Lecture 2: Virus Structure - PDF

Lecture 2 Structure of virus  o Why we study viruses? Some Viruses Cause Disease Rabies Common Cold Smallpox HIV Some Viruses Cause Disease Pepper Mottle Virus Cauliflower Mosaic Virus Rice Tungro Virus...

Lecture 2 Structure of virus  o Why we study viruses? Some Viruses Cause Disease Rabies Common Cold Smallpox HIV Some Viruses Cause Disease Pepper Mottle Virus Cauliflower Mosaic Virus Rice Tungro Virus Papaya Ringspot Virus Tobacco Mosaic Virus Some Viruses Cause Disease Foot & Mouth Disease Classical Swine Fever Porcine Reproductive & Respiratory Syndrome (PRRS) Ebola Avian Flu Some Viruses Cause Disease A ‫اﻧﻔﻠﻮﻧﺰا‬ AH1N1  Some Viruses are Useful Phage Typing of Bacteria e.g. Salmonella spp. classified into strains on the basis of the spectrum of phages to which they are susceptible advantage: Epidemiology ‫ﻋﻠﻢ اﻷوﺑﺌﺔ‬ Some Viruses are Useful Sources of Enzymes e.g RNA polymerase (T7 phage) Genetic Pesticides gene from baculovirus against worms. Some Viruses are Useful o Anti-Bacterial Agents Extrasomatic SARS virus (e.g. NORWEX) o Anti-Cancer Agents Herpes Simplex Virus ‫ﻓﻴﺮوس اﻟﻬﺮﺑﺲ اﻟﺒﺴﻴﻂ‬ Vaccinia Virus Destroy tumor cells not normal cells. ‫ﺗﺪﻣﻴﺮ اﻟﺨﻼﻳﺎ اﻟﺴﺮﻃﺎﻧﻴﺔ وﻟﻴﺲ اﻟﺨﻼﻳﺎ اﻟﻄﺒﻴﻌﻴﺔ‬  Some Viruses are Useful o Gene Vector for Protein Production ‫ﻓﻴﺮوﺳﺎت ﺣﺸﺮﻳﺔ‬ o baculovirus, adenovirus ‫ﻓﻴﺮوﺳﺎت ﺑﺸﺮﻳﺔ ﺗﺴﺒﺐ اﻟﺰﻛﺎم‬ o vaccine component Gene Vector for Treatment of Genetic Diseases o Retrovirus o immunodeficient cases. ‫ﺣﺎﻻت ﻧﻘﺺ اﻟﻤﻨﺎﻋﺔ‬ How we can differentiate between DNA and RNA? By DNAase or RNAase Between double and single stranded NA; by acridine orange stain, which is yellowish green in double stranded and red orange in single stranded.  Host Range Viruses infect all major groups of organisms: vertebrates, invertebrates, plants, fungi, bacteria. Some viruses have a broader host range than others, but none can cross the eukaryotic/prokaryotic boundary. Factors which affect host range include; i) whether the virus can get into the host cell ii) if the virus can enter the cell, is the appropriate cellular machinery available for the virus to replicate? iii) if the virus can replicate, can infectious virus get out of the cell and spread the infection?  Classification of virus o Virus classification is the process of naming viruses and placing them into a taxonomic system. o Viruses are mainly classified by phenotypic characteristics such as morphology, nucleic acid type, mode of replication, host organisms and the type of disease they cause. o Currently, two main schemes are used for the classification of viruses: the International Committee on Taxonomy of Viruses (ICTV) system and Baltimore classification system.  Basis of the Type of Host The virus can be classified on the basis of the type of host. They are:  Animal viruses  Plant viruses  Bacteriophage  Animal Viruses The viruses which infect and live inside the animal cell including man are called animal viruses. Eg; influenza virus, rabies virus, mumps virus, poliovirus etc. Their genetic material is RNA or DNA.  Plant Viruses The viruses that infect plants are called plant viruses. Their genetic material is RNA which remains enclosed in the protein coat. Some plant viruses are tobacco mosaic virus, potato virus, beet yellow virus and turnip yellow virus etc. Bacteriophages Viruses which infect bacterial cells are known as bacteriophage or bacteria eaters. They contain DNA as genetic material. There are many varieties of bacteriophages. Usually, each kind of bacteriophage will attack only one species or only one strain of bacteria.  Classification of viruses Viruses are divided into two large groups: 1. RNA containing viruses. 2. DNA containing viruses. Baltimore classification The Baltimore classification system Based on: – Genetic contents – Replication strategies of viruses – Their manner of mRNA synthesis Viruses were divided into seven groups based on the their nucleic acid and m-RNA production. 1- ds-DNA viruses. 2- ss-DNA viruses. 3- ds- RNA viruses. 4- ss-RNA viruses with positive strands( positive polarity). 5- ss-RNA viruses with negative strands(negative polarity). 6- ss-RNA viruses associated with the enzyme reverse transcriptase. 7- DNA reverse transcribing viruses  1- Double stranded DNA families of medical importance 1- Poxviridae. 2- Herpesviridae. 3- Hepadnaviridae. 4- Adenoviridae. 5- Papovaviridae. 2- Single stranded DNA families. 3- Double stranded RNA families. Single stranded DNA family:1- Parvovoridae. Double stranded RNA family:1- Reoviridae. 4- Single stranded RNA families with positive strands 1-Picornaviridae.2- Caliciviridae.3- Astroviridae.4- Coronaviridae.5- Flaviviradae.6- Togaviridae. The viral genome acts directly as m-RNA. 6-Single stranded RNA viruses associated with the enzyme reverse transcriptase Retroviruses. The viral genome is reverse transcribed into a complementary DNA strand using the enzyme reverse transcriptase.  BALTIMORE CLASSIFICATION The Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus. Group I viruses: contain double-stranded DNA (dsDNA) as their genome. Their mRNA is produced by transcription in much the same way as with cellular DNA. Group II viruses have single-stranded DNA (ssDNA) as their genome. They convert their single-stranded genomes into a dsDNA intermediate before transcription to mRNA can occur. Group III viruses use dsRNA as their genome. The strands separate, and one of them is used as a template Group IV viruses have ssRNA as their genome with a positive polarity. Positive polarity means that the genomic RNA can serve directly as mRNA. Intermediates of dsRNA, called replicative intermediates, are made in the process of copying the genomic RNA. Multiple, full-length RNA strands of negative polarity (complementary to the positive-stranded genomic RNA) are formed from these intermediates, which may then serve as templates for the production of RNA with positive polarity, including both full- length genomic RNA and shorter viral mRNAs.  Group V viruses contain ssRNA genomes with a negative polarity, meaning that their sequence is complementary to the mRNA. As with Group IV viruses, dsRNA intermediates are used to make copies of the genome and produce mRNA. In this case, the negative-stranded genome can be converted directly to mRNA. Additionally, full-length positive RNA strands are made to serve as Group VI viruses have diploid (two copies) ssRNA genomes that must be converted, using the enzyme reverse transcriptase, to dsDNA; the dsDNA is then transported to the nucleus of the host cell and inserted into the host genome. Then, mRNA can be produced by transcription of the viral DNA that was integrated into the host genome. Group VII viruses have partial dsDNA genomes and make ssRNA intermediates that act as mRNA, but are also converted back into dsDNA genomes by reverse transcriptase, necessary for genome replication  DNA VIRUSES DOUBLE STRANDED SINGLE STRANDED COMPLEX NON-ENVELOPED ENVELOPED ENVELOPED NON-ENVELOPED PARVOVIRIDAE POXVIRIDAE HERPESVIRIDAE HEPADNAVIRIDAE CIRCULAR LINEAR PAPILLOMAVIRIDAE ADENOVIRIDAE All families shown are POLYOMAVIRIDAE icosahedral except for (formerly grouped together as the poxviruses PAPOVAVIRIDAE) 15  RNA VIRUSES SINGLE STRANDED SINGLE STRANDED DOUBLE STRANDED positive sense negative sense ENVELOPED NONENVELOPED ENVELOPED NONENVELOPED ICOSAHEDRAL HELICAL ICOSAHEDRAL HELICAL ICOSAHEDRAL FLAVIVIRIDAE CORONAVIRIDAE PICORNAVIRIDAE ORTHOMYXOVIRIDAE REOVIRIDAE TOGAVIRIDAE CALICIVIRIDAE PARAMYXOVIRIDAE RETROVIRIDAE ASTROVIRIDAE RHABDOVIRIDAE FILOVIRIDAE BUNYAVIRIDAE ARENAVIRIDAE 16  ICTV CLASSIFICATION The International Committee on Taxonomy of Viruses began to devise and implement rules for the naming and classification of viruses early in the 1970s Viral classification starts at the level of order and continues as follows, with the taxon suffixes given in italics: Order (-virales) Family (-viridae) Subfamily (-virinae) Genus (-virus) Species Species names generally take the form of Disease virus. 17  Replication of virus 1. Virus attachment and entry 2. Uncoating of virion ‫اﻟﻬﺠﺮة‬ 3. Migration of genome nucleic acid to nucleus 4. Transcription 5. Genome replication 6. Translation of virus mRNAs 7. Virion assembly 8. Release of new virus particles 18 19 20 21 22 23 24 ‫اﻧﺰﻳﻤﺎت ﺗﺤﻠﻞ ال ‪capsid‬‬ ‫‪25‬‬ 26 27 28 29 ‫اﻧﻘﺴﺎم‬ ‫‪30‬‬ Receptor Recognition – CD4+ cells infected by HIV – CD155 acts as the receptor for poliovirus 31