Biology Notes - A2.3 Viruses

Virus Structure

Structural Features of Viruses

Virus structure

• Viruses are non-cellular infectious particles; they are not organisms, as they are not considered to be alive.

• Viruses possess none of the characteristic features used for classifying organism,s so they sit outside of the three-domain classification syst.em

• They are relatively simple in structure and much smaller than prokaryotic cells, with diameters between 20 and 300. nm

  • They can only be seen with an electron microscope.cope

• They have no cellular structures and so no metabolism, so they are considered to be acellular.r

• Structural features common to all viruses include

  • A small size

    • Viruses contain few molecules, sthey o do not form large structures

  • A fixed size

    • Viruses do not grow

  • A nucleic acid core

    • Their genomes are made up of either DNA or RNA

    • Nucleic acids in viruses can be single-stranded or double-stranded

    • Nucleic acids can have a linear or circular structure

  • A protein coat called a ‘capsid’

    • Attachment proteins are present on the outer surface of a capsid that allow viruses to bind to and enter host cells.

  • No cytoplasm

  • Very few, or no, enzymes

• Some viruses have an additional outer layer called a lipid envelope, formed usually from themembrane phospholipidss of the cell they were made

  • Lipid envelope structures can be involved in cell recognition

• All viruses are parasitic in that they can only reproduce by infecting living cells and using their protein-building machinery (ribosomes) to produce new viral particles

  • The energy that viruses need for replication is released by the host cell; viruses do not respire

General virus structure diagram

Virus structure can vary, but all viruses have genetic material and a protein capsid with attachment proteins.

Structural Diversity

Diversity of structure in viruses

• Although simple, there is a huge variety and diversity of virus structure and shape:

  • Genetic material can be either RNA or D,NA which can either double-strandedble or single-stranded

  • Some viruses are enveloped, others are not

  • Viral shapes can be threadlike, polyhedral, and spherical

• Each type of virus can attach to and infect a specific type of host cell; the host cell to which it can attach is determined by the attachment proteins, e.g.

  • HIV infects white blood cells

  • Hepatitis infects liver cells

Virus structure variety diagram

Virus structure varies widely

• Examples of viruses that have different structures are:

  • Bacteriophage lambda

  • Coronaviruses

  • HIV

Bacteriophage lambda

• This is a bacterial virus and it infects the bacterial species Escherichia coli (E. coli)

• It has adouble-strandedd DNA genome contained within its capsid head

• The tail and fibrils enable it to attach itself to its host and insert its DNA into the cell

  • The tail consists of proteins that contract, allowing the virus to move the tail through the bacterial cell wall 

  • DNA from the virus is injected into the host cell through the tail

Bacteriophage lambda structure diagram

A bacteriophage virus

Coronaviruses

• Coronaviruses are a group of viruses that cause respiratory diseases in mammals and birds

  • They can be transmitted via respiratory fluids

• Their structure includes:

  • Single-stranded RNA

  • A spherical shape

  • An envelope outside their capsid

  • Many glycoproteins that project from their surface, producing a "corona" 

• Examples include SARS-CoV-2 (COVID-19), Middle East Respiratory Syndrome (MERS), and Severe Acute Respiratory Syndrome (SARS)

Coronavirus structure diagram

A coronavirus

HIV

• The Human Immunodeficiency Virus is spread by intimate human contact and can only be transmitted by direct exchange of body fluids

• This means HIV can be transmitted in the following ways:

  • Sexual intercourse

  • Blood donation

  • Sharing of needles used by intravenous drug users

  • From mother to child across the placenta

  • Mixing of blood between the mother and child during birth

  • From mother to child through breast milk

• HIV contains:

  • Two RNA strands

  • Proteins (including the enzyme reverse transcriptase)

    • Reverse transcriptase allows the production of DNA from the viral RNA; for this reason, HIV is known as a retrovirus.s

  • A protein capsid

  • A viral envelope consisting of a lipid bilayer and glycoproteins that act as attachment proteins

    • The lipid bilayer is derived from the cell membrane of the host helper T cell from which the particle escaped.

HIV structure diagram

An HIV particle

Replication in Viruses

The Lytic Cycle

Viral replication

• Being non-living, viruses do not undergo cell division

• All viruses are parasitic, meaning they can only reproduce by infecting living cells, referred to as host cells

• To replicat,e all viruses must:

  • Attach to a specific attachment site on the host cell

  • Inject their nucleic acid into the cytoplasm of the host cell

  • Use the protein synthesis machinery of their host cell to produce viral proteins

  • Assemble new viral particles

  • Release the new viral particles from  the host cell

• Viral replication occurs via a lytic pathway, but some viruses undergo a series of events known as the lysogenic pathway between reproductive cycles.

The lytic pathway

• This is named as such because the new virus particles are released during lysis (bursting) of the host cell

  • This is caused by an enzyme called lysozym,e which is coded for by the virus's genetic material

• Lysis occurs after the production of fully functional virus particles called virions

• The steps of the lytic pathway are as follows:

  1. The virus attaches to the cell membrane of the host cell using attachment proteins

  2. The virus infects the host cell by injecting its DNA into the cytoplasm

  3. Next, the virus uses proteins and enzymes within the host cell to produce new virus particles in a process called biosynthesis.

  4. Virus particles are assembled and matured into virions

  5. Finally, the host cell undergoes lysis, releasing the virions into the host organism to infect more cells

Lytic cycle diagram

Viruses use the protein synthesis machinery of host cells to replicate themselves in the lytic pathway.y

The Lysogenic Cycle

The lysogenic pathway

• A key difference between the lytic pathway and the lysogenic pathway is that here new virus particles are not immediately released and will not immediately cause disease once they infect a host ce.ll

• During the lysogenic path,way viral nucleic acid combines with the host DNA

• A viral gene coding for a repressor protein prevents the viral nucleic acid from being transcribed and translated

  • This is called lat,ency and the time during which it occurs is known as a period of lysogeny

• The host cell will continue to function as normal, including reproduction and cell div,ision which means that subsequent cells will contain the virus nucleic acid within the host's genome

  • This can result in continuous production of host cells containing the virus nucleic acid wtheirin its genome

  • This stage of the lysogenic pathway can continue until a lytic event is triggered

• The viral DNA is inactive, or dormant, until a change in the cell's environment triggers the virus DNA to enter the lytic pathway

  • Changes include exposure to UV rays and certain chemicals

Lysogenic cycle diagram

Viruses lie dormant in the lysogenic pathway until the lytic pathway is triggered

Origin of Viruses

• Viruses can infect nearly all living species and are estimated to have been on Earth 3.5 billion years before humans evolved

• There is evidence that viruses evolved alongside other species, a process known as coevolution

  • Around 8 % of the human genome contains small segments of viral DNA thought to be left over from ancient infections

  • These DNA fragments are called endogenous retroviruses (ERVs) and have been passed along and modified over millions of years of evolution

• The origin of viruses is still under debate in the scientific community and among virologists

  • One issue is that viruses are not found in fossils, so there is limited evidence for their evolution

There are three key theories as to the origin of viruses:

Escape theory

• Viruses arose from genetic elements, such as DNA and RNA, that gained the ability to move betweencellsl.s

• These genetic elements became surrounded by an outer boundary, forming a virus particle.

Regressive/reduction theory

• Viruses are remnants of cellular organisms or were once small cells that became parasites of largercellsl.s

• Over ti,me the cellular structures that were no longer needed were sed , leaving behind just viral structur.es

Virus-first theory

• Viruses predate their current cellular hosts

• During evolut,ion we expect simpler organisms to give rise to more complex organisms, so the simple nature of virus particles could indicate that viruses evolved first

Theories of virus origin diagram

There are multiple theories for the origin of viruses

• Viruses are div,erse and this diversity suggests that there may have been different origins for different viruses

  • It is possible that all of the above theories or correct, or indeed that none of them are correct, and that a different process occurredSome features aree common among many viruses, which indicates that convergent evolution may have occurred

• All viruses have a capsid protein outer boundary, and no cytoplasmis contained within this boundary

  • All viruses have genetic material, either DNA or RNA

    • The genetic code is the same as that used by other organisms

  • All viruses are parasitic and cannot replicate or carry out their functions without a host cell

Evolution in Viruses

Viral evolution

• Viruses can undergo evolution extremely rapidly

• Two examples that demonstrate this are:

  • The evolution of influenza viruses

  • The evolution of HIV

• Both of these viruses:

  • Have high mutation rates

    • This is largely because these viruses have RNA as their genetic material; mutations can occur during the process of converting viral RNA into DNA during viral replication.

  • Have large population sizes

  • Have short generation times

• These features mean that both of these viruses can quickly evolve to evade the immune systems of their host.s

Antigenic drift and antigenic shift

Viruses can undergo genetic change either by antigenic drift or antigenic shi.ft

Antigenic drift

• The accumulation of small changes to viral genetic material over time

• Variation in the surface proteins of the virappearsear slowly

• Eventu,ally the host's immune system cannot recognise the virus

• HIV undergoes antigenic drift

Antigenic shift

• A major change occurs in the viral genetic material in a sperioderiod

  • Two or more virus types infect the same cell within the host

  • They combine their genetic material

• Rapid variation is produced in the surface proteins of the virus 

• A new virus is created that is not recognised by the host's immune system

• The influenza virus undergoes antigenic shift

Treating disease caused by rapidly evolving viruses

• Vaccines

  • For rapidly evolving viruses, vaccines need to be changed and updated yearly so that they remain effective

  • This is a successful approach for viruses that undergo antigenic drift because the changes are small and not hugely rapid

    • Although HIV undergoes genetic drift, it does so at an unusually rapid rate ,so a vaccine has not yet been successful.

  • For viruses undergoing antigenic shif,t vaccines are not so successful because the changes are rapid and not predictab.le

• Fast-evolving viruses may need to be dealt with he isolation infected individuals to stop the spread of infection.

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