CDC site UNAIDS Aids Knowledge Base http://www.cdc.gov/hiv/dhap.htm http://hivinsite.ucsf.edu/insite.jsp?page=kb National Institute of Allergy and Infectious Diseases http://www.niaid.nih.gov/default.htm Combination Antiretroviral Therapy June 1998 Am.Acad.Family Physicians http://www.aafp.org/afp/980600ap/maenza.html The Body: Gene Therapy for HIV/AIDS http://www.unaids.org/en/default.asp http://www.thebody.com/treat/expdrugs.html HIV Infection and AIDS, FDA related treatment, testing, fraud, prevention,clinical trials http://www.fda.gov/oashi/aids/hiv.html Interesting article on HIV therapy written for physicians http://www.postgradmed.com/issues/2004/02_04/volberding.htm

HIV 1981 Centers for Disease Control report s of unusual incidence of pneuomonia caused by Pneumocystis carinii and of skin cancers caused by Kaposi's sarcoma. Patient's immune system was imparied. 1982 CDC recognized a new disease: Acquired Immune Deficiencey Syndrome which is abbreviated AIDS. 1983 Two years after appearance of unknown disease the infectious agent was isolated. Now called Human Immunodeficiencey Virus which is abbreviated HIV. 1984 Estimated that 13 million are infected world wide. 1999 More than 15,000 new infections daily. Ninety-five percent in developing countries. Nearly 50% are in women. It is estimated that worldwide there are 34.3 million people infected. 33.0 million adults 1.3 million children younger than 15 years old More than 71 percent (24.5 million) live in Sub-Saharan Africa 16 percent (5.6 million) live in South and Southeast Asia. click me for more info HIV1 is the strain in the U.S. In Africa HIV2 is also seen. The number infected (2000) is about 50% greater than what was predicted in 1990. Start at the begining of this slide for the 10-11 class.

2000 United Nations estimates there are 36.1 million people infected. 3 million died in 2000 alone 16 to 22 million estimated dead since the start of the epidemic. Estimated number of deaths of persons with AIDS is 501,669, including 496,354 adults and adolescents, and 5,315 children under age 15. This is through the year 2002.However, I think that the world wide numbers are more important and should also be mentioned. AIDS is likely to devastate developing nations, while we remain relatively unscathed. Check out the Executive Summary on the United Nations page:http://www.un.org/esa/population/publications/aidsimpact/ AIDSWebAnnounce.htm Here s one quote: Over 22 million people have already lost their lives and more than 42 million are currently living with HIV/AIDS. Even if a vaccine for HIV were discovered today, over 40 million people would still die prematurely due to AIDS. In a 1998 report by the United Nations Population Division refering to 34 developing countries: In addition, 91 per cent of all AIDS deaths in the world have occurred in these 34 countries. reference: http://www.uwmc.uwc.edu/ geography/110/aids/africa_aids.htm

Centers for Disease Control August 9, 2004 Cumulative AIDS CasesThe estimated number of diagnoses of AIDS through 2002 in the United States is 886,575. Adult and adolescent AIDS cases total 877,275 with 718,002 cases in males and 159,271 cases in females. Through the same time period, 9,300 AIDS cases were estimated in children under age 13.Estimated number of deaths of persons with AIDS is 501,669, including 496,354 adults and adolescents, and 5,315 children under age 15. At the global level, the number of people living with HIV continues to grow - from 35 million in 2001 to 38 million in 2003. An estimated 5 million people acquired the human immunodeficiency virus (HIV) in 2003, the greatest number in any one year since the beginning of the epidemic. In 2003, almost three million were killed by AIDS; over 20 million have died since the first cases of AIDS were identified in 1981.

Koch's Postulates cannot be performed. Problems proving that HIV causes AIDS Epidemiological work is difficult because of the long latency (8-10 years from infection to disease). 1.Virus can be isolated from almost all with the disease. Evidence that HIV causes AIDS 2. Advanced disease correlates with higher virus titer. 3. Asymptotic individuals which have detectable HIV coat proteins later develop the disease. 4. Recipients of contaminated blood subsequently develop AIDS. 5. Needlestick injuries with HIV contaminated blood often develop AIDS. 6. About 30% of children born to infected mothers are infected with the virus. Those that are infected go on to develop AIDS. But uninfected siblings do not. 7. AIDS does not appear in a new locality without the prior presence of HIV. 8. The single best argument that HIV causes AIDS is that drugs designed to specifically interfere with the viral life cycle suppress symptoms and extend life. PCR was invented by Kary Mullis, one of two Nobel Laureates in Chemistry in 1993. Peter Duesberg AZT causes AIDS or other drugs cause AIDS. 9-10 am

The Evidence That HIV Causes AIDS http://www.niaid.nih.gov/factsheets/evidhiv.htm Why do I even need to include this info? Por que Kary Mullis y Peter Duesberg son peligroso (OK, here is their argument: http:// www.virusmyth.net/aids/data/kmsdtrib.htm)

IV is a retrovirus. IV is a retrovirus. A more specific name for this one is Lentivirus. Retroviruses are viruses that have a RNA genome hich is replicated via a DNA intermediate within the host cell. HIV is similar to RNA tumor viruses but is much more mplex. ther retroviruses LV Avian leukemia virus (birds) LV Murine leukemia virus (mice) hese viruses have a relatively simple mrna splicing pattern. ALV has 1 splice donor and 1 splice acceptor and produces different mrnas. IV1 9 genes with 4 splice donor and 6 splice acceptor sites and by the process of alternative mrna splicing can produce least 30 different mrnas.

10 10 virions produced per day during latency period. 1/2 life of virion is about 5-8 hours. During a 10 year period about 4 X10 13 virions are produced.

Structure of the HIV virus A coffin-shaped capsid contains 2 copies of RNA genome. It is single stranded. Both are the plus strand. The capsid also contains HIV reverse transcriptase, HIV integrase, HIV RNase and HIV protease. Capsid is made of p24. Protein p17 forms an icosahedral-like container that encloses the p24 sarcophagus. This structure is enclosed by a lipid bilayer. The lipid bilayer was stolen from the host cell. The lipid bilayer contains two very important viral-encoded proteins, gp41 and gp120. Other host-derived proteins may also be present in the membrane.

Life Cycle Reverse transcription complex RTC = RT, IN, p7, Vpr tiny amount of p17. Vpr & IN have nuclear localization signals. Are involved in transport into nucleus. The cellular importin 7 protein is involved in this. Importin 7 is a transporter for ribosomal protein and histones. trimer Reverse transcription complex RTC = RT, IN, p7, Vpr tiny amount of p17. Vpr & IN have nuclear localization signals. Are involved in transport into nucleus. The cellular importin 7 protein is involved in this. Importin 7 is a transporter for ribosomal protein and histones.

Infection and gp120 & gp41 gp120 and gp41 associate with one another. The complete complex is trimeric (3 copies of both gp120 and gp41). Beta turns are presumably exposed in C3 and C4 regions and are important for CD4 binding.

Primary Target: CD4 helper T cells. The normal role of these cells is to stimulate other macrophages to be more effective in destroying pathogens. They coordinate the immune response. These helper T cells have on their surfgace a glycoprotein called CD4. The viral protein gp120 binds CD4. The gp120 protein changes shape and exposes a chemokine binding site. Now it binds the chemokine coreceptor. gp41 causes membrane fusion It is clear that the viral p24 sarcophagus enters the cell. The protein coat is removed and the virus's RNA genome is reverse transcribed in the cytoplasm into a double stranded DNA molecule. Double stranded DNA molecule enters the nuclease HIV integrase inserts it into the host cell's genome. Now called a provirus. Provirus never leaves the genome. CD4 surface glycoprotein is also found on other cells of hematopoietic origin. It is in high concentration on the surface of mature and immature helper T hymphocytes. It is in low concentration on antigen presenting dendritic cells such as follicular dendritic cells in the lymph nodes and blood dendritic cells, monocytes and macrophages. Therefore, early in the infection HIV can infect these cells but at a lower frequency.

How was it shown that CD4 was a receptor? Note: Some cells lines that express CD4 cannot be infected. This indicated that the CD4 receptor was necessary but not sufficient. G418 selects for neor (neomycin resistance gene)

There are at least 12 chemokine receptors that work in vitro. Two are know to work in in vivo. Chemokine receptors CD4 is necessary but not sufficient for HIV entry into CD4+ T-lymphocytes. The chemokines act as coreceptors. 1) CCR5 - macrophages, iv & mucosal membrane transmission. Viruses that can access these typically do not generate syncytiums. Important for the initial infection. Dominates early stage of infection - entry vehicle! 2) CXCR4 - T-cells. Syncytium forming. CXCR4 is cytopathic and appears late in disease course. Rambaut, A., Posada, D., Crandall, K. A. & Holmes, E. C. (2004) Nat Rev Genet 5, 52-61. CCR5 on macrophagesis used dominates as the co-receptor early on - do not show syncytia formation. Later CXCR4 is used. Usually late in infiection. AIDS can progress without going down this path. This is just a common one. Rambaut, A., Posada, D., Crandall, K. A. & Holmes, E. C. (2004) Nat Rev Genet 5, 52-61.

Alleles that confer resistance - AIDS Restriction Genes = ARGs CCR5 32 About 1% of Caucasians, European ancestry AIDS Restriction Genes = ARGS Blocks HIV-1 in homozygotes. Heterozygotes show slow progression. Resistant to the virions that 'normally' start an infection. Some people have a 32 bp deletion in this gene (second extracellular loop). The receptor is not expressed on cell surface. Cells from people with these gene are very resistant to infection. Seems to have no adverse affect These people can still get HIV, remember that during the later stages of the disease that the types of receptors that can be used changes. These people can catch a variant that can use the CXCR4 receptor. CCR2b mutation seems to increase the likelihood of delayed disease progression. CXCR4 3' UTR mutation About 1% Caucasians It delays the onset and the time of death. It is a point mutation in the 3' UTR. Mechanism unknown. Why is the disease more aggressive in some populations? Female sex workers in Nairobi 3.5 years from infection to AIDS More than 3X faster than in Caucasians. Data is starting to emerge that says that in this Nairobi cohort the protective mutation s are not found. Reference: Sarah L. Rowland-Jones. 1998. Survival with HIV infection: good luck or good breeding. TIG 14: 343-345. Good Reference for ARGS is Human genes that limit AIDS. 2004. Stephen J O Brien & George W Nelson. Nature Genetics 36:565-574. Good Reference for ARGS is Human genes that limit AIDS. 2004. Stephen J O Brien & George W Nelson. Nature Genetics 36:565-574.

RANTES is a principal chemokine ligand for CCR5. Elevated circulating RANTES levels have been detected in exposed individuals who avoid infection and also in people infected with HIV-1 who have a delayed onset of AIDS. Stephen J O Brien & George W Nelson Stephen. 2004. Human genes that limit AIDS. Nature Genetics 36:565. 16 Chemokines are cytokines that induce directed chemotaxis.

ARGs are important because They suggest effective therapies. One might tailor the therapy based on the ARGs present. The interpretation of clinical trials. 17

How does HIV kill cells? A healthy individual has about 800 CD4 positive cells per ml of blood. AIDS patients often have about 200 CD4 cells/ ml. The virus replicates by budding through the cell membrane. This does not necessarily kill the cells. Cells dies by autofusion, syncytial formation and apoptosis. Other mechanisms may await discovery. Autofusion

How does HIV kill cells? Syncytium formation Apoptosis An infected cell T helper cell can direct an uninfected T helper to undergo apoptosis. Apoptosis is the process of programmed cell death. During development of an organism it is a normal event to kill off some cells. This is done by telling them to commit suicide. This process is called apoptosis. For instance, in the thymus it is normal to eliminate autoreactive T lymphocytes to establish self-tolerance.

Genes of HIV HIV has a number of overlapping genes. gag, pol and env are related to the genes found in other retroviruses. These three encode polyproteins. Genes that overlap use the same region of the DNA and RNA but are read differently by the ribosomes. 9 genes 15 proteins (http://hivinsite.ucsf.edu/insite?page=kb-02-01-01#s1x) one variant was 9749 bp

Source of Diversity 0.2 errors per genome via reverse transcription Three recombination events per genome per replication cycle. RATE OF RECOMBINATION IS HIGHEST AMONGST ALL KNOWN ORGANISMS. RNA Pol II makes mistakes. Viral generation time of 2.5 days. Produces 10 10 to 10 12 new virions each day. Most cells have 2 or more proviruses. Dual infection is common. Rambaut, A., Posada, D., Crandall, K. A. & Holmes, E. C. (2004) Nat Rev Genet 5, 52-61.

Reverse Transcription Reverse transcriptase does not have any error checking ability therefore it makes many mistakes. About 5-10 errors occur during reverse transcription. 5 R U5 PBS U3 R 3

Reverse Transcription Reverse transcriptase does not have any error checking ability therefore it makes many mistakes. About 5-10 errors occur during reverse transcription. p7 promotes the annealing of trnalys3 p7 coats the RNA and is a CHAPARONE that promotes all types of interactions between the RNA genome & the DNA copy. trna R U5 PBS U3 R

Reverse Transcription Reverse transcriptase does not have any error checking ability therefore it makes many mistakes. About 5-10 errors occur during reverse transcription. R U5 R U5 PBS U3 R p7 promotes the annealing of trnalys3 p7 coats the RNA and is a CHAPARONE that promotes all types of interactions between the RNA genome & the DNA copy. Up to this point is thought to occur during viral assembly. Prior to infecting the next cell.

Reverse Transcription Reverse transcriptase does not have any error checking ability therefore it makes many mistakes. About 5-10 errors occur during reverse transcription. R U5 PBS U3 R R U5 PBS U3 R PBS U3 R

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Galetto et al 2006. JBC 281:2711-2720 Viral recombination Very high replication rates early in infection. Cells very often infected by more than one subspecies. Copy-choice method of viral recombination. 3-30 switching events per each infection cycle At least 10-% of HIV-1 infectious strains are recombinants. Recombination may be a product of the ability of the virus to replicate nicked RNA genomes! 31

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Life Cycle

Integration Preferential integration into sites where RNA pol II is actively transcribing.

Kaposi s sarcoma Human herpesvirus 8 HHV8 Found in all KS High male to female ratio Declining incidence Also seen in those at risk for but without HIV Old paper showed that Tat expression in mouse epithelia would induce something that looked like Kaposi s sarcoma. Cells that are in the tumor do not express Tat. Hengge et al. 2002. The Lancet Infectious Diseases 2:344

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CCR5 principle co-receptor for non-syncytium inducing isolates. The ligand for CCR5 is usually CD8. A very typical progression is: CCR5 ------> CCR3 and CCR2b -------> CXC and CXCR4 As disease advances see appearance of variants that recognize CCR3, CCR2b. Virions that use these receptors are more pathogenic. Late stages of the disease Chemokine receptor family: CCR5, CXC, CXCR4, CCR2b The CXC coreceptor receptor is used. Virions that use the CXC chemokine coreceptor are cytopathic and syncytium inducing. CXCR4 receptor This provides access to a vast number of new targets which were previously unavailable. Skip The progression of receptors may not be valid. This information is from older papers. I have not seen it in more recent papers.