DNA and RNA Virus Replication

• Replication of DNA and RNA viruses involves distinct processes tailored to their genome type.

DNA Virus Replication

• A fraction of the viral DNA is transcribed into early mRNAs before replication.
• Early mRNAs are translated into early proteins, which are essential enzymes for viral DNA replication.
• Viral DNA is replicated in the presence of early proteins.
• A portion of the viral genome is then transcribed into late mRNAs, which are translated into structural proteins.
• The replicated DNA and structural proteins are assembled to form new virus particles.
• Early transcription occurs before replication to produce early proteins needed for DNA/RNA replication.
• Early proteins are enzymes or factors required to copy the viral genome.
• The virus transcribes a portion of its DNA to make early proteins, as the host cell's machinery cannot directly replicate the viral DNA.
• These early proteins are subsequently used to replicate the viral DNA, allowing the virus to create more copies of its genome for packaging into new virions.
• Order of a DNA virus's life cycle:
  • Attachment
  • Penetration
  • Uncoating
  • Early transcription (DNA to mRNA to produce proteins for replication assistance)
  • Early translation
  • Late genome replication
  • Late viral transcription (late genes produce mRNA for structural proteins needed for new viral particle assembly)
  • Late translation (host ribosomes translate late mRNA, such as capsid proteins)
  • Progeny virion assembly
  • Virion release (non-enveloped viruses lyse the host cell, enveloped viruses bud, taking host membrane)

Positive-Sense ssRNA Viruses

• Positive-sense ssRNA virus genome is a single RNA strand with the same polarity as mRNA (messenger RNA).
• Viral RNA can be directly used as mRNA for translation into proteins by the host cell’s ribosomes.
• Positive-strand RNA viruses have RNA that can function as mRNA for the host cell's translation machinery.
• Virus attaches to specific receptors on the host cell surface via viral surface proteins (e.g., poliovirus binds to CD155 receptor).
• Following attachment, the virus enters the host cell by endocytosis or membrane fusion, depending on the virus and host.
• The viral capsid disassembles inside the host cell, releasing the positive-sense ssRNA genome into the cytoplasm.
• The host cell's ribosomes recognize the viral RNA as mRNA and translate it into proteins.
• This produces non-structural proteins essential for viral replication, including RNA-dependent RNA polymerase (RdRp).
• Viral RNA genome serves as a template for RdRp to produce complementary negative-sense RNA strand.
• Negative-sense RNA acts as a template for producing new positive-sense RNA genomes.
• Host cell starts producing structural proteins (capsid components) as replication proceeds.
• Newly synthesized viral RNA genomes and structural proteins assemble in the cytoplasm to form virions.
• New virions are transported to the cell membrane via vesicular trafficking and bud off from the host cell's membrane.
• Some viruses acquire an envelope from the host cell membrane during budding (e.g., hepatitis C), while others do not (e.g., poliovirus).
• The host cell may lyse due to a large number of virions, or release particles in a more controlled manner.
• Released virions infect other cells and spread the infection throughout the host organism.
• Immediate translation occurs, and the viral RNA is translated into protein by the host.
• The virus uses RdRp to replicate its RNA genome, generating genomes for progeny viruses.
• New virus particles are assembled then released to infect other cells.
• The order of a positive-sense single-stranded DNA virus's life cycle:
  • Attachment
  • Penetration
  • Uncoating
  • Translation (positive-sense strands act as mRNA) of non-structural proteins for viral replication
  • Replication (RNA-dependent RNA polymerase produces negative strands to make more positive-sense RNA)
  • Late translation of structural proteins (e.g., capsids)
  • Assembly of new virions in the cytoplasm
  • Budding/lysis and release of virions

Negative-Sense ssRNA Viruses

• Negative-sense ssRNA viruses have an RNA genome complementary to mRNA, thus cannot be directly translated by host ribosomes (e.g., rabies virus, influenza virus).
• RNA-dependent RNA polymerase (RdRp) is packaged within the virus upon entry into the host cell.
• RdRp uses the negative-sense RNA genome as a template to synthesize positive-sense RNA (mRNA)
• The positive-sense RNA is translated by host ribosomes, producing viral proteins.
• After protein production, RdRp replicates the viral genome, synthesizing a positive-sense RNA strand used as a template to make negative-sense RNA genomes.
• Negative-sense RNA genomes are then packaged into new virions.
• Virus attaches via viral surface glycoproteins (e.g., hemagglutinin in influenza) that recognize and bind to cell surface receptors.
• Following attachment, the virus enters the host cell by endocytosis or membrane fusion.
• Since the RNA is negative-sense it cannot be immediately used by the hosts ribosomes and must be converted to positive-sense first
• The RdRp transcribes the negative-sense RNA genome into positive-sense RNA (mRNA).
• Translation produces required proteins for viral replication and transcription.
• Later translation produces structural proteins, for creating the capsid and assembling new virus particles.

Double-Stranded RNA Viruses

• Type III RNA viruses contain double-stranded RNA as their genetic material and are segmented, each segment encoding one polypeptide.
• Viral particle contains RNA-dependent RNA polymerase enzyme.
• Eukaryotic cells do not have an enzyme capable of transcribing double-stranded RNA.
• Positive-strand RNA also serves as a template for the synthesis of complementary negative-sense RNA strand, resulting in the formation of double-strand RNA progeny.
• The viral surface proteins bind to the host cell receptors.
• The virus usually enters the cell via endocytosis
• The virus must transcribe its dsRNA genome into mRNA with its own packaged RdRp.
• RdRp synthesizes mRNA from the positive strand of the dsRNA genome creating mRNA for the host to use for translation
• Early translation produces non-structural proteins, including the RNA-dependent RNA polymerase (RdRp), which is needed for further genome replication and transcription.
• Late translation produces structural proteins, such as the capsid proteins that will form the protective outer shell of the new virus particles.
• A newly synthesized negative-sense RNA strands will be used to make more positive-sense RNA to be packaged into the new virions.
• The viral structural proteins are assembled, then transported to the host cell membrane where budding and release from the cell occurs

Positive-Sense ssRNA Viruses (via DNA Intermediate)

• Positive-sense ssRNA is converted to dsDNA by reverse transcriptase contained in the virus.
• Resultant dsDNA integrates into cell's genome using viral integrase enzyme.
• mRNA and progeny positive RNA genomes are transcribed from integrated DNA by host's RNA polymerase.
• The virus binds using its viral glycoproteins to receptor markers on the body's cells.
• The reverse transcriptase synthesizes a complementary DNA strand (cDNA) from the positive-sense RNA genome.
• Then, the enzyme makes a second strand of DNA, creating a double-stranded DNA intermediate
• The viral integrase enzyme then integrates the viral DNA into the host genome and becomes known as the provirus
• When the host cell activates it will use it's RNA polymerase to uses the proviral DNA and create positive sense RNA out of it.
• The positive sense RNA is used to translate viral proteins and is also used as the genomic RNA to be packaged into new virions
• The viral proteins get translated and turned into structural and non-structural proteins
• Examples of these proteins are replicase, integrase, capsid proteins and envelope glcoproteins
• This creates new viral genomes which can be packaged into the virons
• The cell then goes through the budding stages, which allows it to infect other potential hosts

Replication vs. Transcription

• For DNA viruses, transcription happens first, where viral DNA is transcribed into mRNA.
• Followed by replication, helping to create genomes for new virions.
• For RNA viruses, with positive-sense, replication happens soon after the RNA enters the host cell.
• Transcription of mRNA occurs soon after.
• With negative-sense viruses, replication proceeds the creation of positive-sense RNA used for mRNA.