Classification of Viruses

Basis of Classification

The following properties have been used as a basis for the classification of viruses:

(1) Virion morphology, including size, shape, type of symmetry, presence or absence of peplomers, and presence or absence of
membranes.

(2) Virus genome properties, including type of nucleic acid (DNA or RNA), size of genome in kilobases (kb) , strandedness
(single or double), whether linear or circular, sense (positive, negative), segments (number, size), nucleotide sequence and G + C
content.

(3) Physicochemical properties of the virion, including molecular mass, pH stability, thermal stability, and susceptibility to
physical and chemical agents, especially ether and detergents.

(4) Virus protein properties, including number, size, and functional activities of structural and nonstructural proteins, amino acid
sequence, and modifications (glycosylation, phosphorylation).

(5) Genome organization and replication, including gene order, number and position of open reading frames, strategy of
replication (patterns of transcription, translation), and cellular sites (accumulation of proteins, virion assembly, virion release).

(6) Antigenic properties.

(7) Biologic properties, including natural host range, mode of transmission, vector relationships, pathogenicity, tissue tropisms,
and pathology.

LHT System of Virus Classification

The LHT System of Virus Classification is based on chemical and physical characters like nucleic acid (DNA or RNA),
Symmetry (Helical or Icosahedral or Complex), presence of envelope, diameter of capsid, number of capsomers. This
classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of
Microbiological Societies (1962).

:It is as follows

 Phylum Vira (divided into 2 subphyla)

 Subphylum Deoxyvira (DNA viruses)

 Class Deoxybinala (dual symmetry)

 Order Urovirales

 Family Phagoviridae

 Class Deoxyhelica (Helical symmetry)

 Order Chitovirales

 Family Poxviridae

 Class Deoxycubica (cubical symmetry)

  Order Peplovirales

 Family Herpesviridae (162 capsomeres)

 Order Haplovirales (no envelope)

 Family Iridoviridae (812 capsomeres)

 Family Adenoviridae (252 capsomeres)
 Family Papiloviridae (72 capsomeres)
 Family Paroviridae (32 capsomeres)
 Family Microviridae (12 capsomeres)

 Subphylum Ribovira (RNA viruses)

 Class Ribocubica

 Order Togovirales

 Family Arboviridae

 Order Lymovirales

 Family Napoviridae
 Family Reoviridae

 Class Ribohelica

 Order Sagovirales

 Family Stomataviridae
 Family Paramyxoviridae
 Family Myxoviridae

 Order Rhabdovirales

 Suborder Flexiviridales

 Family Mesoviridae
 Family Peptoviridae

 Suborder Rigidovirales

 Family Pachyviridae
 Family Protoviridae
 Family Polichoviridae

STRUCTURE OF HIV

The complete sequence of the HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution.
[6]
The HIV genome encodes a small number of viral proteins, invariably establishing cooperative associations among HIV
proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. [7]

HIV is different in structure from other retroviruses. The HIV virion is ~100 nm in diameter. Its innermost region consists of a
cone-shaped core that includes two copies of the (positive sense) ssRNA genome, the enzymes REVERSE TRANSCRIPTASE,
integrase and protease, some minor proteins, and the major core protein. [8] The genome of human immunodeficiency virus (HIV)
encodes 16 viral proteins playing essential roles during the HIV life cycle.

HIV-1 is composed of two copies of noncovalently linked, unspliced, positive-sense single-stranded RNA enclosed by a conical
capsid composed of the viral protein p24, typical of lentiviruses.[10][11] The RNA component is 9749 nucleotides long[12][13] and
bears a 5’ cap (Gppp), a 3’ poly(A) tail, and many open reading frames (ORFs).[14] Viral structural proteins are encoded by long
ORFs, whereas smaller ORFs encode regulators of the viral life cycle: attachment, membrane fusion, replication, and assembly.

The single-strand RNA is tightly bound to p7 nucleocapsid proteins, late assembly protein p6, and enzymes essential to the
development of the virion, such as reverse transcriptase and integrase. Lysine tRNA is the primer of the magnesium-dependent
reverse transcriptase.[10] The nucleocapsid associates with the genomic RNA (one molecule per hexamer) and protects the RNA
from digestion by nucleases. Also enclosed within the virion particle are Vif, Vpr, Nef, and viral protease. A matrix composed of
an association of the viral protein p17 surrounds the capsid, ensuring the integrity of the virion particle. This is in turn surrounded
by an envelope of host-cell origin. The envelope is formed when the capsid buds from the host cell, taking some of the host-cell
membrane with it. The envelope includes the glycoproteins gp120 and gp41, which are responsible for binding to and entering the
host cell.

As the only proteins on the surface of the virus, the envelope glycoproteins (gp120 and gp41) are the major targets for HIV
vaccine efforts.[15] Over half of the mass of the trimeric envelope spike is N-linked glycans. The density is high as the glycans
shield underlying viral protein from neutralisation by antibodies. This is one of the most densely glycosylated molecules known
and the density is sufficiently high to prevent the normal maturation process of glycans during biogenesis in the endoplasmic and
Golgi apparatus.[16][17] The majority of the glycans are therefore stalled as immature 'high-mannose' glycans not normally present
on secreted or cell surface human glycoproteins. [18] The unusual processing and high density means that almost all broadly
neutralising antibodies that have so far been identified (from a subset of patients that have been infected for many months to
years) bind to or, are adapted to cope with, these envelope glycans.[19]

The molecular structure of the viral spike has now been determined by X-ray crystallography [20] and cryo-electron microscopy.
[21]
These advances in structural biology were made possible due to the development of stable recombinant forms of the viral spike
by the introduction of an intersubunit disulphide bond and an isoleucine to proline mutation in gp41. [22] The so-called SOSIP
trimers not only reproduce the antigenic properties of the native viral spike but also display the same degree of immature glycans
as presented on the native virus.[23] Recombinant trimeric viral spikes are promising vaccine candidates as they display less non-
neutralising epitopes than recombinant monomeric gp120 which act to suppress the immune response to target epitopes

LIST OF PLANT VIRUSES

A recent MicrobiologyBytes post reported a slightly older Molecular Plant Pathology paper as giving a “Top Ten” ranking for
plant viruses – at least, those of “…perceived importance, scientifically or economically, from the views of the contributors to the
journal”. Specifically, the article authors “…survey[ed] all plant virologists with an association with Molecular Plant
Pathology and ask[ed] them to nominate which plant viruses they would place in a ‘Top 10’ based on scientific/economic
importance”. They got “…more than 250 votes from the international community”, and came up with the following list:

(1) Tobacco mosaic virus (TMV),

(2) Tomato spotted wilt virus (TSWV),
(3) Tomato yellow leaf curl virus (TYLCV),
(4) Cucumber mosaic virus (CMV),
(5) Potato virus Y (PVY),
(6) Cauliflower mosaic virus (CaMV),
(7) African cassava mosaic virus (ACMV),
(8) Plum pox virus (PPV),
(9) Brome mosaic virus (BMV) and
(10) Potato virus X (PVX),
with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus (CTV), Barley yellow dwarf
virus (BYDV), Potato leafroll virus (PLRV) and Tomato bushy stunt virus (TBSV).

ANIMAL VIRUSES

Here is a list of viruses that are found in animals: 1. Papovaviruses 2. Simian Virus-40 3. Adenoviruses 4. Herpesviruses 5. Pox
Viruses 6. Picornavirus 7. Togaviruses 8. Rabies Viruses 9. Influenza Viruses 10. Reoviruses.

1. Papovaviruses:

Papovaviruses are one of the four important dsDNA viruses (e.g. papovaviruses, adenoviruses, herpes viruses and pox viruses)
which produce tumour in many animals.

2. Simian Virus-40 (SV40):

S V40 is an oncogenic virus. It is naked and icosahedral in morphology with a diameter of 45 nm. (Fig. 17.4). Capsid consists of
72 capsomers. SV40 is similar to polyoma virus in size and structure. Polyoma is associated with tumour in mice.

3. Adenoviruses:

Adenoviruses were first isolated in human adenoids (tonsils) from which its name is derived. The adenoviruses are common
pathogens of humans and animals. More than 100 serologically distinct types of adenovirus have been identified including 49
types that infect humans. Moreover, several strains have been the subject of intensive research and are used as tools in mammalian
molecular biology.

Enzymes

Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate chemical reactions. The molecules upon which
enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. Almost
all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. [1]:8.1 Metabolic
pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field
of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry
out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. [2][3]

Enzymes are known to catalyze more than 5,000 biochemical reaction types. [4] Most enzymes are proteins, although a few
are catalytic RNA molecules. The latter are called ribozymes. Enzymes' specificity comes from their unique three-dimensional
structures.

Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Some enzymes can make their conversion
of substrate to product occur many millions of times faster. An extreme example isorotidine 5'-phosphate decarboxylase, which
allows a reaction that would otherwise take millions of years to occur in milliseconds. [5][6] Chemically, enzymes are like any
catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most
other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that
decrease enzyme activity, andactivators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme
inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH.

Some enzymes are used commercially, for example, in the synthesis of antibiotics. Some household products use enzymes to
speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and
enzymes inmeat tenderizer break down proteins into smaller molecules, making the meat easier to chew.

Phosphatidic acids

Phosphatidic acids: those lipids which on hydrolysis give rise to one molecule of glycerol and phosphoric acid and two molecules
of fatty acids.

Structure
General chemical structure of phosphatidic acids
Phosphatidic acid consists of a glycerol backbone, with, in general, a saturated fatty acid bonded to carbon-1, an unsaturated fatty
acidbonded to carbon-2, and a phosphate group bonded to carbon-3.[1][2]
Formation and degradation[edit]
Besides de novo synthesis, PA can be formed in three ways:

 By phospholipase D (PLD), via the hydrolysis of the P-O bond of phosphatidylcholine (PC) to produce PA and choline.[3]
 By the phosphorylation of diacylglycerol (DAG) by DAG kinase (DAGK)

 By the acylation of lysophosphatidic acid by lysoPA-acyltransferase (LPAAT); this is the most common pathway.[4]

PA is degraded by conversion into DAG by lipid phosphate phosphohydrolases (LPPs)[5][6] or into lyso-PA by phospholipase A
(PLA).

The role of PA in the cell can be divided into three categories:

 PA is the precursor for the biosynthesis of many other lipids.

 The physical properties of PA influence membrane curvature.

 PA acts as a signaling lipid, recruiting cytosolic proteins to appropriate membranes (e.g., sphingosine kinase 1[7]).

 PA plays very important role in Phototransduction in Drosophila[8]

The first three roles are not mutually exclusive. For example, PA may be involved in vesicle formation by promoting membrane
curvature and by recruiting the proteins to carry out the much more energetically unfavourable task of neck formation and
pinching.

Cholesterol

Cholesterol (from the Ancient Greek chole- (bile) and stereos (solid), followed by the chemical suffix -ol for an alcohol) is
an organicmolecule. It is a sterol (or modified steroid),[4] a type of lipid molecule, and is biosynthesized by all animal cells,
because it is an essential structural component of all animal cell membranes and is essential to maintain both membrane structural
integrity andfluidity. Cholesterol allows animal cells to function without a cell wall (which in other species protects membrane
integrity and cell viability); this allows animal cells to change shape rapidly.

In addition to its importance for animal cell structure, cholesterol also serves as a precursor for the biosynthesis of steroid
hormones,bile acid[5] and vitamin D. Cholesterol is the principal sterol synthesized by all animals. In vertebrates, hepatic cells
typically produce the greatest amounts. It is absent among prokaryotes (bacteria and archaea), although there are some exceptions,
such asMycoplasma, which require cholesterol for growth.[6]

François Poulletier de la Salle first identified cholesterol in solid form in gallstones in 1769. However, it was not until 1815 that
chemistMichel Eugène Chevreul named the compound "cholesterine".[