VIRUS REPLICATION STRATEGIES Dr Sobia Manzoor MV Lecture

VIRUS REPLICATION STRATEGIES Dr. Sobia Manzoor MV, Lecture 06

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.

• 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.

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.

• 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.

Families and Genera of Viruses that Infect Vertebrates Genome Virus Family Adenoviridae Type Polaritya ds. DNA Both Topology b Linear Anellovirus genus ss. DNA Negative Asfarviridae ds. DNA Circoviridae Genome Replication Segments 1 Enzyme Viral Dd. Dp Intracellular Site Nucleus Circular 1 Cellular Dd. Dp Nucleus Both Linear 1 Viral Dd. Dp Cytoplasm ss. DNA Negative/ ambisense Circular 1 Cellular Dd. Dp Nucleus Hepadnaviridae ds. DNA Both Linear 1 Virion RTase Nucleus/cytoplasm Herpesviridae ds. DNA Both Linear 1 Viral Dd. Dp Nucleus Iridoviridae ds. DNA Both Linear 1 Viral Dd. Dp Nucleus/cytoplasm Papillomaviridae ds. DNA Both Circular 1 Cellular Dd. Dp Nucleus Parvoviridae ss. DNA Either Linear 1 Cellular Dd. Dp Nucleus Polyomaviridae ds. DNA Both Circular 1 Cellular Dd. Dp Nucleus

ds. DNA Both Linear 1 Viral Dd. Dp Cytoplasm Arenaviridae ss. RNA Ambisense Linear 2 Virion Rd. Rp Cytoplasm Arteriviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Astroviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Birnaviridae ds. RNA Both Linear 2 Virion Rd. Rp Cytoplasm Bornaviridae ss. RNA Negative or ambisense Linear 1 Virion Rd. Rp Nucleus Bunyaviridae ss. RNA Negative Linear 3 Virion Rd. Rp Cytoplasm Caliciviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Coronaviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Deltavirus genus ss. RNA Negative Circular 1 RNA pol II Nucleus

Filoviridae ss. RNA Negative Linear 1 Virion Rd. Rp Cytoplasm Flaviviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Hepevirus genus ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Nodaviridae ss. RNA Positive Linear 2 Viral Rd. Rp Cytoplasm Orthomyxoviridae ss. RNA Negative Linear 6 -8 Virion Rd. Rp Nucleus Paramyxoviridae ss. RNA Negative Linear 1 Virion Rd. Rp Cytoplasm Picornaviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm Reoviridae ds. RNA Both Linear 10 -12 Virion Rd. Rp Cytoplasm Retroviridae ss. RNA Positive Linear 2 identical Virion RTase Nucleus/cytoplasm Rhabdoviridae ss. RNA Negative Linear 1 Virion Rd. Rp Cytoplasm Togaviridae ss. RNA Positive Linear 1 Viral Rd. Rp Cytoplasm

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 RNA viruses.

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

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.

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

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

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

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 innate or adaptive. • Innate mechanisms involve apoptosis, interferon production and RNA interference.

• 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.

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

RNA Replication Is Error Prone • The polymerases that catalyze RNA replication and reverse transcription have minimal proofreading activities. • 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

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

Levels of Segmentation Genes, m. RNA and Proteins Viral Rd. Rps 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

• 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 Rd. Rps can initiate RNA synthesis de novo. • However, there are exceptions: Picornavirus Rd. Rps 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 m. RNAs and use them to prime transcription.