tags which localize proteins to the nucleus. Discovered by A.E. Smith in 1984. In SV40 the NLS tag is PKKKRKV. Many virus proteins have an NLS, including T antigen.
Nucleic acid
A macromolecule made of dNTP (DNA) or rNTP (RNA) polymers bound by phosphodiester bonds. A component of a virion, forming the genome.
Nucleocapsid
A component of a virion. A protein and nucleic acid structure. Includes the core and capsid.
Nucleoprotein (NP)
An open reading frame in the Ebola virus genome. Encodes a major protein coating the RNA genome. It is the most-produced protein of Ebola virus; more of it is needed than any other component.
Occlusion body
Nucleocapsids assembled in a virioplasm. Consists of viral RNA and proteins. Can be seen with microscopy.
Oncolytics
Some viruses can be used to kill cancer cells, or a gene can be introduced to cure a genetic disease.
Open reading frame (ORF)
A component for translation. Must have an AUG codon.
Open structure
Structure depends on the length of nucleic acid. If you add more nucleic acid, it gets larger. Helical viruses have open structure.
Order
A taxonomic level. Not all viruses have an order. There are 7 orders of viruses.
Orthomyxoviridae
A family of viruses. Includes influenza virus.
Orthomyxovirus
A genus of negative sense RNA viruses with a linear, segmented genome.
Outbreak
A movie based on the Ebola virus.
P53
An important protein in humans that prevents tumour growth, and is needed for normal replication. It recognizes when cells are replicating uncontrollably, and induces apoptosis. It is an enhancer of gene transcription. T-antigen interferes with P53.
Palisade layer
A fence-like layer that surrounds the core of a nucleocapsid.
Panama Canal
During its construction, mosquitoes had to be controlled to prevent illness and deaths from yellow fever and malaria.
Pandoravirus
A genus of viruses discovered in ice in 2003, and discovered to be a virus in 2013. Shaped like a Greek jar, 1 ?m in size. Affects amoeba hosts. Genome has approximately 2,500 genes.
Papillomavirus
A genus of dsDNA viruses. Causes cancer.
Papovaviridae
A family of isometric viruses. 18 – 26 nm in size. Includes human papillomavirus type 52.
Parainfluenzavirus
A genus of viruses in the family Paramyxoviridae. Causes croup.
Paramyxoviridae
A family of viurses. Includes parainfluenzavirus, respiratory syncytial virus, and viruses which cause measles and mumps.
Paramyxovirus
A genus of negative sense RNA viruses with a linear, non-segmented genome.
Parvoviridae
A family of viruses. Includes human paravirus B19.
Parvovirus

“Small”

A genus of ssDNA viruses with a linear genome. 22 nm in diameter. Affects mammal and insect hosts. Isometric, consisting of 22 pentons. There are no hexons. Only the penton protein gene is required. A small virus.

Pathogenicity

Pathology

A criterion for demarcation of viruses into species. What diseases the virus causes. Includes encephalitis, hepatits.

Penetration
The second sequelae of animal virus infection and virus replication. Common to all viruses. The virus penetrates into the cell. There is fusion or receptor-mediated endocytosis. With naked viruses, there may be direct penetration through the cell membrane (poliovirus, SV40).
Penton
A five-sided capsomere. Located at the 12 apices of an isometric virion. Generally consists of 5 protomers. Important, because they give curvature to the surface of the virion.
Peplomer
Glycoprotein spikes on the envelope of a virion.
Permissive
A cell that allows a virus to replicate inside it. Necessary for the virus to replicate.
Persistent infection
After uncoating, the infected cell has a persistent infection and slow virus release. New viruses are produced and released one at a time, without killing the cell.
Peyton Rouse
Discovered chicken sarcoma in 1910.
Phage
An ssDNA virus in the family Inoviridae. Genome is 9.0 kb, with 9 open reading frames.
Pharaoh Ramses V
Lived in Egypt in 1157 BC. His mummy has pock marks on his face and neck, which may have been caused by smallpox. A sample from the pocks proved this.
Phillip Allen Sharp and Richar J. Roberts
In 1977, discovered splicing of eukaryotic mRNA in adenovirus.
Phosphorylation
A post-translational protein modification. Phosphates are added to the polypeptide. Often a signal to activate or inactivate a process.
Phycodnaviridae
A family of isometric viruses. 130 – 200 nm in size.
Phycodnavirus
A genus of dsDNA viruses. Genome has 407.3 kb, with 472 open reading frames. Affects Emiliana huxleyi hosts. Isometric, T = 1179.
Physiochemical/antigenic properties
A criterion for demarcation of viruses into species. The serotype of a virus.
Picornaviridae
A family of isometric viruses. 22 – 30 nm in size. Includes hepatitis A virus, coxsackievirus A 16, and human rhinovirus 16.
Picornavirus
A genus of positive sense RNA viruses with a linear, non-segmented genome.
Pitch (P)

The pitch between each turn of the helix

P = ? x p

Pneumonia
Caused by RSV, or complications of the flu.
Plague
Caused by Yersinia pestis.
Plant viruses
Research is cheap, and they are easy to grow and handle. Cause many plant diseases.
Plaque
An area on a lawn of cells where a virus has infected the cells, causing a clearing of cells. Analogous to a botanical colony. Not all viruses form plaques. Bacterial or animal cells may be used.
Plaque assay
Similar to a bacterial colony on agar. Permissive cells, such as HeLa cells are diluted to a monolayer, and are often dyed.
Plaque morphology
A phenotype of a virus. The size and/or appearance of a virus plaque.
Plectovirus
A genus of rod-shaped or helical viruses. 14 x 71 nm in size.
Pleomorphic
Changing shape.
Poliovirus
A genus of viruses. The genome is 7,000 bp. A simple virus with 4 capsid proteins. Attaches to receptor pvr, and releases hydrophobic VPI arms into the plasma membrane. Has either membrane invagination into an endosome or penetrates into the plasma membrane as a free virus. The +RNA has a VPg attached to its 5′ end, which is removed in the nucleus and then the +RNA is translated into mRNA. The mRNA is translated into a polyprotein which is cleaved into equal amounts of VP4, 3, 2, and 1, as well as protease RdRp, RNA polymerase, and VPg. Extra unused proteins are wasted. For genome replication, the +RNA is translated into -RNA and then into +RNA, amplifying the amount. It is released from the cell by lysis, and has a maturation phase in which VP0 cleaves into VP2 and VP4. RdRp causes translation of cellular mRNA to halt by cleaving eIF4G. It affects only certain cells of the human body. There is an effective vaccine for it.
Poliovirus receptor (pvr)

CD 155

The receptor that poliovirus attaches to.

Polyadenylation
Increases the life of an mNRA. The poly-A til is chewed up.
Polydnavirus

“Poly-DNA”

A genus of viruses with more than one strand of DNA.

Polymerase (L)
An openin reading frame in the Ebola virus genome. Encodes large protein, the least numerous polypeptide; only one is needed for the Ebola virion. All RNA viruses have an L protein. The polypeptide is cleaved into smaller pieces. A major component of RNA polymerase (RdRp).
Polymerase co-factor VP35
An open reading frame in the Ebola virus genome. Encodes viral protein 35 kDa, the second most numerous polypeptide.
Polyomavirus
A genus of dsDNA viruses with a circular genome. Causes liver cancer. Isometric capsid, consisting only of pentons. Pentons make up the apices as well as triangular faces, with three pentons per triangular face. Only one protomer is needed. Has a small genome, but produces T-antigen.
Polypeptide
A macromolecule made of amino acid polymers bound by peptide bonds. Translated from one mRNA strand.
Polyprotein
A large polypeptide produced by viruses with one reading frame. It is cleaved into smaller polypeptides to form the structural and non-structural proteins of the virus.
Polysaccharide
A macromolecule made of sugar polymers bound by glycosidic bonds. A carbohydrate.
Portals of entry
Points in the human body through which a virus can infect. Includes mouth, respiratory tract, alimentary tract, urogenital tract, anus, skin, capillary, arthropod, scratch or injury, and conjunctiva.
Positive sense RNA (+RNA)

Sense-like

Written 5′ to 3′. The ssRNA genome is in the same sense as mRNA. The +RNA is transcribed into -RNA then into mRNA; this amplifies the amount of mRNA synthesized. The +RNA is transcribed into -RNA then into +RNA for genome replication.

Positive staining
Adding stain to objects you want to see
Post-translational modification
Modification of viral polypeptides in the endoplasmic reticulum and Golgi body. Can include cleavage of a polyprotein, removal of signal sequences, and protein modifications such as glycosylation, phosphorylation, acylation, and sulfation. Splicing always occurs in the nucleus.
Powassan virus
An enterovirus first discovered in Powassan, Ontario.
Poxviridae
A family of viruses. Includes vaccinia and fowlpox.
Poxvirus
A genus of dsDNA viruses with a linear genome with covalently closed ends. One of the larger viruses. Infects orally, but signs of the virus ar visualized on the skin surface.
Primary culture
A kind of tissue culture. Comes directly from tissues. The first cells to form the tissue.
Prokaryotes
Cells that have no nuclear membrane, endoplasmic reticulum, or Golgi body. Coupled transcription and translation in the cytoplasm. The mRNA is polycistronic, and ribosomes are free. There is often a cell wall.
Protease
Breaks up a polyprotein.
Protein
A macromolecule made of one or more polypeptides. A component of a virion, including structural and non-structural proteins.
Proteome
A criterion for demarcation of viruses into genera and families. Analyzed by mass spectrometry. You can test for RNA polymerase enzyme to determine if a virus is negative-sense RNA.
Protomer
A polypeptide subunit of a capsomer.
Pseudo virus
A polypeptide subunit of a capsomer.
Quarantine and burial practices
Very important for the control of spread of disease during an outbreak.
Rabbit fever
Caused by Francisella tularensis.
Rabies virus
A helical virus in the family Rhabdoviridae. 45 x 180 nm in size. Transmitted by animals.
Receptor-mediated endocytosis
The most common way a virus penetrates a cell. The virus is ingested by the cell into an endosome or caveosome. The endosome is acidified, causing release of the nucleocapsid or viral genome from the endosome into the cytoplasm, by various mechanisms.
Release
The sixth sequelae of virus replication. Structural proteins and the viral genome self-assemble into nucleocapsids, and there is viral release by direct release by lysis, budding, or by remaining cell-associated.
Renato Dulbecco et al
Worked in poliovirus plaque assays and tumour virology of Rous sarcoma virus. Won a Nobel Prize in 1975.
Reoviridae
A family of viruses. Includes rotavirus.
Reovirus
A genome of dsRNA viruses with a linear, segmented genome.
Replication
A nuclear molecular process. Copying of nucleic acid to form complementary strands of DNA or RNA. Uses DNA or RNA polymerase, replicase.
Respiratory syncytial virus (RSV)

Bronchiolitis and pneumonia

A childhood illness that is the top cause of bronchiolitis and pneumonia in infants in the USA. Symptoms are flu-like at first; fever, runny nose, and cough. Up to 40% of children with RSV infection will develop wheezing, and up to 2% will require hospitalization. Symptoms tend to be milder in older children and in adults. Caused by a virus in the family Paramyxoviridae.

Respiratory tract
A portal of entry. The virus is breathed into the body. Influenza virus and rhinovirus can infect through this point.
Restriction and modification
A system of bacterial host resistance to foreign DNA. Foreign DNA is recognized by its complementariness and it is prevented from replicated.
Retroviridae
A family of viruses. Includes HIV.
Retrovirus
A genus of positive sense RNA retroviruses with a linear, diploid genome. A complex virus, cone shaped, 80 nm in diameter. The +RNA is transcribed into -ssDNA in the cytoplasm, then transcribed into dsDNA which enters the nucleus and is transcribed into mRNA. The +RNA is transcribed into dsDNA then into +RNA for genome replication. The only viruses with a diploid genome; there are two copies of +RNA in the virion.
Rhabdoviridae
A family of viruses. Incldues rabies virus.
Rhabdovirus
A genus of negative sense RNA viruses with a linear, non-segmented genome.
Rhinovirus

“Nose”

A genus of viruses. Causes the common cold.

Ribosome
Similar in size to a virus. Viruses do not code for ribosomes, and must use host ribosomes. A component for translation. Large and small components are both needed.
Richard Montgomery
Commanded George Washington’s American army in the American Revolutionary war with Benedict Arnold. This army outnumbered the British army, but still lost.
Rideau Canal
An icosahedron-shaped structure was partially submerged in the ice.
Right-handed helix
All screws for carpentry are right-handed. If you turn it clockwise, the screw will go into the wood.
RNA-dependent RNA polymerase (RdRp)
A viral protein needed by RNA viruses for transcription of mRNA. Some viruses carry an RNA polymerase in their virion. Large protein (L) is a major component. It “stutters” as it transcribes; goes back and forth over stretches of adenine, coming off or staying on at certain points. In poliovirus it acts as a protease, cleaving the polyprotein into its parts, as well as cleaving and inactivating eIF4G, halting translation of cellular mRNA.
RNA virus
Includes ssRNA and dsRNA. There is a limit to the size of the genome; 30.0 kb is about the maximum. Most have filamentous morphology due to shearing forces. Need RdRP to trasncribe mRNA.
RNase H
A component for DNA replication. Makes RNA primers.
rNTP
A type of molecule. Includes A, G, U, and C. Components of RNA.
Robert Koch
Developed germ theory in 1874. Developed staining and microscopy to visualize microorganisms in diseased animals. Discovered anthrax endospores. Helped propose the Henle/Koch’s postulates.
Rotavirus
A genus of viruses in the family Reoviridae. Causes severe diarrhea.
Rubella

German measles

A mild virus that usually causes no serious probelms, and is preventable with the MMR vaccine. Can harm the fetus if a pregnant women becomes infected. Symptoms are a low fever and rash that spreads from the face to the rest of the body. Caused by a virus in the family Togaviridae.

SARS
A virus. Genome is 29.8 kb. It was first sequenced by scientists from University of British Columbia. There was an outbreak in Canada.
Satellite
Has a subviral genome.
Scratch or injury
Penetration of the skin to underlying tissues and circulatory system. A portal of entry. The route of cutaneous vaccination, including for smallpox. Rabies virus, Ebola virus, and HIV can infect through this point.
Segmented ssRNA
An RNA virus with the RNA in more than one piece. Each piece encodes about one gene.
Sequelae of animal virus infection
Events that occur during an animal virus infection. Attachment, penetration, and uncoating, followed by either lytic infection, persistent infection, cell transformation, or virus latency.
Serotype
A group of viruses which react to the same antibodies.
Severe diarrhea
A childhood illness that was the top cause of diarrhea-related deaths in young children until introduction of an effective vaccine. Symptoms are vomitting and watery diarrhea, which can dehydrate infants quickly. Children may recover in 24 hours. Caused by rotavirus. Often it can spread on ships due to uncooked seafood, and packed quarters. There are two rotavirus vaccines for infants.
Secreted glycoprotein (sGP)
An open reading frame in the Ebola virus genome. Encodes a major secreted glycoprotein, the fourth least numerous polypeptide. May reduce the effectiveness of the immune system.
Shingles
A disease caused by varicella zoster virus in older hosts. Symptoms include painful, itchy rash on the torso.
Sialic acid

Neuraminic acid

Influenza virus attaches to the receptor for sialic acid.

Sigla
A nomenclature system for viruses. Viruses are named using acronyms. Example: picornavirus (pico-RNA-virus).
Signal peptidase
A peptide that cleaves the Zika polyprotein.
Signal sequence
Localizes a protein to where it needs to be in the cell.
Simeon Ecuyer
A British captain who distributed two blankets and some handkerchiefs inoculated with smallpox as gifts to Native Americans.
Simian virus 40 (SV40)
A virus that uses the host’s DNA polymerase, which is not produced by the cell unless it is replicating. The virus produces a protein that causes the cell to proliferate and produce DNA polymerase. Used as a model because it is large, simple, and easy to replicate. It produces a lot of mRNA, so it is easy to detect and isolate its mRNA. While studying it, scientists discovered 5′ capping, poly-A tails, and nuclear locator signals. It can be used to make vaccines. It has only one capsid protein, a penton. The viral DNA is wrapped in histones so that it resembles cellular DNA. It steals cellular histones as part of its virion structure.
Simple viruses
Viruses with fewer genes
Single stranded DNA (+ssDNA)
A type of DNA virus. Has relatively simple structure. Limited on how large the genome can be. The +DNA is transcribed into dsDNA then into mRNA. The +DNA is transcribed into +DNA for genome replication.
Single stranded RNA (ssRNA)
A type of RNA virus. Can be positive or negative sense, and non-segmented or segmented.
Skin
A portal of entry. The skin must be broken to cause infection. Poxvirus can infect through this point.
Spanish flu

French flu

A disease that caused the Great flu pandemic, and changed the fate of WWI. It affects young people, such as those who were involved in the war.

Sparta
During the Trojan wars, Achilles fought on this side.
Species

” _ virus”

A taxonomic level. There are 2827 species of virus.

Spruce budworm baculovirus
Can be used for biological control of pests. There was an outbreak in Canada.
Strawberry virus
A virus that affects strawberries, transmitted by aphids. In 2013 there was an outbreak in Nova Scotia.
Structural protein
Proteins that form the virion.
Study groups
Local groups which can make recommendations to the ICTV.
Subfamily
A taxonomic level. Not all viruses have a subfamily. There are 22 subfamilies of viruses.
Subunits per turn (?)

The number of subunits per turn of the helix.

P = ? x p

Subviral entity
Similar to a virus, but not a virus. Has no other taxonomic home. Doesn’t replicate the same way virsuses do. Includes satellites, viroids, virusoids, and prions.
Subviral genomes

Non-viral genomes

Always ssRNA and circular. Includes virioides, satellites, and delta agents.

Sugar
A type of molecule. Carbohydrates consisting of C, H, and O.
Sulfation
A post-translational protein modification. Addition of sulfates to the polypeptide. Changes the character of a protein.
Surveillance
Important for efforts to eradicate certain diseases from the world.
Susceptible
A cell which has a receptor for the virus, and may become infected. Necessary for the virus to replicate.
Systematics
The study of biological relationships and evolutionary history.
T-antigen

Tumour antigen

Produced by polyomavirus. Prevents cancer protection mechanisms of the cell, causing unregulated cell growth and tumour genesis. It has a nuclear locator signal, and binds to and interferes with P53. Cells have many antigens and immune responses to T-antigen.

T4 bacteriophage
A complex dsDNA virus in the family Myxoviridae. The head is 110 x 80 nm. The tail is 15 x 110 nm. The tail attaches to the bacteria surface. Genome is linear and circularly permuted.
Taconomy
Science of classifications that make biological sense. Includes ICTV rules for classifying viruses. All taxonomic names are in italics.
Tegument
Matrix of a herpesvirus. Important for the replication cycle.
Tobacco mosaic disease (TMD)
A disease caused by tobacco mosaic virus. There are white necrotic lesions on the leaf surface of a tobacco plant.
Tobacco mosaic virus (TMV)
An RNA virus that causes tobacco mosaic disease. The first virus to be discovered, and much of the initial research into viruses was using this virus. Helical shape, 18 nm in diameter, 300 nm long. Contains 2130 protein units, and 6390 ribonucleic units. Pitch is 2.28 nm. Each protein subunit attaches to three nucleotides. Has a rigid nucleocapsid. The virion is weak and brittle, and can be broken easily.
Togaviridae
A family of viruses. Includes rubella.
Togavirus
A genus of positive sense RNA viruses.
Topoisomerase
A component for DNA replication.
Transcription
A nuclear molecular process. A component of biosynthesis. The basis of Baltimore Classification. Copying of a nucleuc acid template (DNA or RNA) to make primary mRNA. Uses RNA polymerase, transcriptase. Viral mRNA synthesis mechanisms depend on the nature of the genome template.
Transcription factor VP30
An open reading frame in the Ebola virus genome. Encodes viral protein 30 kDa, the third least numerous polypeptide.
Transformation
After uncoating, there is integration of the viral DNA into the cell genome, causing transformation into tumour cells. The gene may be inserted in the genome near a cancer-causing gene. Retroviruses can do this.
Translation
A cytoplasmic molecular process. A component of biosynthesis. Copying of codon triplets of mRNA, beginning with the AUG codon, to make a polypeptide. The cell’s cytoplasmic ribosomes, as well as other components, are needed for translation. The ribosomes starts at the 5′ end of the mRNA, and amino acids are added to the C terminus of the nascent polypeptide.
Transmission
A criterion for demarcation of viruses into species. How the virus is transmitted. Includes coughing, mosquitoes, and ticks.
Triangulation number (T)

Used to calculate the number of capsomeres or protomers of an isometric virus nucleocapsid. Generally, the larger the T value, the larger the virus, but this depends on the size of capsomeres.

Number of capsomers = 10T + 2

Number of protomers = 60T

tRNA
A component for translation.
Tropism
Virus specificity to certain cell types, such as lung cells. Necessary for the virus to replicate.
Troy
During the Trojan wars, Hector fought on this side.
Tyrode’s solution
A mixture of salts used for tissue cultures.
U. Fisher et al
In 1995, discovered nuclear export signals.
Uncoating
The third sequelae of animal virus infection and virus replication. Common to all viruses. The virus uncoats, freeing the viral genome. Occurs in the cellular compartment where it needs to be uncoated.
Urogenital tract

Penile, vaginal (including childbirth), and urinary

A portal of entry. Human herpesvirus, HIV, and HPV can infect through this point.

V.B. Reddy
In 1978, fully sequenced SV40 dsDNA genome, the first “mammalian” genome, which has 5,224 nucleotides.
Vaccinia virus
A complex RNA virus in the family Poxviridae. 200 x 200 x 250 nm in size. Has complex symmetry. Has a lateral body with an outer envelope, enclosing a nucleoid. Has its own enzymes for adding a 5′ cap to its mRNA in the cytoplasm.
Varicella zoster virus

Chickenpox virus

A virus in the family Herpesviridae. Causes chicken pox and shingles in older hosts. A vaccine was recently developed for it, which is free.

Vesicular stomatitis virus (VSV)
A virus used as a base for the VSV-EBOV vaccine. In the same family as rabies virus.
Viral conjunctivitis

Pink eye

Caused by adenovirus in the family Adenoviridae or by herpesvirus in the family Herpesviridae. A childhood virus which causes tearing, redness, itching, and crusty eyelashes. Caused by the same virus as the common cold. Often spreads in schools and day care centres. Most children recover in four to seven days.

Viral genes
A criterion for demarcation of viruses into species. The genomes and proteomes of a virus.
Viral genome
Has limited coding capacity, so many copies of the same protein may be used for the capsid.
Viral protein 0 (VP0)
A viral protein of poliovirus which is equivalent to VP2 and VP4 still not cleaved from each other. The virus is not infectious until VP0 is cleaved into VP2 and VP4; this occurs in a maturation phase.
Viral protein 4 (VP4)
A viral protein of poliovirus. An internal structure protein. It is initially part of VP0.
Viral protein genome linked (VPg)
Attached to the 5′ end of poliovirus +RNA, acting as a primer for translation, binding to the ribosome in several places. It falls off the mRNA during translation. It is cleaved off of in the nucleus for genome replication. It is uridylated, making a poly-U tail.
Viral proteinase (pr)
A component of the Zika virus virion.
Virion
A complete mature infectious virus particle. The physical virus particle, which can be seen. Often symmetrical shape. Consists of the nucleocapsid and envelope. Made up of nucleic acids, proteins, lipids, and carbohydrates.
Viroid
Has a subviral genome.
Virus
Obligate intracellular parasite. Cause many infectious diseases, which may have influenced history. They can help to unravel molecular and cellular structures/processes, and can be harnessed for biotechnology. They may be considered living things, but this is debated. Their bodies are more numerous than any organism, and they are too small to be visualized in a light microscope. Can be serially passaged despite dilution. The components of a virus can crystallize spontaneously to form the virus. Small, soluble particles, less complex than bacteria or fungi, but more complex than a molecule. Contain DNA or RNA covered by a protein shell, and may have an envelope. They cannot be grown on a non-living surface; must have living cells in which to replicate and form a plaque. Host cells are used for energy metabolism, protein synthesis, membrane biogenesis, and cellular scaffolding, a virus replicates by synthesis of viral macromolecules and self-assembly. They are filterable infectious agents; can be separated from larger microbes such as bacteria and fungi. Originally they were not known, and could not be isolated or detected.
Virus isolate

Virus strain, type, serotype, subtype, variant, or genotype

Naming of different viruses. No taxonomic significance to the ICTV.

Virus latency
After uncoating, the virus goes into a dormant state, and stimulus such as a hormone activates it to undergo lytic cycle.
Virus name
Not written in italics. The real thing, which you can put in a test tube and study. Has no taxonomic significance; not bound by rules.
Virus replication cycle

Attachment, penetration, uncoating, biosynthesis, assembly, release, and maturation.

mnemonic: APUBARM

Virus species
Written in italics. The basic unit of virus taxonomy. A man-made abstract concept for organizing virus for purposes of communication and classification.
VPg uridylation

Addition of uridines to the VPg of poliovirus. Creates a poly-U tail which can be transcribed to create a poly-A tail.

VPg + U > VPgU

VSV-EBOV vaccine
A vaccine against Ebola which uses vesicular stomatitis virus as a base. Developed at the National Microbiology Laboratory in Winnipeg. The VSV G envelope protein is exchanged with EBOV GP envelope protein. When introduced to the body, the immune system produces Ebola GP antibodies. This vaccine was used during the Ebola outbreak in Africa.
Wendell M. Stanley
In 1936, discovered that tobacco mosaic virus could be crystallized and viewed by electron microscopy. The crystals were still infectious. This is a chemical property; he thought the agent was a protein.
Walter Reed

An American army surgeon who tested Carlos Finlay’s theory that mosquitoes or filtered serum could transmit yellow fever, but not fomites. A “volunteer” (a soldier) died in one of his experiments in 1901. There were two buildings:

1. Closed and filled with fomites including blankets, clothes, and towels used by patients with yellow fever.

2. Lots of fresh air, with two sections: one protected by mosquito meshing, and the other exposed to mosquitoes.

Only volunteers exposed to mosquitoes developed yellow fever.

Walter Reed and James Carroll
Discovered yellow fever in humans in 1901.
West Nile virus
A virus that is transmitted by mosquitoes. It can become serious. Horses are a dead-end host, however mosquitoes can acquire the virus from humans.
Wilhelm Ellerman and Olaf Bang
Discovered fowl avian leucosis in 1908.
World Health Organization (WHO)
Attempted to control the spread of Ebola during the outbreak in 2014; administered quarantines and buried bodies in mass graves.
Yellow fever (YF)
A disease caused by a Flavivirus. Discovered by Walter Reed and James Carroll in 1901. The first disease in humans discovered to be caused by a virus. There was an outbreak during the Spanish American war in Cuba and Panama in 1898, and the Spanish lost the war due to lack of immunity to the fever. It is transmitted by mosquitoes.
Zika
An isometric positive sense ssRNA virus in the family Flaviviridae. Transmitted by mosquitoes. It spread from Uganda to Brazil, then to North America. The species of mosquito which spreads it lives south of Florida, and there haven’t been any cases in Florida since August 2016. Greatest risk is to pregnant women; causes microcephaly in the fetus. Genome is 10,676 bp. Has one reading frame; the entire genome is translated into a polyprotein with several transmembrane domains, embedded in the endoplasmic reticulum. It is cleaved at specific sites. Components of the virion include C, pr, M, E, and NS 1 – 5. Peptides that cleave the polyprotein include signal peptidase, Golgi protease, and NS3 protease.
Zoonose
A disease spread by more than one animal species, and may be transmitted to people.
Categories: Microbiology