World of Viruses: Final

5′ cap dependent transcription
Transcription of influenza -RNA into mRNA. Occurs in the nucleus. A 5′ cap sequence of host mRNA aligns with the 3′ end of the -RNA, and RNA polymerase cleaves the -RNA, leaving 11 – 13 nucleotides at teh 5′ end of the host RNA. Two nucleotides at the 3′ ed of the host mRNA hybridize with the first two nucleotides in the -RNA; this can acts as a primer for transcription with RNA polymerase. There is polyadenylation via reiterative copying. The mRNA is transported into the cytoplasm.
?1 antitrypsin deficiency inherited emphysema
Lack of ?1 antitrypsin. Occurs in 1 out of 3,500 people. Targets lung and liver cells.
A82V

Ebola virus/H. sapiens/wt/Guinea/2014/Makona-C15

A variant of Ebola which spread quickly and was very infectious. Had a very early A82V substitution due to a non-synonymous C to T substitution at nucleotide 6,283, changing alanine to valine in GP protein. This made it bind more strongly to cellular receptor NPC1, making it more adapted for infection in humans. Additional non-synonymous substitutions increased its virulence. This mutation is the reason for the increased virulence of Ebola in the West African outbreak of 2013 – 2016. It was discovered near Makona River in 2014.

Acute viral infection
A consequence of virus-host interaction. Disease is caused. There can be death, recovery, persistent infection, or immunity. A short-term infection.
Adaptive immunity
Antibody mediated. Humoral, B cells synthesize specific antibodies by plasma cells. Cell-mediated, helper T cells and cytotoxic T cells. Anamnestic; second and subsequent response is faster.
Adeno-associated virus vectors (AAV)
Non-pathogenic in humans. Infect dividing and non-dividing cells. Mediate long-term transgene expression. Non-integrative in the current vector format, episomes. Low immunogenicity. Limited cloning capacity, with a maximum of 4.5 kb. The viral genome can be gutted and packaged with therapeutic genes, resulting in an episomal copy of therapeutic genes and expression for the lifecycle of the cell. The most promising current gene therapy platform. High safety profile. The first approved gene therapy product in the western world. In the US it cured congenital childhood blindness. There are 47 ongoing clinical trials, and 3 of the top 10 biotech start-ups in 2013 were based on AAV gene therapy.
Adenovirus
A relatively benign virus, causing mild diseases of the upper respiratory tract and conjunctivitis. Medium-sized naked virus. Well-studied. Used for gene therapy. Attaches to Car on the cell, with trimeric adenovirus fibre knob.
Airborne spread
The fate of aerosol created from a cough depends on particle size, viscosity of mucous, and rate of expiration. If the particle is greater than 100 ?m, it may fall out and become windborne. If the particle is less than 100 ?m, it is a droplet nuclei.
Albert Sabine
Created the OPV polio vaccine. In 1957 passaged the virus through monkey kidney to duck embryo cells, to develop an attenuated strain. By 1962 it could be taken orally, causing mild infection of the intestines. Tested on 77 million people in the USSR and eastern Europe. Since the 1960s it was grown in human lung diploid cells WI-38.
Alfalfa mosaic virus
A plant virus which associates with the chloroplast membrane.
Alimentary tract
A route of infection. Physical barriers include acid, bile, proteolytic enzymes such as tripsin, IgA, specialized M cells in the ileum, and movement of the intestine slowing down the virus. Barriers mostly acid-resistant. Rotavirus, coronavirus, and Norwalk virus infect by the alimentary tract. Enter the gut through endocytes. Never infect from top of apical, always from the basal membrane; it is a generalized infection.
Amgen
An oncolytic virotherapy company that spent $1 billion making an oncolytic virus. Doesn’t produce the best product, but it was the first company to go into oncolytics.
Andre Rhodes and Arthur Franklin
From 1947 to 1951 grew poliovirus in test tubes of Vero cells.
Angiogenesis
A hallmark of cancer. Production of specific growth factors, including VEG-F that promote new vasculature to form in the tumour. The tumour feeds itself. Vasculature is incomplete and leaky. Viruses benefit from this because it initiates cell cycle.
Anti-attachment
An antiviral drug defense. Includes Win for rhinovirus.
Anti-vaxxer
People who are opposed to vaccinations. Believe that disease levels would have gone down on their own without vaccinations.
Antibodies
An antiviral defense that produces humoral immune response to virus infection. Neutralizes viruses.
Antigen (Ag)
A method of direct detection of viruses. Immunofluorescence, immunohistochemistry, ELISA, latex particle agglutination, agar gel immunodiffusion, hemadsorption, hemagglutination, and western blotting.
Aphid

Aphididae

In the order Hemiptera. There are 4,000 species, 192 of which are vectors for 275 plant viruses. The most important vector of plant viruses.

Apoptosis
Programmed cell death. A defence against a virus. A normal process imporant in development and immunity. A primary defense against invading pathogens. There is a complex triggering system; it is bad to have too much. Webbing between fingers dies by apoptosis in utero.
Apple scar skin viroid
In the genus Apscaviroid. A plant viroid. Has 306 – 369 nucleotides.
Arbo

Arthropod-borne

Includes Zika and West Nile virus. Can be mechanical or biological transmission.

Armantadine
An antiviral target for influenza virus. An M2 antagonist, preventing acidification of endosome and fusion of viral, endosome membranes prior to release of ribonucleoprotein RNA.
Asymptomatic
Subclinical infection. A consequence of virus-host interaction. There can be recovery, persistent infection no longer than a month, or induced immunity.
ATPase
A segment of TAg. ATPase activity.
Attenuated virus vaccine
A type of viral vaccine. A modified live virus. Includes MLV, the rabies virus, OPV, and yellow fever virus. A viral vaccine antiviral defense.
Autogenous
Virus obtained from animals. Sometimes works. Efficacy is variable. Sometimes it is the only choice.
Avocado sunblotch viroid
In the genus Avsunviroid. A plant viroid. Has 246 – 250 nucleotides.
Avoiding immune response
A hallmark of cancer. The body is good at recognizing tumour cells, which produce TAAs, which are visible to our immune system. The tumour creates an immunosuppressive environment through the production of immunosuppressive molecules such as IL-10, TGF?, and IDO, which are produced normally to control the immune system, telling T cells everything is fine.
B19R
A deletion in vaccinia virus. Inhibits interferons. Normally sequesters type I interferons.
BCX4430
An EBOV antiviral. Affects ebolavirus RdRp, acting as nucleotide analogue, causing chain termination. Effective against EBOV, but also affects host RNA.
Benign tumour
Cancer that is localized and non-invasive, and can easily be remove surgically. Usually surrounded by a membrane.
Biological assays
A method of detecting plant viruses. Indicator indexing. Still the official method for woody perennial crop such as fruit trees, grapevines, and strawberries.
Biological transmission
Arthropod-borne viruses where the insect needs an incubation period before it can transmit the disease. The virus amplifies in the insect. With plant viruses it often goes into the salivary glands. Includes yellow fever.
Blood
A route of infection and a route of release of the virus. Blood products or transfusions may spread a virus. Hepititis C and Zika virus may be spread this way. Viremia, HIV, hepatitis B, C, and D and Zika may be released this way.
Bovine spongiform encephalopathy (BSE)

Mad cow disease

A TSE of cattle. First identified in 1986, when more than 160,000 cattle died. Cut down Canadian exported beef, and they had to cull and burn many cattle. Can occur in humans. Transmitted to cattle when they eat offal of other cattle. The offal should be treated with organic solvents, but because they are expensive sometimes it is just boiled, and this can cause BSE transmission. It is no longer allowed to feed cattle offal. It can occur spontaneously. It has a very long incubation period.

Brome mosaic virus
A plant virus which associates with the endoplasmic reticulum membrane.
Bruce Aylward
The director of polio eradication.
Bunyaviridae
A family of viruses which affect plants as well as animals.
Byram Bridle
From the Department of Pathobiology at the University of Guelph. Doing research on oncolytics and cancer immunotherapy.
Cadang cadang viroid
In the genus Cocadviroid. A plant viroid that affects coconuts. 246 – 301 nucleotides.
Cancer
Unregulated growth of certain cells in the body. Includes malignant and benign tumours, and are grouped into classes based on tissues affected, including leukemia, lymphoma, sarcoma, and carcinoma. Cells are transformed by inactivating tumour suppressors p53 or RB, or by oncogenes.
Cap snatching

The 5′ cap of host mRNA is stolen and added to viral mRNA of influenza virus, and there is primer function.

1. Host nuclear mRNA is cleaved by RNase, proving a 3′ OH.

2. GTP is added to the 3′ OH end of the 5′ cellular cap.

3. New GTP binds to penultimate C on the negative viral gRNA.

4. Elongation. Terminal U of gRNA is not transcribed.

Car
Coxsackievirus and adenovirus receptor.
Carcinoma
Cancer in epithelial cells.
Carlavirus
In the family Betaflexiviridae. A group of 55 plant viruses. Non-circulative, non-persistent transmission by aphids.
Cas9
A bacterial nuclease involved in defense against invading phages. Used in CRISPR.
CCR5

CD 195

C-C chemokien receptor

A cell attachment factor, receptor for a virus. The second HIV receptor to be discovered. It is a co-receptor. A group of sex workers lacked this receptor, so they were not infected with HIV.

CD4

Cluster of differentiation 4

A cell attachment factor, receptor for a virus. The first HIV receptor to be discovered.

CD8+T cells
A special group of cells that secrete enzyme, causing other cells to go into apoptosis. Recognizes surface antigens of virus-infected cells. Having a broader range of cells causes peopel to be able to fight HIV better.
Cell is “winner”
Outcomes include: no receptor on the cell, no infection; receptor is present on the cell but does not infect the cell, virus is blocked by Ab; and virus infects the cell but its replication is inhibited by interferons or the cell lacks enzymes the virus needs.
Cell-mediated
An antiviral defence that produces immune response to virus infection. Lyses infected cells.
Central nervous system
Local spread of virus dissemination can occur. Direct localization in blood vessels of the brain and spinal cord via peripheral nerves (rabies, varicella, HSV), lytic infections of neurons (polio, flavivirus, herpesvirus), non-lytic infections (rabies, LCMV), and some slow degeneration (prions, non-viral agents).
Chemotherapy
A prevention measure for viruses.
Chicken embryo
Susceptible to many viruses. Used to grow viruses.
Chickenpox
There was an outbreak in Hong Kong in 2009. They killed all the chickens in the area, and stopped importing live chickens.
Chronic infection
A persistent infection. A consequence of virus-host interaction. Disease is caused. There is recurrent clinical disease, or persistent infection.
Chronic wasting disease
A TSE of mule deer and elk. Occured in wild elk in Canada.
Citrus exocortis viroid
In the genus Pospiviroid. A plant viroid.
Citrus tristeza virus
A plant virus. The most important virus affecting citrus crops. Millions of trees are removed. Weakens the grafting point, and the scion can fall off. Produces seedling yellows in sour orange. Stem pitting, and rope-like depression in Marsh grapefruits, and reduced size and quality of fruit. Reduced size and quality of Valencia sweet orange. Tahiti lime has pitting strain with vein clearing, and vein corking on mature leaves.
Clathrin-dependent receptor mediated endocytosis

Occurs in Semliki Forest virus, a +RNA Togaviridae, as well as in baculovirus and rhabdovirus.

1. Attachment to the cell receptor.

2. Consolidation of viral attachment protein/cell receptor interactions.

3. Formation of clathrin coated pit.

4. Invagination of the pit to form a clathrin-coated vesicle.

5. Clathrin coat is lost as first step to change to early endosome.

6. Acidification of the endosome through proton transport.

7. pH-mediated change in conformation of viral attachment protein to a fusion protein.

8. Fusion between viral membrane and endosomal membrane.

9. Release of nucleocapsid into the cytoplasm.

10. Dissociation of the capsid, releasing viral genome.

11. Genome can be translated.

Closterovirus
In the family Closteroviridae. A group of 25 plant viruses. Non-circulative, semi-persistent transmission by aphids and whitefly.
Connaught Laboratories
At the University of Toronto. Did poliovirus research since the 1930s. Found that growth was better in medium 199. Produced all the poliovirus used by 5 companies to prepare vaccines.
Constantin Levaditi
An Iranian scientist who in 1911 discovered that polio was caused by a filterable virus. Extracted material from nervous tissue and filtered out poliovirus.
Cough
When you cough, the velocity of the aerosol particles are from 2 to 28 m/s.
Cowpea mosaic virus
A plant virus which associates with the endoplasmic reticulum membrane.
Creutzfeldt-Jakob disease (CJD)
A TSE of humans. Caused by nvCJD, a variant of nCJD. May be contracted by eating beef affected by BSE.
CRISPR
Bacterial Cas9 nuclease, guided by RNA for genome editing. Predicting on the introduction of double stranded breaks within genomic DNA. Relies on a guide RNA to bring nuclease target to sequence. Simpler to design than zinc fingers or TALENs, but constrained by PAM sequence.
Cucumber mosaic virus
A plant virus which associates with the vacuole membrane.
Cucumber mosaic virus satellite RNA
A satellite nucleic acid, 332 – 405 nucleotides.
Cucumovirus
In the family Bromoviridae. A group of 3 plant viruses. Non-circulative, non-persistent transmission by aphids.
Custom nuclease
Zinc fingers and TALEs fused to Fokl nucleases for genome editing. Predicated on the introduction of double stranded breaks within genomic DNA.
Cutter Labs
In 1955 produced a batch of polio vaccine for trial on 200,000 subjects. The virus was clumped together when mixed with formaldehyde, and some virus in the centre of the clumps was not killed. It is hard to detect live viruses in large samples. There were 40,00 cases of polio infection, 192 cases of paralytic polio, 53 cases of complete paralysis, and 11 deaths. A filter was later used to solve this problem.
CXCR5

CD 189

C-X-C chemokine receptor

A cell attachment factor, receptor for a virus.

Cycles
A virus has three cycles: replication cycle, pathogenesis, and epidemiology.
Cystic fibrosis
A faulty transport of salt in lung epithelium. Occurs in 1 out of 3,000 Caucasians. Targets airways in the lungs.
Cytomegalovirus (CMV)

Human herpesvirus 5

Causes lifelong congenital diseases. Cells fuse and become large and multinucleate. 20 – 40 thousand people get it every year. It can be latent and come back again. Can make children deaf. Causes 8 thousand permanent disabilities every year. There is no vaccine, however an antiviral can help in children. Spreads in saliva and urine. Has 200 genes.

DC-SIGN

Dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin

A cell attachment factor, receptor for a virus.

Diagnosis
Need a specific diagnosis for clinical cases. For certification of freedom from a specific infection there must be artificial insemination, embryo transfer, blood transfusion, tracking zoonoses, xenotransplantation for humans.
Direct detection
A method of virus detection. Includes visualization, antigen, nucleic acid, or histology.
Disease production
The third step of the pathogenesis cycle. Clinical signs, general and specific. Secondary replication. Replicates in target organs, causing cellular damage, lesions, and clinical disease occurrence. Mechanisms include direct cell damage, cell transformation, inflammatory response, predisposition to bacterial infection (damaged tissue in gut and respiratory tract), immunosuppression (infect immune cells), and immune response.
DNA binding
A segment of TAg. Binds to the Ori.
DNA ligase 1
A component of the SV-40 replication fork. A cellular accessory protein. Seals daughter DNAs.
DNA polymerase ?
A component of the SV-40 replication fork. An RNA primase.
DNA polymerase ?
A component of the SV-40 replication fork. PRocessive DNA synthesis.
DNA vaccine
Just DNA is introduced, which enters cells and produces a viral protein that incites immunity. Works to a certain extent. Hard to get DNA into cells, and to get cells to produce enough protein. Can be used as an Ebola vaccine; muscle cells express NP protein.
Double stranded DNA (dsDNA)
A type of virus. Genome is 5 – 1000 kb. There are 25 total, affecting 7 vertebrates, and non affecting plants.
Double stranded DNA break repair
Induction of a double stranded break at a specific location in the DNA. A repair template is provided containing therapeutic gene or corrected DNA, which is then integrated by homologous recombination and cellular machinery. Delivery of TALEN or CRISPR and repair template is a problem. Requires a large coding capacity. Likely candidates are lentivirus, adenovirus, herpesvirus, and baculovirus.
Double stranded RNA (dsRNA)
A type of virus. Genome is 3 – 32 kb. There are 8 total, 2 affecting vertebrates, and 4 affecting plants.
DpnI
An endonuclease that recognizes methylated A’s in DNA. Used for mapping the Ori of SV-40.
Drift
A way that influenza virus can change its coat proteins. Gradual changes due to single mutations. Enough antigenic shifts allows the change to be sufficiently different that it reacts differently with antibodies. Includes H2a to H2b.
Droplet nuclei
An aerosol particle in a cough that is less than 100 ?m in size. It may become windborne or it may be inhaled. If inhaled, if it is less than 5 ?m it remains within the nasal mucosa, and if it is over 5 ?m it can enter the trachea and alveoli.
dsRNA dependent protein kinase R (PKR)
An interferon regulated gene activated by IFN. Phosphorylates EIF2?, inactivating it and abolishing translation.
dsRNA dependent RNase L
An interferon regualted gene activated by IFN. Digests mRNAs.
Duchenne muscular dystrophy
Lack of dystrophin. Occurs in 1 out of 3,000 males. Targets muscle cells.
E1A
A viral protein of adenovirus which binds to p53, with similar action to TAg of SV-40.
E2F
A cellular transcription protein. It is released from pRB when TAg binds to it, causing transcription of cyclins, DNA polymerase ?, thymidine kinase, DNA ligase, and histones. Results in S-phase: DNA cell replication and cell division.
E7
A viral protein of papillomavirus which binds to pRB, with similar action to TAg of SV-40.
Early promoter
Promotes genes to the left of the Ori of SV-40. Genes include LPI, sT, and LT. Transcribed before DNA replication by host RNA polymerase II. The mRNA is 5′ capped and spliced in the nucleus, then translated in the cytoplasm.
Ebola antivirals
Includes convalescent plasma from Ebola survivors, producing passive immunization, as well as ZMapp, ZMAb, SNALP, BCX4430, and Favipiravir.
Ebola outbreak 2013
The virus had increased virulence due to A28V mutation. WHO did not get involved fast enough due to funding issues.
Ebola vaccine
DNA vaccines, such as NP or GP genes, produces T-cell proliferative and humoral immunity. Prime boosting with DNA, and protein such as poxvirus GP, VS-EBOV. Replication defective chimpanzee recombinant adenovirus expressing GP (likely humans do not have immunity to this virus). BSNP-333-GP recombinant GP rabies vaccine. Filoviruses with envelopes, GP, and NP by baculovirus. Subunits of GP in bacteria.
EcoRI
An endonuclease which cuts the DNA in only one place in SV-40. Used to locate the Ori.
Edward Jenner

A country doctor in 1796. During a smallpox outbreak in Gloucestershire, noticed that milk maids with cowpox from cows rarely contracted smallpox. Concluded that they had become immune to smallpox by exposure to cowpox. Used cowpox scabs as a source of inoculum. Hypothesized that it could “immunize” someone against smallpox. In May 1796, obtained cowpox from a milkmaid and scratched it into the arms of an 8 year old boy, then challenged him with smallpox from a smallpox scab. He got a fever and then survived, and survived another 20 challenges. Jenner then inoculated his sone, but later died from smallpox himself.

1. Immunize someone with cowpox.

2. Allow time for immunity to establish.

3. Monitor for immunity to smallpox.

Electron microscope
A tyep of visualization. Excellent, but has low sensitivity to the virus; a lot of virus is needed. Transmission EM or scanning EM. Transmission EM include negative staining, thin sections, and immune EM.
Electrophoresis
Add SES to separate proteins from each other.
Elite controllers
HIV patients who have a low level of HIV and don’t need as much anti-viral drugs. They have a different way of makign CD8+T cells that recognize virus-infected cells.
End problem
A problem for linear DNA, cellular and viral. How does the gap after the terminal RNA primer fill in? Ends get shorter every time the DNA replicates; at some point critical genes may be deleted. Telomerase adds telomeres, solving this problem.
Endemic
Present in at last one place.
Endoplasmic reticulum (ER)
It has seven regiosn associated with plant virus replication and movement: nuclear pore, microtubule nucleation, rough ER, smooth ER, transitional ER, actin-binding, and plasmadesma.
Enhancer
It bends the DNA so that RNA polymerase II is at the transcription initiation site. Host transcription factors build up on the region in certain places, activating transcription.
Epidemiologically
A prevention measure for viruses. Related control measures are quarantine, sanitation, wildlife control, and vector control.
Epidemiology cycle
A cycle of viruses within a population of hosts.
Episome
An extra-chromosomal circular DNA element. IDLVs insert genes as episomes.
Epithelial surfaces
Local spread of virus dissemination can occur. Can spread on the skin (papilloma virus, pox virus), respiratory (bronchitis: influenza virus, parainfluenza virus), and intestinal (diarrhea: rotavirus).
Eradication
Success of eradication depends on surveillance and reliable diagnostics, quarantine, containment, ring vaccination, and vaccination quality control. Cheap and stable vaccine that elicits durable cellular and humoral immunity. Short incubation period, no insect vectors, and only human hosts.
Excretion of viruses
A way a virus may be transmitted. The virus is excreted in respiratory, oral, fecal, milk, skin, or urogenital tract.
Eyes

Conjunctiva

A route of infection. Common in swimming pools.

Familal hypercholesterolemia
A deficiency in factor IX. Occurs in 1 out of 30,000 males. Targets liver cells.
Fatal familial insomnia (FFI)
A TSE of humans. Inherited from parents.
Favipiravir
An EBOV antiviral. Used for influenza. Nucleotide analogue which preferntially inhibits viral RdRp. Allows for transcription, but inserts chain-terminators.
Feces

Fecal oral transmission

A route of release of the virus.

Feline immunodeficiency virus (FIV)
The cat version of HIV. It is a lentiviral vector.
Feline leukemia virus
A virus that causes leukemia in cats.
Fen1
A component of the SV-40 replication fork. A cellular accessory protein. A 3′ – 5′ RNA exonuclease, least rntd.
Fetus
Local spread of virus dissemination can occur. Congenital infection. Some viruses cross the placenta (LCM, avian leucosis virus). Clinical outcome is fetal death and abortion (variola, parvo B19), an congenital defects (CMV, rubella).
First generation adenovirus
The first generation of adenovirus for gene therapy. Rendered non-replicative by deletion of E1 gene. Had moderate coding capacity, and could be easily manufactured. Can transduce dividing and non-dividing cells, and can be retargeted by switching out fibre genes. It also expressed viral proteins, which were what caused the death of Jesse Gelsinger.
Flaccid paralysis
A symptom of poliomyelitis. Can be caused by many things. Hospitals need to quarantine anyone with this symptom, in case it is polio.
Flavivirus
A viral disease which could be eradicated.
Flumist
A nasal spray vaccine for influenza. Quadrivalent. An attenuated live virus. Protects against: A/Bolivia/559/2013 (H1N1, same as A/California/7/2009), A/NewCaldeonia/71/2014 (H3N2, same as A/HongKong/4801/2014), B/Brisbade/60/2008, and B/Phuket/3073/2013. The virus is mutated so it is not infectious. A very low dose, but the person may get a fever.
Fluviral
An IM injection vaccine for influenza. Trivalent. A split virion. Protects against: A/California/7/2009 (H1N1), A/HongKong/4801/2014 (H3N2), and B/Brisbane/60/2008.
Fluzone
An IM injection vaccine for influenza. Quadrivalent. A split virion. Protects against: A/California/7/2009 (H1N1), A/HongKong/4801/2014 (H3N2), B/Brisbane/60/2008, and B/Phuket/3073/2013.
Fraenckel-Conrat
In 1955 used TMV self-assembly to discover RNA was a genetic material besides DNA.
Gaetan Dugas
An individual who was said to be the first AIDS patient in North America. His blood and the blood of his partners were tested. He was labelled as “Patient O”, for “Outside of California”, but the O was misconstrued as a zero, forming “Patient zero”. Using a phylogeny with a superimposed molecular clock it was determined that he was not the first person with AIDS in North America.
Gamma globulin
Can protect against poliovirus.
Gardasil 9-L1
A protein made by yeast cells, which is used as a vaccine that guards against 9 different viruses.
Gaucher’s disease
A defect in the enzyme glucocerebrosidae. Occurs in 1 out of 450 Ashkenazi Jews. Targets bone marrow cells and macrophages.
Gene therapy
Use of viruses to deliver genetic payload to correct defects by addition of a functional gene copy. Various viral systems may be used. Delivery of a functional copy of a nucleic acid to a patient’s cells in order to correct a genetic disorder. Most successful are in recessive monogenic disorders, where a single functional copy is enough to correct. Viruses are an ideal platform for delivery of nucleic acid, since they are evolved for this purpose. However, viruses can cause diseases and immune reactions, and most viruses express genes for a limited time with no permanent correction.
Generalized infection
A type of virus dissemination. The virus spreads from local sites to the target organ by lymphatic and hematogenic spread (viraemia), or by nerves. You start to see the disease when the virus reaches target organs. Includes measles and rabies.
Genetic changes
There can be changes in genes and pathogenesis. Increase or decrease virulence (attenuated live vaccine strains decrease virulence). Alteration in tropism, host specificity, and range (TGEV enteric to respiratory coronavirus, canine parvovirus). Alteration in receptor binding sites. Development of drug resistance (HIV, influenza A virus). Changes in the antigenic determinates on viral surfaces (HIV, influenza viruses). Changes in temperature sensitivity (influenza virus vaccine).
Genital secretions
A route of release of the virus. Includes HIV, herpesvirus, hepatitis B and C, Zika, and Ebola.
Gerstmann-Straussler-Scheinker disease (GSS)
A TSE of humans.
GM-CSF

Cytokines

An addition in vaccinia virus. A granulocyte/macrophage colony stimulating factor. Produces immune reaction in normal cells. Alters the immune system, counteracting tumour immunosuppressive environment.

GM1

Ganglioside 1

Glycosphingolipid with sialic acid. A cell attachment factor, receptor for a virus.

GP
A protein in EBOV which functions in attachment. A trimer, cleaved into GP1 and GP2 by endosomal cathepsin protease. Binds to NPC1, and fuses membranes in the endosome to release the nucleocapsid.
GP1
A component of GP. Has a mucin-like domain, and a glycan cap of GP, subject to proteolysis.
GP3
A component of GP. Remains in the virus membrane, exposing the NPC1 binding domain. Has an RBD receptor domain, which include A82V.
Grapevine fanleaf virus
A plant virus transmitted by nematodes. Causes chlorosis, and bad, small grapes with low sugar content.
Grapevine leafroll disease complex
A plant virus. Has different symptoms in Pinot red (dark leaves), vs. Chardonnay varieties (yellow leaves). One of the most damaging viral diseases of grape in the world. Transmitted by nematodes. Displays different symptoms depending on combination of scion and rootstock. Leaves have discolouration of veins, and leaf rolling. The virus is filamentous and flexible with a rattlesnakc structure.
Grapevine yellow speckle viroid
In the genus Apscaviroid. A plant viroid.
H1N1
An influenza virus with HA1 and NA1. No had seen it before, and it had elements from pigs and chickens. There was a lot of hype, but it turned out to not be a big deal. WHO overreacted rather than underreacted.
Haemophilia
A deficiency in factor VII. OCcurs in 1 out of 10,000 males. Targets liver, muscle, fibroblast, or bone marrow cells. Causes bleeding disorders ranging from mild to severe. A single functional copy will correct the disease phenotype.
Hallmarks of cancer
Tumours arise through genetic changes which favour immortality. Tumours flourish in what should be a hostile environment. Tumour microenvironment is extremely immunosuppressive. Tumours deregulate cellular energetics, avoid immune destruction, resist cell death, and induce angiogenesis. It is a double-edged sword. Many of the same pathways involved in malignancy are also involved in successful viral infection, such as proteins that evade apoptosis, avoid detection by the immune system, and deregulate cellular energetics. This makes cancer cells very sensitive to viral infection. Cancer cells do not display proteins seem on normal cells, and antibodies can target specific surface markers.
Helicase
A segment of TAg. Helicase activity and ssDNA binding activity.
Hemagglutinin (HA)
A structural protein of influenza virus A, coded by segment 4. 550 amino acids. A homo-trimer receptor. Binds to sialic acid, and causes membrane fusion. There are 17 subtypes, H1 – H17. Attaches to red blood cells, causing the cells to stick together. Has a hydrophobic component to aid with fusion of endosome and viral envelope. An envelope protein, translated on the endoplasmic reticulum membrane. Interaction with sialic acid has low affinity. Interaction of many HA to many sialic acids leads to high avidity. In the human upper respiratory epithelium, there is mostly ? (2,6) linked sialic acid. In the human lower respiratory tract there is mostly ? (2,3) linked sialic acid. Duck gut epithelium has ? (2,3) link, and pigs have both ? (2,6), allowing for co-infection.
Hemoglobinopathies thalessemias
A structural deficit in the ? or ? globin gene. Occurs in 1 out of 600 people in certain ethnic groups.
Hepatitis delta
A human satellite virus. Circular -RNA, 1682 nucleotides. An RNA satellite of hepatitis B virus, which it needs for its envelope. Can only replicate in cells infected with hepatitis B. Dependent on host for genome replication. Transcription to 800 nucleotides mRNA using host RNA polymerase II. Polyadenylated by polyA signal AAUAAA. Two polypeptides form from a single ORF: small delta antigen and large delta antigen. Replication to antigenome RNA by host RNA polymerase I, with rolling circle replication. vRNA is encapsulated by small delta antigen, and the nucleocapsid is enveloped by hepatitis B envelope, with large, medium, and small glycoproteins, as well as large delta antigen. RNA acts as a ribozyme.
Herpes
Has a generalized infection. It spreads through the blood or central nervous system.
Herpesvirus assembly

A complex virus that requires a scaffold during assembly, which is removed once the capsid is in place. Linear DNA is replicated by circular replication, producing a very long DNA sequence that is recognized by sequences in the capsid. One unit length of DNA is pulled in, and stopped at intersections between copies. Its final envelope is derived from the endoplasmic reticulum.

1. The DNA genome conceter is produced by rolling circle replication.

2. Transport of MT NC to the DNA replication site. UL32 and UL17, as well as UL15.

3. Terminase complex: UL15, ATPase; UL28, recognition and binding “packaging” sequence (pac2/pac2)on vDNA.

4. The terminase complex binds internal pac sequences on DNA, and a single portal penton.

5. Pac remains associated with the portal.

6. One genome length of DNA is “reeled” into the MT capsid until the next pac sequence.

7. Capsid is stabilized by UL25 and UL17.

8. Cleavage at DR1 of both pac sequences, at the portal, with one nucleotide overhang.

9. Genomic DNA in the capsid remains linear.

10. Unpackaged DNA is relegated to reconstitute the pac sequence.

Herpesvirus maturation/egress

1. The virion buds through the inner nuclear membrane, into the endoplasmic reticulum lumen. UL31, UL34, and US3 disrupts the nuclear lamina, and picks up some VP16, and some tegument proteins (first source of tegument proteins, from the nucleus).

2. De-envelopment by fusion with the endoplasmic reticulum membrane (second source of tegument proteins, from the cytoplasm).

3. Re-envelopment by budding into the Golgi lumen.

4. Budding out of the Golgi network, picking up a second envelope.

5. Fusion with the plasma membrane, losing the Golgi-derived membrane.

Herpes simplex virus 1 (HSV-1)
A DNA virus. After fusion with the plasma membrane, the tegument is in the cytoplasm, and the nucleocapsid is in an endosome. The empty nucleocapsid is aligned to the nuclear pore, and is transported through with dynein motors on microtubules. DNA is injected through the nuclear pore complex.
Hexamer assembly
A segment of TAg. Zinc finger assembly at the Ori.
Hop stunt viroid
In the genus Hostuviroid. A plant viroid.
Horizontal transmission
A way a virus may be transmitted. Direct contact or indirect contact vectors. Things people may have touched. The virus is on the abiotic surface, not replicating.
Host range
A segment of TAg. Virus production.
Hsc70
A segment of TAg. Cell chaperone binding activity.
Human herpesvirus 4
A virus that causes Burkitt’s lymphoma or nasopharangeal carcinoma.
Human herpesvirus 8
A virus that causes Kaposi sarcoma.
Human immunodeficiency virus (HIV)
Men who have sex with men have higher occurence. It is zoonotic and came from primates in Africa. The disease knocks out immune cells and the patient dies from an infection, and can have Kaposi’s sarcoma. The SU (GP120) attachment protein attaches to the CD4 cell receptor. CD4 has a Phe43 region that goes into a hydrophobic cavity of SU. Enters the nucleus during mitosis when the nuclear membrane is absent. Infects cells which are supposed to monitor and kill infected cells. In order to control, cells must be shocked into becoming lytic.
Human papillomavirus
A virus that causes 70% of cervical cancer. A vaccine may be made with yeast cells that overproduce L1 surface protein. L1 crystalizes into an empty icosahedron with no nucleic acid, which is injected as a vaccine.
Iatrogenic introduction
A route of infection. Viruses may be spread during hospitalization.
Iceberg concept of infection

1. Most infections have exposure but not infection.

2. Vaccines cause infection but no symptoms.

3. Mild symptoms.

4. Severe symptoms.

Inactivated polio vaccine (IPV)
Created by Jonas Salk. A killed, inactivated virus. Caused no mutation or reversions to virulence. Produced okay immunodeficiency in patients. Had better take in the tropics than OPV. Sufficient immunity to prevent myelitis. Some vaccines did not raise immunity. The antigen structure was altered by formaldehyde. Immunity is in the blood, not intestines. Needed several boosters, requiring lots of virus. More costly: required inactivation and testing. There was a shortage of monkeys for kidney cells for production. Failure of inactivation is always a possibility.
Inactivated tumour suppressors
A mechanism of transformation of cancer cells. Tumour suppressors inactivated incldue p53 and RB.
Inactivated virus

Killed virus

A viral vaccine antiviral defence. Includes seasonal influenza split virus, hepatitis A virus, IPV, and autogenous animal vaccines. Tested for sterility not efficacy.

Inclusion body
Cells are infected and the virus replicates. Either intranuclear bodies or intracytoplasmic bodies, depending on the virus. When tissues are observed you can start to diagnose with inclusion bodies. Seen when the virus is replicating.
Increasing tumour specificity
A necessary step in making a safe virus for oncolytic virotherapy. Limits viral replication to tumour cells: disables the viruses’ ability to modulate the immune system, and targets entry to tumour cells. Predicated on the alteration within the tumour cell, weakening the virus so it can’t replicate in normal tissue. Uses alteration in the tumour to complement engineered viral defects.
Incubation period
The time which occurs from infection until specific clinical signs are seen. Varies among viruses. Many factors, including amount of virus, type of virus, and size and breed of the animal. Before clinical signs there are unspecific signs such as headache, indication of infection. Some individuals are infectious during the incubation period.
Indirect detection
A method of virus detection. Serological tests with antibody. Serological tests include ELISA, virus neutralization, indirect immunofluorescence assay, agar gel immunodiffusion, hemagglutination-inhibition, counter-immunoelectrophoresis, complement fixation, western blotting, and IgM class-specific antibody assay.
Influenza A virus
A -RNA virus in the genus Influenzavirus A, in the family Orthomyxoviridae. Affects birds and humans. It is helical and enveloped, 80 – 20 nm in diameter, pleomorphic. The genome is in eight segments, with a total of 13,588 nucleotides. Virion structural proteins incldue: HA, NA, M1, M2, NP, PB1, PB2, PA, and NEP/NS2. It has vRNA, gRNA, mRNA, cRNA, and panhandle vRNA. In 1918 there was a world pandemic, causing 20 – 60 million deaths (difficult to estimate). The two surface glycoproteins, HA and NA are key antigens in host response to influenza virus in natural infection or vaccination. There can be many combinations of HA and NA types. Birds are reservoirs; ducks can have it without getting sick. Each chromosome has a specific tag, which is recognized during assembly so that the virion has one of each chromosome.
Influenza B virus
Affects humans only.
Influenza C virus
Affects humans and pigs.
Influenza vaccine
There are many variants of influenza, and a complex mixture is needed for vaccines.
Influenza virus attachment
It binds to sialic acid receptors. Penetrates via receptor-mediated endocytosis.
Influenza virus biosynthesis
Viral -RNA is transcribed into +RNa using host mRNA capped primers, stealing host 5′ caps with cap snatching. There is reiterative replication of a poly-U segment, producing a poly-A tail in the mRNAs. Splicing of mRNA occurs in the nucleus, and then mRNAs are transported to the endoplasmic reticulum or plasma membrane. At low NP concentration, PB2 (cap binding protein) and PA (endonuclease) of the RNA polymerase complex have initiation of host mRNA 5′ caps and PB1 (of RdRp), forming mRNA. As NP concentrations increase, influenza switches from mRNA production to gRNA production without a primer, and a single Appp is all that is needed at the 5′ end of a new +cRNA strand. PA has a role in non-primed transcription to +cRNA, and a role in non-primed transcription from full length +cRNA to full length -gRNA, and PB2 has no function. All 8 gRNA molecules then fit into one virion.
Influenza virus polyadenylation
Reiterative copying of the poly-U near the 5′ end of the -RNA influenza virus template during transcription. During mRNA synthesis, RNA polymerase binds to the 5′ end of the -RNA template, and the 3′ end threads through. As it nears the 5′ end of the template, the RNA polymerase blocks itself from continuing beyond the poly-U tract, and it is pulled tight, still attached. There is reiterative copying of an oligo-U, forming a poly-A tail on the mRNA. At about 150 A’s, mRNA synthesis stops, and mRNA is released.
Influenza virus release
The nucleocapsid assembles in the nucleus. Fusion of the transport vesicle with the plasma membrane brings envelope proteins to the plasma membrane, and the nucleocapsid buds through the plasma membrane, bringing envelope proteins with it, and releasing the virion from the cell.
Influenza virus uncoating
The globular head of HA trimer interacts with sialic acid receptors from the plasma membrane. There is invagination, and dynamin-mediated plasma membrane fission, forming an endosome containing the enveloped virus. Acidification of the endosome mediates a conformational change of HA to a fusogenic protein: a loop turns into a coil, displacing the globular head to the side, and exposing the hydrophobic fusion peptide, which inserts into the inner leaf of the endosomal membrane. H+ ions from the endosome are transported into the virion through M2 channels, and the lowered pH allows partial dissociation of viral ribonucleoprotein. Fusion between viral and endosomal membranes occurs, mediated by HA fusion peptide, through hemifusion intermediate, allowing for release of vRNAs into the cytoplasm. Viral ribonucleoproteins have NLSs, and nucleocapsids are imported to the nucleus, where it uncoats and 5′ cap dependent transcription of mRNA occurs.
Influenzavirus A
A genus of viruses. Includes influenza virus A.
Innate immunity
First response to infection, due to pathogen-association molecular patterns such as viral dsRNA recognized by Toll receptor 3. Secretion of cytokines such as interferon. Activation of the complement system (cell lysis and opsonisation for destruction). Antigen presentation by macrophage and neutrophils. Activation of adaptive immune response.
Insulffation
Taking material from the pus of someone with a mild case of smallpox, and blowing it up the sinuses, or mixing it with water and introducing it with a swab. Common practice in China in 200 BC.
Integration deficient lentivirus (IDLV)
The latest generation of lentivirus platform. Integration deficient: DNA exists as an episome. Expression is for the lifetime of the cell. Mutant integrase maintains RT activity, but can’t integrate. Can only carry 8 kb, but is more benign and quiescent than other vectors.
Intercellular movement
The second stage of movement of a plant virus. Through plasmodesmata.
Interferon (IFN)
A cellular antiviral protein, part of innate immunity. Produced in virus-infected cells. Effective only in neighboring uninfected cells. Activates interferon regulated genes, including dsRNA dependent RNase L and PKR. A potent antiviral that induces an antiviral state within a cell. Decreases cell metabolism and protein translation, preventing viruses from replicating. Occurs all the time in our bodies. Many tumour cells  are interferon defective. VSV inhibits interferon production. The first defense against the virus, before the virus replicates.
Intergenomic sequences (IGs)
Identical, designed so that RNA polymerase stops at the termination signal, or sometimes passes over. It is a specific sequence. There is reiterative transcription of poly-U tract, making a poly-A tail. It is capped with capping enzyme action of RNA polymerase in the cytoplasm.
International Committee on Taxonomy of Viruses
Met in 2010 in Paris at the Pasteur Institute. Canadians including Eric Castens, Helene Sanfacon, Curtis Suttle, and prof. Krell.
Interrupt transmission

Disinfection

A prevention measure for viruses. Sources of virus may be clinical cases, carriers, and animal products.

Intracellular movement
The first stage of movement of a plant virus. On the cytoskeleton and vesicular transport.
Intracytoplasmic body
Inclusion bodies found in bovine respiratory syncytial virus.
Intranuclear body
Inclusion bodies found in adenovirus.
Iron lung
A chamber in which pressure goes up and down, enabling a person paralysed from poliomyelitis to breathe. The person will need to live in the iron lung forever.
Isolate virus
A method of virus detection. Isolate from exudate, excretion, secretion, tissue, or feces. The “golden standard”. The only method that can detect unexpected agents. Supply of particles for further characterization and archiving. Large quantities of material as a diagnostic material. It is slow, expensive, technically demanding, needs a specialized laboratory, and some agents cannot be propagated.
ISVP

Infectious subviral particle of reovirus

3 is depleted ?1 myristated.

Janet Parker
A medical photographer who died of smallpox in Birmingham, in the UK in 1978. Was working in a lab studying smallpox, where it was drawn up into the air system of the building. Her boyfriend, Henry Bedson, was the last person to die of smallpox.
Jennerex
A private oncolytic virotherapy company in Ottawa. Uses vaccinia and rhabdovirus.
Jesse Gelsinger
A young man with ornithine transcarbamylase deficiency. Was in the first known and published gene therapy experiment, and received a first generation adenovirus encoding a corrective gene for his disease. He had a fever going into the experiment. The virus produced viral genes which caused a cytokine strom that targeted his liver, and deregulation of production of immune cytokines lead to shock that was fatal. A harsh lesson for gene therapy: an exceptional cost. His death set back gene therapy research.
John Franklin Enders
Scaled up poliovirus production of his boss, Thomas Wellers. With Wellers and Robbins, won the Nobel Prize in 1954.
Jonas Salk
Created the IPV polio vaccine. Poliovirus, plus formalin (inactivated polio virus), produced an inactivation curve. Provided immunity in monkeys. Trials were done on 1,829,916 people in Michigan in 1952 – 1953, found the vaccine to be safe and 70 – 90% effective. It was declared “Safe, Effective, and Potent”. There was celebration, and Salk visited the White house.
Joseph Meister
A 9 year old boy who contracted rabies in 1885, and was saved by Louis Pasteur, who gave him an attenuated virus, with an intraperitoneal inoculation (injected into the belly).
Karl Landsteiner
In 1909 demonstrated the aetological nature of poliovirus by injecting monkeys.
Kinase
Phosphorylation activity.
Kleinschmidt analysis
Uses an electron microscopic to visualize circular DNA of polyomavirus. Cytochrome C is added to the solution to make DNA easier to see.
Koch’s postulates
It is unethical to test Koch’s postulates for human diseases. Evidence that viruses cause cancer is circumstantial.
Kaposi sarcoma
Common in AIDS patients. Decreased immunity causes suceptibility to herpesvirus 8.
Kuru

“Trembling”

A TSE of humans, caused by a prion, affecting native Fore tribes of New Guinea. Causes trembling and inability to sit without support. It was determined by Carleton Gajdusek to be spread by ritualistic funerary cannibalism. Older men ate the meat, and younger boys ate leftovers including the brain, which gave them Kuru. Affects the area of the brain controlling movement.

Laboratory diagnosis
Detects the virus. The ideal diagnostic procedure is fast, simple, sensitive, specific, and low cost. It must be a standardized test with reagants of good quality, miniaturized assays to conserve reagents, automated with high-tech instruments, and with computerized analysis and printouts. There are specialized laboratories for diagnosis.
Lady Mary Mortley Montague
In 1717 her brother died of smallpox, and she caught it herself. Her husband was British Ambassador to the Ottoman Empire. She observed that local women would inject themselves with smallpox, and have fever for two days, after which they would be healthy. She then allowed her son to be variolated with smallpox, and in 1721 her daughter. Experimented on orphans and prisoners to prove its safety. Inoculated the children of the Princess of Wales.
Large delta antigen
A polypeptide of hepatitis delta, 21 amino acids. From the same ORF as small delta antigen. Uses RNA editing so that UAG is changed to UGG, tryptophan, so it is longer than small delta antigen.
Large T-antigen (LT)
An early transcript of SV-40. The protein is transported into the nucleus where it binds to the ORI, and recruits cellular DNA polymerase for DNA replication, and stimulates transcription of late transcripts. A component of the SV-40 replication fork. Hexameric.
Late promoter
Promotes genes to the right of the origin of replication in SV-40. Genes include VP1, VP2, VP3, and VP4. Transcription occurs after DNA replication, stimulated by LT, in greater amounts than early transcripts. The mRNA is 5′ capped and spliced in the nucleus, then transported to the cytoplasm. The structural proteins are transported into the nucleus, and assembly around replicated minichromosomes.
Latent infection
A persistent infection. Neither the cell nor the virus wins. The virus infects the cell but its replication is “suspended” in a latent infection. There are no new progeny viruses.
Ldlr

Low density lipoprotein receptor

A cell attachment factor, receptor for a virus.

Leaf beetles

Chrysomelidae

In the order Coleoptera. There are 20,000 species, 48 of which are vectors for 30 plant viruses.

Leafhoppers

Cicadellidae

In the order Hemiptera. There are 1,500 species, 49 of which are vectors for 31 plant viruses.

Lentiviral vectors
Viruses such as HIV and FIV. Used for gene therapy ex vivo. Naturally integrate into the human genome. Can be engineered to maintain integration without viral replication. Encoded therapeutic genes will become part of the chromosome. You can’t control or predict the integration site; it may activate proto-oncogenes, causing cancer. Integrates into the host genome in a stable fashion. Long-term stable expression of the transgene. High-efficiency infection of dividing and non-dividing cells. Low immunogenicity. Inserts can be up to 8 kb. Can target specific cells through modification of surface proteins. Low virus yield. Currently there are 22 ongoing clinical trials.
Leptomycin B
An antiviral target for influenza virus. Transport of RNP to the cytoplasm.
Level 3 lab
Does work on SARS, influenza virus, and HIV.
Level 4 lab
Does work on EBOV and Marburg virus.
Light microscope
A type of visualization. Visualizing inclusion bodies in infected cells.
Localized infection
A type of virus dissemination. The virus enters the host into the target organ. You can start to see the disease right away. Includes rhinovirus.
Louis Pasteur
Weakened rabies virus by passing it through rabbits, then drying their spinal cords. Tested it first on dogs and found that it worked. In July 1885, a 9 year old boy, Joseph Meister, was bitten by a rabid dog, and Pasteur gave him 13 inoculations of rabies vaccines, and the boy survived. In October 1885, a 15 year old boy contracted rabies, and Pasteur gave him 8 injectsion and he survived. This is the first example of viral attenuation.
Luteovirus
In the family Luteoviridae. A group of 27 plant viruses. Circulative, non-propagative transmission by ahpids.
Lymphatic spread
Local spread of virus dissemination can occur. Tissue macrophages in lymphatic ducts, local lymph nodes, and the blood stream. May be inactivated and processed. Some replicate in macrophages or lymphocytes.
Lysozyme
A physical barrier to infection. An antimocrobial in tears, mucous, saliva, and milk.
Lytic infection

Cytocidal

The virus infects the cell, it replicates, and the cell is destroyed. New progeny viruses are produced.

M protein
A matrix protein beneath the envelope of VSV. It physically blocks nuclear pores, and mRNA cannot exit the nucleus to be translated. The virus can still replicate in the cytoplasm.
M51
An amino acid deletion in a protein of VSV. Deletion of nucleotide 51. Causes it to be unable to inhibit interferon production. The virus cannot block mRNA export in normal cells, but can in cancer cells.
Malignant tumour
Cancer that gives rise to metastasis, allowing new tumours to develop at remote sites.
Mapping Ori

Identifying essential viral genes for DNA replication. Plasmid DNA is replicated in E. coli dam cells had methylated A’s, and were susceptible to being digested. Plasmid DNA replicated in mammalian or insect cells did not have methylated A’s. A different experiment also found the Ori in the same location.

1. Grow plasmids with suspect Ori’s in E. coli dam cells.

2. Transfect plasmids into infected cells.

3. If the plasmid does not replicate, only input DNA (A-met) will remain. Does not have an Ori.

4. If the plasmid replicates, then new plasmids will not be methylated.

5. Extract DNA from infected cells, treat with DpnI, and do southern blot and probe with plasmid vector. Or transfect bacteria and isolate the plasmid.

March of Dimes
A program supporting poliovirus research in 1938. Dedicated to children’s health. Founded by President Franklin D. Roosevelt, who had contracted polio. After Salk developed IPV in 1952, it raised money for production of the vaccine.
Marnavirus
A linear dsDNA virus, 1181 kb. In the family Mimiviridae. It is parasitized by the virophage sputnik.
Matrix protein 1 (M1)
A structural protein of influenza virus A, coded by segment 7. 252 amino acids; the unspliced protein of segment 7. Interacts with RNP and glycoproteins for RNP nuclear export, assembly, and budding. Matrix protein between the membrane and nucleocapsid, holding everything together. A nucleocapsid protein, transported to the nucleus for assembly.
Matrix protein 2 (M2)
A structural protein of influenza virus A, coded by segment 7. 97 amino acids ; the spliced protein of segment 7. An ion channel protein, functioning in assembly and budding. Important during uncoating: it causes acidification of the inside of the virion, causing NP to come off the RNA. The nuclear export signal in the mRNA is spliced, and it is transported to the cytoplasm. An envelope protein, translated on the endoplasmic reticulum membrane.
Max Theiler
From Harvard/Rockefeller. In 1927 found that yellow fever was a filterable agent. Did intracranial inoculation of mice with YFV from infected monkey liver; needed to get through the blood-brain barrier. Passaged the virus from mouse to mouse, and tested the relative virulence in monkeys. The passaged virus became less virulent. Devleoped Dakar (Senegal) YFV vaccine. There were several unacceptable fatalities. Attenuated the virus further, growing it in mouse embryo cells, and passaging through chicken embryo tissues. Tested by immunizing monkeys. Found the vaccine protective with no deaths. For mass production as a human vaccine, attenuated the virus grown in embryonated chickens. Won the Nobel Prize in 1951.
Maximum clade credibility (MCC)
It was used to show that the Caribbean was the source of HIV in North America, with it starting in New York. North American HIV genome sequences based on novel 1978 HIV samples. Caribbean sequences were from Los Alamos National Laboratories for HIV database. The end of an arm represents a unique HIV genome sequence. Nodes represent the last common ancestor for the arms, and year of divergence. The length of the arm represents years to accumulate the number of nucleotide substitutions between arms.
Mealybugs

Pseudococcidae

In the order Hemiptera. There are 6,000 species, 19 of which are vectors for 10 plant viruses.

Measles virus
A virus in the family Paramyxoviridae. Has generalized infection. It looks localized, but there are other symptoms. Has an attenuated strain that restricts entry to tumour cells. The ideal platform for oncolytics, because attachment and fusion are controlled by separate surface proteins, and it can be retargeted. May be used to make a tumour vaccine. All babies are vaccinated for measles.
Mechanical transmission
Arthropod-borne viruses where the insect bites the host, and the virus is transmitted on mouthparts of the insect. There are not many. The virus gets killed quickly.
Medium 199
A medium used for growing poliovirus, developed by Leone Farrell at the University fo Toronto. Used today for most cells.
Mercury
A very small amount is used in vaccines to prevent contamination with fungus or bacteria.
MHCI
The receptor to which SV-40 attaches to the cell. Breaks up proteins of viruses so there are surface antigens, recognized by CD8+T cells.
Microtubules
Transport vesicles containing some viruses. Uses dynein/actin filaments. Disrupted by nocodazole.
Milk
A route of release of the virus. You should not drink non-pasteurizezd milk. Includes cytomegalovirus.
Mimiviridae
A family of large dsDNA viruses that affect amoebae. Includes marnavirus.
Minichromosome
The DNA of SV-40 with histones. Resembles a cellular chromosome. Nucleoproteins of the histones are taken from the host in the nucleus. Distance between histones is the same as in cellular DNA. The chromosome is hyperwound into a supercoil.
Mucous secretions
A physical barrier to infection. Traps pathogens. A good source of IgA.
Multi-partite
A virus which requires several particles to be infectious. Many plant viruses are multi-partite.
Murine leukemia virus (MLV)

The first retrovirus to be used in gene therapy. Used to correct bone marrow cells ex vivo for a fatal immune disorder. Cured the disease, but caused leukemia in two out of eleven patients.

1. Stem cells removed from the body.

2. Cultured in a dish and transduced with virus.

3. Corrected cells are selected and re-inoculated to the patient.

National immunization days (NID)
Days when WHO comes into an area, and vaccinates all children below the age of 5 for poliovirus.
National polio day
October 24th. Polio is still endemic in three countries, with 32 cases.
Natural live virus
Includes smallpox virus variolation and cowpox virus vaccination.
Necrotic local lesion assay
In 1928 Francis Holmes spread abrasives (celite or carborundum) on a leaf surface, and rubbed leaf blades with a finger and a dilution stock of virus. Counted the number of local lesions, and calculated the titer of the original viral stock. Reminiscent of plaque assays of bacteriophages.
Negative-sense single stranded RNA (-RNA)
A type of virus. Genome is 9 – 19 kb. There are 11 total, 8 affecting vertebrates, and 5 affecting plants.
Nepovirus
In the family Secoviridae. A group of 39 plant viruses. Non-circulative, semi-persistent transmission by nematodes.
Neuraminidase (NA)
A structural protein of influenza virus A, coded by segment 6. 454 amino acids. A homo-trimer. Cleaves sialic acid glycosidic bonds from the receptor, releasing the virus from the cell. There are 10 subtypes, N1 – N10. An enzyme that digests neuraminic acid, and eliminates receptors. An envelope protein, translated on the endoplasmic reticulum membrane.
Nigeria
There is a lack of government, making it hard to vaccinate everyone. There is fear of recolonization. In the past, vulnerable populations were used for medical experiments. There are tribal beliefs that vaccines are a scheme of the USA to sterilize the population. Some villages were not vaccinated for polio, and now have polio endemics.
NLS
A segment of TAg. The nuclear locator signal.
Nocodazole
Disrupts microtubules. Prevents transport of herpesvirus and adenovirus capsids to the nucleus.
Non-persistent
Transmission of a virus on an insect that happens very quickly.
Non-propagative
Transmission of a virus on an insect requiring circulation to replicate.
Non-structural protein 1 (NS1)
IFN antagonist. A structural protein of influenza virus A. 230 amino acids, coded on segment 8. The most abundant protein of influenzavirus. Acts as an interferon that antagonizes capases and polymerase A. Prevents interferon from blocking the virus, and prevents an apoptosis cascade. Interferes with polyadenylation. A nucleocapsid protein, transported to the nucleus for assembly. A multifunctional protein. Binds and sequesters dsRNA infected cells, preventing activation of dsRNA induced IFN gene and dsRNA dependent RNase L and PKR. Binds to specific proteins directly. Has functions in replication and splicing.
None
A consequence of virus-host interaction. The host is resistant to the virus.
Nonspecific resistance
A type of resistance in hosts. Includes receptor, cellular factors, interferons, nutrition, age, sex, hormones, lactation, concurrent infection, fever, or acquired immunodeficiencies.
NPC1
The cellular receptor to which EBOV binds. GP2 exposes its C binding domain, which is then bound by RBD.
Nuclear export/non-structural protein 2 (NEP/NS2)
A structural protein of influenza virus A, coded by segment 8. 121 amino acids. Functions in RNP nuclear export and RNA synthesis. Despite its name it is a structural protein. The nuclear export signal in the mRNA is spliced, and it is transported into the cytoplasm. A nucleocapsid protein, transported to the nucleus for assembly.
Nucleic acid
A method of direct detection of virues. PCR, RT-PCR, qPCR, hybridization method, southern blot hybridization, dot blot hybridization, in situ hybridization, restriction endonuclease analysis, RFLPs, and sequencing.
Nucleic acid-based
A method of detecting plant viruses. Includes hybridization (southern blot and northern blot), PCR, qPCR, RT-PCR, qRT-PCR, and metagenomics (next generation sequencing).
Nucleoprotein (NP)
A structural protein of influenza virus A, coded on segment 5. 498 amino acids. Functions in RNA binding, synthesis, and RNP nuclear import. Each nucleoprotein associates with 20 nucleotides. Comes off the RNA when uncoating, due to acidification. AS concentrations rise, more of it binds to RNA, preventing it from being transcribed. This causes the switch from mRNA production to gRNA production. Gets nucleocapsids out of the nucleus. Has an NES.
Nucleorhabdovirus
A plant virus which associates with the nuclear membrane.
Oncogene
A mechanism of transformation of cancer cells. Can be activated by integration of viral DNA, containing a strong promoter, adjacent to the cellular oncogene. Viruses may have their own oncogene that they insert, such as c-src of Rouse sarcoma virus. We have many quiescent oncogenes which can cause cancer when activated by strong promoters.
Oncolytic virotherapy
Use of viruses, natural or engineered, to specifically replicate in and destroy tumour cells but not normal tissue. Engineering viruses to be more tumour-specific. Combines virotherapy with immunotherapy. Fast and emerging in the field of cancer therapy. Early worked involved unmodified, impure human viruses, causing tumours to shrink but patients died from the virus. Engineering a safer virus is necessary. It can debulk cancer, but not cure it. Combined strategies to recruit immune cells may be used. Next generation will combine with TAAs to make a tumour vaccine. The perfect oncolytic virus is targeted exclusively to tumour cells using surface markers, recruits immune cells to the tumour, aided by GM-CSF, acts as a vaccine by expressing TAAs on MHC molecules, and counteracts the tumour immunosuppressive environment (produces pro-immue cytokines, IL-12, IL2). Billions of virions are injected into the body. Oncolytics involves tumours, viruses, and immune system. Each patient will need a specific approach to their cancer. Clinical trials are happening.
Oncolytics Biotech
An oncolytic virotherapy company in Calgary.
Open reading frame (ORF)
Starts with an AUG sequence, and ends with a termination sequence.
Oral polio vaccine (OPV)
Created by Albert Sabine. Long-lasting, durable immunity. Broad immune response, protecting against all three strains of polio: IgG, IgM, and IgA. Lifelong immunity in the intestines. Immune response to protective antigen VP1. Contact immunity: spread to non-vaccinated individuals. More cross-reactive vs. inactivated. Low cost, easy to transport, and easy administration. Eliminated wild type viruses from the community. There is possibility of mutation. Spread to contacts is non-consensual. Vaccine derived poliovirus. Not standardized due to mutations. It is a problem in immunodeficiency diseases. Had poor take in the tropics because it needs to be refrigerated. Kidney cells may have been contaminated with other viruses such as polyomavirus and SV-40. Still used today. It is given to children on a lump of sugar, which is preferred to an injection.
Oral sessile papilloma
A virus which affects free-ranging Atlantic bottlenose dolphin.
Origin of replication (Ori)
The site in SV-40 DNA where DNA replication starts. DNA to the left contains early transcripts, and DNA to the right contains late transcripts. There are 400 base pairs. Has enhancer regions that were the first enhancer regions to be described. Has a TATA box to initiate transcription. Has a core region, without which the DNA cannot replicate. When they were trying to locate it, they isolated SV-40 DNA intermediates without replication, linearized the DNA with EcoRI, and prepared the DNA for Kleinschmidt electron microscopy. There were intermediates with small to large “Ori” bubbles, with the centre always 1.6/3.4 kb from each end, suggesting that the Ori was this distance from the EcoRI site, and cell replication is bidirectional. If the DNA has an Ori, it should replicate in a eukaryotic cell.
Orthomyxoviridae
A family of -RNA viruses. Includes the genus Orthomyxovirus.
Orthomyxovirus

“Mucous”

A gene of -RNA viruses in the family Orthomyxoviridae. Includes influenza virus. Affects the mucous membranes of the lungs. Three genera, Influenzavirus A, Influenzavirus B, and Influenzavirus C. Has receptor-mediated endocytosis, and then the viral membrane fuses with the late endosome membrane, releasing the nucleocapsid.

Osman Hussein Ibrahim
A polio eradication worker who died from a stray bullet in 2010 while trying to do polio vaccination and education in Somalia.
p53

Guardian against cancer

A cellular tumour suppressor protein, discovered using TAg immune precipitates. Prevents abnormal cell division. When activated, it transcribes genes p21, inhibiting cell cycle or inducing apoptosis in virus infected cells. Concentration is normally low, but insult to the cell or viral infection leads to increased concentrations. Viral proteins such as TAg, E7, and E1A (adenovirus and papilloma virus), binds to it, inactivating it, so that it cannot induce apoptosis or prevent division. This can be a mechanism of transformation of cancer cells.

P53
A segment of TAg. Binds to p53.
p300
Important for histone modification. Binding represses early gene transcription.
Panspermia
The theory that viruses originated from outer space. It is not widely accepted. How would viruses survive and replicate in space?
Papaya ringspot virus (PRSV)
A plant virus. Affected Puna Island in Hawaii. Causes defoliation of trees. Transgenic papayas have resistance. Transmitted by aphids. It stays in the soil and roots, so you cannot replant an affected field.
Paramyxoviridae
A family that includes measles virus.
Paramyxovirus
Includes measles virus. MV-H attaches to SLAM receptor, and there is fusion with the plasma membrane. Initial binding is low affinity, but there is consolidation of binding through multiple virus attachment proteins and cell receptor interactions, producing high avidity.
Pararetrovirus
A plant virus that replicates with reverse transcriptase, but does not integrate into the genome of the plant host.
Parvovirus
A small virus, but it still cannot fit through the nuclear pore. It produces phospholipase which destroys the nuclear membrane at the nuclear pore.
Pathogenesis cycle

A cycle of viruses within an individual host. Mechanisms by which viruses cause disease. A stage-by-stage development.

1. Routes of infection.

2. Virus dissemination.

3. Disease production.

4. Release of virus.

5. Transmission of virus.

PB-F2
A protein of influenza virus A, on segment 1. 87 amino acids. Formed from leaky scanning over the ORF of PB1. It escapes from the cell and goes into immune cells to increase apoptosis.
Pea enation mosaic
A plant virus which associates with the nuclear membrane.
Peach latent mosaic viroid
In the genus Pelamoviroid. A plant viroid. Has 337 – 399 nucleotides.
Persistent infection
The virus is the “winner”. The virus infects the cell, it replicates, but the cell survives. New progeny viruses are produced at a steady, low rate. Long-term infection of the host. The virus is not cleared, nad there is a host-parasite relationship. Includes latent infection, chronic infection, and slow infection.
Physical barriers to infection
Non-specific and innate. Includes skin, epithelial layers with tight junctions, tears, urine flow, earwax, nasal hairs, mucous secretions, cilia that sweep viruses away from the nose and lungs, antimicrobial chemicals such as lysozyme, stomach acids, digestive enzymes, macrophages, and neutrophils.
Phytorhabdovirus
In the family Rhabdoviridae. A group of 32 plant viruses. Circulative, propagative transmission by aphids and leafhoppers.
Plants
A major food source for humans and animals. Uses solar energy to produce chemical energy. Provides oxygen we breathe. Pleasant to look at, and are a source of building materials. 19% of species on Earth are plants.
Plant virus
Over 957 virus species, 49% of total. 73 genera and over 49 families. Many genera and speices are not assigned to a higher taxon, and are “floating”. There are no dsDNA or retroviruses. Most contain +RNA. Half have rod or filamentous morphology. Many are multi-partite, transmitted by vectors such as insects and nematodes, and lack a lipid envelope. Families which also have animal viruses include Bunyaviridae, Rhabdoviridae, and Reoviridae. Enters into the plant cells through vegetative propagation material (cuttings, budwood, grafting: common in fruit crops and vegetatively propagated crops), mechanical transmission through wounds or abrasians (rub-inoculation, tools, field equipment and machinery, mites, fungi). Humans are the most important vector for many. Has three stages of movement in infected plants: intracellular movement, intercellular movement, and systemic movement. Detected by biological assays, protein-based, or nucleic acid-based methods. Difficult to control: no pesticides available. Controlling vectors can lead to resistance to insecticides. Breeding for virus-resistant cultivars uses natural resistance genes, which are hard to find, and difficult to incorporate into commercial cultivars. Cross protection, certified virus-free propagation stock, and genetic engineering and RNA silencing may be used to control. Most do not cause symptoms in the host.
Planthoppers

Fulgoroidea

In the order Hemiptera. There are 1,900 species, 28 of which are vectors for 24 plant viruses.

Plum pox virus

Sharka

A plant virus. Crops are lost or unmarketable. Spreads very quickly.

Pol?
A segment of TAg. DNA polymerase ?-binding primase activity.
Poliomyelitis
A disease caused by poliovirus. In 1950, the only treatment was the iron lung. 200,000 cases occured per year in the 1950s, and 2,100 deaths per year: a fatality rate of 1%. Symptoms include flaccid paralysis. The person may not be able to breathe.
Poliovirus
Docks to the cell at CD 155 receptor with FP1 attachment protein. There is rearrangement, loss of lipid, and insertion of the hydrophobic N terminus of VP1 into the membrane, forming a pore. VP3 is displaced and vRNA is released through the VP1 pore. WIN compounds in canyon prevwent rearrangement of VP1. There are three types: A, B, and C (now called 1, 2, and 3). It remains in the blood for a long time. Can be grown, and a vaccine needs all three types to be effective in the blood. It is contracted by being eaten, from fecal contamination. It is a naked virus, and can survive in the stomach. It affects nervous tissues and causes poliomyelitis. If it never leaves the blood it causes no symptoms. Immune response in the blood can prevent damage to nervous tissue. There was an outbreak in the 1950s. There is no animal reservoir.
Poliovirus eradication
In 1988 WHO said they would eradicate polio by 2000. Global eradication will require surveillance, NIDs, mop-ups of house-to-house immunization, and containment. Cases declined after introduction of IPV and OPV. There were 1,977 cases in the USA in 2006, and 1,604 cases globally in 2009. Countries where it has not been eradicated include Nigeria, India, Pakistan, and Afghanistan. There are tribal fears that immunization is a Western ploy to sterilize the population. Eradicated from Canada and USA in 1979. There is a problem with circulating vaccine derived poliovirus. Switching from trivalent PV 1, 2, and 3 (tOPV), to bivalent PV1 and 3 only (bOPV). Switching to IPV. Hopefully it will be eradicated worldwide by 2018.
Poly-A sequence
A sequence in the genome of SV-40, opposite on the circular DNA to the origin of replication. Signals for transcription to stop. The RNA is cleaved back a little, then the sequence is further polyadenylaed. Sometimes the RNA polymerase passes over the sequence, producing late transcript mRNA longer than is normal; these have sequences complementary to early transcrips, and can hybridize to form dsRNAs.
Polyepitope
It may be possible to find a conserved epitope of the stalk of HA of influenza virus, rather than the head, for a more general influenza vaccine.
Polymerase acidic (PA)
A structural protein of influenza virus A, coded by segment 2. 716 amino acids. Has endonuclease activity and some protease activity. Forms a polymerase complex with PB1 and PB2. It is unclear why it has protease activity. Has no function when NP concentration is low. When NP concentration is high, it has a role in non primed transcription to positive, full length RNA, and its transcription into negative viral gRNA.
Polymerase basic 1 (PB1)
A structural protein of influenza virus A, coded by segment 1. 757 amino acids. A part of RNA-dependent RNA polymerase. Forms a polymerase complex with PA and PB2.
Polymerase basic 2 (PB2)
A structural protein of influenza virus A, coded by segment 3. 759 amino acids. Functions in binding the 5′ cap of host mRNAs. Forms a polymerase complex with PA and PB1. Has no function when NP concentrations are high.
Polyomaviridae
A family of viruses. Includes Polyomavirus.
Polyomavirus
A genus of viruses in the family Polyomaviridae. Causes cancer. Includes SV-40, JCV, BKV, and KIPV.
Positive-sense single stranded RNA (+RNA)
A type of virus. Genome is 2 – 30 kb. There are 39 total, 9 affecting vertebrates, and 23 affecting plants.
Potato black ringspot virus
A plant virus in the family Comoviridae. Affects potato.
Potato leafroll virus
A plant virus in the family Luteoviridae. Affects potato.
Potato mop-top virus
A plant virus in the family Pomovirus. Affects potato.
Potato spindle tuber viroid (PSTV)

In the genus Pospiviroid, in the family Viroid. A plant viroid that affects potato. 339 nucleotides.

1. Circular viroid RNA enters the cell and nucleus. Goes right through the nuclear pore.

2. Transcribed by host RdRp with rolling circle RNA, forming a long linear concatameric cRNA with multiple copies of the viroid genome.

3. cRNA enters the nucleolus and is transcribed.

4. Concatenated vRNA is cleaved by host RNase III.

5. Linear monomeric vRNA is circularised by DNA ligase I.

6. Circular ssRNA enters adjacent cells through plasmodesmata.

Potato virus A
A plant virus in the family Potyviridae. Affects potato.
Potato virus M
A plant virus in the family Betaflexiviridae. Affects potato.
Potato virus S
A plant virus in the family Betaflexiviridae. Affects potato.
Potato virus T
A plant virus in the family Betaflexiviridae. Affects potato.
Potato virus U
A plant virus in the family Comoviridae. Affects potato.
Potato virus X (PVX)
A plant virus in the family Alphaflexiviridae. Affects potato. Associates with the endoplasmic reticulum membrane.
Potato virus Y
A plant virus in the family Potyviridae. Affects potato.
Potato yellow dwarf virus
A plant virus in the family Rhabdoviridae. Affects potato.
Potato yellow mosaic virus
A plant virus in the family Geminiviridae. Affects potato.
Potyvirus
In the family Potyviridae. A group of 186 plant viruses. Non-circulative, non-persistent transmission by aphids.
Poxviridae
A family of vaccinia viruses. Same platform as the smallpox vaccine. Has a high safety profile. Attenuated versons have missing key immune-modulating genes, including vaccinia virus.
Poxvirus
Infection causes inclusion bodies in the cytoplasm.
pRB
A cellular tumour suppressor protein. Binds to E2F transcriptional activator proteins, so that cell transcription is low, and there are less cell division proteins. TAg binds to it through the J domain co-chaperone, inactivating it and causing it to release E2F, which then activates transcriptions of cyclins, DNA polymerase ?, thymidine kinase, DNA ligase, and histones. Results in S-phase: DNA replication and cell division.
Presumptive diagnosis
Uses history, clinical signs, epidemiology, post-mortem histology, and response to treatment.
Primer
A component of the SV-40 replication fork. One primer is for the leading strand, and multiple primers are for the lagging strand.
Prion
An infectious agent smaller than a virus, that causes TSEs. A protein, about 250 amino acids long. Includes PrPSC.
Proliferating cell nuclear antigen (PCNA)
A component of the SV-40 replication fork. Replaces DNA polymerase ?/DNA primase when TAg binds to Rep protein C. Keeps DNA polymerase ? on the template. A cellular accessory protein. Sliding clamp to “zip up” nascent dsDNA.
Propagative
Transmission of a virus on an insect, where it replicates in the insect as well as the plant host.
Protein-based
A method of detecting plant viruses. Includes ELISA (enzyme-linked immunosorbent assay), western blot, and immunosorbent EM.
PrPC
A cellular protein. Protease-sensitive. Water-soluble. 43% ? helix, 3% ? sheet. It attaches to the end of a PrPSC fibril, and is converted into PrPSC.
PrPSC

Prion protein scrapie

A modified form of cellular PrPC. Causes BSE and scrapie. Modifies normal PrPC into PrPSC. Forms an amyloid fibre that elongates as more PrPC is converted to PrPSC. Fibrils can fragment and further elongate, forming more fibrils. Fibrils can puncture cell membranes. Protease-resistant. Water-insoluble. 34% ? helix, 43% ? sheet. It forms spontaneously or is ingested. Has the same sequence as PrPC, but different polypeptide folding.

Pseudovirus
A virus constructed so that it contains the attachment protein you want. Used to create a phylogeny of EBOV and test the virulence of A28V strain. An experimental system where the virus can express in cells without replicating.
Rabies
Has a generalized infection. It spreads through the nerves to the brain. A dangerous virus. The vaccine needs to be attenuated. Wild animals can be vaccinated by putting the vaccine in meat bait.
Rb
A segment of TAg. Binds to retinoblastoma.
RdRp

RNA-dependent RNA polymerase

A protein of influenza virus. Carried with the virus, for mRNA production. It is important in the switch from transcription to replication.

Receptor mediated endocytosis (RME)

Occurs in naked viruses such as adenovirus.

1. Firbe attaches to AdV receptor (Car)/integrin.

2. AdV pentamers of penton based are bound to cell integrin, vitronectin.

3. REM stimulates invagination, forming a clathrin-coated pit.

4. Endosome is formed and clathrin is recycled.

5. AdV fibres dissociate.

6. Acidification of the endosome.

7. Destabilization of the rest of the capsid. Some pentons are removed.

8. Destabilization capsid is released from the endosome.

9. Capsid is further transported to a nuclear pore on microtubules with dynein motor.

10. Further dissociation of the capsid at the nuclear pore complex.

11. AdV DNA and core proteins V and VII are imported into the nucleus.

12. Nuclear histones H1 binds to hexon proteins.

13. Importins 7 and ? bind to H1:hexons.

14. Hexon-protein (proteins V and VII) enter nucleus.

15. Further disassembly of the capsid.

16. Viral DNA/protein VII (NP) is imported into the nucleus.

Recombinant vaccines
A live virus. A viral vaccine antiviral defence. Includes VSV-EBOV virus.
Release of insects with dominant lethal gene (RIDL)
Releasing male insects that carry a transposon of a lethal gene. The gene has an activator and promoter drive by its own product, causing toxic buildup. It is bound by a tetragrade, with which the insects are treated so they can reproduce. In the wild, all progeny will die. The insect fluoresces red under UV light so they are easy to identify. Used to control screwworm in cattle and tsetse flies which carry malaria.
Release of virus
The fourth step of pathogenesis cycle. Cell injury. Includes respiratory, feces, skin, urine, milk, genital secretions, or blood.
Reovirus
A dsRNA virus. The -RNA strand is transcribed within the virion, and the +RNA strand escapes through a pore in a penton capsomere, to be used as an mRNA template. Has partial proteolysis in lysosomes, removing the outer capsid. More capsid protein is removed by proteolysis. The core escapes the lysosome. Causes severe diarrhea in children (“don’t leave home”). Has 11 – 12 segments of dsRNA. Has two capsid layers, one of which is removed, leaving behind a subviral particle with pentameric turrets, each responsible for one dsRNA strand.
Reoviridae

A family of viruses which affect plants as well as animals. A dsRNA virus. The dsRNA is hidden in the subviral particle, because it stimulates antiviral response. RNA-dependent protein kinase R induces interferons. Ribonuclease L cleaves mRNAs. Only one penton has a portal. For transcription:

1. Negative RNAs form a circle within RdRp, one at each turret, within the subviral particle.

2. The template for +RNA is capped and non-polyadenylated, and extruded through the pentons of the subviral particle.

3. The +RNA is used as mRNA.

4. Nascent, non-capped +RNA strands, conservative, with one strand used as a template.

5. Nascent subviral particles are formed.

6. The -RNA strand is copied within a new SVP.

7. -RNA within the subviral particle.

8. Template for +RNAs extrude through pentons of the subviral particle.

9. +RNA is used as mRNA.

10. For replication, nascent +RNA strands.

11. Nascent subviral particles.

12. -RNA strand is copied within the new subviral particle.

Replication cycle

A cycle of viruses within a host cell.

1. Attachment.

2. Penetration.

3. Uncoating.

4. Transcription.

5. Translation.

6. Genome replication.

7. Assembly.

8. Release.

Replication factor C (RfC)
A component of the SV-40 replication. A cellular accessory protein. Loads PCNA onto replicated DNA.
Resistance of hosts
Resistance or susceptibility is multifactorial. Includes nonspecific and specific resistance.
Resistance of virus
Viruses may be resistant to heat, pH extremes, desiccation, and UV/gamma irradiation.
Respiratory
Oronasal secretion. A route of release of the virus. Coughing, mucous, talking, sneezing, and kissing.
Respiratory tract
A route of infection. Includes airborne spread. Physical barriers include mucous blanket and ciliated cells, IgAs, particles over 5 – 10 ?m may be trapped. Local vs. generalized barriers.
Retargeting viruses
Mutate attachment proteins of a measles virus so it can no longer attach to its natural receptor. Leave the fusion protein intact, and add a new targeting molecule on the surface, usually a single chain antibody fragment.
Retinoblastoma protein (RB)
Regulates transition from G to S phase of cell cycle. Stops cell division by binding to E2F during G1. Cdk 4 phosphorylates RB into pRB, which then releases E2F, causing cell division. Viral proteins may bind to RB, such as TAg or E7, freeing E2F, allowing cells to divide continuously. This can be a mechanism of transformation of cancer cells.
Retrovirus (HTLV-1)
Currently there are 58 ongoing clinical trials using it for gene therapy. A virus that causes T-cell leukemia.
Rhabdoviridae
A family of viruses that includes VSV. Affects plants as well as animals.
Rhabdovirus
Includes rabies virus. Has receptor-mediated endocytosis, and then the viral membrane fuses with the late endosome membrane, releasing nucleocapsid.
Rhinovirus
After 6 days of infection, the ciliated cells of tracheal epithelium have an abnormal texture.
Rimantadine
An antiviral target for influenza virus. An M2 antagonist, preventing acidification of endosome and fusion of viral and endosome membranes prior to release of ribonucleoprotein and RNA.
Rinderpest
A measles virus of cattle. Millions of cattlw ere lost. Initial control methods were to stop movement of cattle. Vaccination of cattle was successful in Africa, eradicating the disease. It is transmitted animal-to-animal.
RNase H1
A component of the SV-40 replication fork. Removes RNA primer from the RNA:DNA duplex. A cellular accessory protein.
Roger Beachy
In the 1980s discovered coat protein-mediated protection.
Rosalind Franklin
In 1956 described RNA in a TMV particle.
Rouse sarcoma virus
A virus that causes sarcoma in chickens. The first virus discovered to cause cancer. When they discovered it, they thought all cancers were caused by viruses. Contains the oncogene src.
Routes of infection
The first step of the pathogenesis cycle. Entry into the host. Includes respiratory tract, alimentary tract, skin, urogenital tract, eyes, transplants, blood, surgical treatment, and iatrogenic introduction.
RpA
A component of the SV-40 replication fork. A cellular accessory protein. A primase: ssDBP and unwinding helicase.
Ernst Ruska
In 1938, took the first electron micrograph of TMV particles.
S phase
A phase in cell cycle where the cell is committed to DNA replication. TAg induces the host cell to enter S phase.
Sarah Wootton
From the Department of Pathobiology at University of Guelph. Doing research on AAV vectors and precise genome editing.
Satellite
An infectious agent smaller than a virus, bigger than a viroid. A subviral particle. Linear or circular, ssDNA or ssRNA. 220 – 1500 nucleotides. Does not encode enzymes for replication. Dependent on conventional helper viruses. Includes satellite nucleic acids, and satellite viruses. Includes virusoids, satellite tobacco necrosis virus, and hepatitis delta.
Satellite DNA
A satellite nucleic acid with an ssDNA genome. Uses helper virus coat/envelope. Uses helper virus for genome replication.
Satellite nucleic acids
A type of satellite. Satellite ssDNA or ssRNA (circular or linear), 220 – 1500 nucleotides. Doesn’t encode protein coat. Genome replication is dependent on a helper virus, which provides coat proteins. Includes strawberry latent ringspot satellite RNA and cucumber mosaic virus satellite RNA.
Satellite RNA

 A satellite nucleic acid, with circular or linear ssRNA. Uses helper virus coat/enevelope. Uses helper virus for genome replication.

1. Linear satellite RNA enters the cell.

2. Satellite RNA circularizes and acts as a template.

3. Rolling circle replication generates a linear, concatameric cRNA.

4. cRNA is cleaved into monomer copy RNA units which circularize.

5. Copies are transcriped to concatameric satellite RNA.

6. cRNA (from step 3) is transcribed into concatameric satellite RNA, which can enter the cycle againt at step 2.

Satellite tobacco necrosis virus
A satellite virus.
Satellite virus
A tyep of satellite. RNA or DNA genome. Encodes its own coat/envelope. Uses helpper virus for genome replication. Helper viruses include chronic bee paralysis virus and adenovirus. RNA satellite virus replication to linear cRNA concatamers in the cytoplasm. cRNA is transcribed into vRNA, and there is self-cleavage to the mature form. Includes virophages, virusoids, and hepatitis delta.
Scrapie
A TSE of sheep and gaots, caused by PrPSC. The first TSE to be discovered. Worldwide distribution. Fatal neurodegeneration. Genetic variations of susceptibility among different breeds. Incubation period is as long as 8 years. Spreads through contact with the placenta and placental fluids: transmitted to offspring. Animals scrape themselves against fence posts
Segment 1
A -RNA segment of influenza virus A. Has a 5′ cap and a poly-A tail. Has two ORFS, coding PB1 and PB1-F2.
Segment 2
A -RNA segment of influenza virus A. Has a 5′ cap and a poly-A tail. Codes PA.
Segment 3
A -RNA segment of influenza virus A. Has a 5′ cap and poly-A tail. Codes PB2.
Segment 4
A -RNA segment of influenza virus A. Has a 5′ cap and a poly-A tail. Codes HA.
Segment 5
A -RNA segment of influenza virus A. Has a 5′ cap and a poly-A tail. Codes NP.
Segment 6
A -RNA segment of influenza virus A. Has a 5′ cap and poly-A tail. Codes NA.
Segment 7
A -RNA segment of influenza virus A. Has a 5′ cap and a poly-A tail. Codes two proteins by differential splicing, by a stop and start mechanism in the NUAAUGN junction. Codes M1 and M2, which have the same start sequence, but different splicing, sharing only 9 amino acids. There is also a theoretical M3.
Segment 8
A -RNA segment of influenza virus A. Has a 5′ cap and poly-A tail. Codes two polypeptides by differential splicing, NS1 and NEP/NS2. Both have the same start sequence.
Semi-persistent
Transmission of a virus on an insect, requiring longer time to inoculate into a new plant. Doesn’t replicate in the insect.
Severe acute respiratory syndrome (SARS)
A deadly, very contagious coronavirus. Originated in China in one hotel. People were living in close proximity with animals. Major microbiologists of the world worked togehter to identify the pathogen. It is spread in cough droplets. Kills 4% of victims. Caused economic collapse, but quarantine efforts controlled it.
Severe combined immunodeficiency (SCID)

Bubble boy syndrome

A deficit in a single gene, adenosine deaminase (ADA) in 25% of patients. Rare incidence. Targets bone-marrow cells or T lymphocytes. It was cured using gene therapy in an experiment in which two of the eleven subjects developed leukemia.

Shift
A way that influenza can change its coat proteins. Radical changes due to exchange of viral chromosomes, and re-assortment. Includes H2N2 and H3N2. May occur if a pig gets influenza from a duck and a human at the same time: it is a “mixing bowl” for influenza chromosomes and re-assortment. When two different viruses infect the same cell. New virus combinations of the eight chromosomes form, which can have different HA and NA genes. New viruses may be better or worse than either original virus.
Sialic acid receptor
The receptor to which influenza virus A attaches to the cell.
Siman virus 40 (SV-40)
A simple dsDNA virus in the genus Polyomavirus. Icosahedral shape, with 72 capsomers, T = 7. All capsomers are pentameric, with 12 pentavalent and 60 hexavalent. It is 40 nm in diameter, with a genome of 5,243 bp. Virion proteins include VP1, VP2, VP3, and VP4. Non-structural proteins include sT and LT. Virus DNA is circular and has histones to form a minichromosome. Attaches to MHCI via a GM1 ganglioside. Penetrates with receptor-mediated endocytosis into a caveolae and the endoplasmic reticulum. Uncoating mechanism is unknown. DNA to the left of the orgin of the replication contains early transcripts, and DNA to the right is for late transcripts. Early genes are promoted by early promoters, and transcribed by RNA polyerase II. 5′ capping and alternative splicing occurs in the nucleus, and mature mRNAs are transported into the cytoplasm. DNA replication involves LT, bi-directional transcription in a theta circle, and host nucleosome acquisition. Assembly of capsomers begins in the cytoplasm and is completed in the nucleus. VP4 induces cell lysis for release. Maturation occurs during morphogenesis.
Single-stranded DNA (ssDNA)
A type of virus. Genome is 2 – 9 kb. There are 7 total, 2 affecting vertebrates, and 2 affecting plants.
Skin
A route of infection, and a route of release of the virus. Physical barriers include keratin. Virus enters through breaks in the skin. Entry through skin if there are wounds or bugs. Intact skin is an excellent barrier against viruses. Rabies virus and WNV infect through animal or insect bites. Virus release by formation of a rash and fluid of the lesion. A physical barrier to infection. Keratinized, unbroken skin surface is acidic and dry, colonized with “good” bacteria, and has desquamation of skin.
SLAM
Signalling lymphocyte activation molecule. The receptor to which paramyxovirus attaches.
Small circular satellite of rice yellow mottle virus (scRYMV)
A viruoid that stelas coat protein from rice yellow mottle virus, a plant subemovirus.
Small delta antigen
A polypeptide of hepatitis delta, 195 amino acids. From the same ORF as long delta antigen. Stops at 3′ UAG termination codon.
Small T-antigen (sT)
An early transcript of SV-40. The mRNA is 5′ capped and spliced in the nucleus, then translated in the cytoplasm.
Smallpox
Had a high global incidence in the 20th century, and high mortality, causing 2 million deaths per year in 1966. Survivors are severely disfigured. There was international motification to eradicate it. Many people who died of smallpox are buried in permafrost, and there is some fear that global warming will melt the ice and release the disease. Isolates of strains from the past can be extracted from bodies buried in permafrost. People who raid tombs can get smallpox from the ancient corpses of people who died of smallpox. The body needs to be burned to destroy the virus.
Smallpox eradication
WHO worked to eradicate smallpox 1966 – 1980. Diagnostics, surveillnace, and ring vaccination. Last natural case was in 1977, Ali Maow Maalin, from Somalia. A medical photographer, Janet Parker died in the UK in 1978. The last person to die of smallpox was Henry Bedson, in 1978. In 1980 WHO declared smallpox to be eradicated.
SNALP

Stable nucleic acid lipid particles

An EBOV antiviral. TKM-100802 lipid nanoparticles with siRNA that prevent translation of viral mRNA.

Specific resistance
A type of resistance in hosts. Includes specific immune response from vaccination or preveious infection, humoral immune response, cellular immune response, or interferons.
Split virion
A virus grown in chick embryos, inactivated by UV and formaldehyde, purified by centrifugation, disrupted by sodium deoxycholate, and preserved in themerosol. Used in fluviral and fluzone. An inconsequential amount of mercury is used as a prservative, so the preperation is not contaminated.
Sputnik
A virophage. Has circular dsDNA, 18.3 kb. A parasite of marnavirus.
ssDNA template
A component of the SV-40 replication fork.
Stomach
A physical barrier to infection. Very few viruses can survive the stomach; only naked viruses, including enterovirus.
Strawberry latent ringspot satellite RNA
A satellite nucleic acid, 1118 nucleotides.
Subunit vaccine
Just protein of a virus. A viral vaccine antiviral defence. Includes human papilloma virus L1 major capsid protein, and hepatitis B surface GP.
Surgical treatment
A route of infection. Viruses may be spread on surgical instruments when they are not disinfected or sterilized properly. In Japan there was a case of this where someone with dialysis died. cCJD can spread this way.
SV-40 replication fork
There are two, one leading strand and one lagging strand. Components include ssDNA template, LT, DNA polymerase ?, RNA primers, DNA polymerase ?, RpA, RfC, PCNA, RNase H1, Fen 1, and DNA ligase 1.
Systemic movement
The third stage of movement of a plant virus. Through phloem and sieve elements.
T antigen (TAg)
A multifunctional protein of SV-40. Binds to the Ori of SV-40 and recruits DNA polymerase ?, initiating elongation in DNA synthesis. Stimulates host DNA replication so the host cell enters S-phase. Represses early promoters, and stimulates late promoters. Binds p300 histone acetylase, to repress early genes, but not late genes. Acts as an oncogene protein; inhibits host p53 and pRB proteins, enhancing host DNA replication and inhibiting cellular apoptosis. Transforms susceptible cells, immortalizing them. Has protein kinase activity. Its segments were mapped by looking at mutants.
TAg Ori binding

1. TAg binds to the Ori as two hexameric structures.

2. ATP binds to TAg, activating it, opening the dsDNA into two strands, acting as a helicase.

3. TAg binds to Rep protein A, DNA polymerase ?/DNA primase, and topoisomerase, resulting in a short RNA primer annd short DNA on both strands.

4. TAg binds Rep protein C, replacing DNA polymerase ?/DNA primase with DNA polymerase ? and PCNA.

5. TAg acts as a helicase, and repeats steps 1 – 4 at the fork.

TAg temporal regulation

After DNA replication, TAg reduces early gene transcription and promotes late gene transcription.

1. TAg is in high concentration until DNA synthesis occurs.

2. TAg binds TATA box, reducing TAg early mRNAs.

3. TAg depresses late repression by binding cellular repressors RXR and TR?1. Limited amounts of repressors are diluted as DNA concentration increases.

4. TAg activates cell transcription factors, which bind to SV-40 enhancers to increase late mRNAs.

5. TAg interacts with TEF-1, TBP, and TFIIA.

TALENs
Engineered domains consisting of a DNA binding domain (TALE), and an effector domain (Fokl nuclease). 33 – 34 amino acid sequences that bind specific nucleotides. Can target virtually any sequence when arranged in tandem.
Tamiflu

Oseltamivir

An antiviral target for influenza virus. Works only for early infections.

TATA box
An early gene promoter. TAg binds to it. RNA polymerase and TFIID cannot bind to it.
Theodor Diener
A USDA plant pathologist. Discovered plant viroids in 1971. Won the National Medal of Science in 1987.
Theta replication
Replication of a circular DNA strand. Topoisomerase I and II are involved.
Third generation adenovirus
An adenovirus used for gene therapy, with no viral genes and very limited immune response. Huge coding capacity of 36 kb. Can be targeted by swapping fibre genes. Can transduce dividing and non-dividing cells. Difficult to produce, requiring special packaging cell lines. Gene expression is transient, for only 30 days. Used exclusively for cancer gene therapy, in 72 ongoing clinical trials.
Thomas Francis
From the University of Michigan. In 1943, developed an influenza vaccine. Virus was grown in chicken embryos, inactivated with formaldehyde to kill the virus, and preserved with mercury. Reduced incidence from 7.11% to 2.22%. However, this vaccine did not work in 1947 when a new strain arose.
Thomas Weller
Was the boss of John Franklin Enders. In 1946 grew poliovirus in Vero cells. Won the Nobel Prize.
Thymidine kinase (TK)
A deletion in vaccinia virus, which provides a nucleotide pool for replication.
TMV capsid proteins (TMV CP)
The first transgenic resistance against a plant virus was transgenic plants expressing this protein. Delayed onset of the disease. Coat protein-mediated resistance. Excess CP from transgene blocks virus disassembly, leading to resistance against the virus.
Tobacco mosaic virus (TMV)
A plant virus. In the genus Tobamovirus, in the family Virgaviridae. One of the first viruses discovered and conceptualized in 1898. Associates with the endoplasmic reticulum membrane. Virions form a herringbone structure in mesophyll cells. Affects tobacco (Nicotiana tabacum). Causes local necrotic lesions. Stable in dead plant debris in the soil. Infectious in cigars and cigarettes, and can survive for 100 years. A model for pioneer studies. Has mechanical transmission. Has 16.3 capsid proteins per helical turn, 2,130 per virion. The genome threads through the virion, building up as double discs. The 5′ segment threads through the growing helix. Encodes a 126 kDa protein (MTR and HEL), and a 183 kDa readthrough protein (MTR, HEL, and POL). There no polyprotein or proteolysis. It moves through the plant following photo-assimilates.
Tobacco rattle virus
A plant virus which associates with the mitochondrial membrane.
Tomato bushy stunt virus
A plant virus which associates with the peroxisome membrane.
Tomato leaf curl virus satellite
A DNA beta satellite, 2794 nucleotides.
Tomato spotted wilt virus
A plant virus which associates with the mitochondrial membrane.
Toll receptor 3
On the outside of the cell. Can sense dsRNA. Part of the complement system, and can activate cytolysis.
Topoisomerase I
Produces one nick in the DNA to unwind the supercoil during DNA replication.
Topoisomerase II
Produces two nicks in the DNA to unwind the supercoil and separate daughter DNA strands after DNA replication. The strands are broken, allowing the two circular DNAs to become detached.
Toronto technique
Developed by Leone Farrell in 1953. A technique for bulk growth of poliovirus vaccine, using 5 L bottles, and gently rocking them to oxidize cells. Required 165 monkeys per week for cells.
Tospovirus
In the family Bunyaviridae. A group of 5 plant viruses. Circulative, propagative transmission by thrips.
Transformation

Oncogenesis

The virus is the “winner”. The virus infects the cell and transforms it.

Transmissible spongiform encephalopathy (TSE)
Causes spongiform brain amyloid plaques. Caused by prions. Includes scrapie, BSE, Kuru, and Creutzfeldt-Jakob disease. Neurodegenerative, transmissible, with long incubation period. Fatal, with pathological changes confined to the central nervous system. Produces brain symptoms similar to Alzheimer’s disease.
Transmission of virus
The fifth step of the pathogenesis cycle. Shedding and persistence. How a virus reaches another susceptible individual. This is the opportunity for intervention of viruses. Viruses may be spread in food products, wind transportation of animals, animal products, humand migrating birds, vaccines, semen, and eggs. Includes excretion of viruses, horizontal transmission, and vertical transmission.
Transplants
A route of infection. Organ transplants, if the person who had the the organ had the virus. Rabies may be transmitted this way.
Tulip mosaic virus
Produces stripes in the tulip petals.
Tumour associated antigens (TAA)

Neo-antigens

Presented on tumour-cells. The immune system recognizes them as not “self”. May be added to an oncolytic virus and overproduced, so that immune cells are recruited by viral infection and added cytokines.

Tumour formation
A consequence of virus-host interaction.
Tumour vaccine
A vaccine of a measles virus presenting TAAs of cancer cells. Causes the immune system to react to cancer cells. Recruit and “educate” anti-tumour T-cells.
Turnip crinkle virus satellite
An RNA satellite, 230 nucleotides.
Turnip yellow mosaic virus
A plant virus which associates with the chloroplast membrane.
Tymovirus
In the family Tymoviridae. A group of 21 plant viruses. Circualtive, non-propagative transmission by beetles.
Unspliced mRNA
Most cellular mRNA is spliced, except histones, which also lack a poly-A tail. Mature mRNA is recognized by a 5′ cap, 3′ poly-A tail, and exon junctions. If all are present transcript export TREX is activated. Viral mRNA (HIV, influenza) is unspliced, and will lack an exon bindign junction, requiring NS1 protein for export.
Urbanowics et al
Surveyed 16,010 isolates for gp protein mutations during the West African EBOV outbreak of 2013 – 2016. Generated recombinant murine leukemia virus “pseudoviruses” with each mutation, expressing luciferase. Entry of pseudoviruses was tested in bat and human cells, and measured by presence of luminescence. It was seen that A82V mutants had twice as much luminescence in humans than in bats.
Urine
A route of release of the virus. Viruria (arenaviruses).
Vaccine
The ideal vaccine provides protective immunity, raises strong humoral and cell-mediated immunity, provides mucosal and systemic immunity, is safe, low seropositivity, grows to high titres in multiple cell lines. For RNA viruses, there should be no chance of integration into host DNA (except for retrovirues), and there is no chance of re-assortment with wild-type viruses.
Vaccination

“Cow”

A prevention measure for viruses. Originally tested empirically. Results in buildup of adaptive immunity. Humoral immunity, antibody production by B cells. Abs neutralize viruses by preventing attachment, and stimulate destruction of virus and infected cells. Cell mediated immunity via T cells. Immune cells are activated to destroy virus-infected cells tagged by Abs. Produces antibodies that remember the virus.

Vaccinia virus
An engineered poxvirus for oncolytic virotherapy. Has three deletions, and one addition: B19R, vVEG-f, TK, and GM-CSF. In a normal cell, there is induction of interferon, a low nucleotide pool, and no cycle progression. All engineered defects are complemneted by tumour cells.
Variolated
Ingrafted with a live virus. Lady Mary Mortley Montague variolated her children with smallpox in 1717. Benjamin Jestsy variolated his family with smallpox that same year. The British variolated troops in 1775. George Washington variolated his troops in 1777, a bit too late to take Quebec.
Vascular endothelial growth factor (VEG-F)
A growth factor produced by cancer cells to promote angiogenesis. Interacts with epidermal growth factor to start cell cycle. A virulence factor that vaccinia virus cannot replicate without. Vaccinia virus produces another version, vVEG-f.
Vero cells
Green monkey kidney cells. Used to grow polio virus.
Vertical transmission
A way a virus may be transmitted. Transmission from parent to offspring. In animals, it may be by germ plasm, placenta, milk, or eggs. In plants it may be by pollen, ovary, and seeds.
Vescicular stomatitis virus (VSV)

A -RNA virus in the family Rhabdoviridae. Not normally a human pathogen. Bullet shaped, with M protein beneath its envelope. An early oncolytic virus with tropism for neutral tissue. Has a matrix protein that blocks cellular mRNA export, inhibiting interferon production; a M51 mino acid deletion removes this block. Intergenic regions between ORFs. Transcription is by re-initiation: RNA binds to the “leader” intergenic region. For all downstream ORFs, the upstream one needs to be transcribed. For genome replication it switches from mRNA to gRNA, requiring high concentratiosn of antitermination N protein.

1. Initiates at “leader” intergenic region.

2. Terminates at the second IG, producing an N mRNA.

3. Re-initiates at the IG between the first and second ORF, producing a P mRNA.

4. Continues downstream for all transcripts.

5. Transcription stops at the “gene ends” sequence a the IG junction: 3′-AUACUUUUUUU-5′.

6. RNA polymerase slips on the poly-U sequence, causing reiteration.

7. Multiple slips on poly-U sequnece generate an mRNA poly-A tail, and there is dissociation of the mRNA.

8. Reiteration at the “gene start” sequence: 3′-UUGUC-5′ of the next ORF.

9. 5′ capping of a new mRNA.

Viral polymerase
An antiviral drug defence. Includes AZT for HIV.
Viral specific proteins
An antiviral drug defence. Includes protease inhibitors for HIV, ion channel blockers for influenza, and neuraminidase inhibitor for influenza.
Viral VEG-F (vVEG-F)
A deletion in vaccinia virus in VEG-F. An engineered viral defect complemented by the tumour cell. The virus cannot replicate unless the host cell is producing VEG-F, and only cancer cells produce it.
Viroid

viroidae

An infectious agent smaller than a virus, a subviral particle. A small circular ssRNA, 120 – 475 nucleotides. Non-coding, no capsid. Infectious only to plants. Parasites of cellular transcription proteins. Genome replicates in the host nucleus or chloroplast, depending on viroid, with rolling circle replication requiring host RNA polymerase. Can cause serious diseases. Includes cadang cadang viroid of coconuts, and potato spindle tuber viroid.

Virophage
A large dsDNA satellite virus. A parasite of larger dsDNA viruses, using helper virus transcriptional machinery for its own replication and coat/envelope. Includes sputnik.
Virulence
Capacity of a virus to cause disease. A relative term to measure pathogenicity. Multigenic. Determinants include genetic basis (genes, gene products), host tissue and specificity (tropism), infecting viral dose, route of infection, and dissemination of virus within the host.
Virus
Normally they make you sick and can cause damage, but can also be used for oncolytic virotherapy and gene therapy.
Virus detection
Includes isolating virus, direct detection, and indirect detection.
Virus dissemination
The second step of the pathogenesis cycle. Dissemination within the host. Includes localized infection and generalized infection. Local spread can occur on epithelial surfaces, lymphatic spread, central nervous system, or fetus.
Virus elimination
Virus-free stock material certification programs for plant viruses. Includes shoot tip tissue culture and meristem culture, thermotherapy, and chemotherapy (ribavirin). Indexing to ensure plant materials are free from certain viruses. Certification of clean stock materials by government agencies. The United States National Clean Plant Network (NCPN) is involved, and Canada is following suit.
Virusoid
A satellite virus. Circular ssRNA genome, 220 – 238 ribonucleotides. Co-infection with a virus and viroid. Uses helper virus coat/envelope. Dependent on host for genome replication. Only one encodes a protein. Affects only plants. Replicates like a viroid RNA using host plant RdRp. RNA has hammerhead ribozyme activity (functions like an RNase). Ribozyme allows cleavage to monomeric virusoid RNA. Coat protein is from a helper virus. Includes scRYMV.
Visualization
A method of direct detection of viruses. Includes light microscope and electron microscope.
VP1
A late transcript of SV-40. There are 360 copies in the virion; it is the most-produced protein of SV-40.
VP2
A late transcript of SV-40. It is carboxy-end co-terminal with VP3 and VP4, and the proteins are produced by differential RNA splicing. The protein is hydrophobic near its amino end.
VP3
A late transcript of SV-40. It is carboxy-end co-terminal with VP2 and VP4, and the proteins are produced by differential splicing.
VP4

Viroporin 4

A late transcript of SV-40. It is carboxy-end co-terminal with VP2 and VP3, and the proteins are produced by differential splicing. It may induce cell lysis for virus release.

VSV-EBOV
Recombinant VSV that expresses GP of EBOV, used as an Ebola vaccine. Developed in Winnipeg.
Walter Reed
In 1901 found that yellow fever was transmitted by mosquitoes, and also tested for fomite transmission.
Watson
In 1954 discovered the helical structure of the TMV particle.
Wei Zhang
A virologist at the University of Toronto doing research on ubiquination of viral proteins to destroy them, fighting the virus.
Wendell Stanley
In 1935 discovered viruses are proteinaceous in nature. Crystalized TMV particles.
Whitefly

Aleyoididae

In the order Hemiptera. There are 1,200 species, 3 of which are vectors for 43 plant viruses.

Windborne
Aerosol particles from a cough of any size may become windborne. Affected by low temperature, cloud cover, high humidity, rainfall, high population density, and negative pressure ventilation.
Winnipeg
Has the only level 4 virus research lab in Canada, doing experiments on EBOV with pigs and sheep. The lab has negative pressure, so that air is sucked into the room, and never blown out. Workers must wear suits with positive pressure. It takes a day to do a one-hour experiment due to safety precautions. Looking for interferons for EBOV. On November 7, 2016, a virologist working in the lab noticed a rip in his suit. He was put into quarantine for 21 days.
World Health Organization (WHO)
Analyzes the influenza virus trends from the previous year, and tries to predict which strains are most likely to become problematic. Protect against these strains in vaccines. Three vaccines are available: fluviral, fluzone, and flumist.
Yellow fever virus (YFV)
Walter Reed found it to be transmitted by mosquitoes in 1901. Survivors remain resistant. It was a serious disease, causing fatality in 20 – 40%. It is still a problem, causing about 200,000 cases annually, mostly in Africa and South America.
YFV 17D
An attenuated strain of yellow fever virus developed 60 years ago. Still used today. Started with a low neurovirulent YFV from Asibi, Ghana. Passaged 53 times in Rhesus monkeys, sometimes through mosquitoes to monkeys. Passaged 18 times in embryonic mouse tissues. Passaged 50 times in minced whole chicken embryo tissues. Passaged 152 times in minced whole chicken embryos with nervous tissue removed. Somewhere between passage 89 and 114, the virus is mutated sufficiently to lose its neurovirulence. Currently it is produced at the Pasteur Institute.
Zanamivir

Neuraminidase

An antiviral target for influenza virus. Cleaves off sialic acid receptor, allowing for virus release from cell surface. The virus remains stuck to sialic acid receptor on the cell, and cannot spread.

Zika virus
Transmitted by mosquitoes. There was a request for emergency funding for research, but the USA republican government denied funding, and now Zika is found in Florida.
ZMAb
An EBOV antiviral. Three neutralizing mAbs. Made in Canada.
ZMapp
An EBOV antiviral. A mixture of three “humanized” murine chimeric monoclonal antibodies vs. human Ebola virus grown in tobacco (plantibodies), and purified. Produces an anti-antibody response to some antibodies. Made in Canada.
Zucchini yellow mosaic virus
A plant virus. Produces shoestring leaves: severely deformed leaves, and crooked, severely deformed, and unmarketable fruits.
Categories: Microbiology