Case 5
Virus
Viruses are noncellular genetic elements that use a living cell for their replication (= obligate
intracellular microbes) and have an extracellular state. Viruses are ultramicroscopic particles
containing nucleic acid (DNA or RNA) surrounded by protein. These proteins can be structural, e.g.
capsid, and non-structural, e.g. enzymes and polymerases. In some cases, the viruses contains lipids,
such as (glyco)proteins, which make up the membrane-like envelope.
• Outside the host cell, the virus particle is also known as a virion. The virion is metabolically
inert and does not grow or carry on respiratory or biosynthetic functions.
• Thus, a virus is alive, a virion is not!
• Viruses vary considerably in size and shape. The smallest viruses are about 0.02 μm (20
nanometres), while the large viruses measure about 0.3 μm (300 nanometres). Smallpox
viruses are among the largest viruses; polioviruses are among the smallest.
• Bacteriophages are viruses that multiply within bacteria. These viruses are among the more
complex viruses. They often have icosahedral heads and helical tails. The virus that attacks and
replicates in Escherichia coli has 20 different proteins in its helical tail and a set of numerous
fibres and “pins.” Bacteriophages contain DNA and are important tools for viral research.
Viruses differ from bacteria. Bacteria are small and single-celled, but they are living organisms that do
not depend on a host cell to reproduce. Due to these differences, bacterial and viral infections are
treated differently. For instance, antibiotics are only helpful against bacteria, not viruses. Viruses are
much smaller than bacteria. The diameter of a typical virus is about 20-300 nm. This is considerably
smaller than a typical E. coli bacterium, which has a diameter of roughly 1000 nm.
,Viral structure
Certain viruses contain ribonucleic
acid (RNA), while other viruses have
deoxyribonucleic acid (DNA). The
nucleic acid portion of the viruses is
known as the genome. The nucleic
acid may be single-stranded or
double-stranded; it may be linear or
a closed-loop, and it may be
continuous or occur in segments.
The genome of the virus is always surrounded by a protein coat known as a capsid, which is a structure
that packages, protects, and transports a virus during transmission of one host to another and from a
host to its target cell. Capsid proteins are always encoded by the virus genome, meaning that it’s the
virus (not the host cell) that provides instructions for making them. Viral Attachment Proteins (VAPs)
are structure on the surface of the capsid, which mediate the interaction of the virus to the target cell.
There are two types of VAPs: (1) Hemagglutinin (HA) and (2) Neuraminidase (NA).
A capsid is formed from a number of individual protein molecules called capsomeres. Capsomeres are
arranged in a precise and highly repetitive pattern around the nucleic acid. A single type of capsomere
or several chemically distinct types may make up the capsid. The combination of genome and capsid
is called the viral nucleocapsid.
A number of kinds of viruses contain envelopes. An envelope is a membrane-like (lipid) structure that
encloses the nucleocapsid and is obtained from a host cell during the replication process. The envelope
contains viral-specified proteins that make it unique. Viruses with envelopes do not provide
instructions for the envelope lipids. Instead, they "borrow" a patch from the host membranes on their
way out of the cell. Envelopes do, however, contain proteins (VAP) that are specified by the virus,
which often help viral particles bind to host cells. Among the envelope, viruses are those of herpes
simplex, chickenpox, and infectious mononucleosis.
, • Naked capsid viruses (Viruses WITHOUT an envelope) are more resistant to extreme
conditions: dryness, ranges of pH, different detergents, and remain infectious for a longer time
on different types of surfaces. Therefore, these types of viruses are transmitted via surfaces
such as keyboards, toilet seat, public transport, and door handles.
• Enveloped viruses (viruses WITH an envelope) are less resistant to the extreme conditions as
mentioned above and thus more susceptible to these conditions. Therefore, these types of
viruses need to be transmitted through bodily fluids, through sexual intercourse, blood
transfusion, sneezing, needles.
The nucleocapsids of viruses are constructed according to certain symmetrical patterns and they come
in many forms, but they often take one of the following shapes (or a variation of these shapes):
• Icosahedral – icosahedral capsids have twenty faces, and are named after the twenty-sided
shape called an icosahedron. E.g. yellow fever, polio, and head colds
• Filamentous – filamentous capsids are named after their linear, thin, thread-like appearance.
They may also be called rod-shaped or helical. E.g. rabies virus
• Head-tail – these capsids are kind of a hybrid between the filamentous and icosahedral shapes.
They basically consist of an icosahedral head attached to a filamentous tail
, Viral classification
Viral classification can be based on (1) the difference in genome (DNA or RNA) and (2) presence or
absence of an envelope.
The larger the genome, the more information (genes) it can carry and the larger the capsid or envelope
structure required to contain the genome. Notably, DNA and RNA viruses always use the same genetic
code as living cells. If they didn’t, they would have no way to reprogram their host cells.
In case of DNA viruses, there is a subdivision in double-stranded and single-stranded DNA, either being
enveloped or naked. In case of RNA viruses, they could be (+)RNA, (-)RNA, (+/-)RNA, or (+)RNA via DNA.
• (+)RNA = RNA virus that has the same form as mRNA
• (-)RNA = RNA virus that is complementary to mRNA
• (+/-)RNA = RNA virus that has double-stranded RNA
• (+)RNA via DNA = RNA virus whose replication goes from RNA to DNA, instead of the other
way around = Retrovirus.
RNA viruses mostly replicate in the cytoplasm, because eukaryotic host cells cannot replicate RNA but
can only transcribe. The RNA viruses, thus, need to carry the enzyme viral RNA polymerase in order to
replicate, except for (+)RNA viruses → because, although they need this RNA polymerase, (+)RNA
viruses are basically mRNA, so they can encode for these RNA-dependent RNA polymerases on their
genome. Once this genome enters the host cell, they can immediately go to the ribosomes and
translate this gene encoding the RNA-dependent RNA polymerase into the active enzymes.
• RNA viruses are also more prone to mutation.
Common features of (+)stranded RNA viruses: they have a positive polarity, so they can act directly
as mRNA, and therefore, they can be directly translated into viral enzymes. This means that naked
genomic RNA is directly infectious, it doesn’t need anything else. Furthermore, positive-stranded RNA
viruses can use host enzymes.
• E.g. (+)RNA: HAV, HCV, HEV (hepatitis A, C, and E virus), and norovirus
Common features of (-)stranded RNA viruses: they are the complementary strand of mRNA, and
therefore, not directly infectious. These (-)stranded RNA viruses need to carry their own RNA-
dependent RNA polymerase in their virion, since we humans do not have this. The location of gene
expression and replication varies for these types of viruses. And so far, all (-)RNA viruses that are known
have an envelope.
