Viral Replication & Genetics

What is the function of DNA-dependent DNA polymerase (DDDP) in virus replication?

DNA-dependent DNA polymerase (DDDP) synthesizes new DNA strands using an existing DNA template, and it is essential for the replication of DNA viruses and cellular organisms.

What is the role of DNA-dependent RNA polymerase (DDRP) in virus replication, and how does it differ from RNA-dependent RNA polymerase (RDRP)?

DNA-dependent RNA polymerase (DDRP) transcribes DNA into RNA, which is essential for converting DNA into messenger RNA (mRNA) for protein synthesis. Many DNA viruses rely on the host cell's RNA polymerase for transcription. RNA-dependent RNA polymerase (RDRP) is used by RNA viruses to replicate their RNA genome.

What is the function of ribosomes in protein synthesis, and what are the key binding sites?

Ribosomes are composed of proteins and ribosomal RNAs and synthesize proteins by translating messenger RNA (mRNA) from the 5' to 3' end. The key binding sites are the A-site (aminoacyl), P-site (peptidyl), and E-site (exit), with the P-site being the second binding site for tRNA.

What is the rule for viral genomes in relation to mRNA and ribosomes?

All viral genomes must make mRNA that can be read by the host ribosomes, and there are no known exceptions. This classification was proposed by Dr. David Baltimore.

What is the replication strategy for Group 1 (Class I) viruses?

Group I (Class I) Viruses – Replication Strategy 1. Genome Type:

• Double-stranded DNA (dsDNA)

2. Replication Site:

• Most replicate in the host cell nucleus

• Exception: Poxviruses replicate in the cytoplasm (they bring their own enzymes)

Group 1 viruses use the host cell's DNA-dependent DNA polymerase for replication and DNA-dependent RNA polymerase for transcription. They require dividing cells and can push cells into a replicative state (except Parvovirus).

What is the replication strategy for Group 2 (Class II) viruses?

Group 2 ssDNA viruses must first convert their single-stranded genome into double-stranded DNA using the host's DNA polymerase. Most ssDNA viruses have circular genomes and replicate via rolling circle replication (RCR).

What is the replication strategy for Group VII (Class VII) viruses?

: Group VII viruses use reverse transcription. Their genome is converted into RNA by the host’s RNA polymerase, and then reverse transcriptase makes DNA from this RNA, which integrates into the host genome.

What are the characteristics of viruses in Group VII (Class VII)?

Group VII viruses have double-stranded DNA genomes that are segmented. The gap in one strand is repaired to create a complete dsDNA genome before transcription. They also involve an RNA intermediate (dsDNA-RT) and reverse transcription in their replication cycle. Example: Hepadnaviridae (Hepatitis virus).

What is the replication strategy for Group III (Class III) viruses?

Group III viruses are double-stranded RNA viruses that carry their own RNA-dependent RNA polymerase (RDRP). They use this enzyme to transcribe their RNA genome into mRNA and replicate their genome. An example is rotavirus.

What is the replication strategy for Group IV (Class IV) viruses?

Group IV viruses are positive-sense single-stranded RNA viruses. Their genome serves as mRNA, which can be immediately translated by the host’s ribosomes. They use RNA-dependent RNA polymerase (RDRP) to replicate their RNA genome. Examples include poliovirus and coronavirus.

: What is the replication strategy for Group V (Class V) viruses, and what makes some of them ambisense?

Group V viruses are negative-sense single-stranded RNA viruses. Their RNA genome must first be converted into positive-sense RNA by the virus's RNA-dependent RNA polymerase (RDRP) before translation and replication can occur. Some Group V viruses are ambisense, meaning their genome contains both positive-sense and negative-sense regions, allowing some parts of the genome to be directly used as mRNA while other parts need to be transcribed into complementary RNA.

What is the replication strategy for Group VI (Class VI) viruses?

Group VI viruses are single-stranded RNA viruses with a DNA intermediate. Their RNA genome is converted into DNA by the viral reverse transcriptase enzyme (RT). This DNA is then integrated into the host's genome, and the host's transcription machinery is used to make viral mRNA. An example is HIV.

How do DNA viruses replicate within a host cell?

DNA viruses typically enter the host cell’s nucleus. The host’s DNA-dependent RNA polymerase transcribes the viral genes into mRNA, and the viral DNA-dependent DNA polymerase replicates the viral genome.

How do RNA viruses replicate within a host cell?

RNA viruses replicate and transcribe in the cytoplasm. Positive-sense RNA viruses (+ssRNA) can be directly translated into proteins and serve as templates for replication. Negative-sense RNA viruses (-ssRNA) must first be converted into positive-sense RNA by the viral RNA-dependent RNA polymerase (RDRP). Retroviruses (like HIV) use reverse transcriptase to convert their RNA genome into DNA, which then integrates into the host’s genome.

What are the key functions of gene products in a viral genome?

Gene products in a viral genome are responsible for protein synthesis (mainly in giant viruses), replication of the viral genome, assembly and packaging of the genome, regulation and timing of the replication cycle, modulation of host defenses, and spread to other cells and hosts.

What does the viral genome regulate in terms of the replication cycle?

The viral genome regulates the timing and regulation of the replication cycle, ensuring efficient genome replication, assembly, and packaging, as well as modulating host defenses and enabling spread to other cells and hosts.

What are some key characteristics of viral genomes in terms of protein synthesis and membrane biosynthesis?

Viral genomes do not encode the complete protein synthesis machinery or proteins involved in membrane biosynthesis

What are the differences between viral genomes and host chromosomes regarding centromeres and telomeres?

Viral genomes do not contain classical centromeres or telomeres found in standard host chromosomes. However, as more genomes are sequenced, more genes are being discovered.

What are some ways viral genomes can change?

Viral genomes can change through mutations, recombination, re-assortment, complementation (helper virus), and transcapsidation (phenotypic mixing).

What is transcapsidation in viral genome changes?

Transcapsidation (phenotypic mixing) is a process where two viruses infect the same host cell and exchange viral capsid proteins, leading to a hybrid virus with mixed phenotypic characteristics.

: What is a mutation in the viral genome and how does it occur?

A mutation is a change in the DNA or RNA of a virus, including nucleotide addition, deletion, or rearrangement. Mutations occur spontaneously and readily in viral genomes.

What are the consequences of mutations in viral genomes?

Mutations can create new virus strains with properties different from the parental virus, may have no effect or be detrimental, or may produce antiviral drug resistance or alter the antigenicity or pathogenicity of the virus.

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: Why are viral polymerases error-prone?

Viral polymerases are error-prone because they lack a genetic error-checking mechanism, which leads to many mutations during genome replication.

How do mutation rates compare between RNA viruses and DNA viruses?

RNA viruses generally have higher mutation rates than DNA viruses due to the lack of an error-checking mechanism in their replication process.

What is antigenic drift and how does it occur in viruses like influenza?

Antigenic drift is the slow accumulation of point mutations in a viral protein, such as hemagglutinin (HA) in influenza. This occurs due to RNA polymerase's poor fidelity, resulting in replication errors and changes in the viral protein that allow the virus to escape neutralizing antibodies.

How does antigenic drift lead to the need for new flu vaccines?

Antigenic drift causes gradual changes in viral proteins like HA, which allows the virus to escape immune recognition, requiring the development of new flu vaccines every year or two to address the new viral strains.

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What is viral recombination and how does it occur?

Recombination is the exchange of nucleic acids (DNA or RNA) between similar viruses. This process involves the breaking and reforming of nucleic acid molecules, leading to the mixing of characteristics from each virus, such as in HSV-1 + HSV-2 or SARS-coronavirus.

How can recombination affect a virus?

Recombination can result in new viral strains with mixed characteristics, potentially altering the virus's behavior, pathogenicity, or immune escape mechanisms.

What is reassortment in influenza viruses, and why is it important for surveillance?

Reassortment occurs when viruses with segmented genomes, like influenza, infect the same host and mix their RNA segments. This can result in the packaging of new genomic segments into the virus capsid, creating new strains. Surveillance is crucial for tracking reassortment events to predict and control potential epidemics or pandemics, such as those caused by avian (bird) flu.

How does reassortment contribute to influenza pandemics?

Reassortment can lead to antigenic shift, where new RNA segments are mixed into influenza viruses, resulting in a novel virus. This can cause a pandemic if the new strain is highly contagious and the population lacks immunity. Pandemics are typically associated with Influenza A viruses.

What is complementation in the context of viral infections?

Complementation occurs when a defective virus, which cannot replicate due to missing or non-functional essential genes, infects a cell alongside a wild-type virus. The wild-type virus provides the missing function, allowing both viruses to replicate.

How does a mixed infection lead to complementation in viral genomes?

In a mixed infection, two types of viruses infect the same cell. The defective virus relies on the functional genes from the wild-type virus to complete its replication cycle, leading to the complementation process and the replication of both viruses.

What is transcapsidation in viral infections?

Transcapsidation is the process where a defective viral genome is replicated and then packaged into a functional capsid. This may require capsid proteins or viral attachment proteins (VAPs) from another virus.

What is an example of transcapsidation in viral infections?

An example of transcapsidation is the Hepatitis D virus, which requires the Hepatitis B surface antigen (HBsAg) to package its defective genome into a functional capsid for replication.

What are the major steps in viral replication?

The major steps in viral replication include attachment, entry, uncoating, genome replication, protein synthesis, assembly, and release. These steps occur using the host cell’s energy, machinery, and substrates, with processes not provided by the cell being encoded in the viral genome.

How do viruses overcome the biochemical limitations of the host cell during replication?

Viruses overcome the cell's biochemical limitations by encoding processes in their genome that are necessary for viral replication and protein synthesis, with variations depending on the structure of the virus (e.g., DNA or RNA genome, enveloped or naked capsid).

What is an acute viral infection?

An acute infection is rapid and self-limiting, with the virus causing symptoms quickly and often being cleared by the immune system in a short time.

What is a latent viral infection?

A latent infection is dormant and can reactivate later, often causing symptoms after a period of inactivity.

What is a persistent viral infection?

A persistent infection is long-term, lasting for the life of the host, with the virus remaining stable and characteristic for each virus. Most persistent infections likely begin as an acute infection.

What defines a persistent viral infection?

A persistent infection occurs when the primary infection is not cleared by the immune response, and the virus continues to produce particles, proteins, and genomes, often with the viral genomes remaining even after proteins are no longer detected.

What factors contribute to the likelihood of a persistent viral infection?

Persistent infections are more likely when cytopathic effects are absent and host defenses are reduced. Viral immune modulation can also play a role in maintaining the infection.

What is the mnemonic to remember the steps of viral replication?

"A purple apple might redden"

• A - Attachment

• P - Penetration

• A - Uncoating

• M - Maturation

• R - Replication

• R - Release

• Early Phase: viral phasew

• • Recognize an appropriate target cell

  • Attach to the cell

  • Penetrate the plasma membrane and be taken up

  • Release (uncoat) viral genome into the cytoplasm

  • Deliver genome to the nucleus (if necessary)

• Late Phase:

• Genome replication

• Viral macromolecular synthesis

• Viral assembly and release

• What is the eclipse phase in viral replication?

The eclipse phase refers to the uncoating of the genome from the capsid or envelope during the early phase. This abolishes the infectivity and identifiable structure of the virus.

What is the latent phase in viral replication?

The latent phase (not to be confused with latent infection) is the period when extracellular infectious virus is not detected.

What is the first step in every viral infection?

Recognition and attachment. The virus attaches to the surface of the host cell through a specific reaction between virion attachment proteins or spikes and receptors on the host cell's surface.

What role do neutralizing antibodies play in viral infections?

Neutralizing antibodies block the attachment of the virus to the host cell, preventing the virus from entering and infecting the cell.

What is the difference between a susceptible and a permissive cell in viral infections?

• Susceptible: A cell that has viral receptors, allowing the virus to attach.

• Permissive: A cell that supports viral replication and production of progeny virus.

What is viral tropism?

Viral tropism is the preference of a virus to infect and replicate in a specific cell or tissue type.

What is viropexis?

Viropexis, or viral-induced pinocytosis, is a process where cells internalize virions through endocytosis, allowing viruses to enter host cells and initiate replication.

How do viruses penetrate host cells?

Virus penetration is closely linked to attachment and is an essential step in infection. Enveloped viruses enter by direct fusion with the plasma or endosomal membrane or through viropexis. Non-enveloped viruses use endocytosis, viropexis, or direct entry.

How do enveloped viruses penetrate host cells?

Enveloped viruses penetrate host cells through direct fusion. Examples include Paramyxoviruses, herpesviruses, and some retroviruses (HIV). Viral envelope proteins (spikes) bind to host cell receptors, promoting fusion of the viral envelope with the plasma membrane. This process is facilitated by viral envelope proteins like the F protein of RSV and Gp41 of HIV. After fusion, the nucleocapsid complex is released into the cytoplasm.

How do enveloped viruses penetrate host cells via viropexis?

Enveloped viruses can enter host cells through viropexis. Viral spikes bind to host cell receptors, leading to the surrounding of the virion by the plasma membrane and the formation of an endosomal vesicle. Examples include Orthomyxoviruses (influenza viruses), Togaviruses (rubella virus), Rhabdoviruses (rabies), and Coronaviruses.

How do non-enveloped viruses penetrate host cells?

Non-enveloped viruses penetrate host cells by binding their naked capsid to the plasma or endosomal membrane. This binding exposes hydrophobic regions of the capsid, allowing entry into the cytoplasm via viropexis. Example: Rhinovirus (Picornaviridae).

What happens during viral uncoating and transport?

The viral capsid undergoes programmed degradation, often influenced by pH and proteases, to release nucleic acids into the host cell. Capsid components and viral ribonucleoproteins (vRNPs) may assist in genome transport. Most DNA viruses transport their genome to the nucleus, while poxviruses replicate in the cytoplasm. Some RNA viruses, like retroviruses and orthomyxoviruses (e.g., influenza), also transport their genome to the nucleus.

How do transcription and replication differ among viruses?

Transcription and replication vary significantly based on the virus group. DNA viruses and RNA viruses use different strategies, often relying on host or viral polymerases. Many effective antiviral drugs target these steps to inhibit viral replication.

How is gene expression organized in DNA viruses?

DNA viruses express genes in a defined sequence:

• Early genes: Encode regulatory proteins and enzymes.

• Late genes: Involved in DNA synthesis and structural protein production.

How do viruses overcome the limitation of monocistronic mRNA for protein synthesis?

• DNA viruses: Generate mRNA through splicing as they replicate inside the host nucleus, using the host's machinery.

• RNA viruses:

  • Segmented genome: Each segment encodes one protein.

  • Negative-sense RNA viruses: Produce a nested set of mRNAs.

  • Positive-sense RNA viruses: Use a polyprotein that is cleaved into mature proteins by a protease enzyme.

What is the process of viral assembly or encapsidation?

• The process of enclosing the viral genome in a protein capsid.

• Initiates at a specific locus on the genome called the packaging site.

• Only viral nucleic acid is packaged.

• Segmented genomes ensure all parts are present.

• Essential viral proteins must be packaged.

What are the mechanisms of viral egress or release?

• Lysis (cell death): Both non-enveloped and enveloped viruses.

  • Example: Rhinovirus.

• Exocytosis: Viruses exit the cell via exocytosis.

  • Example: Flaviviruses, Pox virus.

• Budding: Typically for enveloped viruses, where the virus acquires its envelope from the host cell membrane.

  • Example: Influenza, Herpesvirus, HIV.

What is latent viral replication and what are examples of viruses that exhibit latency?

• Latent Viral Replication:

  • A state where the virus remains dormant within a host cell, replicating its genome but not producing new viral particles, until triggered to reactivate and resume the lytic cycle.

  • Type of persistent infection where no infectious virus is produced, and only a few viral proteins are made.

• Examples of Latent Viruses:

  • Retroviruses (HIV)

  • Adenoviruses (Adenovirus)

  • Hepadnaviruses (Hepatitis B)

  • Herpesviruses (HSV, EBV, VZV, CMV)

  • Papovaviruses (Papillomavirus)

  • Parvoviruses (Adeno-associated virus - AAV)