Viruses

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VirusesChapter 6Talaro

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Viruses of bacteria, Archaea and eukaryotes

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Size of Viruses Smaller than bacteriaPass through a filter

Once called “filterable agents”

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Taxonomy of Viruses

• Originally based on disease

• Now based mainly on three criterion

• Nucleic acid type (DNA or RNA)

• Strategy for replication

• Morphology and size

• Naming and classification decided on by International Committee on Taxonomy of Viruses (ICTV)

•Order, Family, Subfamily, Genus, Species – Subspecies, strain etc.Naming: -virales Order; -viridae, Family; -virinae Subfamily; -virus

Genus, Species Epithet usually in English

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Taxonomy of Viruses(Continued)

• Ex. 1, Poliovirus

Genus & Species: Enterovirus human poliovirus 1

Family: Picornaviridae

Order: Not decided by ICTV

• Ex. 2, Rabies Virus

Genus & Species: Lyssavirus rabies virus

Family: Rhabdoviridae

Order: Mononegavirales

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Species Concept in Virology

• What is a virus “species”?

After many years of controversy, in 1991, the ICTV accepted the definition of a virus species proposed by van Regenmortel (1990), as follows: "A virus species is defined as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche." Members of a polythetic class are defined by more than one property and no single property is essential or necessary. One major advantage in this definition is that it can accommodate the inherent variability of viruses and it does not depend on the existence of a single unique characteristic.

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Isolation, Cultivation, and Identification

• Much more problematic than cultivation of organisms

• Requires host cell for replication

• Often times propagation of host cell is challenging

• Mammalian tissue culture expensive and time consuming

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Viral Identification• Usually too small to see without electron microscopy

• Nanometer range

• Antibodies detect viral coat proteins•Western blot / ELISA technique to identify

(ELISA- Enzyme-Linked ImmunoSorbent Assay) •May also use tissue culture and observe characteristic cytopathic effects

• Newer methods use PCR to amplify virus specific DNA or RNA sequences

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Composition of Viruses -Viral genomes i. double-stranded DNA ii. single-stranded DNA iii. double-stranded RNA iv. single-stranded RNA

- Nucleic acid can be organized as i. circular molecule ii. one or more linear molecules

- Viruses range from simple (4 genes) to complex (100s of genes)

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dsDNA

(-) & (+) ssDNA

dsRNA

(-) ssRNA

(+) ssRNA (for DNA)

(+) ssRNA (for mRNA)

(+) sense, template or transcribed strand

(-) antisense or non-template stand

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Capsids - Protein shell enclosing

the genome

- Built of large number

of proteins called

capsomeres

- Capsid can be composed

of 100s of same or

different capsomeres

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Helical Shaped Viruses

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Icosahedral Shaped Viruses

• 20-sided with 12 corners

• Vary in the number of capsomers

• One edge is called a facet

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Viral Envelopes - Not found in all viruses

- Surrounds capsid

- Derived from host cell (budding)

- May have viral proteins and

glycoproteins embedded

- Assists the virus in infecting

its host

- Example is influenza

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Viral Life Cycles Host Ranges - Viruses can only reproduce within a host cell - Viruses usually infect hosts by binding to receptors on the cell surface - Some viruses can infect many types of cells or many types of species (rabies for example) - Most viruses can only infect a few types of cells = limited host range - Eukaryotic viruses often attack specific tissues

Cold virus = cells of upper respiratory trackAIDS virus = T cells & macrophages of immune systemHepatitis = Only liver cellsPolio = Intestinal & nerve cellsRabiesvirus = Nerve cells

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Viral Mutation Rate No proof-reading enzymes sono repair

- Mutation rate 1 in 10,000 nucleotides (depends upon the virus)

- Low-fidelity RNA polymerase (means not so accurate)

- May recombine with different strains of the same virus- Reassortment of nucleic acid

- Occasionally (rarely), acquire traits from completely different virus

- DNA & RNA viruses

Viral Replication Cycles

Bacteriophage dsDNA

Influenza Virus (-) sense ssRNA

Human Immunodeficiency Virus (+) sense ssRNA for DNA

6 Steps in Phage Replication

1. Adsorption – binding of virus to specific molecule on host cell

2. Penetration – viral genome enters host cell

3. Replication – viral components produced

4. Assembly - viral components assembled

5. Maturation – completion of viral formation

6. Release – viruses leave cell to infect other cells

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Lytic Cycle Virulent

Lysogenic Cycle Temperate

Bacteria eater

20Fig 6.11

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-Viral genome has a promoter-Bacterial RNA polymerase transcribes viral genes

-EARLY STAGE PROTEINS-Viral genes adjacent to the promoter are transcribed

- Proteins that stop host transcription- Proteins that stimulate viral replication- Viral nucleases digest host genome- Stimulate late gene transcription

-LATE STAGE PROTEINS- Viral genes that code for viral capsid proteins- Proteins that lyse the host cell

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Virus infects hostHost’s RNA polymerasetranscribes EARLY genes

Early proteinsstop transcriptionof host’s genes

Early proteinstimulates viral genomereproduction, digest hostgenome & stimulate lategene transcription

Early proteinstimulates transcriptionof LATE genes. Lyse

host

Viral capsidproteins

operon

Lytic Stage

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Lysogenic Phage Cycle - Phage able to reproduce without destroying host - Temperate phages are able to use both the lytic and lysogenic cycles - When phage DNA enters cell, it uses site-specific recombination to insert its DNA into the host’s

chromosome = prophage - The phage DNA is replicated and passed to daughter cells each time the bacteria divides - Occasionally, the prophage exits the bacterial DNA and engages in the lytic cycle - Exit from the lysogenic stage is often triggered by environmental cues/stresses

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Temperate phage

Bacterium growing well lysogenic cycle

Bacterial host stressed or damaged lytic cycle

Regulatory proteins cI CroCompete for promoter sites

Constant Growth

Cro cI Lysogenic

STRESS or UV Damage cI Cro Lytic

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STRESS or DAMAGECro protein activates promotersfor phage DNA replication &cell lysis

GOOD GROWTHcI accumulates & activatespromoters for integration Lysogenic Cycle

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Animal VirusAdsorption

Penetration

Duplication/Synthesis

Assembly

Release

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Adsorption - Glycoproteins on the envelope bind to specific receptors on the host membrane

- Cell receptor is also a glycoprotein

- Envelopes fuse, viral capsid & genome are transported inside cell

- The receptors are involved in normal cell functions

- Rabies virus attaches to acetylcholine receptor on nerve cells

-HIV attaches to the CD4 receptor on T and some other cells of the immune system

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Penetration

Endocytosis

Fusion with cell membrane

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Release by Budding or Exocytosis

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Cytopathic Effects1. Changes in size & shape2. Cytoplasmic inclusion bodies3. Nuclear inclusion bodies4. Cells fuse to form multinucleated cells5. Cell lysis6. Alter DNA7. Transform cells into cancerous cells (called

Transformation but do not get confused with bacterial transformation)

• Can see these effects microscopically in tissue culture cells infected with virus

Influenza (-) sense RNA virus

Spanish Flu Epidemic20 million deaths

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Negative Sense RNA Virus

- An RNA virus whose genome is complementary to

mRNA

- Contains an RNA-dependent RNA polymerases

required for the synthesis of mRNA

Influenza virus

- Genome consists of eight different negative sense

ss RNA strands

- Strands 1 through 6 each encode one protein

- Strands 7 & 8 encode two proteins

(+) RNA = mRNA

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Lipoprotein envelope Glycoprotein spikes

HemagglutininBinds to a receptor foundon eukaryoticrespiratory mucosa cells

NeuraminidaseHydrolyzes the protectivemucous coating, assists in viralbudding, prevents virions fromsticking together & helps in penetration

RNA + nucleoprotein

Matrix

Nonspecific

Polymerase

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- Enveloped viruses do not always kill host cell- Virus can be continuously shed from infected cell(factory)

Viral glycoproteins bind tohost cell receptors

Virus enters by endocytosis

Viral RNA isreleased

Viral RNA is translated

Virionassembled

Viral RNA dependentRNA polymerase makes (+) RNA

(-)(-)

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- Influenza viruses can infect humans, pigs, sea mammals & birds- Typically, one virus can only infect one type of host- Occasionally, some viral strains can infect another animal host - Genome segments can be exchanged when two different viral strains infect the same host- Some of the exchanged RNA segments encode for glycoproteins- The virus can have glycoproteins from several hosts: swine, human & bird- The same virus will appear as a “new” virus to the human immune system because of different glycoproteins

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Each year, new strains of influenza emerge from southern China.

The domestic duck is the main reservoir of influenza viruses in southern China. Geese are infrequently infected and chicken rarely.

The domestic pig serves as the host for both avian and human influenza viruses. These viral

strains recombine their genes to give rise to a novel influenza virus capable of human-to-human transmission.

Reassortment

Functional virions that contain combinations ofof genomic segments fromintracellular “pools” of viral strains

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Influenza A viruses Infect humans, horses, pigs, ferrets and birds.

A major human pathogen, that incites epidemics and pandemics. 15 known haemagglutinin (HA) serotypes and 9 known neuraminidase (NA) serotypes have been identified. Pigs and ducks are important reservoirs, that produce genetically/antigenically diverse viruses. The viruses are transferred back to humans via close contact between humans and animals.

Influenza B virusesOnly infects mammal and incite a mild form of influenza. Does not have distinguishable serotypes like influenza A.

Influenza C viruses

Only infects mammals, but it is unclear if they cause disease.Genetically and morphologically distinct from A and B types.

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Novel Influenza A Strains Incite Pandemics1918 Spanish flu1957 Asian flu1968 Hong Kong flu1977 Russian flu

Avian flu (H5N1) 1997- Type A virus- Easily transferred & highly virulent in chickens & wild birds- Not easily transferred to humans to date- 105 human deaths in 186 confirmed cases (WHO Mar 24, 2006)

- Human deaths are associated with close exposure to infected chickens- H5N1 is not transmissible via aerosol droplets- Concern & debate regarding the no. of mutations required to make this possible

Human Flu Transfers May Exceed ReportsBy DONALD G. McNEIL Jr.Published: June 4, 2006The New York Times

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Birds and Influenza H5N1 Virus Movement to and within North AmericaJohn H. Rappole* and Zdenek Hubálek†*Smithsonian Institution, Washington, DC, USA; and †Academy of Sciences, Valtice, Czech RepublicEmerging Infectious DiseasesVol. 12, No. 10 • October 2006

Figure 2. Map of known routes for natural interhemispheric bird movement: route 1, migrants breeding in Alaska and wintering in East Asia; route 2, migrants breeding in East Asia and wintering along the Pacific Coast of North America; route 3, migrants breeding in Iceland or northwestern Europe and wintering along the Atlantic Coast of North America; route 4, vagrants from West Africa carried by tropical storm systems across the Atlantic to eastern North America.

How will H5N1 reach North America?

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“The bird flu virus, known as A(H5N1), belongs to a group of influenza viruses known as Type A, which are the only ones that have caused pandemics. It has been steadily advancing around the world, first appearing in Asia, then Europe and

Africa. The apparent lethality of A(H5N1), combined with its inexorable spread, are what have made scientists take it seriously. The

virus lacks just one trait that could turn it into a pandemic: transmissibility, the ability to spread easily from person to person. If the virus acquires that ability, a worldwide epidemic could erupt.

The A(H5N1) strains circulating now are quite different from the A(H5N1) strain detected in Hong Kong in 1997, which killed 6 of 18 human victims. Over time,

A(H5N1) seems to have developed the ability to infect more and more species of birds, and has found its way into mammals -- specifically, cats that have eaten infected birds.”

The New York Times Sunday, June 4, 2006

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Aerosols – suspensions of fine dust and moisture in the air that containpathogens