Lesson 7: Virus Genome replication and Gene expression

Virus genome replication and gene expression are critical steps in the viral life cycle that enable the production of new viral particles. These processes vary depending on the type of virus, particularly whether the virus has a DNA or RNA genome, and whether it is single-stranded or double-stranded.

1. Virus Genome Replication

DNA Viruses:

• Double-Stranded DNA (dsDNA) Viruses:
  • These viruses, replicate either in the host cell nucleus (smaller viruses) or in the cytoplasm (bigger viruses).
  • The viral DNA is transcribed into mRNA by the host’s RNA polymerase.
  • Host or viral DNA polymerase then replicates the viral DNA to produce new copies.
• (a) ds DNA viruses that replicate exclusively nuclear:
• Double-stranded DNA (dsDNA) viruses that replicate exclusively in the nucleaus are more common compared to those that replicate in the cytoplasm.
• These viruses rely on the host’s nuclear machinery for DNA replication, transcription, and RNA processing.
• They depend on the host’s DNA-dependent RNA polymerase II to transcribe their DNA, and typically rely on host replication factors.
• Examples: Adenoviridae, Herpesviridae (Herpes Simplex Virus, Varicella-Zoster Virus, Epstein-Barr Virus, and Cytomegalovirus), Polyomaviridae (JC virus and BK virus), Papillomaviridae (Human Papillomaviruses).
  
• (b) ds DNA viruses whose replication occurs in the cytoplasm:
• Double-stranded DNA (dsDNA) viruses that replicate exclusively in the cytoplasm and are less common compared to those that replicate in the nucleus.
• These viruses are unique among dsDNA viruses because they do not need to enter the nucleus as they carry their own  DNA-dependent RNA polymerase and other essential enzymes, transcription machinery, and other necessary factors, allowing them to be entirely independent of the host nucleus.
• DNA replication occurs by a bidirectional process (similar to that in host cells), starting at a specific origin of replication on the viral DNA.
• Examples: Poxviridae family (Variola virus, Vaccinia virus, Monkeypox virus, Molluscum contagiosum virus) and Asfarviridae (African Swine Fever virus).
  

Summary Table (ds DNA viruses)

• Single-Stranded DNA (ssDNA) Viruses:
  • ssDNA viruses, replicate in the nucleus.
  • Upon entry into the nucleus, the host’s DNA polymerase recognizes the ssDNA as damaged DNA and synthesizes a complementary DNA strand, forming a double-stranded DNA (dsDNA) intermediate. This process is called second-strand synthesis.
  • This dsDNA is then used as a template for transcription and replication.
  • After early proteins are produced, replication of the viral genome begins. The replication process typically proceeds through a rolling circle replication or strand displacement mechanism, depending on the type of ssDNA virus.
  • Example: Parvoviridae (e.g., Parvovirus B19), Circoviridae (e.g., Porcine Circovirus), Anelloviridae (e.g., Torque Teno Virus):

Summary Table (ss DNA viruses)

• dsDNA virus genome with RNA intermediate:
  • The replication of double-stranded DNA (dsDNA) viruses that involve an RNA intermediate occurs in the nucleus.
  • The replication cycle involves reverse transcription to convert the RNA back into DNA using a reverse transcriptase.
  • Inside the nucleus, the partially double-stranded rcDNA is converted into covalently closed circular DNA (cccDNA) by host DNA repair enzymes (repair of the gapped genome). This cccDNA serves as a stable template for the transcription of viral RNAs and remains in the nucleus of infected cells, sometimes for the life of the cell, acting as a viral reservoir.
  • Examples: Hepadnaviruses like the Hepatitis B virus (HBV)

RNA Viruses:

RNA viruses replicate their genomes using various strategies, which can differ depending on whether they are single-stranded (ssRNA) or double-stranded (dsRNA), and whether the genome is positive-sense (+) or negative-sense (−).

• Positive-Sense Single-Stranded RNA (+ssRNA) Viruses:
  • The replication takes place in the cytoplasm
  • These viruses have RNA genomes that function directly as mRNA, which can be immediately translated into viral proteins by the host’s ribosomes upon entry into the host cell.
  • Viral RNA-dependent RNA polymerase (RdRp) synthesizes a complementary negative-sense RNA (−ssRNA) strand, which serves as a template for producing more +ssRNA genomes.
  • The newly synthesized −ssRNA intermediate is used by the RdRp to generate multiple copies of +ssRNA.
  • Example: Picornaviruses (e.g., Poliovirus, Rhinovirus), Flaviviruses (e.g., Hepatitis C Virus, West Nile Virus), Coronaviruses (e.g., SARS-CoV-2).

• Negative-Sense Single-Stranded RNA (-ssRNA) Viruses:
  • Replication takes place either in the nucleus or cytoplasm
  • Negative-sense RNA viruses must first synthesize a positive-sense RNA strand before viral proteins can be translated.
  • The viral genome is not directly translatable (is complementary to the mRNA), so the virus brings its own RNA-dependent RNA polymerase (RdRp) within the virion.
    RdRp synthesizes a complementary +ssRNA strand using the −ssRNA genome as a template, which is then translated into proteins.
  • RdRp replicates the viral genome by synthesizing more −ssRNA using the +ssRNA as a template. This results in the production of more negative-sense RNA genomes, which are packaged into new virions.
  • Examples: Orthomyxoviruses (e.g., Influenza Virus), Rhabdoviruses (e.g., Rabies Virus), Filoviruses (e.g., Ebola Virus).
• (a) Non segmented genomes (order Mononegvirales): –ss RNA genome transcribed by the virion RdRp to produce mRNAs, which also serve as the template for subsequent genome replication. Replication occurs in the cytoplasm.
  
• (b) segmented genomes (Orthomyxoviridae): Replication occurs in the nucleus, with monocistronic mRNAs for each of the virus genes produced by the virus.
  
• Double-Stranded RNA (dsRNA) Viruses:
  • Replication occurs in the cytoplasm
  • These viruses contain a genome composed of two RNA strands, one positive-sense and one negative-sense.
  • RdRp synthesizes new dsRNA genomes by using the +ssRNA as a template to synthesize the complementary −ssRNA.
  • The newly formed dsRNA genome remains protected within viral particles during replication.
  • The viral RdRp also replicates the dsRNA genome within a viral replication complex.
  • Example: Reoviruses (e.g., Rotavirus)

• Positive-sense RNA viruses with DNA intermediate (+ss RNA-DNA intermediate)
  • Replication takes place in the nucleus
  • These viruses are unique because contain a viral enzyme reverse transcriptase that converts the single-stranded RNA genome into double-stranded DNA (dsDNA).
  • The viral dsDNA is transported into the nucleus, where it integrates into the host cell genome with the help of the viral enzyme integrase.
  • The integrated viral DNA, known as a provirus, can remain latent or be actively transcribed.
  • The host cell’s machinery replicates the integrated viral DNA as part of the cell’s own DNA. New viral RNA genomes are synthesized from the integrated proviral DNA.
  • Example: Retroviruses such as HIV (Human Immunodeficiency Virus) and HTLV (Human T-lymphotropic Virus).

Summary of RNA Virus Replication Mechanisms:

2. Virus Gene Expression

• Transcription of ds DNA viruses:
  • Early transcription: The host’s machinery (or the virus’s own enzymes) transcribes early genes from the viral DNA. These early genes often code for proteins that regulate viral replication and modulate host defenses. In nuclear-replicating viruses, this step takes place in the nucleus. For cytoplasmic-replicating viruses, the virus brings or encodes its own transcription machinery.
  • Late transcription: After DNA replication, late viral genes are transcribed. These genes typically code for structural proteins (such as capsid proteins) and enzymes needed for virion assembly.
  • For the gaped ds DNA viruses with RNA intermediate the host’s RNA polymerase II transcribes the cccDNA to produce various viral mRNAs, including those encoding viral proteins and the pre-genomic RNA (pgRNA). The pgRNA is a longer RNA molecule that acts as the template for reverse transcription, and it also serves as the mRNA for viral core and polymerase proteins.
• Transcription of ss DNA viruses:
  • The ss DNA converted to dsDNA intermediate serves as a template for transcription by the host’s RNA polymerase II.
  • Viral early genes are transcribed into mRNA, which is then translated into viral proteins (e.g., proteins needed for genome replication).
  • Some ssDNA viruses also encode their own replication proteins, which assist in genome replication and packaging.
  • Once sufficient copies of the viral genome have been made, late genes are transcribed and translated. These typically code for structural proteins needed to assemble new viral particles (capsids).
• Transcription of  +ss RNA Viruses
  • The +ssRNA genomes that are not immediately packaged into new virions are translated to produce structural proteins (e.g., capsid proteins, glycoproteins).
  • These proteins are required for assembling new virions.
  • Once sufficient copies of the viral genome have been made, late genes are transcribed and translated. These typically code for structural proteins needed to assemble new viral particles (capsids).
• Transcription of  -ss RNA Viruses
  • The newly synthesized +ssRNA from -ss RNA functions as mRNA, which is translated by the host’s ribosomes to produce viral proteins, including more RdRp and structural proteins.
• Transcription of  ds RNA Viruses
  • Inside the viral capsid, the viral RNA-dependent RNA polymerase (RdRp) transcribes the negative-sense RNA strand into positive-sense RNA.
  • The +ssRNA is then released into the cytoplasm for translation by host ribosomes.
• Transcription of +ss RNA-DNA intermediate Viruses
  • When active, the host’s RNA polymerase II transcribes the integrated proviral DNA into viral mRNA and full length genomic viral RNA.
• Translation:
  • Viral mRNA for all viruses is translated by the host cell’s ribosomes in the cytoplasm to produce viral proteins.
  • These proteins include enzymes required for viral replication, structural proteins (viral capsid, viral envelope proteins) for assembling new virions, and regulatory proteins that modulate host cell functions.
• Post-Translational Modifications:
  • Many viral proteins undergo post-translational modifications, such as glycosylation or cleavage, to become fully functional.
  • For example, some viral glycoproteins are processed in the host’s endoplasmic reticulum and Golgi apparatus before being transported to the site of virion assembly.

Key Points:

• The replication and gene expression strategies of viruses are tightly integrated with the host cell’s machinery.
• Viruses often manipulate host cell processes to prioritize the synthesis of viral components over host cell components.
• The complexity and specific mechanisms of replication and expression vary widely among different types of viruses.

This detailed orchestration allows viruses to efficiently produce progeny and propagate infection within the host.