Virus II

Virus Abundance

  • No known species is immune to virus infection.

  • Viruses attack a wide range of organisms including bacteria, archaea, plants, and animals.

  • Viruses are ubiquitous in nature and play a significant role in evolution.

  • There is considerable variation in the replication mechanisms and life cycles of different viruses.

Virus Replication Process

  1. Attachment (Adsorption)

    • The virus binds to a receptor on the host cell surface, which is often a protein, but can also be sugars, lipids, or complexes of these.

    • There is a diverse range of surface receptors utilized by different viruses. Some viruses utilize the same receptor while others can bind to multiple receptors.

  2. Penetration (Injection)

    • The process by which the virus enters the host cell to release its genetic material.

    • In animal cells, which have a mobile lipid bilayer membrane, crossing the membrane is relatively easy.

      • Non-enveloped viruses enter via endocytosis.

      • Enveloped viruses enter via fusion, followed by an uncoating step to release the viral nucleic acid.

    • In plant cells, the rigid cell wall makes penetration much more difficult.

      • Viruses typically enter via damage to the cell wall or through vectors (e.g., animals feeding on plants).

    • In bacterial cells, which also have a rigid cell wall, mechanisms are needed for entry:

      • Tail fibers bind and flex, tail pins bind, and the tail sheath contracts to push the tail core through the bacterial wall, allowing nucleic acid to be injected.

  3. Synthesis of Nucleic Acid and Protein

    • Once inside the host, viruses leverage the host cell machinery to replicate their nucleic acid and synthesize necessary proteins for the capsid and replication.

    • The order of protein synthesis events (e.g., early or late proteins) is tightly regulated depending on the virus type.

    • DNA viruses and RNA viruses rely on the host's machinery in different ways:

      • RNA-dependent RNA-polymerase is not present in host cells, which leads RNA viruses to synthesize it themselves.

      • Some RNA viruses can directly use their genomic RNA as mRNA, whereas others require transcription.

    • Retroviruses like HIV convert their single-stranded RNA (ssRNA) into double-stranded DNA (dsDNA) via reverse transcription using the reverse transcriptase enzyme. This dsDNA can then be used as a template for further viral synthesis.

  4. Assembly and Packaging (Maturation)

    • Viral components (e.g., proteins and nucleic acid) are assembled into mature virions directed by the viral DNA through the host's biosynthesis processes.

  5. Release

    • The new virions can be released from the host cell through:

      • Budding: The host cell may survive the process with the virus acquiring an envelope as it exits.

      • Lysis: The host cell is destroyed, releasing virions into the environment.

Lytic vs. Lysogenic Cycles

  • The two distinct processes of viral replication:

    1. Lytic Cycle:

      • The viral DNA attaches to a host cell and injects its DNA.

      • New phage DNA and proteins are synthesized and assembled into phages.

      • Eventually, the cell lyses, releasing new phages into the environment.

    2. Lysogenic Cycle:

      • The phage DNA integrates into the bacterial chromosome, becoming a prophage.

      • As the bacterium reproduces, it copies the prophage and passes it on to daughter cells, leading to a large population of bacteria with the prophage.

      • Conditions may induce the prophage to exit the bacterial chromosome and initiate a lytic cycle, resulting in viral replication and cell lysis.

Horizontal Gene Transfer

  • Horizontal gene transfer: Transfer of genetic material from one lineage to another.

  • Vertical gene transfer: Transfer of genetic material from parent to offspring.

  • Viruses can incorporate into the host genome, as in humans where 8% of the genome consists of endogenous retroviruses.

  • Upon re-emergence, viruses can carry pieces of host genetic material to new infections, facilitating genetic exchange between species.

Examples of Large Viruses

  • Mimivirus, Mamavirus, Megavirus:

    • Large viruses that infect amoebae, ranging from 400-800 nm in size.

    • E. coli is approximately 2μm x 500 nm and contains about 1000 protein-coding genes.

    • Some genes present are found only in cellular organisms, underscoring evolutionary connections.

  • Sputnik Virophage:

    • A small virus that can solely infect amoeba when already infected by a mimi/mamavirus. It cannot infect amoeba independently.

  • Pandoravirus:

    • Contains approximately 2500 protein-coding genes, with only 6% similarity to genes from other viruses or cellular organisms.

    • Recognized for containing the largest viral genome, twice that of megavirus, and primarily infects amoebae.

  • Pithovirus:

    • Discovered in Siberian permafrost, estimated to be approximately 30,000 years old.

    • Measures about 1.5μm x 500 nm and specifically infects amoebae.

  • Medusavirus:

    • Discovered in 2019, it infects amoebae and causes the host to form a thick hardened shell, effectively “turning it into stone.”

    • Indicates evidence of horizontal gene transfer with eukaryotes, raising questions regarding the direction of this transfer.

  • Polydnaviruses:

    • Virus that infects insects, specifically in parasitoid wasps.

    • This virus is typically incorporated into the wasp genome and reproduces in the wasp’s reproductive system, injected along with eggs to enter the host's blood cells, effectively reducing the host's immune response.