46 Introduction to viruses

Viruses are typically described as obligate intracellular parasites, acellular infectious agents that require the presence of a host cell in order to multiply. Viruses that have been found to infect all types of cells – humans, animals, plants, bacteria, yeast, archaea, protozoa…some scientists even claim they have found a virus that infects other viruses! But that is not going to happen without some cellular help.

Virus Characteristics

Viruses can be extremely simple in design, consisting of nucleic acid surrounded by a protein coat known as a capsid (Figure 9.24). The capsid is composed of smaller protein components referred to as capsomers. The capsid+genome combination is called a nucleocapsid.

Viruses can also possess additional components, with the most common being an additional membranous layer that surrounds the nucleocapsid, called an envelope. The envelope is actually acquired from the nuclear or plasma membrane of the infected host cell, and then modified with viral proteins called peplomers. Some viruses contain viral enzymes that are necessary for infection of a host cell and coded for within the viral genome. A complete virus, with all the components needed for host cell infection, is referred to as a virion.

Virus Genome

While cells contain double-stranded DNA for their genome, viruses are not limited to this form. While there are dsDNA viruses, there are also viruses with single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), and single-stranded RNA (ssRNA). In this last category, the ssRNA can either be positive-sense (+ssRNA, meaning it can transcribe a message, like mRNA) or it can be negative-sense (-ssRNA, indicating that it is complementary to mRNA). Some viruses even start with one form of nucleic acid in the nucleocapsid and then convert it to a different form during replication.

Virus Structure

Viral nucleocapsids come in two basic shapes, although the overall appearance of a virus can be altered by the presence of an envelope, if present. Helical viruses have an elongated tube-like structure, with the capsomers arranged helically around the coiled genome. Icosahedral viruses have a spherical shape, with icosahedral symmetry consisting of 20 triangular faces. The simplest icosahedral capsid has 3 capsomers per triangular face, resulting in 60 capsomers for the entire virus. Some viruses do not neatly fit into either of the two previous categories because they are so unusual in design or components, so there is a third category known as complex viruses. Examples include the poxvirus with a brick-shaped exterior and a complicated internal structure, as well as bacteriophage with tail fibers attached to an icosahedral head.

Virus Replication Cycle

While the replication cycle of viruses can vary from virus to virus, there is a general pattern that can be described, consisting of five steps:

1. Attachment – the virion attaches to the correct host cell.
2. Penetration or Viral Entry – the virus or viral nucleic acid gains entrance into the cell.
3. Synthesis – the viral proteins and nucleic acid copies are manufactured by the cells’ machinery.
4. Assembly – viruses are produced from the viral components.
5. Release – newly formed virions are released from the cell.

Attachment

Outside of their host cell, viruses are inert or metabolically inactive. Therefore, the encounter of a virion to an appropriate host cell is a random event. The attachment itself is highly specific, between molecules on the outside of the virus and receptors on the host cell surface. This accounts for the specificity of viruses to only infect particular cell types or particular hosts.

Penetration or Viral Entry

Many unenveloped (or naked) viruses inject their nucleic acid into the host cell, leaving an empty capsid on the outside. This process is termed penetration and is common with bacteriophage, the viruses that infect bacteria. With the eukaryotic viruses, it is more likely for the entire capsid to gain entrance into the cell, with the capsid being removed in the cytoplasm. An unenveloped eukaryotic virus often gains entry via endocytosis, where the host cell is compelled to engulf the capsid resulting in an endocytic vesicle, allowing the virus access to the cell contents. An enveloped eukaryotic virus gains entrance for its nucleocapsid through membrane fusion, where the viral envelope fuses with the host cell membrane, pushing the nucleocapsid past the cell membrane. If the entire nucleocapsid is brought into the cell then there is an uncoating process to strip away the capsid and release the viral genome.

Synthesis

The synthesis stage is largely dictated by the type of viral genome, since genomes that differ from the cell’s dsDNA genome can involve intricate viral strategies for genome replication and protein synthesis. Viral specific enzymes, such as RNA-dependent RNA polymerases, might be necessary for the replication process to proceed. Protein production is tightly controlled, to insure that components are made at the right time in viral development.

Assembly

The complexity of viral assembly depends upon the virus being made. The simplest virus has a capsid composed of 3 different types of proteins, which self-assembles with little difficulty. The most complex virus is composed of over 60 different proteins, which must all come together in a specific order. These viruses often employ multiple assembly lines to create the different viral structures and then utilise scaffolding proteins to put all the viral components together in an organised fashion.

Release

The majority of viruses lyse their host cell at the end of replication, allowing all the newly formed virions to be released to the environment. Another possibility, common for enveloped viruses, is budding, where one virus is released from the cell at a time. The cell membrane is modified by the insertion of viral proteins, with the nucleocapsid pushing out through this modified portion of the membrane, allowing it to acquire an envelope.

Viral replication strategies of DNA viruses and RNA viruses in host cells

Bacteriophage

Viruses that infect bacteria are known as bacteriophage or phage. A virulent phage is one that always lyses the host cell at the end of replication, after following the five steps of replication described above. This is called the lytic cycle of replication.

There are also temperate phage, viruses that have two options regarding their replication. Option 1 is to mimic a virulent phage, following the five steps of replication and lysing the host cell at the end, referred to as the lytic cycle. But temperate phage differ from virulent phage in that they have another choice: Option 2, where they remain within the host cell without destroying it. This process is known as lysogeny or the lysogenic cycle of replication.

A phage employing lysogeny still undergoes the first two steps of a typical replication cycle, attachment and penetration. Once the viral DNA has been inserted into the cell it integrates with the host DNA, forming a prophage. The infected bacterium is referred to as a lysogen or lysogenic bacterium. In this state, the virus enjoys a stable relationship with its host, where it does not interfere with host cell metabolism or reproduction. The host cell enjoys immunity from reinfection from the same virus.

Exposure of the host cell to stressful conditions (i.e. UV irradiation) causes induction, where the viral DNA excises from the host cell DNA. This event triggers the remaining steps of the lytic cycle, synthesis, maturation, and release, leading to lysis of the host cell and release of newly formed virions.

So, what dictates the replication type that will be used by a temperate phage? If there are plenty of host cells around, it is likely that a temperate phage will engage in the lytic cycle of replication, leading to a large increase in viral production. If host cells are scarce, a temperate phage is more likely to enter lysogeny, allowing for viral survival until host cell numbers increase. The same is true if the number of phage in an environment greatly outnumber the host cells, since lysogeny would allow for host cells numbers to rebound, ensuring long term viral survival.

Lysogens can experience a benefit from lysogeny as well, since it can result in lysogenic conversion, a situation where the development of a prophage leads to a change in the host’s phenotype. One of the best examples of this is for the bacterium Corynebacterium diphtheriae, the causative agent of diphtheria. The diphtheria toxin that causes the disease is encoded within the phage genome, so only C. diphtheriae lysogens cause diphtheria.

Eukaryotic Viruses

Eukaryotic viruses can cause one of four different outcomes for their host cell. The most common outcome is host cell lysis, resulting from a virulent infection (essentially the lytic cycle of replication seen in phage). Some viruses can cause a latent infection, inserting their viral DNA into the host cell genome, allowing them to co-exist peacefully with their host cells for long periods of time (much like a temperate phage during lysogeny). Some enveloped eukaryotic viruses can also be released one at a time from an infected host cell, in a type of budding process, causing a persistent infection. Lastly, certain eukaryotic viruses can cause the host cell to transform into a malignant or cancerous cell, a mechanism known as transformation.

Viruses and Cancer

There are many different causes of cancer, or unregulated cell growth and reproduction. Some known causes include exposure to certain chemicals or UV light. There are also certain viruses that have a known associated with the development of cancer. Such viruses are referred to as oncoviruses. Oncoviruses can cause cancer by producing proteins that bind to host proteins known as tumour suppressor proteins, which function to regulate cell growth and to initiate programmed cell death, if needed. If the tumour suppressor proteins are inactivated by viral proteins then cells grow out of control, leading to the development of tumors and metastasis, where the cells spread throughout the body.

Case study

A 7-year-old female koala (Phascolarctos cinereus), rescued from a roadside near a rural veterinary clinic, presented with lethargy (lack of energy), weight loss, and mild dyspnoea (Subtle increased respiratory rate or depth). Physical examination revealed generalised lymphadenopathy (swollen lymph nodes), and haematology showed a marked lymphocytosis (increased lymphocyte count). PCR testing confirmed koala retrovirus (KoRV) infection, and further diagnostics supported a diagnosis of KoRV‑associated lymphoma, a common neoplastic condition in koalas due to viral integration into the host genome and subsequent oncogene activation.

KoRV-associated neoplasia has limited treatment options in free-ranging wildlife. Management in this case focused on supportive care, including fluid therapy, nutritional support, and stress minimisation.

Given the poor prognosis and welfare considerations, euthanasia was elected. KoRV has a significant role in cancer development in koalas and challenges are faced by rural clinics managing infectious oncogenic diseases in Australian native wildlife.

 

Viral Classification

Since viruses lack ribosomes (and thus rRNA), they cannot be classified within the Three Domain Classification scheme with cellular organisms. Alternatively, Dr. David Baltimore derived a viral classification scheme, one that focuses on the relationship between a viral genome to how it produces its mRNA. The Baltimore Scheme recognises seven classes of viruses.

DNA viruses

Class I: dsDNA

DNA viruses with a dsDNA genome, like bacteriophages T4 and lambda, have a genome exactly the same as the host cell that they are infecting. For this reason, many host enzymes can be utilised for replication and/or protein production. The flow of information follows a conventional pathway: dsDNA → mRNA → protein, with a DNA-dependent RNA-polymerase producing the mRNA and the host ribosome producing the protein. The genome replication, dsDNA → dsDNA, requires a DNA-dependent DNA-polymerase from either the virus or the host cell.

The virus often employs strategies for control of gene expression, to ensure that particular viral products are made at specific times in the virus replication.  In the case of T4, the host RNA polymerase binds to the viral DNA and begins transcribing early genes immediately after the DNA is injected into the cell. One of the early viral proteins modifies the host RNA polymerase so that it will no longer recognise host promoters at all, in addition to moving on to transcribe genes for middle-stage viral proteins. A further modification (catalysed by middle-stage viral proteins) further modified the RNA polymerase so it will recognise viral genes coding for late-stage proteins. This ensures an orderly production of viral proteins.

The replication of several dsDNA viruses results in the production of concatemers, where several viral genomes are linked together due to short single-stranded regions with terminal repeats. As the genome is packaged into the capsid a viral endonuclease cuts the concatemer to an appropriate length.

There are several animal viruses with dsDNA genomes, such as the pox viruses and the adenoviruses. The herpesviruses have several notable features, such as the link of several members with cancer and the ability of the viruses to remain in a latent form within their host. A productive infection results in an explosive viral population, cell death, and development of disease signs, during which neurons are infected. A latent infection develops in the neurons, allowing the virus to remain undetected in the host. If the viral genome is reactivated, a productive infection results, leading to viral replication and disease signs again.

Class II: ssDNA

The flow of information for ssDNA viruses, such as the parvoviruses, will still follow the conventional pathway, to a certain extent: DNA → mRNA → protein. But the viral genome can either have the same base sequence as the mRNA (plus-strand DNA) or be complementary to the mRNA (minus-strand DNA). In the former case, a DNA strand that is complementary to the viral genome must be manufactured first, forming a double-stranded replicative form (RF). This can be used to both manufacture viral proteins and as a template for viral genome copies. For the minus-strand DNA viruses, the genome can be used directly to produce mRNA but a complementary copy will still need to be made, to serve as a template for viral genome copies.

The replicative form can be used for rolling-circle replication, where one strand is nicked and replication enzymes are used to extend the free 3’ end. As a complementary strand is synthesised around the circular DNA, the 5’ end is peeled off, leading to a displaced strand that continues to grow in length.

Class VII: DNA viruses that use reverse transcriptase

The hepadnaviruses contain a DNA genome that is partially double-stranded, but contains a single-stranded region. After gaining entrance into the cell’s nucleus, host cell enzymes are used to fill in the gap with complementary bases to form a dsDNA closed loop. Gene transcription yields a plus-strand RNA known as the pregenome, as well as the viral enzyme reverse transcriptase, an RNA-dependent DNA-polymerase. The pregenome is used as a template for the reverse transcriptase to produced minus-strand DNA genomes, with a small piece of pregenome used as a primer to produce the double-stranded region of the genomes.

RNA viruses

Class III: dsRNA

Double-stranded RNA viruses infect bacteria, fungi, plants, and animals, such as the rotavirus that causes diarrheal illness in humans. But cells do not utilise dsRNA in any of their processes and have systems in place to destroy any dsRNA found in the cell. Thus the viral genome, in its dsRNA form, must be hidden or protected from the cell enzymes. With very few exceptions, cells also lack RNA-dependent RNA-polymerases, necessary for replication of the viral genome so the virus must provide this enzyme itself. The viral RNA-dependent RNA polymerase acts as both a transcriptase to transcribe mRNA, as well as a replicase to replicate the RNA genome.

For the rotavirus, the viral nucleocapsid remains intact in the cytoplasm with replication events occurring inside, allowing the dsRNA to remain protected. Messenger RNA is transcribed from the minus-strand of the RNA genome and then translated by the host ribosome in the cytoplasm. Viral proteins aggregate to form new nucleocapsids around RNA replicase and plus-strand RNA. The minus-strand RNA is then synthesised by the RNA replicase within the nucleocapsid, once again insuring protection of the dsRNA genome.

Class IV: +ssRNA

Viruses with plus-strand RNA, such as poliovirus, can use their genome directly as mRNA with translation by the host ribosome occurring as soon as the unsegmented viral genome gains entry into the cell. One of the viral genes expressed yields an RNA-dependent RNA-polymerase (or RNA replicase), which creates minus-strand RNA from the plus-strand genome. The minus-strand RNA can be used as a template for more plus-strand RNA, which can be used as mRNA or as genomes for the newly forming viruses.

Translation of the poliovirus genome yields a polyprotein, a large protein with protease activity that cleaves itself into three smaller proteins. Additional cleavage activity eventually yields all the proteins needed for capsid formation, as well as an RNA-dependent RNA-polymerase.

The formation of a polyprotein that is cut into several smaller proteins illustrates one possible strategy to an issue faced by many +ssRNA viruses – how to generate multiple proteins from an unsegmented +ssRNA genome? Other possibilities include:

• subgenomic mRNA – during translation, portions of the viral RNA may be skipped, resulting in different proteins than what is made from the viral RNA in its entirety.
• ribosomal frame-shifting – the ribosome “reads” the mRNA in groups of three nucleotides or codon, which translate to one amino acid. If the ribosome starts with nucleotide #1, that is one open reading frame (ORF), resulting in one set of amino acids. If the ribosome were to move forward where nucleotide 2 is the starting nucleotide that would be ORF #2, resulting in a completely different set of amino acids. If the ribosome were to move forward again where nucleotide 3 is the starting nucleotide that would be ORF#3, resulting in an entirely different set of amino acids. Some viruses have viral genes that deliberately overlap within different ORFs, leading to the production of different proteins from a single mRNA.
• readthrough mechanism – a viral genome can have stop codons embedded throughout the sequence. When the ribosome comes to a stop codon it can either stop, ending the amino acid sequence, or it can ignore the stop codon, continuing on to make a longer string of amino acids. For viruses with the readthrough mechanism, they acquire a variety of proteins by having stop codons that are periodically ignored. Sometimes this function is combined with the ribosomal frame-shifting to produce an even greater variety of viral proteins.

Class V: -ssRNA

Minus-strand RNA viruses include many members notable for humans, such as influenza virus, rabies virus, and Ebola virus. Since the genome of minus-strand RNA viruses cannot be used directly as mRNA, the virus must carry an RNA-dependent RNA-polymerase within its capsid. Upon entrance into the host cell, the plus-strand RNAs generated by the polymerase are used as mRNA for protein production. When viral genomes are needed the plus-strand RNAs are used as templates to make minus-strand RNA.

Class VI: +ssRNA, retroviruses

Despite the fact that the retroviral genome is composed of +ssRNA, it is not used as mRNA. Instead, the virus uses its reverse transcriptase to synthesise a piece of ssDNA complementary to the viral genome. The reverse transcriptase also possesses ribonuclease activity, which is used to degrade the RNA strand of the RNA-DNA hybrid. Lastly, the reverse transcriptase is used as a DNA polymerase to make a complementary copy to the ssDNA, yielding a dsDNA molecule. This allows the virus to insert its genome, in a dsDNA form, into the host chromosome, forming a provirus. Unlike a prophage, a provirus can remain latent indefinitely or cause the expression of viral genes, leading to the production of new viruses. Excision of the provirus does not occur for gene expression.

Methods of inactivating viruses

Viruses can be inactivated using physical, chemical, and biological methods, depending on the setting (clinical, laboratory, or environmental).

Physical methods include heat, radiation, and filtration. Moist heat (for example autoclaving) is highly effective because it denatures viral proteins and damages nucleic acids, while dry heat is less efficient but still useful for heat‑stable materials. Ultraviolet (UV) radiation inactivates viruses by causing nucleic acid damage that prevents replication, although it has limited penetration. Filtration can remove viruses from fluids when appropriately small pore sizes are used.

Chemical methods involve disinfectants and antiseptics. Alcohols, chlorine compounds, iodine, hydrogen peroxide, and quaternary ammonium compounds disrupt viral envelopes and denature proteins, making them particularly effective against enveloped viruses. Non‑enveloped viruses are generally more resistant and require stronger agents.

Biological and pharmaceutical methods include antiviral drugs and immune responses, which inhibit viral replication rather than directly destroying viral particles.

Other infectious agents including prions and viroids

Viroids

Viroids are small, circular ssRNA molecules that lack protein. These infectious molecules are associated with a number of plant diseases. Since ssRNA is highly susceptible to enzymatic degradation, the viroid RNA has extensive complementary base pairing, causing the viroid to take on a hairpin configuration that is resistant to enzymes. For replication viroids rely on a plant RNA polymerase with RNA replicase activity.

Prions

Prions are infectious agents that completely lack nucleic acid of any kind, being made entirely of protein. They are associated with a variety of diseases, primarily in animals, although a prion has been found that infects yeast. The prion protein is found in the neurons of healthy animals (PrPC or Prion Protein Cellular), with a particular secondary structure. The pathogenic form (PrPSC or Prion Protein Scrapie) has a different secondary structure and is capable of converting the PrPC into the pathogenic form. Accumulation of the pathogenic form causes destruction of brain and nervous tissue, leading to disease symptoms such as memory loss, lack of coordination, and eventually death.

Case study

A 6-year-old Holstein–Friesian dairy cow, part of a herd in southern England, presented to a rural veterinary practice with progressive behavioural changes, including nervousness, hypersensitivity to stimuli, and altered gait. Over several weeks, the cow developed ataxia, tremors, and difficulty rising, suggestive of a neurological disorder. Given the age, breed, and region, bovine spongiform encephalopathy (BSE) was considered a key differential, and the animal was humanely euthanised with post-mortem testing confirming the diagnosis.

Bovine spongiform encephalopathy is a fatal prion disease characterised by the accumulation of misfolded prion protein in the central nervous system, leading to spongiform degeneration of brain tissue. It most commonly affected adult dairy cattle, particularly Holstein–Friesians, during outbreaks in the United Kingdom, where contaminated meat-and-bone meal was historically used in feed. There is no treatment for BSE, and management relies on strict surveillance, feed bans, and biosecurity measures to prevent transmission and protect both animal and public health.