Subviral Entities and Viral Evolution What are they and where did they all come from?

Subviral Entities and Viral Evolution

Subviral Entities and Viral Evolution

What are they and where did they all come from?

What are they and where did they all come from?

Subviral entitiesSubviral entities

Viroids They are small single stranded infectious RNAs

with a circular genome that is self-complementary Their RNA genomes of 246-375 nucleotides long

are much smaller than the smallest RNA virus known

They are capable, however, of autonomous replication

They appear to encode no proteins and are not classified under the Baltimore viral classification scheme

Their genomes all contain 5 regions called domains.

Viroids They are small single stranded infectious RNAs

with a circular genome that is self-complementary Their RNA genomes of 246-375 nucleotides long

are much smaller than the smallest RNA virus known

They are capable, however, of autonomous replication

They appear to encode no proteins and are not classified under the Baltimore viral classification scheme

Their genomes all contain 5 regions called domains.


A central conserved domain (C) A P domain containing a run of purines

which appears to be involved in the pathogenic effects of the viroid.

A V domain of variable sequence Left (T1) and right (T2) terminal domains

A central conserved domain (C) A P domain containing a run of purines

which appears to be involved in the pathogenic effects of the viroid.

A V domain of variable sequence Left (T1) and right (T2) terminal domains

Viroid structureViroid structure


Viroids are transmitted through vegetative propagation of the host, by seeds, by aphids, or through mechanical damage. Therefore there is no need for a receptor on the host that the viroid must bind to as a first step in its replication.

If viroids don’t encode any proteins (i. e., a replicase), how then do they replicate?

Viroids are transmitted through vegetative propagation of the host, by seeds, by aphids, or through mechanical damage. Therefore there is no need for a receptor on the host that the viroid must bind to as a first step in its replication.

If viroids don’t encode any proteins (i. e., a replicase), how then do they replicate?


They use the host cell RNA polymerase II. It appears as if the extensive double stranded helical arrangement of the RNA competes effectively with normal DNA for the enzyme!

The host cell RNA polymerase I may also play a role in the viroid replication

They appear to use a rolling circle mode of replication

The genomic strand (+) serves as a template for the synthesis of a concatameric, linear antigenomic strand of RNA using the host cell RNA polymerase II.

They use the host cell RNA polymerase II. It appears as if the extensive double stranded helical arrangement of the RNA competes effectively with normal DNA for the enzyme!

The host cell RNA polymerase I may also play a role in the viroid replication

They appear to use a rolling circle mode of replication

The genomic strand (+) serves as a template for the synthesis of a concatameric, linear antigenomic strand of RNA using the host cell RNA polymerase II.


The antigenomic concatameric strand is a template for synthesis of a concatameric genomic strand using the host RNA polymerase I.

The concatamers are cleaved to genomic length.

The DNA is ligated to form the circular genome.

Details on how the last two steps occur are lacking.

The antigenomic concatameric strand is a template for synthesis of a concatameric genomic strand using the host RNA polymerase I.

The concatamers are cleaved to genomic length.

The DNA is ligated to form the circular genome.

Details on how the last two steps occur are lacking.

Model of viroid replicationModel of viroid replication


Viroids cause plant diseases – how do they cause disease? Their P domains are complementary to 7S RNA, a

molecule that is involved in protein translocation after synthesis.

The formation of viroid-7S RNA hybrids might prevent the 7S RNA from functioning properly in the translocation of newly synthesized proteins.

This could lead to the alteration in plasma membrane derived structures that is seen in viroid infections.

Viroids cause plant diseases – how do they cause disease? Their P domains are complementary to 7S RNA, a

molecule that is involved in protein translocation after synthesis.

The formation of viroid-7S RNA hybrids might prevent the 7S RNA from functioning properly in the translocation of newly synthesized proteins.

This could lead to the alteration in plasma membrane derived structures that is seen in viroid infections.


Other RNA containing subviral entities Include satellite viruses, satellite RNAs,

virisoids, and the hepatitis delta virus All of these differ from viroids in that they are

not autonomous. To replicate, they require that the host cell be co-infected with a helper virus that provides essential functions in their replication and transmission cycles Satellite viruses, virisoids, and satellite RNAs infect

plants Hepatitis delta virus infects animals

Other RNA containing subviral entities Include satellite viruses, satellite RNAs,

virisoids, and the hepatitis delta virus All of these differ from viroids in that they are

not autonomous. To replicate, they require that the host cell be co-infected with a helper virus that provides essential functions in their replication and transmission cycles Satellite viruses, virisoids, and satellite RNAs infect

plants Hepatitis delta virus infects animals

A comparison of viroids and other infectious RNAs

A comparison of viroids and other infectious RNAs

Subviral entitiesSubviral entities Hepatitis delta virus particles are enveloped with a

membrane containing three envelope proteins of hepatitis B virus (the helper virus).

Within the envelope is the nucleocapsid containing the covalently closed circular, single-stranded negative sense RNA genome complexed with multiple copies of the major gene product of this RNA, the delta antigen.

The delta antigen contains two RNA binding domains, a nuclear localization signal, and a multimerization domain characteristic of members of proteins in the leucine zipper family. Many of these proteins are known to play a role in transcriptional regulation.

Hepatitis delta virus particles are enveloped with a membrane containing three envelope proteins of hepatitis B virus (the helper virus).

Within the envelope is the nucleocapsid containing the covalently closed circular, single-stranded negative sense RNA genome complexed with multiple copies of the major gene product of this RNA, the delta antigen.

The delta antigen contains two RNA binding domains, a nuclear localization signal, and a multimerization domain characteristic of members of proteins in the leucine zipper family. Many of these proteins are known to play a role in transcriptional regulation.


After entry and uncoating, the genome and associated delta antigen are transported to the nucleus where the genome is transcribed and replicated by the host cell RNA polymerase II!

How this occurs is unknown since these enzymes normally cannot use RNA as a template to make a complementary copy of RNA!

RNA is transcribed to the antigenomic + RNA Transcription also generates a subgenomic

mRNA that is capped, polyadenylated, and translated into the delta antigen. Generation of this subgenomic RNA may be via interrupted replication or by ribozyme activity of the RNA itself.

After entry and uncoating, the genome and associated delta antigen are transported to the nucleus where the genome is transcribed and replicated by the host cell RNA polymerase II!

How this occurs is unknown since these enzymes normally cannot use RNA as a template to make a complementary copy of RNA!

RNA is transcribed to the antigenomic + RNA Transcription also generates a subgenomic

mRNA that is capped, polyadenylated, and translated into the delta antigen. Generation of this subgenomic RNA may be via interrupted replication or by ribozyme activity of the RNA itself.

Hepatitis delta virus replication and transcription

Hepatitis delta virus replication and transcription


The mRNA may be edited by cellular enzymes to alter the first translational terminator resulting in a delta antigen protein that is 19 amino acids longer than that expressed from the unedited mRNA.

The short form (unedited) of the delta antigen is required for genome replication (inhibits mRNA synthesis)

The long form (edited) suppresses replication and promotes assembly. It has a lipid attached to it that permits it to interact with the cytoplasmic membrane in the location where hepatitis B surface protein is located.

The mRNA may be edited by cellular enzymes to alter the first translational terminator resulting in a delta antigen protein that is 19 amino acids longer than that expressed from the unedited mRNA.

The short form (unedited) of the delta antigen is required for genome replication (inhibits mRNA synthesis)

The long form (edited) suppresses replication and promotes assembly. It has a lipid attached to it that permits it to interact with the cytoplasmic membrane in the location where hepatitis B surface protein is located.

Hepatitis delta antigenHepatitis delta antigen


HDV is spread by blood contamination and causes a pathology similar to that caused by other hepatitis viruses.

The severity of the disease results from co-infection with HBV or superinfection of an HBV-positive individual with HDV. Fatality rates can be as high as 20%.

An interesting note is that the antigenomic RNA has sequences complementary to mammalian 7S RNA suggesting that HDV may interrupt normal protein translocation by forming HDV-7S RNA hybrids

HDV is spread by blood contamination and causes a pathology similar to that caused by other hepatitis viruses.

The severity of the disease results from co-infection with HBV or superinfection of an HBV-positive individual with HDV. Fatality rates can be as high as 20%.

An interesting note is that the antigenomic RNA has sequences complementary to mammalian 7S RNA suggesting that HDV may interrupt normal protein translocation by forming HDV-7S RNA hybrids


Prions Cause spongiform encephalopathies in man

and other mammals The diseases that they cause in man are Kuru and

Creutzfeldt-Jakob disease (and recently, mad cow disease also called variant Creutzfeldt-Jakob disease )

Do not appear to contain any nucleic acid! They are infectious proteins! The name prion comes from proteinaceous infectious agent plus “on” a suffix originally used to denote particles in physics!

Prions Cause spongiform encephalopathies in man

and other mammals The diseases that they cause in man are Kuru and

Creutzfeldt-Jakob disease (and recently, mad cow disease also called variant Creutzfeldt-Jakob disease )

Do not appear to contain any nucleic acid! They are infectious proteins! The name prion comes from proteinaceous infectious agent plus “on” a suffix originally used to denote particles in physics!


Prion proteins (PrP) are 27-30 kd in size

In electron micrographs PrP appears as large macromolecular fibrils similar to but distinct from the amyloid fibrils seen in Alzheimer’s disease victims

Prion proteins (PrP) are 27-30 kd in size

In electron micrographs PrP appears as large macromolecular fibrils similar to but distinct from the amyloid fibrils seen in Alzheimer’s disease victims

Prion fibrilsPrion fibrils


How do prions replicate? Studies have shown that PrP is encoded

by a chromosomal gene that is expressed at the same level in the brains of both infected and non-infected animals.

The normal gene product PrPc (c for cellular) is a glycoprotein of 33-35 kd. It is attached to the plasma membrane by a glycosylphospphatidylinositol (GPI) anchor where it may act as a cell surface receptor involved in signal transduction in neurites.

How do prions replicate? Studies have shown that PrP is encoded

by a chromosomal gene that is expressed at the same level in the brains of both infected and non-infected animals.

The normal gene product PrPc (c for cellular) is a glycoprotein of 33-35 kd. It is attached to the plasma membrane by a glycosylphospphatidylinositol (GPI) anchor where it may act as a cell surface receptor involved in signal transduction in neurites.

Subviral entitiesSubviral entities The conversion of PrPc into fibrils is a multistep

process: PrPc has four alpha helical regions in its native

conformation. The triggering event is the conversion of two of the

alpha helices into an anti-parallel beta pleated sheet conformation. This molecule is termed PrPsc and this is the infectious form of the molecule that catalyzes the conversion of native PrPc molecules to the PrPsc

conformation. Proteolytic removel of 67 amino acids from the N-

terminus of PrPsc produces a molecule that aggregates into the amyloid fibrils seen in the disease.

Some types of prion disease (Creutzfeldt-Jakob disease) appear to arise spontaneously (as described above) rather than via infection, while others are clearly via infection with a PrP (Kuru, mad cow disease)

The conversion of PrPc into fibrils is a multistep process:

PrPc has four alpha helical regions in its native conformation.

The triggering event is the conversion of two of the alpha helices into an anti-parallel beta pleated sheet conformation. This molecule is termed PrPsc and this is the infectious form of the molecule that catalyzes the conversion of native PrPc molecules to the PrPsc

conformation. Proteolytic removel of 67 amino acids from the N-

terminus of PrPsc produces a molecule that aggregates into the amyloid fibrils seen in the disease.

Some types of prion disease (Creutzfeldt-Jakob disease) appear to arise spontaneously (as described above) rather than via infection, while others are clearly via infection with a PrP (Kuru, mad cow disease)

Prion structurePrion structure

Viral evolutionViral evolution

What is the origin of subcellular entities (includes viruses)? There are three different theories:

One theory, called the regressive theory, asserts that viruses are the degenerative progeny of other obligate intracellular parasites

According to this theory, viruses are entities that have regressed to the point that they have dispensed with all but a few genes and they rely entirely upon their host for their metabolic needs, especially protein synthesis

The problem is that this does not explain where RNA viruses came from

There is also a huge difference between Chlamydia and viruses (see chart on next slide). An intermediate form, that would be predicted by the theory, has never been found.

What is the origin of subcellular entities (includes viruses)? There are three different theories:

One theory, called the regressive theory, asserts that viruses are the degenerative progeny of other obligate intracellular parasites

According to this theory, viruses are entities that have regressed to the point that they have dispensed with all but a few genes and they rely entirely upon their host for their metabolic needs, especially protein synthesis

The problem is that this does not explain where RNA viruses came from

There is also a huge difference between Chlamydia and viruses (see chart on next slide). An intermediate form, that would be predicted by the theory, has never been found.

Regression of bacteria to viruses (regressive theory)Regression of bacteria to

viruses (regressive theory)


The cellular constituent theory also proposes that viruses developed after their hosts. According to this theory, viruses are thought to have descended from normal cellular DNAs or RNAs that developed the ability to replicate themselves autonomously

This mechanism requires that free DNA molecules acquire an origin of replication and gene or genes encoding a viral capsid

RNA molecules would also have to acquire a gene encoding a replicase

Transposons and retrotransposons that can move around in cellular DNA may have contributed to this process

The cellular constituent theory also proposes that viruses developed after their hosts. According to this theory, viruses are thought to have descended from normal cellular DNAs or RNAs that developed the ability to replicate themselves autonomously

This mechanism requires that free DNA molecules acquire an origin of replication and gene or genes encoding a viral capsid

RNA molecules would also have to acquire a gene encoding a replicase

Transposons and retrotransposons that can move around in cellular DNA may have contributed to this process

Viral evolutionViral evolution Retrotransposons move by a three step

process: the retrotransposon is first transcribed into an RNA molecule which is then reverse transcribed back into a cDNA molecule which then reinserts into a new location.

The prebiotic RNA model asserts that the RNA viruses are the descendents of self-replicating prebiotic RNA molecules that became parasites within true cells when they in turn evolved.

This theory is based on current ideas that suggest that the first genetic material to develop was RNA.

The theory does not consider how DNA viruses arose

Retrotransposons move by a three step process: the retrotransposon is first transcribed into an RNA molecule which is then reverse transcribed back into a cDNA molecule which then reinserts into a new location.

The prebiotic RNA model asserts that the RNA viruses are the descendents of self-replicating prebiotic RNA molecules that became parasites within true cells when they in turn evolved.

This theory is based on current ideas that suggest that the first genetic material to develop was RNA.

The theory does not consider how DNA viruses arose

Theories of viral originTheories of viral origin


What factors affect viral evolution? Mutation – the polymerases of RNA viruses

and the small DNA viruses do not have proofreading capabilities, so mutations are quite common and can lead to rapid evolution (antigenic drift with influenza virus)

Recombination – the creation of new molecules by combining or substituting pieces of nucleic acid particularly when host cell genes are recombined into a viral genome (transduction)

What factors affect viral evolution? Mutation – the polymerases of RNA viruses

and the small DNA viruses do not have proofreading capabilities, so mutations are quite common and can lead to rapid evolution (antigenic drift with influenza virus)

Recombination – the creation of new molecules by combining or substituting pieces of nucleic acid particularly when host cell genes are recombined into a viral genome (transduction)


Reassortment with viruses having segmented genomes – when a host cell is coinfected with viruses of two different strains, new viruses may contain various combinations of genetic segments from both viruses (antigenic shift with influenza virus)

Reassortment with viruses having segmented genomes – when a host cell is coinfected with viruses of two different strains, new viruses may contain various combinations of genetic segments from both viruses (antigenic shift with influenza virus)

Emerging virusesEmerging viruses

What is meant by the word “emerge”? This may refer to a virus that has been present

in the human population for a long time, but some change in the virus or in the host (susceptible population) results in the disease that the virus produces emerging into an epidemic form: Polio is a disease of civilization. Children used to get

the disease early in life through contaminated water. However, with the development of sanitation and water treatment, individuals often did not get the virus until later in life. The risk of developing paralytic poliomyelitis rises markedly in individuals over the age of 5.

What is meant by the word “emerge”? This may refer to a virus that has been present

in the human population for a long time, but some change in the virus or in the host (susceptible population) results in the disease that the virus produces emerging into an epidemic form: Polio is a disease of civilization. Children used to get

the disease early in life through contaminated water. However, with the development of sanitation and water treatment, individuals often did not get the virus until later in life. The risk of developing paralytic poliomyelitis rises markedly in individuals over the age of 5.


Changes in population density may allow a virus that requires a sizable population to maintain itself to cause continuing disease when the population density increases – measles is an example of this

New techniques may allow us to identify previously unidentified viruses – hepatitis C and human herpesvirus 8 which causes Kaposi’s sarcoma are examples of this

Changes in population density may allow a virus that requires a sizable population to maintain itself to cause continuing disease when the population density increases – measles is an example of this

New techniques may allow us to identify previously unidentified viruses – hepatitis C and human herpesvirus 8 which causes Kaposi’s sarcoma are examples of this


Zoonotic viruses can cross the species barrier to cause human diseases – the modern ease of movement and the encroachment of humans into previously unpopulated areas may contribute to this

Some zoonotic viruses have humans as a dead end host (i.e., no human to human transmission occurs) (Sin Nombre hantavirus and West Nile virus)

Some zoonotic viruses can cause human diseases in which human to human transmission may occur (Ebola virus, SARS virus,Lassa fever virus)

Some zoonotic viruses may mutate to become human viruses (HIV)

Zoonotic viruses can cross the species barrier to cause human diseases – the modern ease of movement and the encroachment of humans into previously unpopulated areas may contribute to this

Some zoonotic viruses have humans as a dead end host (i.e., no human to human transmission occurs) (Sin Nombre hantavirus and West Nile virus)

Some zoonotic viruses can cause human diseases in which human to human transmission may occur (Ebola virus, SARS virus,Lassa fever virus)

Some zoonotic viruses may mutate to become human viruses (HIV)

Emergence of new virusesEmergence of new viruses

HIV-SIV genetic relationships

HIV-SIV genetic relationships

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Subviral Entities and Viral Evolution What are they and where did they all come from?