VIRUS REPLICATION STRATEGIES Dr. Sobia Manzoor MV, Lecture 06

1. VIRUS REPLICATION STRATEGIESDr. Sobia ManzoorMV, Lecture 06

2. Introduction • Replication of genetic information is the single most distinctive characteristic of living organisms, which is accomplished with great economy and simplicity among viruses. • To achieve the expression, replication, and spread of their genes, different families of viruses have evolved diverse genetic strategies and life cycles that exploit the biology and biochemistry of their hosts in a variety of ways.

3. Each infection represents an encounter between the genetic program of a virus and that of its host, defining host-viral relationships. • This also create opportunities for the rational development of antiviral drugs and for domesticating viruses as expression vectors, live attenuated vaccines, and pesticides.

4. Diversity of Viral Genome Structures Different families of viruses have different genomes: • Double-stranded (ds) / single-stranded (ss) viruses • DNA / RNA viruses • positive, negative, or mixed (ambisense) polarity • linear or circular topology • single or multiple segments The coding strategies of arenaviruses (family Arenaviridae) and members of the Phlebovirus genus of the Bunyaviridae differ from those of other negative-sense RNA viruses in that some proteins are coded in viral-complementary RNA sequences and others are coded in the viral RNA sequence. The term ambisense RNA has been proposed to denote these unique coding arrangements.

5. Each variation has consequences for the pathways of genome replication, viral gene expression, and virion assembly. • Viral taxonomy above the family level is variable, with only 10 of 71 virus families being assigned to the three orders that are currently recognized.

6. Families and Genera of Viruses that Infect Vertebrates

9. Viral Pathways and Enzymes • As intracellular parasites, all viruses depend heavily on functions provided by their host cells. • Nevertheless, almost all viruses encode and express unique proteins including enzymes, and many viruses exploit pathways of information transfer. • This is particularly evident among the RNAviruses.

10. Variation In Replication Strategies Whatever the structure and replication strategy of their genomes, all viruses must express their genes as functional mRNAs early in infection in order to direct the cell's translational machinery to make viral proteins. mRNA positive sense Complement negative sense

11. RNA Viruses These viruses replicate their genomes via one of two unique biochemical pathways: • RNA-dependent RNA synthesis (RNA replication), • RNA-dependent DNA synthesis (reverse transcription) followed by DNA replication and transcription. Both pathways require enzyme activities that are not usually found in uninfected host cells and must therefore be encoded in the viral genome and expressed during infection. In some families of RNA viruses, the corresponding polymerase and other associated enzymes with the viral genome are co-packaged during the viral assembly.

12. DNA viruses • Most DNA viruses undergo transcription, replication and assembly in the nucleus, the site of cellular DNA transcription and replication. • The exceptions are the poxviruses, iridoviruses, and African swine fever virus, which replicate their DNA genomes partly or completely in the cytoplasm

13. In contrast, most RNA viruses replicate in the cytoplasm. • Retroviruses integrate DNA copies of their genomes into cellular chromosomes. • Other notable exceptions are the orthomyxo- and bornaviruses, whose linear negative-sense RNA genomes replicate in the nucleus. • The circular RNA genome of hepatitis delta virus also replicates in the nucleus.

14. Pathways of primary mRNA synthesis by DNA viruses of animals • ds DNA ss DNA Cellular DNA Polymerase Cellular RNA Pol II ds DNA mRNA + Pathways of primary mRNA synthesis by DNA viruses of animals. *Hepadnaviruses replicate via reverse transcription of an ssRNA intermediate Cellular RNA Pol II

15. Evasion of Host Cell Defense • Many viruses express gene products that act to circumvent one or more of the several different antiviral defense mechanisms developed by host organisms . • Host defense mechanisms can be innateor adaptive. • Innate mechanisms involve apoptosis, interferon production and RNA interference .

16. Adaptive mechanisms of immunity include the cell- and antibody-mediated immune responses • In different viruses, different mechanisms inhibit apoptosis, intercept/suppress interferon, obstruct RNA interference, and either evade or suppress different arms of the adaptive immune response.

17. Pathways of primary mRNA synthesis by RNA viruses of animals • Pathways of primary mRNA synthesis by RNA viruses of animals. How RNA viruses produce mRNA at the start of infection depends on the nature of the viral genome. ds, double stranded; ss, single stranded.

18. RNA Replication Is Error Prone • The polymerases that catalyze RNA replication and reverse transcription have minimal proofreadingactivities. • Error rates are about 10,000 times higher than those encountered during DNA replication. • RNA viruses can evolve up to 1 million times faster than DNA-based organisms

19. Quasispecies • A quasispecie provides a fertile source of phenotypic variants that can respond rapidly to changing selection pressures by shifting its composition.

20. Levels of SegmentationGenes, mRNA and Proteins Viral RdRps generally appear somewhat restricted in their ability to access internal promoter sites on RNA templates, within the host cells. Through evolution, different RNA virus families have found three solutions: • Proteolytic processing of poly protein precursors to derive final protein products. e.g. the picorna-, toga-, flavi-, and retrovirus families

21. In some other systems, different cis-acting RNA signals are largely responsible for determining the relative template activities of the complementary strands. However, different host factors are involved here as well. • Unlike the enzymes that replicate DNA that usually require primers, most RdRps can initiate RNA synthesis de novo. • However, there are exceptions: Picornavirus RdRps use a small viral protein (Vpg) that is first covalently uridylated, and then used as a primer for viral RNA synthesis. • In another mechanism of priming, the enzymes encoded by orthomyxo- and bunyaviruses cleave short capped oligonucleotides from host mRNAs and use them to prime transcription.