Virus

A virus is a Submicroscopic Organism that replicates only inside the
living cells of an organism. Viruses can infect all types of life forms, from
animals and plants to microorganisms, including bacteria and archaea. The
study of viruses is known as virology.
When infected, a host cell is forced to rapidly produce thousands of
identical copies of the original virus. When not inside an infected cell or in
the process of infecting a cell, viruses exist in the form of independent
particles or virions.

It consists of:
(i) The genetic material, i.e. long molecules of DNA or RNA that encode
the structure of the proteins by which the virus acts.
(ii) A protein coat, the capsid, which surrounds and protects the genetic
material.

(iii) An outside envelope of lipids. The shapes of these virus particles range
from simple helical and icosahedral forms to more complex structures.
Most virus species have virions too small to be seen with an optical
microscope as they are one hundredth the size of most bacteria.

Microbiology

Life properties:

They have been described as “organisms at the edge of life”, since they
resemble organisms in that they possess genes, evolve by natural
selection, and reproduce by creating multiple copies of themselves through
self-assembly.
Although they have genes, they do not have a cellular structure, which is
often seen as the basic unit of life. Viruses do not have their
own metabolism, and require a host cell to make new products.
They therefore cannot naturally reproduce outside a host cell although
bacterial species such as rickettsia and chlamydia are considered living
organisms despite the same limitation.
Accepted forms of life use cell division to reproduce, whereas viruses
spontaneously assemble within cells. They differ from autonomous
growth of crystals as they inherit genetic mutations while being subject to
natural selection.

Structure:

Viruses display a wide diversity of shapes and sizes, called “morphologies”.
In general, viruses are much smaller than bacteria. Most viruses that have
been studied have a diameter between 20 and 300 nanometers.
A complete virus particle, known as a virion, consists of nucleic acid
surrounded by a protective coat of protein called a capsid.

These are formed from identical protein subunits called
capsomeres. Viruses can have a lipid “envelope” derived from the host cell
membrane.
The capsid is made from proteins encoded by the viral genome and its
shape serves as the basis for morphological distinction.
Virally-coded protein subunits will self-assemble to form a capsid, in
general requiring the presence of the virus genome. Complex viruses code
for proteins that assist in the construction of their capsid.
Proteins associated with nucleic acid are known as nucleoproteins, and the
association of viral capsid proteins with viral nucleic acid is called a
nucleocapsid.

Helical:

These viruses are composed of a single type of capsomere stacked around
a central axis to form a helical structure, which may have a central cavity,
or tube.
This arrangement results in rod-shaped or filamentous virions which can be
short and highly rigid, or long and very flexible. The genetic material
(typically single-stranded RNA, but ssDNA in some cases) is bound into the
protein helix by interactions between the negatively charged nucleic acid
and positive charges on the protein.
Overall, the length of a helical capsid is related to the length of the nucleic
acid contained within it, and the diameter is dependent on the size and
arrangement of capsomeres. The well-studied tobacco mosaic virus is an
example of a helical virus.

Icosahedral

Most animal viruses are icosahedral or near-spherical with chiral
icosahedral symmetry. A regular icosahedron is the optimum way of
forming a closed shell from identical sub-units.
The minimum number of identical capsomeres required for each triangular
face is 3, which gives 60 for the icosahedron. Many viruses, such as
rotavirus, have more than 60 capsomers and appear spherical but they
retain this symmetry.
To achieve this, the capsomeres at the apices are surrounded by five other
capsomeres and are called pentons. Capsomeres on the triangular faces
are surrounded by six others and are called hexons. Hexons are in
essence flat and pentons, which form the 12 vertices, are curved.

Envelope:

Some species of virus envelop themselves in a modified form of one of
the cell membranes, either the outer membrane surrounding an infected
host cell or internal membranes such as nuclear membrane or endoplasmic
reticulum, thus gaining an outer lipid bilayer known as a viral envelope.

This membrane is studded with proteins coded for by the viral genome and
host genome; the lipid membrane itself and any carbohydrates present
originate entirely from the host.
The influenza virus and HIV use this strategy. Most enveloped viruses are
dependent on the envelope for their infectivity.

Complex:

These viruses possess a capsid that is neither purely helical nor purely
icosahedral, and that may possess extra structures such as protein tails or
a complex outer wall.
Some bacteriophages, such as Enterobacteria phage T4, have a complex
structure consisting of an icosahedral head bound to a helical tail, which
may have a hexagonal base plate with protruding protein tail fibres.
This tail structure acts like a molecular syringe, attaching to the bacterial
host and then injecting the viral genome into the cell.
The poxviruses are large, complex viruses that have an unusual
morphology. The viral genome is associated with proteins within a central
disc structure known as a nucleoid.

The nucleoid is surrounded by a membrane and two lateral bodies of
unknown function. The virus has an outer envelope with a thick layer of
protein studded over its surface. The whole virion is slightly pleomorphic,
ranging from ovoid to brick-shaped.

Classification:

Classification seeks to describe the diversity of viruses by naming and
grouping them on the basis of similarities. In 1962, Andre Lwoff,Robert
Horne, and Paul Toumier were the first to develop a means of virus
classification, based on the Linnaean hierarchical system.
This system based classification on phylum, class order, family, genus, and
species. Viruses were grouped according to their shared properties and the
type of nucleic acid forming their genomes.
In 1966, the international committee on Taxonomy of Viruses (ICTV) was
formed. The system proposed by Lwoff, Horne and Tournier was never fully
accepted by the ICTV because small genome size viruses and their high
rate of mutation make it difficult to determine their ancestry beyond order.

ICTV classification:

The International Committee on Taxonomy of Viruses (ICTV) developed
the current classification system and wrote guidelines that put a greater
weight on certain virus properties to maintain family uniformity.

A unified taxonomy (a universal system for classifying viruses) has been
established. Only a small part of the total diversity of viruses has been
studied. As of 2019, 4 realms, 9 kingdoms, 16 phyla, 2 subphyla, 36
classes, 55 orders, 8 suborders,168 families,103 subfamilies,1,421 genera,
68 subgenera, and 6,589 species of viruses have been defined by the
ICTV.
The general taxonomic structure of taxon ranges and the suffixes used in
taxonomic names are shown hereafter. As of 2019, the ranks of subrealm,
subkingdom, and subclass are unused, whereas all other ranks are in use.

Realm (-viria)

Subrealm (-vira)
Kingdom (-virae)
Subkingdom (-virites)
Phylum (-viricota)
Subphylum (-viricotina)
Class (-viricetes)
Subclass (-viricetidae)
Order (-virales)
Suborder (-virineae)
Family (-viridae)
Subfamily (-virinae)

Baltimore classification:

The Baltimore Classification of viruses is based on the method of
viral mRNA synthesis
The Nobel Prize-winning biologist David Baltimore devised the
Baltimore classification system. The ICTV classification system is used in
conjunction with the Baltimore classification system in modern virus
classification.
The Baltimore classification of viruses is based on the mechanism
of mRNA production. Viruses must generate mRNAs from their genomes to
produce proteins and replicate themselves, but different mechanisms are
used to achieve this in each virus family.
Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA
or DNA, and may or may not use reverse transcriptase (RT). In addition,
ssRNA viruses may be either sense (+) or antisense (−). This classification
places viruses into seven groups:

I:ds DNA:Viruses (e.g. Adenoviruses, Herpesviruses, Parvoviruses)
II:ssDNA Viruses(+ strand or ―sense‖) DNA (e.g. Parvoviruses )
III: dsRNA Viruses (e.g.Reoviruses)
IV:(+)ssRNA viruses(+ strand or sense) RNA (e.g.Coronaviruses,
Picornaviruses,Togaviruses) .
V:ssRNAViruses(strandorantisense)RNA(e.g.Orthomyxoviruses,Rhabdovir
uses)
VI: ssRNA-RT Viruses (+ strand or sense) RNA with DNA intermediate in
life-cycle (e.g. Retroviruses)
VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g.
Hepadnaviruses)

VZV is in Group I of the Baltimore Classification because it is a dsDNA
virus that does not use reverse transcriptase.

Epidemiology:

Viral epidemiology is the branch of medical science that deals with the
transmission and control of virus infections in humans. Transmission of
viruses can be vertical, which means from mother to child, or horizontal,
which means from person to person.
Vertical transmission include hepatitis B virus and HIV, where the baby is
born already infected with the virus.
Horizontal transmission is the most common mechanism of spread of
viruses in populations. Transmission can occur when: body fluids are
exchanged during sexual activity, e.g., HIV.
Blood is exchanged by contaminated transfusion or needle sharing, e.g.,
hepatitis C.

Exchange of saliva by mouth, e.g., Epstein–Barr virus;
Aerosols containing virions are inhaled, e.g., influenza virus; and insect
vectors such as mosquitoes penetrate the skin of a host, e.g., dengue.
The rate or speed of transmission of viral infections depends on factors that
include population density, the number of susceptible individuals, (i.e.,
those not immune), the quality of healthcare and the weather.

Epidemiology is used to break the chain of infection in populations during
outbreaks of viral diseases.
Control measures are used that are based on knowledge of how the virus
is transmitted. It is important to find the source or sources of the outbreak
and to identify the virus.
Once the virus has been identified, the chain of transmission can
sometimes be broken by vaccines. When vaccines are not available,
sanitation and disinfection can be effective.
Often, infected people are isolated from the rest of the community, and
those that have been exposed to the virus are placed in quarantine.

To control the outbreak of foot-and-mouth disease in cattle in Britain in
2001, thousands of cattle were slaughtered. Most viral infections of humans
and other animals have incubation periods during which the infection
causes no signs or symptoms.
Incubation periods for viral diseases range from a few days to weeks, but
are known for most infections.
Somewhat overlapping, but mainly following the incubation period, there is
a period of communicability—a time when an infected individual or animal
is contagious and can infect another person or animal.

When outbreaks cause an unusually high proportion of cases in a
population, community, or region, they are called epidemics. If outbreaks
spread worldwide, they are called pandemics.