Viruses

What is a retrovirus?

- an RNA virus that contains RNA AND reverse transcriptase - they can make a DNA copy from RNA!

How do enveloped viruses get their envelope?

- animal viruses acquire their envelope (membrane) by BUDDING - in the host cell membrane, there are genes in the virus that cause the host cell to chemically modify its membrane - neuraminidase is a viral-coded protein that is imbeded into the host cell membrane --> this allows the virion to exit the cell with the cell membrane enclosing around it, allowing it to bud off surrounded with the modified host cell membrane

What is lysogenic conversion? KNOW THIS VERY WELL!!!

- bacterial cells that have a prophage in them - most genes of the virus are NOT expressed in the host cell, so it's not causing the host cell to make more copies of the virus - but some (small # of genes) genes, maybe one, may be expressed and they're giving the host cell a new characteristic - so lysogenic conversion refers to the conversion of a host cell into a cell with a new characteristic because of a viral gene that it's carrying

Why would scientists scoff at the idea that an infectious agent could be just made up of protein w/o any nucleic acid?

- bc proteins can't replicate themselves - only nucleic acids can be replicated, transcribed, and translated - we have no knowledge of it being reversed (protein being the template, going to RNA, going to DNA)

What is the iceberg concept of viral infection?

- big at the bottom (most cases), and gets smaller and more serious as you move to the top - largest # of cases: exposed to the virus and it doesn't gain entry or the body immediately eliminates it, so you're not even aware that you've been exposed to a bunch of diseases - viral multiplication without visible change, or incomplete maturation, infection without clinical illness (asymptomatic infection) - inclusion body formation or cell transformation or cell dysfunction, leading to moderate severity and mild illness - fewest # of cases/most virulent: inclusion body formation or cell transformation or cell dysfunction, leading to classic and severe diseases, leading to a higher rate of lysis of cell and death of organisms

Compare and contrast the Marburg Virus and Ebola Virus!

- both are hemorrhagic (discharge of blood from a ruptured blood vessel) viruses - in picture, genes were color coded based on function, and both viruses' genomes were visibly almost identical - clearly, the two highly serious viruses are closely related to each other (prob came from same ancestor)

Tell me about the shape of viruses!

- capsid (protein structure) is shaped as an ICOSAHEDRON (20-sided 3-dimensional structure made up of 20 equilateral triangles) - in many viruses, the capsid is made up of single globular proteins (individual protein molecules = CAPSOMERES) that come together to form triangles, and triangles come together to make up the icosahedron - icosahedron capsid surrounds the nucleic acid - the entire structure, if outside the cell, is called a VIRION - icosahedral shape: very common viral shape of animal viruses (ex: human infections)

Tell me about helical/rod-shaped viruses!

- capsomeres form a hollow rod-shaped capsid by building in a spiral/helical manner - nucleic acids are spiraling inside of the rod/capsid - ex: tobacco mosaic virus, ebola, etc.

Tell me about viral classification!

- different from classification of living things, but in similar pattern - viral taxonomy: order, family, subfamily, genus, and type species - naming is totally different (don't have to be latin, don't have to be two words)

Tell me about the Hantavirus!

- discovered in 1993 - early strains were known in Europe 100s of years earlier, but this was a new strain that showed up in the US - described as a killer in southwest US - first Pennsylvanian died of it in winter 1997 in Lehigh Valley Hospital - causes severe respiratory infection - every year 10-50 ppl in the US are infected with Hantavirus respiratory syndrome, and 1/3 of them die - 35% is a high mortality rate, but to put it in perspective 2.5 million ppl die each year

What happened in 1983?

- doctors in california had young healthy men coming to them with extremely rare diseases like pneumocystis carinii and kaposi sarcoma - eventually figured out that it was a previously unknown virus aka HIV - HIV is way more complicated than tobacco mosaic virus: it's an RNA virus that carries two copies of its genome, it has a protein coat, but it has enzymes that can make DNA copies out of the viral RNA, and has an envelope that is chemically related to the cytoplasmic membrane of human cells - there are drugs that can help patients live a longer life, but no drug can cure the patient - HIV caused a pandemic, but it is now on the drop - highest density of disease is in Africa

Tell me about the replication of HIV!

- enveloped RNA virus that has a lysogenic cycle - gets entry into the cell, has reverse transcriptase, makes double stranded DNA copy from its single stranded RNA (HIV carries 2 copies of single-stranded RNA) - double stranded DNA copy of genes of HIV get incorporated into the nucleus of cells and can stay there for 5 years, maybe 10 years - at some point, they separate and that's when the HIV viruses go through their lytic cycle, making more copies of the HIV virion - HIV virions leave the cells by budding to then attack more cells

Tell me about viruses!

- extremely simple - most are extremely small (one order to two orders of magnitude smaller than bacteria) - simplest viruses just have nucleic acids (either DNA or RNA bc we haven't found any that carry both) and a protein coat --> all DNA viruses make their host cells make RNA copies of their genes --> only some RNA viruses make their host cells make DNA copies of their genes - some viruses carry enzymes (never metabolic enzymes) for DNA/RNA replication - some viruses have an envelope --> enveloped viruses are easier to kill (influenza, HIV) --> nonenveloped viruses are harder to kill (norovirus, which causes intestinal infection, is particularly difficult to kill in the environment) - there are a vast variety of viruses that attack EVERY KIND of LIVING THING --> every species of bacteria has phages that can attack it --> every amoeba, algae, protozoan, plant, fungi, and animal has viruses that can attack it - outside their host cells, viruses can't do anything - they are totally inert! --> can't move, can't detect environmental signals (light and temperature), no metabolism --> which is why could argue that viruses are not living - inside a host cell, they become a home invader of a host cell by taking control of it and force the host cell to replicate the virus --> could argue that viruses are living, but only inside their host cell

What is orthomyxoviridae?

- family of RNA viruses with multiple segments of antisense enveloped RNA - influenza belongs to this family

How do DNA and RNA viruses do their maturation differently?

- for DNA viruses, maturation is predominantly in the nucleus (but a few mature in the ER, membranes, or cytoplasm) vs. - for RNA viruses, maturation is predominantly in the plasma membrane (but a few mature in the ER, golgi, or cytoplasm)

How do DNA and RNA viruses do their nucleocapsid replication differently?

- for DNA viruses, nuclecapsids are replicated predominantly in the nucleus vs. - for RNA viruses, nucleocapsids are replicated predominantly in the cytoplasm

Tell me about human virus shedding!

- for viruses to continue their lifetime, they need to shed - shedding is usually from same body site as entry

How do DNA and RNA viruses do their genome replication differently?

- genome replication for most of the DNA viruses happen in the nucleus, but the pox virion genome replication happens in the cytoplasm vs. - most RNA viruses do their genome replication in the cytoplasm (only a few do their replication in the nucleus)

Tell me about the lysogenic cycle! START HERE

- human viruses that have a lysogenic cycle: cold sores, fever blisters, genital herpes, chicken pox, and HIV - can insert their viral DNA into host cell's DNA and stay quiet for a while (weeks, months, years), and then virus comes out and leads to the lytic cycle

Tell me about animal viruses!

- in addition to having a capsid, some animal viruses also have an envelope (membrane) around the capsid AND nucleic acid is also surrounded by a capsid made up of capsomeres - envelope has chemical characteristics of the host cell of virus + has additional chemicals (ex: spikes) that the virus forces the host to add onto it - ex: influenza has an envelope, HIV has an envelope, some cold viruses do, but most don't

Tell me about zika!

- in flavivirus family - sense single-stranded RNA virus (linear), which serves as the genome and mRNA - surrounded by protein coat and envelope - spherical enveloped and 50nm in diameter (small) - surface proteins are arranged in icosahedral symmetry - 2 virus encoded membrane proteins - genome is all mapped out and we know what most of them do!

Tell me about the replication of influenza virus!

- influenza virus: enveloped antissense RNA virus - when it gains entry into the cell, it gets an extra membrane around its envelope - cell destroys all of those membranes, and uncoats the virus, releasing RNAs that enter the nucleus - bc antissense, causes cell to transcribe sense strand RNA from antisense - more antisense RNA is made to go into the new virion - sense strand RNA which is now mRNA goes out into the cytoplasm where it gets translated - golgi bodies are involved - once the virions are constructed, they bud out through the cell membrane and gain their envelope from it

Tell me about gastrointestinal infections!

- intestinal viruses must overcome: acid, bile salts, and proteolytic enzymes. - acute gastroenteritis ranges from mild watery diarrhea to severe vomiting, diarrhea, and prostration. - rotaviruses (primarily attacks children, but we now have vaccine), noroviruses (can tolerate stomach acid very well, don't have vaccine for this), and other caliciviruses commonly cause gastroenteritis --> if you're vomiting w/o diarrhea, it's prob norovirus - herpes simplex and Epstein-Barr viruses infect the mouth but not intestines - entero-, corono-, and adeno-viruses infect intestines but are usually asymtomatic. - polio viruses (mostly eliminated) and hepatitis A (transmitted via water)cause systemic disease but do not attack the intestines.

How do you work with bacterial viruses?

- like we create a lawn for the kirby-bauer test, we have a petri dish with base agar in it and have a tube with soft agar (same nutrients but less agar so flows better), add the host, and add the virus - pour all that on top of the base agar and spread it over the entire surface - as bacteria start to divide, the viruses will attach to the nearest bacterial cell and go through their lytic cycle - virions are released, and attack neighboring healthy cells - this goes through several cycles before you end up with an area with no more bacterial cells which makes that area clear, and this shows up on the plate (light blue is where the lawn is and where bacteria is not infected, but the dark blue spots aka PLAQUES is bc all the cells in that location had been destroyed by the virus - if want to do further work, sterilize needle and touch it to one of the plaques, and inject the live virus inoculation into another tube/plate

Tell me about complex viruses!

- lots of different shapes within complex group of viruses - T-even bacteriophage: some bacterial viruses look like a "lunar lander" --> made up of tail fibers, baseplate (recognize receptors on cell surface), pins, sheath, DNA, and capsid head (not icosahedron bc not equilateral triangles) --> when attach to cell surface, sheath contracts and DNA is injected

Summarize the types of viral infections of animal cells and the results on the host cells!

- lytic cycle: if virus becomes active and takes control of the cell to make new copies, and can end in 2 ways: 1. cell is destroyed and virions are released 2. the lytic cycle could end with the particles budding out and the cell living for a while - lysogenic cycle: DNA attaches to the host cell DNA and doesn't become acive for a while, but at a later time could become lytic - oncogenic: some viruses can result in oncogenes and result in cancer

How do viral diseases spread in humans?

- most common path of spread is in BLOOD (viremia) or lymph, free or in cells - those that infect the nervous system spread through nerves --> herpes and rabies move in nerves

Tell me about congenital infections!

- most viral infections of the mother do not cross the placenta. - rubella and cytomegalovirus (IMPORTANT) are the most common cause of congenital infections - herpes simplex (genital herpes), varicella-zoster, hepatitis B, measles, mumps, HIV, parvovirus, and some enterorviruses may cause congenital infections - congenital infections may result in fetal death, premature birth, intrauterine growth retardation, developmental malformaiton, or persistent postnatal infection - developmental malformations include: congenital heart defects, cataracts, deafness, microcephaly, and limb hypoplasia. - babies could be infected at birth from maternal fluids with viruses or, more rarely in the first few weeks of life - HIV may be transmitted via breast milk.

Tell me about skin infections!

- most viruses gain entry though abrasions: pox- papiloma- and herpes simplex viruses. - some viruses are introduced by arthropod bites: arboviruses. - some enter through transfusions or needles: hepatitis B, HIV (these come in through injections) - most viruses that enter through the skin become SYSTEMIC, some remain in the skin: papillomaviruses and molluscum contagiosum. - measles rash results from a respiratory origin. - measles and arbovirus rashes- not infectious, as are rashes from pox- and herpes-viruses (bc most are infectious)

Tell me about human oncoviruses and their effects on cell growth!

- most will cause immediate acute disease (ex: warts, hepatitis B), but can also cause chronic cancer (ex: cervical, penile, and oropharyngeal cancer, liver cancer)

Tell me about the replication of Herpes simplex Type 1!

- once inside the cell, because animal cells have nuclei and generally nucleic acid synthesis happens in the nucleus and protein synthesis happens in the cytoplasm, both are involved in replication of Herpes simplex Type 1, an enveloped DNA virus that causes fever blister 1. protein molecules on the surface of the envelope match receptors on the animal cytplasmic membrane, allowing the nucleocapsid of Herpes simplex Type 1 to enter the cell and leave the envelop outside 2. the viral cell uncoats its nucleocapsid, and releases its DNA into the nucleus 3. viral DNA is transcribed into mRNA 4. early transcribed viral mRNA exits to the cytoplasm to be translated into early proteins/enzymes 5. enzymes/proteins enter the nucleus to cause later genes on the virus to be transcribed 6. later genes get transcribed and exits to the cytoplasm to be translated, and the cycle repeats! (there are early, middle, and late proteins) 7. viral DNA gets replicated inside the nucleus, and then the viral proteins that make up the capsid migrate into the nucleus, and construction of the new virions happen in the nucleus 8. Herpes simplex Type 1 then buds out of the nucleus without gaining a membrane, travels to the golgi apparatus, which causes the golgi to modify membranes of the golgi, and virus gains its envelope (this is not very common bc most viruses gain envelope from plasma membrane when exit the cell) 7. this lytic cycle of Herpes simplex Type 1 ends up with budding, NOT explosion of the cell

Tell me about the lytic cycle!

- once virus gains entry into host cell, takes over the host cell, and makes the host cell into a virus factory - so host cell's enzymes, ATP, amino acids, and nucleic acids are now being used to build viral parts and assembled (this process is all directed by viral genes) - viruses don't grow, they get assembled from a bunch of parts into one object - get released from the host cell, resulting in two pathways (both are sucky for the host cell): 1. INSTANT DEATH OF CELL: (ex: cold) after the host cells have made hundreds and thousands of new virions, the last viral gene being expressed makes lysozyme, causing lysis of cells with the release of virions and causing all the cold symptoms (release of cytokines causes congestion and runny nose) 2. SLOW DEATH OF CELL that results in death from exhaustion LOL story of my life: some viruses, especially those with envelopes, like influenza and HIV, don't cause the cells to explode - the viral particles line up against the cytoplasmic membrane and push their way through via budding (so that they are surrounded by the membrane)

How do viruses pull off having a small amount of genomic DNA?

- overlapping genes! (first found in viruses, but we also have them!) - to use the same nucleotide in more than one gene and get more genes than you would normally get if they were not overlapping --> downside: if there is one mutation, it could affect multiple genes :( - there are 6 overlapping genes of Polyomaviruses in 5 thousand base pairs!

Tell me about the lysogenic cycle!

- primarily DNA viruses, but retroviruses also can do the lysogenic cycle --> retroviruses carry RNA but can do reverse transcriptase so can make DNA copy - a large percentage (90%) of bacterial viruses can do the lysogenic cycle, and they are aka "TEMPERATE PHAGES" - at some point, every virus goes from the lysogenic cycle to the lytic cycle; otherwise the virus wouldn't be able to move from one organism to another

How do prions get replicated?

- prions are a normal protein that's part of the nervous system called PrpC --> we have a gene that makes this protein --> when it's folded normally, it functions normally and is involved with transmission of nerve impulses BUT - the same sequence of amino acids could fold in a different way and not function for nerve transmission, and instead causes properly-folded neighboring proteins to also fold improperly - it's a spreading disease! - nerve function then declines, eventually leading to death

What are prions?

- protein infectious agents (NO NUCLEIC ACID) responsible for certain chronic animal diseases involving the nervous system and leading to death - there are not many known diseases caused by prions: --> scrapie (sheep) --> kuru (humans) --> creutzfeldt-jakob (human version of mad cow) --> mad cow (cow DUH) --> chronic wasting disease (deer + elk) - stanley prusiner got the noble prize for discovering prions

Tell me about oncogenic viruses!

- proto oncogenes are normal genes that stimulate cell division (are turned off in most parts of the body and most common in epithelial cells, skin, hair, and bone marrow) - oncogenic viruses contain modified oncogenes that inappropriately stimulate infected cells to divide and become cancerous - oncogenic viruses are lysogenic (attached to the DNA and genes get turned on which stimulates cell division) - most cances are caused by errors in replication or external factors, but 10% of human cancers are caused by oncogenic viruses, both DNA and Retroviruses - DNA oncogenic viruses: Adenoviridae, Herpesviridae, Poxviridae, Papovaviridae, Hepadnaviridae

How would a bacteria cell defend against viruses?

- restriction enzymes can chop up viral DNA, not allowing it to be replicated inside the host cell --> were designed evolutionarily to defend against viruses... --> they recognize certain sequences that are common in viruses but aren't common in the host cell, so will chop up viral DNA - but not all that successful bc we're still getting sick!! --> bacteria are still being taken over by viruses!

How does a virus decide after it enters the cell whether it's going to go lysogenic or lytic?

- several conditions determine whether the virus will go lysogenic or lytic!

Tell me about viroids!

- short strands of naked RNA (not surrounded by protein coat) responsible for some plant diseases - really tiny and have very few genes - have DNA characteristics and are copied by DNA-dependent RNA polymerase of the host - also have enzymatic activity bc RNA can have enzymatic activity!

Why is lysogenic conversion "pretty amazing"??

- the distinguishing characteristic of clostridium botulinum is its toxin, but the botulinum toxin is actually coded for by a virus gene from a lysogenic virus that clostridium botulinum carried!! - corynebacterium diptheriae, which causes diptheria, also produces a diptheria toxin that causes a membrane to develop in the throat area, which is also caused by a lysogenic virus!! - shows that the major characteristics of some bacterial diseases are carried not by their own bacterial gene, but by viral genes from a lysogenic conversion

Tell me about virusoids!

- the few species that we know about of RNA that infects humans - formally called satellite RNAs - covalently closed, circular infectious ssRNAs - encode one or more gene products - require a helper virus for replication --> ex: human hepatitis D virus is a virusoid and it has so little genetic information that it can't cause hepatitis by itself - it can only cause an infection if the person is co-infected with hepatitis B virus

Tell me about repiratory infections!

- the most common entry point for viral infections - many remain localized such as cold viruses, others become systemic: chickenpox, measles, rubella - diagnosis can often be made from symptoms. Symptoms range from mild, to severe, to death, especially in children and the elderly - respiratory infections are the greatest infectious killers of children younger than 5 years old, followed by gastrointestinal infections

What is the concern about avian influenza if we don't handle birds?

- there are these highly virulent flu influenza viruses that birds have been getting and has been killing lots and lots of birds - it's not transmitted by respiratory route - it's transmitted by direct contact, so it's not that dangerous for people who don't handle birds - however, the avian influenza virus is an RNA virus and instead of having a single piece of RNA that makes up its whole genome like HIV, the avian virus is a segmented virus that has several pieces of RNA all of which together make up its genome (making it highly highly virulent) - avian virus is highly virulent, while human virus is highly contagious (transmitted by respiratory route) - a pig could get infected with lots of different strains of viruses - it could be infected with a human virus that is transmitted by the respiratory route, but it could also be infected with the avian virus by contact route - if there is exchange of DNA from both viruses, the new virus is both highly contagious and highly virulent - which is why they are expecting millions and millions of people to die, it's just a matter of time...

Why do new viruses keep showing up?

- they mutate - they've been in low numbers, so nobody's been paying attention to them - somehow they cross over from animals to people - because of travel, they may enter a new realm and start infecting a lot of people

Tell me about central nervous system infections!

- virions gain entry via blood or through either sensory or motor neurons. - meningitis and/or encephalitis are caused by: herpes-, toga- flavi-, entero-, rhabdo-, paramyxo-, and bunya-viruses. - pathological reactions include: necrosis, inflammation, and phagocytosis by glial cells - some symptoms are due to autoimmune disease

What are the main characteristics of latent disease from lysogenic viruses?

- when first get infected (acute), get symptoms upon infection - then, symptoms go away entirely - then sometime later, they come back in the latent infection - some viruses have long term chronic symptoms, which is called a persistent infection (different from a latent infection bc latent infection has no symptoms whatsoever after acute infection) which has some symptoms as it increases and persists

How do you work with animal viruses?

- you have a monolayer of host animal cells in tissue culture - you infect it with a virus and get changes in the host cells wherever the virus infects (plaques) - a lot of viruses that infect humans will also infect birds, so have developed many ways to inject virions into fertilized chicken eggs --> with different viruses, will inject different parts of the egg --> can get viruses to multiply in the chicken embryo, which is how influenza vaccines are developed --> have millions of fertilized chicken eggs and inject them with influenza and chicken will hatch in 21 days, so sometime before 21 days, you kill the chicken embryos :'( --> then purify the antigens from the viruses, and then use those to make the vaccine --> hospital micro labs do this in some degree, but most just send the unknown virus to another more equipped lab

Tell me about zika virus!

- zika virion measures approximately 50 nm across - contains multiple protein types both within and at the surface of the lipid membrane - transmitted by mosquitoes - named after a river valley in Africa - it's been known for 50 years: it's not a new virus, it just had a major outbreak in brazil - proved to cause microcephaly, where babies are born with very small brains and lifelong disabilities - second outbreak showed to have a lot less cases of microcephaly and there's a suggestion that it might require co-infection with dengue fever (which is very common in brazil) - several people in florida got infected with zika from mosquito bites

What do viruses do once they get to their target organ systems? (4)

1. a lot of times, viruses may cause infection but symptoms are mild and body overcomes it so you hardly or don't know you've been infected --> ex: west nile virus can cause very serious brain damage, but most of the time, it doesn't (your body kinda is aware that it's in your body and removes it) 2. some viruses kill cells 3. some impair functions but do not kill cells (and it's the damage that lead to symptoms) 4. some symptoms are caused by release of cytokines from injured cells, so it's not specifically the virus causing the symptoms, it's your own cells releasing chemicals to combat the virus

What are the steps to the bacterial lytic cycle?

1. attachment: the phage attach to specific receptors on the cell wall of host cell 2. penetration: following attachment, phage DNA is injected into the host cell, leaving the phage coat outside 3. if the bacterium is not successful in destroying the viral DNA via its restriction endonucleases, the virus will take over 3. transcription: phage DNA is transcribed, producing phage mRNA, which utlizes host cell enzymes, ribosomes, tRNAs, and ATP, to be translated to phage proteins 4. replication of phage DNA and synthesis of proteins/enzymes: phage coat proteins, capsomeres, other protein components, and DNA are produced separately - host DNA degraded 5. assembly: phage components are assembled into mature virions 6. release: the host cell lyses and releases many infective phages, leading to attachment of neighboring healthy host cells

What are the 5 viruses that have a lysogenic cycle?

1. cold sores 2. fever blisters 3. genital herpes 4. chicken pox 5. HIV

What are the three different shapes of viruses?

1. icosahedral 2. complex 3. spiral/helical

What are three common shapes for viruses?

1. icosahedron 2. helical/rod-shaped 3. complex

What are the 2 mechanisms of animal virus entry?

1. if animal virus has an envelope: --> protein molecules on the surface of the envelope that match receptors on the animal cytplasmic membrane --> animal virus pushes into the host cell plasma membrane --> viral envelope stays attached to the cell membrane and just the nucleocapsid of virus comes into cell, while viral envelope merges with the host cell plasma membrane --> the host cell then uncoats the virus in an attempt to destroy the virus, releasing the viral RNA/DNA (NOT a good idea bc allows virus to take over) 2. but for most viruses that don't have an envelope: - have proteins that connect with the receptors on the animal cytoplasmic cell membrane - animal cells can do phagocytosis/pinocytosis, so host cell membrane surrounds the viral particle, and creates a vesicle that imprisons the virus - in attempt to destroy the virus by destroying the capsid, release the viral nucleic acids, allowing animal viruses to gain entry into the cell and take over

What are the 2 paths to viral multiplication?

1. lytic cycle (most viruses) 2. lysogenic cycle

What are the two different types of viral replication?

1. lytic cycle: (ex: cold) viruses gain entry into the epithelial cells of the respiratory tract, take over, and force the cells to make copies of the viruses, and at the end, they explode the cells, giving you the cold symptoms - then infect other cells and give you irritation (sneeze and cough) 2. lysogenic cycle: (ex: fever or cold sores) show up, disappear, and show up again

What is the bare minimum of a virus?

1. nucleic acid 2. protein coat

What are other features in classification of viruses?

1. shape of capsid (icosahedron, spiral, or complex) 2. DNA/RNA sequence

What are two categories of organisms that don't have the bare minimum of viruses (nucleic acid + protein coat)?

1. viroids 2. virusoids

Walk me through the lysogenic cycle of a bacterial virus!

1. virus recognizes receptors on the host cell surface 2. injects DNA into host cell 3. viral DNA attaches to host cell DNA and for the most part, the genes are not expressed --> the integrated DNA is called a PROPHAGE/PROVIRUS (provirus = prophage in bacteria) 4. if bacterial DNA divides and replicates, it also makes copies of the viral DNA along with its own DNA, and so viruses are being replicated even though there's no outward sign of the virus 5. this can continue for a long time - many cell replications 6. at some point, the viral DNA separates from the bacterial host cell DNA, and goes into the lytic cycle 7. so now, viral genes are transcribed, viral proteins are being translated, and end up producing many new virions and get released one way or the other

How do we first classify a virus? What's the second step? Third? Fourth?

1. we first classify a virus by ITS HOST! - no animal virus can ever infect a plant and vi sa versa 2. is it a DNA or RNA virus? 3. is it single stranded or double stranded? is it sense, antisense, double stranded, multiple segments, or retrovirus? 4. is it enveloped or not?

Tell me about VERTEBRATE viral classification!

10 families of DNA viruses: - most are double stranded DNA viruses (8), but some are single-stranded DNA viruses (2) --> double-stranded DNA viruses are made up of 4 enveloped and 4 non-enveloped DNA viruses --> single-stranded DNA viruses are ONLY made up of non-enveloped DNA viruses 18 families of RNA viruses: - divided into sense single stranded RNA viruses and antisense single stranded RNA viruses --> sense single stranded: the RNA that it carries is messenger RNA (so can be directly translated into protein w/o nucleic acid replication)! --> antisense single stranded: carry the compliment of messenger RNA (so CAN'T be translated directly, need to first transcribe mRNA from antisense RNA that virus carries) - also contains 2 familes of double stranded RNA, 1 family of retrovirus, and 1 family of antisense enveloped multiple segments (orthomyxoviridae)

How many known human viruses (and associated pathologies) are there?

122

How do we characterize influenza?

2 proteins: H and N - influenza strains are characterized by different strains of H protein and different strains of N protein - both H and N proteins are involved with how the cells attach to their host cells

How many human virus families are there?

22

How many known species of all types of viruses are there?

4404

Tell me about the first step of the lytic cycle!

ATTACHMENT is 1st step: - different viruses are designed to attach at different locations of the host cell - can inject DNA through a sex pilus (bc it is a protein tube that is hollow and is able to be injected into) - can inject DNA into flagellum (also hollow protein tube, so can get directly into cytoplasm) - can inject DNA directly into cell itself --> bacteriophages have certain proteins that recognize receptors on the cell surface, they attach, and then inject their DNA

What viral pandemic has not happened yet, but people who know about it are paranoid about?

AVIAN INFLUENZA PANDEMIC aka bird flu - expected it to have killed millions of people already, but hasn't happened yet! - high mortality rate: ~60% - people who have gotten it so far have gotten it directly from birds (ex: ppl who handle birds get it from the birds) - kill millions and millions of birds in the country to try to prevent the spread of the virus

What is the ultimate way in how we classify viruses?

DNA/RNA sequencing!

True or false: most animal viruses are single stranded or double stranded RNA.

FALSE! - most PLANT viruses are single stranded or double stranded RNA!

True or false: most bacteriophages studied so far are sense single stranded RNA viruses.

FALSE! - most bacteriophages studied so far are DOUBLE-STRANDED DNA

True or false: in animal viruses, the protein coat stays outside, and only the DNA is inserted.

FALSE: in BACTERIAL viruses, the protein coat stays outside, and only the DNA is inserted

What's the cure for prions?

NOTHING! - there's no cure OR vaccine for prions - if you get infected by a prion, you will continually lose more and more nerve function until YOU DIE

What is an example of a giant virus and tell me about them!

PANDORAVIRUS - it's 2um long - the size of staph. aureus and can see with even just a light microscope! giant cells are: 1. associated with amoebas (we haven't found any human viruses this large) 2. contain large genomes

How was viruses first discovered?

TOBACCO MOSAIC VIRUS! - splotches on leaves that lowers the worth of tobacco leaves - 1880's disease of tobacco was destroying Dutch cigar industry Martinus Beijerinck in Holland and Dimitri Iwanowski in Russia showed the cause was in the juice and would pass through a bacterial filter and could not grow on its own: - both independently found that if touch sterile needle to infected leaf and then touch a healthy tobacco leaf, will cause splotch - also found that these microbes could go right through a bacteria filter that was supposed to catch bacteria, showing that it is smaller than bacteria - also tried to grow it, and couldn't, which means they either didn't have a suitable medium to grow it, or it couldn't grow outside living tissue! Iwanowski was still thinking it was some kind of small bacterium and didn't have the right formula to demonstrate that, while Beijerinck was thinking that it was something different - in general, there are a lot of plant viruses that cause a lot of problems for food production

True or false: most phages are non-enveloped but enveloped phages exist.

TRUE!

True or false: there is a great range in amount of genetic information in different viruses.

TRUE! - ex: H-1 parovirus is single stranded DNA with only 5,176 bases vs. herpes simplex I with double stranded DNA with 152,260 pairs of bases - some viruses get by with very few genes (very little genetic information), and others have a lot!

True or false: both double-stranded and single-stranded RNA AND DNA viruses exist.

TRUE! - there are 2 single stranded DNA viral families, 8 double stranded DNA viral families - 16 single stranded RNA viral families, and 2 double stranded RNA viral families

TRUE OR FALSE: there are some bacterial viruses that can push out through the cell membrane and cell wall without causing the cell to explode.

TRUE! there are some cases of EXTRUSION in which they don't gain an envelope as they exit and just push out of the wall to exit on its own

True or false: there are some viruses that are bigger than the smallest bacteria.

TRUE! viruses come in a variety of sizes :) and the largest viruses are bigger than the smallest bacteria!

True or false: there are human disease that have their characteristics because they're caused by lysogenic viruses.

TRUE: - the Herpes family of DNA viruses has lots of lysogenic species - ex: 80% of herpes simplex 1 infect the face area, and 20% infect the genital area - ex: 80% of herpes simplex 2 infect the genital area, and 20% infect the face area - so for fever blister, you get infected and pretty much every human being has been infected with herpes simplex 1 - so get infected with it, get the sore (when the virus is lytic), and then the sore goes away, and what happens is, the viral DNA travels up the nerve fiber to the nerve cell nucleus and incorporates itself in one of the chromosomes of the nerve cell for some length of time (weeks, months, years) - some time later, it travels back down the nerve cell to the same area of skin and erupts again in the lytic cycle, causing a fever blister, which can happen over and over again (genital herpes works the same way) - herpes varicella zoster causes chicken pox --> so get chicken box ~5 yrs old, get lytic cycle in the form of pox all over skin --> pox goes away and maybe when you're 50 or 60, you get another eruption in skin bc DNA of chicken pox virus was hiding in nerve cells and for whatever reason got active again, traveled back down to the skin and caused shingles (which is more severe than chicken pox bc in adults, immune system isn't as active as it is in younger ppl) - HIV is an RNA virus that can unusually also do the above cycle

True or false: there is a commission that meets annually that keeps track of viral classification.

TRUE: it's called the official international committee on taxonomy of viruses - the orders, families, subfamilies, genera, and species are continually increasing every year

True or false: there are different incubation periods for different viruses.

True!! they can be as fast as 1-2 days (influenza) and as long as 1-10 years (AIDS)...

What is the structure called if a virus is outside a cell?

VIRION!

What happened in 1935?

Wendell Stanley crystallized the tobacco mosaic virus, showing that its outside surface was chemically very simple - we now know that the virus is a spiral RNA virus - it's rod shape with RNA nucleic acids but its protein coat revolves around it in a spiral

What is the difference between bacterial obligate intracellular parasites and viruses?

bacterial obligate intracellular parasites: - have plasma membrane - can do binary fission - may or may not pass through bacteriological filters, whereas viruses can (bc so smol!) - process both DNA and RNA - have ATP-generating metabolism - contain ribosomes - are sensitive to antibiotics - are not sensitive to interferon (chemical that vertebrates make in response to a viral infection), whereas viruses are

What is interferon?

chemical that vertebrates make in response to a viral infection - gets into the blood and causes adjacent human cells to become more resistant to viral infection - there's research about using interferons as a drug to cure viral diseases (and it also has anticancer activity!) - problem: interferons are specie-specific :( you need human interferons and extracting animal interferons won't work :(

Where do most non-enveloped viruses do their genome replication?

cytoplasm

Tell me about cell tropism when it comes to viruses!

different viruses have affinities for certain organs (liver for hepatitis viruses) - there are 4 hepatitis viruses (a,b,c,d) and they aren't related to each other, but all of them attack the liver - encephalitis viruses that you acquire from mosquito bites, the virus travels in the blood stream and attacks the brain, but not other organs in particuar

How do humans recover/not recover from infections?

host either: 1. recovers 2. retains persistent infection, or 3. dies from the disease

What's the strange thing about zika?

it is sexually transmitted! - we don't know about another systemic virus that is sexually transmitted! --> ex: malaria is not sexually transmitted

How do most human viral diseases enter humans?

most enter via mucosa of RESPIRATORY or DIGESTIVE tracts, some to blood by vectors or punctures.

Where do most human viral diseases replicate in humans?

most viruses replicate at site of entry after they enter (ex: warts), while some move systemically, and others do not. ex: measles is actually a respiratory virus, but then disseminates throughout the body and becomes systemic and moves to the skin to get a measles rash

What is the definition of virus?

noncellular infectious agent that causes host cell to make copies of it

Where do most enveloped viruses do their genome replication?

nucleus!

What is one disease that we're on the verge of eradicating in the world right now?

polio!

The 2 most common killers of children are:

respiratory infection and intestinal infections (respiratory and diarrheal diseases) - respiratory disease caused by viruses are extremely common (the biggest cause of illness)

What is the difference between a sense single stranded RNA virus and an antisense single stranded RNA virus?

sense single stranded (8): the RNA that it carries is messenger RNA (so can be directly translated into protein w/o nucleic acid replication)! - separated into 4 enveloped and 4 non-enveloped vs. antisense single stranded (6 families): carry the compliment of messenger RNA (so CAN'T be translated directly, need to first transcribe mRNA from antisense RNA that virus carries) - ONLY enveloped (6)

What is one disease that is completely eradicated in the world?

small pox!

What is the clinical illness/cause of symptoms for human viruses?

some symptoms are caused by release of cytokines from injured cells, so it's not specifically the virus causing the symptoms, it's your own cells releasing chemicals to combat the virus - ex: cold virus - symptoms of congestion and runny nose are due to cytokines chemical messengers released by the killed cells from the virus (it's not virus causing symptoms, it's your own cells sending messages to try to combat the virus)

What is extrusion?

the exiting of a virus without budding

In the steps to the bacterial lytic cycle, where would transduction play a role?

transduction: genetic recombination bacteria - step 4 (assembly): bc it could take up the host cell DNA by accident while being assembled into infective viral phages

What does viral clearance involve?

viral clearance involves host defenses: interferon, other cytokines, humoral- and/or cell-mediated immunity (whole immune system) interferon: chemical that your infected cell with a virus sends out into the blood and increases defenses of other cells against that virus

Define virion.

virion: viral particle outside the cell that needs to gain entry into a host cell

What is the size of viruses and how does it compare to cells?

viruses: 10-500 nm vs. bacterial cell: 1,000 nm animal cell: 200,000 nm plant cell: 400,000 nm

How does the nucleic acid content of viruses compare to that of cells?

viruses: contain either DNA or RNA, but never both vs. cells: always contain BOTH DNA and RNA

How does the enzyme content of viruses compare to that of cells?

viruses: contain very few, if any enzymes (only for nucleic acid synthesis/replication) vs. cells: contain many enzymes

How does the internal components of viruses compare to that of cells?

viruses: lack ribosomes and enzymes for harvesting energy (metabolic) vs. cells: contain ribosomes and enzymes for harvesting energy (metabolic)

How does multiplication of viruses compare to multiplication of cells?

viruses: multiply only within cells (outside the cell, they are metabolically inert), protein coat and nucleic acid separate prior to multiplication vs. cells: most are free-living and multiply in the absence of other cells, entire cell remains intact during multiplication even during binary fission