1. VIRUS REPLICATION STRATEGIES Dr. Sobia Manzoor MV, 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
Virus Family
Genome
Genome Replication
Type
Polaritya
Topologyb
Segments
Enzyme
Intracellular Site
Adenoviridae
dsDNA
Both
Linear 1
Viral DdDp
Nucleus
Anellovirus genus
ssDNA
Negative
Circular
Cellular DdDp
Asfarviridae
Cytoplasm
Circoviridae
Negative/
ambisense
Hepadnaviridae
Virion RTase
Nucleus/cytoplasm
Herpesviridae
Iridoviridae
Papillomaviridae
Parvoviridae
Either
Polyomaviridae

7. dsDNA
Both
Linear 1
Viral DdDp
Cytoplasm
Arenaviridae
ssRNA
Ambisense 2
Virion RdRp
Arteriviridae
Positive
Viral RdRp
Astroviridae
Birnaviridae
dsRNA
Bornaviridae
Negative or ambisense
Nucleus
Bunyaviridae
Negative 3
Caliciviridae
Coronaviridae
Deltavirus genus
Circular
RNA pol II

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

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 RNA viruses.

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 innate or 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 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

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 Segmentation Genes, 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.