BICD 136 Review for lectures 6-8

Virology Is a virus alive? Why or why not? Sort of alive, viruses are very small, smallest subunit but cannot replicate by itself, cannot reproduce any of its own components cannot live outside the body, no sexual reproduction Define obligate intracellular parasite, glycoprotein. Intracellular parasite is a parasite that lives within the cell, glycoproteinis a proteins linked ina chain Describe the basic viral structure and lifestyle. They decinigrate, enter the cell, hijack it Reconstitution: Virus puts itself back together Forces itself in, puts its rna there, replicates, destroys or leaves cells Genetic material on the insdie, made up of RNA and DNA, protein coating, and an optional lipid envelope, sometimes made up of proteins What components must be synthesized within the cell in order to build new viruses? All the proteins must be synthesized within the cell, sometimes the lipid envelope can be stolen from pre existing membranes Describe the structure of HIV. (nucleic acid, 3 enzymes, structural proteins, lipid envelope, sugar) Nucelic acid is RNA two single stranded RNA, 3 znymes: protease responsible for snipping the glycoproteins at the end, integrase: complexes with viral RNA transports it to the nucleus and implements it into a chromosome, reverse transcriptase: makes Viral NDA from the viral RNA Strulctural proteins: gp41 gp 120 gp 41 harpoons it, gp 120 is responsible for binding to CD4

Lipid envelope stolen from cell, sugar lines the cell, hides it from the immune system Viruses are categorized as RNA or DNA viruses. Which is HIV? lentiviruses? retroviruses? HIV is a lenti virus, also a retrovirus, not all lentivrisues are RNA, retrovirsuses allRNA Which viruses are diploid? What does that mean? Retroviruses are all diploid, have two single strand RNA Which genes characterize retroviruses in particular? What are their functions? Gag: makes capsid protein, nucleocapsid protein and matrix proteub, Pol: makes integrase, RT and protease and env: makes gp41 and gp 120 How did retroviruses get their name? They ability to go against the central dogma of biology, goes from RNA to DNA, reverse transcription Are all RNA viruses retroviruses? no Describe the infection cycle of HIV. adsorption; GP120 binds to CDR and co receptor(CCR5 or CXCR4) penetration via endocytosis and membrane fusion; uncoating; HIV is endocytosed into the cell, gp41 harpoons the cell, pulls two membranes closer together The endosomal membrane, and viral envelope fuse together The core is dumped into the cytoplasm Capsid is shed Viral RNA and enzymes spilled into the cytoplasm production & integration of provirus; Rt makes a ds copy of viral RNa Integrease complexes with viral DNA, goes into nucleus Integrase medaiets adding the viral DNa randomly into the chromosome Forming the provirus production of messenger RNA, genomic RNA, and viral proteins;

assembly and release of new viruses; cellular processes produce the protein pieces through normal machinery env proteins are insertred directly into the cellular membrane gag polyprotein and gag/pol poltyproteins are created, congegrate directly below the cellular membrane buds off maturation leaves cell, after it buds off, the protease cuts the gag poly proteins and gag/pol poly proteins reforms the capsid into the shape of a bullet What does HIV bind to on a cell? Which cells have these? Macrophages and T4 cells, CCR5 CXCR4 and CD4 Explain R5 and X4 viral strains. R5 binds to CCR5, CXCR4 coreceptor, two different strains What is tropism? Tropism is the area and cellular niche that the virus infects, decided by the cells that it has the ability to bind to, which is determined by the receptors and co receptors Why are some Caucasians resistant to HIV infection? Some cacuasions have a natural resistence to CCR5, some htero wild, reduces infectiiblity, some homo mutate, very resistant to infeciton What are the different ways in which biologists/virologists use the term receptor? Receptor is where the virus hooks on What sequences are found on the ends of the genomic RNA, the provirus, the mRNA? HR1 and HR2s What are the roles of the HIV enzymes? Protease: later cleaves gag poly proteins and gag/pol poly proteins, reforms it as a capsid bullet Reverse transcriptase Forms DS viral DNA from SS RNA, reverse transcription, goes against central dogma of biology Integrase: complex with viral DNA, migrates to the nucleus, mittgates random insertion of viral DNA into genome, forms pro virus

How is reverse transcriptase different from DNA polymerase, and how does this affect the virus? Not as good, many more mutations, doesnt self check or regulate itself, makes DS DNA from SS RNA Explain the role of RNA splicing in the regulation of HIV gene expression. At different splicing levels, different things ar made, initially making lots and lots of splicing, making enzymes, then when rev is created enough, regulates splicing, and rev protein goes into nucleus to suppress splicing, binds to PREsite, suppressing splicing, helps with export of RNA Makes genomic RNA How does HIV produce more than one protein from one gene? Differnet levels of splicing, protease then splices the polyproteins later one What is the pre-integration complex (PIC)? How does integrase mediate the integration of the provirus? It complexes with the viral RNA andmigrates itinto the nucleus, which then inserts it into an active chromsome What is a provirus? Explain its importance to the virus, to the cell, to the organism. Pro virus is the Viral DNA that has been inserted into a host cells chorosome. It is importantto the virus, because it is the way additional RNA and proteins are made. Important to the cell because the cellular machinery is what is responsible for creating the viral RNA, creates the thing that destroy sit Distinguish lytic and non-lytic infections. Lytic infections burst and destroy the cell when the virus buds off, nonlytic cells do not necessarily kill the cell What are latency and reactivation? What is the significance of the viral reservoir? Latency is when a virus is not actively being produced, because the part of the chromosome it is inserted into, is not active. Reactivation is when the piece of cellular mechanism is reactivated, and the virus is produced once again

Viral reservoir is when there is a certain level of cellular latency, it makes it so that the virus doesnt ever go away full How does HIV kill T4 cells? Kills the cells via: CTC: kills infected cells via normal infection manner Cell cell fusion: syncytia: multi nucleaticed cell mass Budding: if it happens enough, eventually kills the cell by destroying the membrane too much Insertion of provirus can take place to critical gene, kill cel Aptosis, cell cuicide What effect does HIV have on macrophages? Gets infected not realy killed Why does HIV mutate so much? RT is very apt tomistakes, doesnt have the ability to regulate its mistakes. Can eventually changeamino acid sequence, can then maybe change 3d structure, can maybe providechange in primary function MAY provide eveolutionary advantage Explain the significance of mutations in the envelope gene. Changes gp 41 and gp 120, can evade where antibodies binds, evades antibodies Explain the significance of mutations in the gene encoding the enzymes. Drugs block specific enzymes, changing the strucut oe of a n enzyme makes the drug ineffective for the most part Be able to describe (or graph) the course of the infection in terms of T4 cells, blood Ab levels, and viral load. Explain the trends in each. Testing Define: seropositive, seronegative, seroconversion, reactive test, window period Seropositive: enough antibodies in the blood to test positive for an ELISA test Seonegative: not enough AB to test positive duing AB test Seroconversion is when enough AB are built up to test the antibodies

Reactive test is a test that reacts with antibodies, corresponding pieces of antibodies are on wells, put the blood, washes it, puts secondary antibodies that attach to the back of the HIV antibodies, stained in some way, wash Window period is when the person is hIV positive, but does not test +, VERY INFECTIOUS When did the HIV antibody test first become available? 1985 Explain the HIV antibody test. Is it direct or indirect? ndirect What does it tell you? What doesnt it tell you? Tells us if antibodies against HIV is present or not, doesnt tell us if HIV is actually present, doesn tell us the viral load What is an ELISA? Enzyme linked immunosorbant assa\y How is this test used? (screening, confirmatory?) Why? What are the advantages? It is used for intial screening, do two more if one is positive, if two positive, do western blot: quick, not many false positive Which bodily fluids can be tested by ELISA? Blood, serum, semen, cervical fluid, breast milk How is it performed? What are the problems with ELISA tests in general, and why do they occur? Doesnt show up if enough antibodies, false negatives if in the window period or nt enough, fals positive if medical condition producers similar antibodies, or has vaccine, or mother was infected What is a rapid test? advantages? disadvantages? Antibody test, takes less than 20 minuets, doesnt take very long to do, quick results, can screen, disadvantage: high false positive What happens if the first test is positive? Do two more then western blot What is a Western blot?

Takes hours days for results, cuts up into pieces, electrophorsesis, cut intro strips, compared to known HIV sample How is this test used? (screening, confirmatory?) Why? What are the advantages? Confirmatory, EXTREMLEY accurate, but slow. How is it performed? What are the problems with a Western blot? slow Explain the test for HIV genetic sequences. Is it direct or indirect? direct What does it tell you? What doesnt it tell you? Tgells you viral load and if there is the virus present, doesnt tell you your favourite colour What are the names of this test? Early test, PCR test Why isnt this test done more commonly? Very very expensive What are problems with this test? Very expensive, takes longer What are advantages of the test? Extremely accurate How sensitive is this test? Very very accurate In what situations is it very valuable? Explain. Viral load, stage of infection, very high false positive rate Distinguish between a rapid test and an early test. Rapid test is an ab test that takes less than 20 minutes, used to screen, early test is PCR test, much smaller window Where might a person go to get tested? Ltos of places baby Explain confidential tests and anonymous tests. Confidential test Is connected to you r name, put in your official heatlh record, reported minus your name to federal CDC Anonymous test you are a number, not connected to you

What are the CDC recommendations regarding testing? Get tested once a year, more so if high risk, IVDU, or multiple partners per year What laws apply in CA? Opt in, have to getg counseling to get the test, have to report to CDC, have to tell parents if under 18 Transmission and Risk Factors Can most viruses infect skin upon skin contact? Why? No, skins part of immune system, kills it Dyes from exposure to aid, and drying, and the low pH of the skin Describe different possible routes of infection by viruses. Mucous membrane, direct acces to blood supply What factors cause the demise of HIV once it is out of the body? Drying up, exposre to sunlight, heat, alcohol or bleach Can HIV be spread by skin contact? Why? CAN if there is lesions in the skin, but otherwise cannot, skin kills it What is necessary for HIV to be transmitted directly from one person to another? Exchange of bodily fluids In which bodily fluids is HIV found? Saliva, serum, lymph, blood, semen, cervical fluid, sweat, tears Can HIV be spread in saliva? Explain. No, it is killed by immune system in the saliva, and the viral count is too low to provide an effective dise Explain the significance of the infective dose. Measure of the dose that is required for a statistically possible/likely infection to take place, >10,000 You should understand all the primary routes of HIV transmission. What are their relative efficiencies? (You dont have to memorize the numbers.) Most effective blood transmission> vertical > ivdu> sex How significant are they worldwide? World wide most common is IVDU and heterosexual What are the most common modes of transmission, in order, in the U.S. and Africa? Africa: heterosexu>vertical>IVDU

USA: msm>hetersex>ivdu>vertical You should be able to make the case, using evidence, that HIV is not spread by casual contact. You dont have to remember specific studies and numbers, but you should be able to present a cogent summary of the data. Which variables must be considered when evaluating the risk of transmission? Other stds, viral load, susceptibility, stage of infection, health, type of activity, strain of HIV, time fluid stays, volume of fluid, recpipetients genetic make up How does HIV infect a person sexually? Breaks through the mucous membrane of the vagina or penis How does the efficiency of HIV transmission (sexually) compare to that of other STDs? Much less effective How soon after HIV infection, does a person become infectious to others? Distinguish mucus membranes from skin. Why are they more susceptible to infection? More m cells, thinner, more moise, no keretainised layer How do STDs and circumcision influence transmission of HIV? Explain in detail. Increases the risk, higher concentration of immune cells, more activated, concentrated in genetial region, also increases viral load of infected partner, and increases the chance of exposure, another place for transmission of bodily fluids What is the relative risk of different modes of sexual transmission? Anal>sex>oral> kissing aExplain each. How can you avoid becoming infected? Use condom, make sure the person is on meds, dont ejaculate in body, use lube reduce number of partners

What factors are important to consider when using a condom (to ensure its effectiveness)? What ti is made of, latex or polyurethane, that it isnt expired, that you use one that fits, use lube Why are women more susceptible to infection than men in a heterosexual relationship? Fluid stays there, semen has higher viral count, larger volume, higher surface area of mucous membranes What behavioral, sociological, and biological factors predispose a population to a sexually transmitted HIV epidemic? multiple partners, genetics, IVDU, no condom use, concurrent sexual partners, not treating STIs Why is HIV spread heterosexually more in Africa than in N. America and Europe? Concurrent sexual partners, increased risk because of no comdoms, dry sex, localized in gay population, no tthat much cross over (What biological and social factors are different between the regions?) How are babies infected by their HIV-positive mothers? Explain. In vitrovirus can pass though placent During birth blood can get into mucous membrane eyes etc Breast feeding: virus present in breastmilk How significant is IVDU as a means of HIV transmission globally? in the U.S.? Very signifigant in certain areas such as uikraine, not a HUGE deal in africa, big deal in USA comparatively to other infectins, second most How does IVDU lead to the infection of others outside the IVDU community? Have sex with non IVDU partners nad vertical transmission (sexual partners and babies) How would you counsel an IVD user if he did not have access to sterile needles? To not share needles with other people, What are NEPs? Are they common? legal? In San Diego?

needle exchange program, give them dirty needles, they give youclean needles, legal in certain areas, gray area, in san diego county not legal, in certain cities it is, cannot take any federal funds In what other ways might HIV be transmitted? Shaving etc etc Can HIV be spread by insects? How do we know this? No, doesnt have the same infection patterns as malaria, kids not infected who play outside during dusk, only sexually active [people, figured out by African scitneis, mosquito doesnt transfer blood back, only saliva, insect gut kills it How significant is the risk to/from health care workers? examples? Signifigant TO health care workers, needle stick, spattering of blood Very insignificant FROM health care workers, only a few, such ad the dentist who gave it to six patietns on purpose What are universal precautions? Basic prevention methods such as: gloves, masks, coats, sterilization of tools, sterile work space, safe How is the blood supply protected against contamination with pathogens, including HIV? Do all three tests, AB test, PCR test, test for proteins Does knowing how to prevent HIV transmission make one safe from infection? It doesnt really, it gives us the information on how to prevent it What has to happen? We need to make behavioral changes