Viral genetics

SIGNIFICANCE: The composition and structures of virus genomes are more varied than any identified in the entire bacterial, botanical, or animal kingdoms. Unlike the genomes of all other cells, which are composed of DNA, virus genomes may contain their genetic information encoded in either DNA or RNA. Viruses cannot replicate on their own but must instead use the reproductive machinery of host cells to reproduce themselves.

What Is a Virus?

Viruses are submicroscopic, obligate intracellular parasites. This definition differentiates viruses from all other groups of living organisms. There exists more biological diversity within viruses than in all other known life-forms combined. This is the result of viruses successfully parasitizing all known groups of living organisms. Viruses have evolved in parallel with other species by capturing and using genes from infected host cells for functions that they require to produce their progeny, to enhance their escape from their host’s cells and immune system, and to survive the intracellular and extracellular environment. At the molecular level, the composition and structures of virus genomes are more varied than any others identified in the entire bacterial, botanical, or animal kingdoms. Unlike the genomes of all other cells composed of DNA, virus genomes may contain their genetic information encoded in either DNA or RNA. The comprising a virus genome may be single-stranded or double-stranded and may occur in a linear, circular, or segmented configuration.

The Need for a Host

It must be understood that virus particles themselves do not grow or undergo division. Virus particles are produced from the assembling of pre-formed components, whereas other agents actually grow from an increase in the integrated sum of their components and reproduce by division. The reason is that viruses lack the genetic information that encodes the apparatus necessary for the generation of metabolic energy or for protein synthesis (ribosomes). The most critical interaction between a virus and a host cell is the need of the virus for the host’s cellular apparatus for nucleic acid and for the synthesis of proteins. No known virus has the biochemical or genetic potential to generate the energy necessary for producing all biological processes. Viruses depend totally on a host cell for this function.

Viruses are therefore not living in the traditional sense, but they nevertheless function as living things; they do replicate their own genes. Inside a host cell, viruses are “alive,” whereas outside the host they are merely a complex assemblage of metabolically inert chemicals—basically a protein shell. Therefore, while viruses have no inner and cannot reproduce on their own, they carry with them the means necessary to get into other cells and then use those cells’ own reproductive machinery to make copies of themselves. Viruses thrive at the host cells’ expense.

Replication

The sole goal of a virus is to replicate its genetic information. The type of host cell infected by a virus has a direct effect on the process of replication. For viruses of prokaryotes (bacteria, primarily), reproduction reflects the physical simplicity of the host cell. For viruses with eukaryotic host cells (plants and animals), reproduction is more complex. The coding capacity of the genome forces the virus to choose a reproductive strategy. The strategy might involve near-total reliance on the host cell, resulting in a compact genome encoded for only a few essential proteins (+), or could involve a large, complex virus genome encoded with nearly all the information necessary for replication, relying on the host cell only for energy and ribosomes. Those viruses with an RNA genome plus messenger RNAs (mRNAs) have no need to enter the nucleus of their host cell, although during many often do. DNA genome viruses mostly replicate in the host cell’s nucleus, where host DNA is replicated and the biochemical apparatus required for this process is located. Some DNA viruses (poxviruses) have evolved to contain the biochemical capacity to replicate in their host’s cytoplasm, with a minimal need for the host cell’s other functions.

Virus replication involves several stages carried out by all types of viruses, including the onset of infection, replication, and release of mature from an infected host cell. The stages can be defined in eight basic steps: attachment, penetration, uncoating, replication, gene expression, assembly, maturation, and release.

The first stage, attachment, occurs when a virus interacts with a host cell and attaches itself—binds with a virus-attachment protein (antireceptor)—to a cellular receptor molecule in the cell membrane. The receptor may be a protein or a carbohydrate residue. Some complex viruses, such as herpesviruses, use more than one receptor and therefore have alternate routes of cellular invasion.

Shortly after attachment the target cell is penetrated. Cell penetration is usually an energy-dependent process, and the cell must be metabolically active for penetration to occur. The virus bound to the cellular receptor molecule is translocated across the cell membrane by the receptor and is engulfed by the cell’s cytoplasm.

Uncoating occurs after penetration and results in the complete or partial removal of the virus and the exposure of the virus genome as a nucleoprotein complex. This protein complex can be a simple RNA genome or can be highly complex, as in the case of a containing a RNA genome responsible for converting a virus RNA genome into a DNA provirus.

How a virus replicates and the resulting expression of its genes depends on the nature of its genetic materials. Control of gene expression is a vital element of virus replication. Viruses use the biochemical apparatus of their infected host cells to express their genetic information as proteins and do this by using the appropriate biochemical language recognized by the host cell. Viruses include double-stranded DNA viruses such as papovaviruses, poxviruses, and herpesviruses; single-stranded sense DNA viruses such as parvoviruses; double-stranded RNA reoviruses; single-stranded sense RNA viruses such as flaviviruses, togaviruses, and claiciviruses; single-stranded such as filoviruses and bunyaviruses; single-stranded sense RNA with DNA intermediate retroviruses; and double-stranded DNA with RNA intermediate-like hepadnaviruses.

During assembly, the basic structure of the virus particle is formed. Virus proteins anchor themselves to the cellular membrane, and, as virus proteins and genome molecules reach a critical concentration, assembly begins. The result is that a genome is stuffed into a completed protein shell. The process of maturation prepares the virus particle for infecting subsequent cells and usually involves the cleavage of proteins to form matured products or conformational structural changes.

For most viruses, release is a simple matter of breaking open the infected cell and exiting. The breakage normally occurs through a physical interaction of proteins against the inner surface of the host cell membrane. A virus may also exit a cell by budding. Budding involves the creation of a lipoprotein envelope around the virion prior to the virion’s being extruded out through the cell membrane.

Viral genetics offers a number of opportunities. For example, researchers have studied wastewater for viral clues to the spread of diseases. Monitoring wastewater can be used to detect emerging viral pathogens and changes to existing viruses such as the SARS-CoV-2 coronavirus that causes COVID-19.

Key Terms

• capsidthe protective protein coating of a virus particle
• ribosomea cytoplasmic organelle that serves as the site for amino acid incorporation during the synthesis of protein
• virionsmature infectious virus particles

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