BIO 102: GENERAL BIOLOGY II
CHARACTERISTICS, IDENTIFICATION AND CLASSIFICATION OF VIRUSES
A virus is a tiny infectious particle that can reproduce only by infecting a host cell.
Viruses are infectious microbes/agents with fairly simple, acellular organization with both living
and nonliving characteristics. They possess only one type of nucleic acid, either DNA or RNA (but
not both) surrounded by a protein coat called a capsid (and sometimes, in addition, substances such
as lipids and carbohydrates). Each capsid is composed of protein subunits called capsomeres. The
outermost proteins of the virus particle allow the virus to recognize the correct host cell and gain
entry into its cytoplasm.Viruses can reproduce only within living cells and are obligatory
intracellular parasites. They commandeer the host cell and use its resources to make more viruses,
basically programming it to become a virus factory.
Viruses are quite different from prokaryotic and eukaryotic microorganisms. They are smaller than
prokaryotic and eukaryotic cells. Their sizes range from about 10 to 300 or 400 nm in diameter.
All viruses have a nucleocapsid composed of a nucleic acid surrounded by a protein capsid that
may be icosahedral, helical, or complex in structure.
Capsids are constructed of protomers that self-assemble through non-covalent bonds. A
membranous envelope often lies outside the nucleocapsid.
Despite their simplicity in comparison with cellular organisms, viruses are extremely important
and deserves of close attention because the study of viruses has contributed to safe public health,
research, and medical applications. It has also contributed significantly to the discipline of
molecular biology.
A complete virus particle or virion consists of one or more molecules of DNA or RNA enclosed
in a coat of protein, and sometimes also in other layers. These additional layers may be very
complex and contain carbohydrates, lipids, and additional proteins.
Viruses can exist in two phases: extracellular and intracellular.
Virions, the extracellular phase, possess few if any enzymes and cannot reproduce independent of
living cells. In the intracellular phase, viruses exist primarily as replicating nucleic acids that
induce host metabolism to synthesize virion components; eventually complete virus particles or
virions are released.
Viruses differ from living cells in at least three ways:
(1) their simple, acellular organization;
(2) the presence of either DNA or RNA, but not both, in almost all virions (human cytomegalovirus
has a DNA genome and four mRNAs); and
(3) their inability to reproduce independent of cells and carry out cell division as prokaryotes and
eukaryotes do.
Also note the following:
Living characteristic of viruses Non-living characteristic of viruses
The reproduce at a fantastic rate but They are acellular i.e. they contain no cytoplasm or
only in living host cells cellular organelles.
They can mutate They carry out no metabolism on their own and must
replicate using the host cell’s metabolic machinery i.e.,
viruses do not grow or divide. Instead new viral
components are synthesized and assembled within the
infected host cells.
Viruses are totally dependent on a host cell for replication. They are strict intracellular parasites
and cannot be grown in synthetic culture Media.
NB: Virology - the study of viruses.
A brief history of the discovery of Virus
Although the ancients did not understand the nature of their illnesses, they were acquainted with
diseases, such as rabies, that are now known to be viral in origin. In fact, there is some evidence
that the great epidemics of A.D. 165 to 180 and A.D. 251 to 266, which severely weakened the
Roman Empire and aided its decline, may have been caused by measles and smallpox viruses.
Smallpox had an equally profound impact on the New World.
The word ‘virus’ (Latin word for Poison) was used to describe the cause of tobacco mosaic disease
(TMD).
A Russian botanist Dimitri Ivanowski in 1892 discovered the source of TMD. Initially the source
of the disease was taught to be bacterial. Other scientists including Martinus W. Beijerinck in 1899
concluded that the causative agent was not a bacterium but instead, possibly a chemical, like a
biological poison called toxin. A virus is extremely smaller than a bacterium and can be visible
using electron microscope (SEM and (TEM).
In order to survive and reproduce viruses must infest a cellular host making them obligate
intracellular parasites. The genome of a virus enters a host cell and direct the production of the
viral components, proteins and nucleic acids needed to form new virus particles called virions.
New virions are made in host cell by assembly of viral components. The new virions transport the
viral genome to another host cell to carry out another round of infection.
Hosts and viral transmission
Viruses can infect every type of host cell including those of the plants, animals, fungi, protists,
bacteria and archaea. Most viruses are only able to infect the cell of one or a few species of
organism. This is called the Host Range. However, having a wide host range is not common and
viruses will typically only infect specific hosts and only specific cell types within those hosts.
The viruses that infect bacteria are called bacteriophages and those that infect only fungi are called
mycophages. There are even some viruses called virophages that infect other viruses.
The structure of a T bacteriophage
Viruses may cause abnormal growth of the cell or cell death, alter the cell’s genome or cause little
noticeable effect in the cell. Viruses can be transmitted through direct contacts, indirect contacts
with formites or through a vector. In humans a wide variety of viruses are capable of causing
various infections and diseases. Some of the deadliest emerging pathogens in humans are viruses.
We have few treatments or drugs to deal with viral infections making them difficult to eradicate.
Basic characteristics of viruses:
These characteristics highlight the unique biology of viruses and distinguish them from other
microorganisms like bacteria and cells.
1. Structure:
- Consist of a protein coat (capsid) surrounding a nucleic acid core (genome)
- May have a lipid envelope (membrane) derived from host cell
2. Size:
- Typically range from 10 - 400 nanometers (nm) in diameter
- Smaller than bacteria, larger than most molecules
3. Genome:
- Composed of either DNA (double-stranded) or RNA (single-stranded)
- Genome size varies from a few kilobase pairs (kb) to over 200 kb
4. Replication:
- Require host cell machinery for replication and transcription
- Can replicate in host cell cytoplasm or nucleus
5. Host Range:
- Specific viruses can infect specific hosts (e.g., humans, animals, plants, bacteria)
- Some viruses can infect multiple hosts (e.g., zoonotic viruses)
6. Transmission:
- Spread through various routes (e.g., airborne, contact, vector-borne, fecal-oral)
- Can be transmitted vertically (from parent to offspring) or horizontally (between individuals)
7. Pathogenesis:
- Can cause a range of diseases, from mild to severe and life-threatening
- May induce immune responses, inflammation, and tissue damage
8. Evolution:
- Evolve rapidly due to high mutation rates and recombination
- Can develop resistance to antiviral drugs and immune responses
9. Metabolism:
- Do not carry out metabolic processes like cells do
- Rely on host cell metabolism for energy and nutrient supply
10. Response to Environment:
- Can survive outside host cells for varying periods
- May be sensitive to temperature, pH, and other environmental factors
Identification of Virus
Virus identification is the process of determining the type of virus present in a sample and this is
crucial for the following purposes:
1. Diagnosis: Accurate diagnosis of viral infections.
2. Treatment: Appropriate treatment and management of viral diseases.
3. Prevention: Development of effective vaccines and prevention strategies.
4. Research: Understanding virus evolution, transmission, and pathogenesis.
Methods for Virus Identification
The choice of method depends on the specific context, sample type, and resources available.
However the following are the commonly used methods:
1. Morphology: Electron microscopy (EM) to visualize virus shape and size.
2. Serology: Antibody-based tests (e.g., ELISA, Western blot) to detect viral antigens.
3. Molecular Biology involving the use of:
- PCR (Polymerase Chain Reaction) to amplify viral DNA/RNA.
- RT-PCR (Reverse Transcription PCR) to detect RNA viruses.
- Nucleic Acid Sequencing to determine viral genome sequence.
4. Cell Culture: Isolation of viruses in cell culture.
5. Virus Isolation: Growth of viruses in animals or eggs.
6. Biochemical Tests: Involving detection of viral enzymes or proteins.
7. Next-Generation Sequencing (NGS): High-throughput sequencing technologies.
Challenges in Virus Identification:
1. Virus Variability: High mutation rates and recombination.
2. Limited Sample Material: Small sample sizes or degraded samples.
3. Multiple Infections: Co-infections with multiple viruses.
4. New or Emerging Viruses: Unknown or uncharacterized viruses emergence.
Classification of Viruses
Viruses are classified into several groups based on their nucleic acid’s characteristics, capsid
symmetry, the presence or absence of an envelope, replication methods, and host organisms. The
main classification systems are:
1. Based on Presence or Absence of an Envelope.
There are two categories
- Naked or non-enveloped viruses: They are formed from only a nucleic acid and capsid.
DNA
OR Capsid
RNA
- Enveloped viruses: They are formed with a nucleic acid, packed capsid surrounded by a lipid layer.
Lipid layer
DNA
OR
RNA
2. Baltimore Classification
This system of classifying viruses developed by David Baltimore, categorizes viruses based on
their genetic material and replication strategy into;
- Class I: Double-stranded DNA viruses (e.g., Adenovirus, Herpesvirus)
- Class II: Single-stranded DNA viruses (e.g., Parvovirus)
- Class III: Double-stranded RNA viruses (e.g., Rotavirus)
- Class IV: Single-stranded RNA viruses with positive sense (e.g., Coronavirus, Picornavirus)
- Class V: Single-stranded RNA viruses with negative sense (e.g., Influenzavirus)
- Class VI: Retroviruses (e.g., HIV)
3. International Committee on Taxonomy of Viruses (ICTV) Classification:
- Domain: Riboviria (RNA viruses) or Varidnaviria (DNA viruses)
- Kingdom: e.g., Orthornavirae (infecting animals), Plantae (infecting plants)
- Phylum: e.g., Negarnaviricota (negative-sense RNA viruses)
- Class: e.g., Lenarviricetes (retroviruses)
- Order: e.g., Herpesvirales
- Family: e.g., Herpesviridae
- Genus: e.g., Simplexvirus
- Species: e.g., Human alphaherpesvirus 1 (Herpes simplex virus 1)
4. Host-based Classification:
- Animal viruses
- Plant viruses
- Bacteriophages (infecting bacteria)
- Fungal viruses
Other classification systems include:
- Morphological Classification: based on virus shape and structure
The shape can be either helical, polyhedral or complex.
- Serological Classification: based on antigenic properties
- Genomic classification: based on genome sequence and organization
Each classification system provides unique insights into the characteristics and relationships
among viruses. By combining these approaches, scientists can better understand the diverse world
of viruses and develop effective strategies for prevention, diagnosis, and treatment.
