Introduction to DNA Viruses Basic Properties of DNA Viruses: Genome is DNA Single- or double-stranded linear molecules, single or double-stranded circular molecules, highly base-paired single-stranded circular DNA Replicate their genome using host or viral DNA polymerase Genome is larger and more stable than RNA viruses Most DNA Viruses replicate in the nucleus ONly Poxviridae and Asfariviridae replicate in the cytoplasm Viruses with Single Stranded DNA Genomes  Parvoviridae Circoviridae Anelloviridae Viruses with Double Stranded DNA Genomes Poxviridae Herpesviridae Adenoviridae Papillomaviridae Polymaviridae

Papillomaviridae Characteristics of Papillomavirus Unenveloped icosahedral virions (t=7) DNA Genome Circular Genome replication is catalyzed by host DNA polymerases VERY host specific; cross species transmission is rare VERY difficult to grow in laboratory; replication only occurs in terminally differentiating epithelial cells Warts Keratinized skin tumors or proliferative squamous cell lesions on mucosal surfaces Warts spread by direct contact Warts are usually benign  Genome Expression Have a single stranded regulatory region URR Mrna are transcribed by host RNA pol II Happens before DNA replication  The first products are E1 (nuclear phosphoprotein) and E2   E1 is required binds to viral DNA replication origin ( do not need DNA polymerase) ○ E2 (regulates viral transcription and is also required)  E5: activates cell proliferation ○ E6: bind p53 ( leads to death) but removing p53 can lead to tumor  E7: bind to Rb prevents phosphorylation ○ In HPV infected cell Rb binds to E7 causing Rb to continue proliferation  In normal cel Rb binds directly to E2F to stop proliferation   Disease: Anogenital HPV Cervical Cancer HPV 16 and 18

Adenoviridae Characteristics of Adenoviruses Naked icosahedral virus (25 icosahedral capsid) Linear ds DNA genome Transcription and genome replication are nuclear First isolated in the adenoids (or tonsils)  Virion Structure naked icosahedral viruses T=25 Long and distinct fiber projections Genome Organization 5ʼ ends of the genome are covalently linked to terminal protein (TP; primer for DNA replication,E2)  Encode a viral DNA polymerase (E2B) Encode for genes that move cells into S phase (E1A,E1B) In Transcription: Transcripts are capped and polyadenylated and mRNAs are extensively spliced Adenovirus Replication Cycle Attachment –spike protein Endocytosis Delivery of DNA to nucleus Early gene transcription DNA replication –viral DNA pol Late gene transcription Assembly (nuclear) Release with cell death Proteins E1A: induces S phase; inhibits transcription of interferon response genes; blocks transcription of MHC class 1 genes E1B: induces s phase; inhibits apotosis E2: directly involved in viral DNA replication E3 genes inhibit apoptosis and down-regulate MHC Class I expression E4 encodes proteins needed for viral mRNA transcription; mRNA transport; viral DNA replication Diseases Common Cold Pharyngitis Gasteroenteritis Pneumonia Oncolytic Adenoviruses

Poxviridae Characteristics of Poxviridae Large enveloped virus Brick shaped DS DNA genome that is a covalently closed circle. Virus replication occurs completely in the cytoplasm Two human viruses ( variola that causes smallpox) & moluscom contagiosum virus Genome Structure Single stranded self complementary circular molecule Disease Smallpox caused by variola and exclusive to humans Transmission is contact and aerosol Gives you life long immunity Eradicated with vaccine Molluscum contagiosum Only in humans Transmission direct contact ○ Rabbit myxoma virus Introduced american virus in australia in order to control the virus and become less virulent Australian rabbits became resistant Replication Transcribed from opposite directions and have 3 diff. Promoters:(early,intermediate and late) Early: transcribe before uncoating basically all proteins need for synthesis of early mRNA Need to promote cell growth and suppress both immune systems RNA pol, VIRAL EARLY TRANSCRIPTION FACTOR AND POLY a Intermediate: transcribed after uncoating, protein needed for DNA replication Late: after DNA is replicated Encode for structural proteins and are needed to package DNA and virion Assembly happens in cytoplasm

Retroviridae   Virion Structure Enveloped Virus 2 copies (identical) of mRNA for DS DNA genome. Each is bound by a molecule of tRNA Characteristics Genome replication uses reverse transcriptase (RT) RNA dependent DNA polymerase Double stranded DNA copy of the viral genome is stably integrated into the host cell genome. This is called the provirus. Exogenous Retroviruses retroviruses are passed horizontally (virions are produced) Endogenous Retroviruses Endogenous retroviruses are found in the germ-line. Offspring inherit endogenous retroviruses through the germ-line. Comprise of about 8% of the human genome. Genome Organization  Simple Retroviruses Gag, PR, Pol, Env genes only  Gag (for group-associated antigen) encodes the GAG polyprotein Pol gene encodes the polymerase (POL) polyprotein Env encodes the envelope (ENV) polyprotein Complex Retroviruses Have slightly larger and more complex genomes. Encode a variety of regulatory and accessory proteins  Proteins   Proteins of the virus core or capsid, gag gene products Matrix (MA): Has role in virus assembly. Capsid (CA): Major structural protein, role in assembly. Nucleocapsid (NC): A basic protein (+charge) that binds the viral genome. Facilitates reverse transcription.   (Protease, PR) :cleave viral polyproteins at specific sites  Products of the pol gene  Reverse transcriptase (RT): viral genome synthesis  Integrase (IN): insertion of retroviral ds DNA into the host cell genome (Protease, PR) : cleaves precursor polyproteins in the newly budded (but immature) virion Products of the env gene Surface glycoprotein (SU): attachment Transmembrane glycoproteins (TM): fusion Replication Overview  Attachment  Penetration (fusion)  Nucleocapsid is released into cytoplasm  Reverse transcription of viral RNA to generate a double stranded DNA copy Viral DNA is integrated into the host cell DNA (viral IN protein). The integrated DNA is called the ‘provirus’  After integration, virus may be latent, or expression of mRNA can occur immediately  Synthesis of viral mRNA (by host cell RNA polymerase)  Synthesis of viral proteins  Capsid assembly (package RNA genome) and budding  Maturation (cleavage of gag-pol precursor)   Integration The integration of a retrovirus activates a cellular proto-oncogene. ○ Integration is random (as regards the host genome) and may disrupt cellular genes - in rare instances this can lead to transformation

HIV/AIDS Replication  HIV Attachment & Entry Surface protein gq120 mediates attachment ( it binds to CD4 which is found on helper T cells & macrophages) HIV & SIV require coreceptors for binding (CCR5, CXCR4) HIV fuses with cells at the plasma membrane HIV has a fusion domain at its N-terminus HIV Transcription & functions of TAT & REV TAT- small HIV proteins essential for HIV replication and functions as an activator of transcription TAT binds to HIC RNA region called TAR, in absence of TAT there is a full-length mRNA transcribed. REV - required for expressions of HIV structural proteins, interacts with unspliced & singly spliced viral mRNAs to facilitate export from nucleus In absence of REV, only multiple spliced viral mRNAs are exported from nucleus. TAT & REV are synthesized early ○ Assembly, Release & Maturation  Gag & pol polyproteins are assembled as uncleaved precursors  PR cleaved polyproteins to final products Proteins inhibitors are effective wat to stop production of infectious HIV AIDS  Develop as result of untreated HIV Depletion of CD4+ T cells First symptom is CD4+ T-cell below 500 cells/microliter of blood Full blown aids occurs when cd4+ below 500 cells/microliter  Transmission Sexual Parental inoculation or blood transfusion Mother to infant Breast milk Detection HIV infection ELISA West Blot Assay Nucleic acid testing (PCR)

Hepadnaviridae Characteristics of Virus Causes Hepatitis B known as the serum hepatitis Partially double stranded DNA The partially double-stranded DNA genome, associated with a molecule of P, is found within the core. Genome Structure Orf S = S glycoprotein Orf P = Polymerase (RT) Orf C= Capsid protein Longer version of Capsid protein is HBeAG (secreted protein (E) not present in the virion) Orf X = X protein (nonstructural protein with regulatory function) Replication Attachment and fusion at the plasma membrane Nucleocapsid released into the cytoplasm Nucleocapsid traffics to nucleus Genome released into nucleus Genome converted (cellular proteins) to covalently closed circular DNA  Transcription (cellular RNA polII) of mRNAs and pregenomes (pgRNA)  Disease Causes Hepatitis B Transmission via exchange of body fluids Also vertical transmission from mothers to infants - HBV much more infectious than HIV Acute disease: Liver damage occurs but virus is cleared  Chronic disease: Cirrhosis of the liver and primary hepatocellular carcinoma (HCC) Can lead to Hepatocelluar Carcinoma