Lecture 4 Viral genetics - PowerPoint Presentation

1. Lecture 4Viral geneticsDr.Luma amer

2. Viral geneticsViruses are simple creatures, lacking an energy-generating system and having very limited biosynthetic capabilities. The smallest viruses have only a few genes; the largest viruses have as many as 200. Genetically, however, viruses have many features in common with cells, e.g. viruses are subject to mutations, the genomes of different viruses can recombine to novel progeny, the expression of the viral genome can be regulated, and viral gene products can interact. An enormous variety of genomic structures are among viral species; as a group, they contain more structural genomic diversity than plants, animals, & other microbes. There are millions of different types of viruses, but only about 5,000 types are described in detail. As of 2015, Virus genome database has more than 75,000 complete genome sequences, but there are doubtlessly many more to be discovered.

3. Viral geneticsThe virus particles of some virus families, such as those belonging to the Hepadnaviridae, contain a genome that is partially double-stranded and partially single-stranded. For most viruses with RNA genomes and some with single-stranded DNA genomes, the single strands are said to be either positive-sense (called the plus-strand) or negative-sense (called the minus-strand), depending on if they are complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA polymerase before translation.

4. Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the Primary structure of DNA or RNA. Nucleotides consist of 3 components: Nitrogenous base ; Adenine, Guanine,Cytosine,Thymine (present in DNA only),Uracil (present in RNA only)5-carbon sugar which is called deoxyribose (found in DNA) and ribose (found in RNA).One or more phosphate groupsBasic arrangement of nucleotides in DNABasic structure of nucleotide

5. Viral geneticsIn general, RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate during replication, and have a maximum upper size limit. Errors in the genome when replicating render the virus useless or uncompetitive. To compensate for this, RNA viruses often have segmented genomes; the genome is split into smaller molecules;thus reducing the chance that an error in a single-component genome incapacitate the entire genome. In contrast, DNA viruses generally have larger genomes because of the high fidelity of their replication enzymes. Single-strand DNA viruses are an exception, as mutation rates for these genomes can approach the extreme of the ssRNA virus case.[

6. Viral geneticsGenetic Change in VirusesThe mechanisms by which genetic changes occur in viruses. Two principal mechanisms are involved: mutation and recombination. Alterations in the genetic material of a virus may lead to changes in the function of viral proteins. Such changes may result in the creation of new viral serotypes or viruses of altered virulence.Genetic mutations:Mutations arise by one of three mechanisms: (1) by the effects of physical mutagens (UV light, x-rays) on nucleic acids (2) by the natural behavior of the bases, and (3) through the fallibility of the enzymes that replicate the nucleic acids. The first two mechanisms act similarly in all viruses; hence, the effects of physical mutagens and the natural behavior of nucleotides are relatively constant.

7. Viral geneticsMutation Rates and OutcomesDNA viruses have mutation rates similar to those of eukaryotic cells because, like eukaryotic DNA polymerases.The error rate for DNA viruses is low mutation rate.The RNA viruses, however, lack a proofreading function in their replicatory enzymes, and some have mutation rates higher than DNA. Even the simplest RNA viruses, which have about 7,400 nucleotides per genome, generated mutants frequently.

8. Type of mutationA:Point mutation: base substitution1. Silent mutation5’ AUG UUU ACA AAA CUG UAA met- phe- thr- lys- leu- COOH5’ AUG UUU ACC AAA CUG UAA 3’ Point mutation: base substitution met-phe- thr- lys- leu- COOH

9. Mutation2:Induced mutationRadiation: ultraviolet --> thymine dimer CATTCC ---- > CAT=TCC GTAAGG GTA AGG

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11. B:Frame shift mutation1. Insertion5’ AUG UUU CUC AUC ACC 3’ met- phe- leu- Ile- thr5’ AUG AUU UCU CAU CAC 3’ met- Ile- Ser- His- His

12. Type of viral mutation(2)2. Plaque morphology mutants large/small plaque mutant3. Deletion mutants defective interfering particle (DI particle)4. Drug resistant mutant

13. PHENOTYPIC ALTERATION •Conditional Lethal:Multiply under some conditions but not others - wild-type (wt) grows under both sets of conditions•Temperature -sensitive (ts) mutants do not grow at higher temperature•Cold-sensitive mutants do not grow at low temperature•Host-range mutants do not grow in all the cell types that the wt does.

14. PLAQUE SIZE: may show altered pathogenicity.DRUG RESISTANCE: important in the development of antiviral Agents.• “HOT MUTANTS”(one type of ts)–grow better at elevated temperature than wt–less susceptible to feverATTENUATED MUTANTS–milder (or no) symptoms–vaccine development–pathogenesis

15. Interactions among virusesInteractions among viruses: When two or more viruses infect the same host cell. They may interact in a variety of ways (genetics and non-genetic interaction). A)) Recombination: Recombination results in the production of progeny virus (recombinant) that is different from either parent. Reassortment is the term used when viruses with segmented genomes, such as influenza virus, exchange segments. 1. Classic recombination 2. Re-assortmentGenetic reactivation: This phenomenon represent special cases of recombination, reactivate latent virus that has infected a host cell to lytic stage.Multiplicity reactivation: recombination between inactive virus particles produce viable genome, which is genetically stable. If double stranded DNA viruses are inactivated using ultraviolet irradiation, we often see reactivation if we infect cells with the inactivated virus at a very high multiplicity of infection (i.e. a lot of virus particles per cell) - this is because inactivated viruses cooperate in some way.

16. RNA virus reassortment

17. DNA virus recombination

18. Recombenation Interaction between virus(2)#Genetic reassortment parentsReassortant mutant

19. B))Complementation: Viral gene products of one or two defective viruses. Interaction at the functional level, NOT the nucleic acid level mutants which can complement are generally in different genes (usually).C )) Phenotypic mixing: complementation of genotype with heterologous phenotype .The genome of virus type A can be coated with the surface proteins of virus type B .

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22. D ))Interference: Counteraction between viruses.When two viruses infect simultaneously one host cell, the virus A may inhibit replication of virus B. Range of interference occurrence :between the different species of viruses; between the same species of viruses; between the inactivated viruses and live viruses.Significance of interference: Advantage a. Stop viral replication and lead to patient recovery. b. Inactivated virus or live attenuated virus can be used as vaccine to interfere with the infection of the virulent virus.Disadvantage May decrease the function of vaccine when bivalent/trivalent vaccine is used.

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