1. Viruses that Use Reverse Transcriptase during Replication The retroviruses have an RNA genome that is converted to DNA by RT after infection. The hepadnaviruses and caulimoviruses have a DNA genome that is replicated via an RNA intermediate. The mode of replication of these various viruses is otherwise similar. The foamy viruses are retroviruses which appear to contain the DNA phase of the replication cycle in the virion, at least in part.

4. HIV MMTV ASLV Budding ImmatureMatureEarlyLate Released Virions

5. Maturation Retrovirus Particles Cleavage After of by of Gag Budding ImmatureMature MLV M-PMV HTLV -1 HIV-2

6. Maturation of Retrovirus Virions Maturation of virions after release from the cell occurs by cleavage of the Gag polyprotein by the viral protease The protease is a homodimer of a polypeptide of 99 residues The active site consists of two aspartic acid residues, one contributed by each monomer in the homodimer The protease is active in precursor polypeptides as well as after release Because dimerization is required for the enzyme to be active, high concentrations of the precursor polypeptides are required for cleavage to occur, which are normally present only in the assembled virion

7. SCHEMATIC OF A RETROVIRUS

8. Retroviral Genome is an Dimer RNA

14. Retrovirus Replication of a

18. Retrovirus Reverse Transcriptase The subunit composition of active RT differs among retroviruses MLV RT appears to function as a monomer containing pol and RNaseH HIV-1 RT functions as a heterodimer p66 contains both pol and RNaseH domains p51 contains only the pol domain ASLV RT also functions as a heterodimer The larger subunit contains the pol, RNaseH, and IN domains The smaller subunit contains only the pol and RNaseH domains

23. Genome Organization of Retroviruses

26. Transcriptional Activators Tax protein of PTLV/BLV activates transcription Transcription factors bind to TRE in U3 region Tax interacts with these to increase their activity Tat protein of lentiviruses activates transcription Tat of visna interacts with transcription factors Requires sequence element in U3 Tat of HIV binds to TAR element at 5’ end of RNA This increases transcription by an unknown mechanism

28. Regulation of Splicing and Export of mRNAs By REV

29. Leukemia-Sarcoma Viruses The simple retroviruses can cause leukemia, neurological disease, and other diseases Leukemia takes many years to develop and the mechanisms are complex They can also cause sarcomas and other tumors upon incorporation of a cellular oncogene The incorporated oncogene is usually mutant so that it no longer responds to regulatory signals Oncogenes are of many types and function to regulate the cell cycle

32. Primate T-Cell Leukemia Viruses (PTLV) Formerly called human T-cell leukemia (or lymphotropic) viruses (HTLV) PTLV-1 causes T-cell leukemia in ~1% of infected humans after a very long latent period (20-30 years) ATL (adult T-cell leukemia) is rapidly fatal once it arises PTLV-1 can also cause a neurological disease called HAM (HTLV-1-associated myelopathy) HAM develops in ~1% of infected humans and is characterized by demyelination of the spinal cord accompanied by an inflammatory response

34. Patient with Adult Acute T-cell Leukemia

35. Human Immunodeficiency Virus There are two HIVs, called HIV-1 and HIV-2. By the end of 2000, 22 million people had died of AIDS and 36 million were living with HIV infection. Acute immunodeficiency syndrome is characterized by a decline in CD4 T-cells, destruction of lymph nodes, and progressive loss of immune function. Neurological disease is also a common feature of AIDS. HIV requires CD4 as a receptor as well as a chemokine coreceptor. Virus responsible for primary infection usually requires CCR5 as a coreceptor (M-tropic virus). In late stage disease virus requiring CXCR4 usually arises (T-tropic virus). The immune system, especially CTLs, are important in controlling the virus during the long latent period. With decline in immune function, virus replication accelerates and AIDS develops.

40. Lymph Node Germinal Centers in HIV Disease The follicular dendritic cell network within the germinal center of a lymph node is stained pink with an antibody. This network degenerates over time following HIV infection.

45. AIDS in Africa In a number of subSaharan African countries, 24-36% of adults aged 15-49 are infected with HIV. In 9 subSaharan countries, 20-30% of children less than 15 years old are AIDS orphans. The prospects for a vaccine remain remote, and developing countries cannot afford the drug regimes that are successful in the U.S., nor could compliance with the strict demands of >20 pills per day and close observation by medical professionals be expected even if the drugs were available. 25 million people in subSaharan Africa are infected with HIV.

49. Inhibitors of HIV Replication The first inhibitors used were nucleoside analogues that inhibited HIV RT Therapy with a single analogue soon failed because mutations in RT arose within a few months that made it resistant to the analogue Using two analogues was more successful but ultimately failed because resistant mutants arose The development of protease inhibitors that better inhibit virus replication has led very successful therapy in about half of of HIV patients Protease inhibitors are used in combination therapy with two nucleoside analogues to inhibit RT Such therapy reduces virus to undetectable levels but does not eradicate the infection It is unknown if such triple therapy will ultimately fail because of the appearance of resistant variants