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12: Viruses

Introduction

An infectious agent of small size and simple composition that can multiply only in living cells of animals, plants, or bacteria. The name is from a Latin word meaning “poison.” Viruses consist of genetic material—either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—surrounded by a protective coating of protein, called a capsid, with or without an outer lipid envelope.

The study of viruses is called virology.

Virus classification (Systematic position)

  • A universal system for classifying viruses, and a unified taxonomy, has been established by the International Committee on Taxonomy of Viruses (ICTV) in early 1990s .
  • The ICTV system shares many features with the system used for classifying cellular organisms.
  • Viruses are generally classified by the organisms they infect, animals, plants, or bacteria.
  • There are several differences however; the classification of cellular organisms starts with the Kingdom, while viruses start with Order.

  • The names of like all taxonomic groups - orders, families, subfamilies, genera - are written in italics with the first letter capitalised. Species names are italicised and have the first letter of the first word capitalized,but virus names are not .
  • The names of orders must be single word end with the suffix -virales.
  • A family name must be a single word end with the suffix - viridae
  • A Sub-family name must be a single word end with the suffix - virinae.
  • A genus name must be a single word ending in ...virus.
  • Virus and virus taxon nomenclature are not based on proposed International Code of Bionomenclature (BioCode).

Currently (2008), 5 orders, 84 families and 2,083 species of virus have been defined and many families have not yet been classified into orders. 5orders are Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, Picornavirales.

Today, the primary criteria used to differentiate virus orders, families, and genera are as follows:

  • The type and organization of the viral genome
  • the strategy of viral replication
  • the structure of the virion

Classification by genome type :- seven groups are:-

DNA viruses:-

DNA and RNA Reverse Transcribing viruses:-

  1. Group I - dsDNA viruses (double stranded DNA)such as the herpes virus and the chickenpox virus.
  2. Group II - ssDNA viruses (single stranded DNA)viruses such as the parvo virus.

RNA viruses:-

  1. Group III, - dsRNA viruses (double stranded RNA)
  2. Group IV, - (+)ssRNA viruses (positive single stranded RNA or mRNA like) such as the Sars virus, the yellow fever virus and many other well known viruses
  3. Group V - (-)ssRNA viruses (negative single-stranded RNA) such as the measles virus, the mumps virus and the rabies virus.

DNA and RNA Reverse Transcribing viruses:-

  1. Group VI - ssRNA-RT viruses (single stranded RNA)such as HIV
  2. Group VII - dsDNA-RT viruses (double stranded DNA) such as the hepatitis B virus.

The Group VI viruses use the enzyme to reverse-transcribe their RNA into DNA and then insert the transcribed DNA into the host organism's DNA, where it is replicated whenever a cell divides. The Group VII viruses transcribe their DNA into an RNA form, then transcribe the RNA back into DNA to be inserted into the host's DNA and replicated.

Discovery of viruses

  • In 1892 Russian scientist Dmitry I. Ivanovsky first discovered Tobacco mosaic virus - the virus pathogenic on higher plants.During studying mosiac tobacco disease, he found that the agent causing the disease was small enough for pass though ceramic filter that are small enough to trap all bacteria.
  • The Dutch scientist Martinus W. Beijerinck (1898 ) first surmised that the virus under study was a new kind of infectious agent which was filterable.The infectious agent could diffuse through agar agar; hence he concluded that it must be fluid in nature.Which he designated contagium vivum fluidum,meaning that it was a live, reproducing organism that differed from other organisms.
  • Loeffler and Frosch (1898) discovered first animal-pathogenic virus found that foot and mouth disease of cattle also was caused by a filterable agent-virus.
Important discoveries in Virology after 1900
Important discovery Name of scientists and years of discovery
Bacteriophages, or viruses that infect bacteria or eaters of bacteria. Frederick Twort (1915) and Felix D'Hérelle (1917)were first to describe. (
First time isolated a virus. (1933) M. Schlesinger (1933)
Isolate TMV (tobacco mosaic virus) in crystalline form .Crystals were made up of proteins. W. M. Stanley (1935).
Presence of contained RNA in addition to protein in TMV crystals . Bawden and Pirie (1938).
Mechanism of replication in bacteriophages S. Luria, M.Delbruck and Lwoff(1942-48).
First successful cultivation of a virus (polio virus) in tissue culture American scientists John Enders, Thomas Weller, and Frederick Robbins (1949)
Proteins are non-infective and nucleic acids are infective parts of a bacteriophage. A. Hershey and M. Chase(1952)
Vaccination against polio J. Salk and A. Sabine(1957)
Ultrastructure of TMV R. Franklin, A. klug and K.C. Holmes (1955-57)
Discovery of bacteriophage with single-stranded DNA R. L. Sinsheimer (1959)
Viruses attacking cyanobacteria i.e., blue green algae- Cyanophages R. S. Schafferman and M. E. Morris (1963)
RNA-directed DNA synthesis (Reverse transcriptase) H. Temin and D. Baltimore(1964-70)
Unified system of classification of virus A. Lwoff, R.W. Home and P. Toumier (1960)
Attempts at Artificial synthesis of virus A. Komberg et al. (1967-72)
Virus caused cancer in primates Schidolovski and R. Ahmad 1973
AIDS virus Momtagnier et. al. (1983); Robert Gallo et. al.(1984)

Size of viruses

  • Usually, the size of viruses ranges from 20-300(or 350 nm).The smallest virus is Coliphage F2 measuring about 2 nm.
  • The longest known plant virus is Citus Tristeza virus - rod shapes measuring 2000 X 12 nm.
  • The smallest plant virus is satellite tobacco necrosis virus measuring 17 nm which can replicate in the host cell only if Tobbacco necrosis virus is also present.

Shape of viruses:-

There are mainly two types of shapes found amongst viruses: rods, or filaments, and spheres. The rod shape is due to the linear array of the nucleic acid and the protein subunits making up the capsid. The sphere shape is actually a 20-sided polygon (icosahedron).

  • Filamentous (tubular); e.g., tobacco mosaic virus
  • Polyhedral (roughly spherical); e.g., adenovirus (causes respiratory infections, different than rhinovirus which causes colds)
  • Combined (polyhedral head attached to a filamentous tail); e.g., E. coli bacteriophage T4.

General structure of a virus

Viruses occupy a special taxonomic position: they are not plants, animals, or prokaryotic bacteria (single-cell organisms without defined nuclei).Viruses can’t be grown in the absence of the host cell: obligate intracellular parasites. Although they may seem like living organisms because of their reproductive abilities, viruses are not a living organisms .Viruses are too small to be seen under the light microscope (~65 nm).

Structure

  • All viruses have a very simple nucleoproteinaceous structure -which consist of acentral core of genetic material either DNA or RNA (but not both).
  • The core is surrounded and protected by a protein coat (the capsid).
  • Some viruses are also enclosed by an envelope of fat and protein molecules.
  • In its infective form, a complete virus particle that consist of DNA or RNA molecule enclosed in a coat of protein is called a virion.
  • Each virion contains at least one unique protein synthesized by specific genes in its nucleic acid.
  • Viroids (meaning "viruslike") are disease-causing organisms that contain only nucleic acid and have no structural proteins.
  • Other viruslike particles called prions are composed primarily of a protein tightly integrated with a small nucleic acid molecule.

The viral genome or Nucleic Acid: -

  • The viral genome (nucleic acid ) of each virus contains all genetic information for the synthesis of all proteins.
  • In almost all free-living organisms, the genetic information is in the form of double-stranded DNA arranged as a spiral lattice joined at the bases along the length of the molecule (a double helix).
  • Viruses contain either DNA or RNA -this feature differentiates viruses from all cellular forms of life which contain both DNA and RNA types of nucleic acid in each cell.
  • Majority of animal viruses have double stranded DNA(dsDNA), rarely single or double stranded RNA (dsRNA)as genetic material.
  • The structure of the nucleic acid in a virion may be either linear or circular.
  • The genetic information of viruses is either encoded by single-stranded RNA (most plant viruses), double-stranded RNA (wound tumor viruses), single-stranded DNA (gemini-viruses) or double-stranded DNA (cauliflower mosaic-virus: CaMV).
  • All double-stranded DNA viruses consist of a single large molecule.
  • Most of double-stranded RNA(dsRNA) viruses have segmented genomes, with each segment usually representing a single gene that encodes the information for synthesizing a single protein.
  • In most of viruses, the genomic RNA is known as a positive strand because the genomic RNA acts as mRNA for direct synthesis (translation) of viral protein.
  • Several large families of animal viruses, and one family Rhabdoviridae which includes both plant and animal viruses contains genomic single-stranded RNA, termed a negative strand.
  • which is complementary to mRNA.
  • All of these negative-strand RNA viruses have an enzyme, called an RNA-dependent RNA polymerase (transcriptase).
  • Which must first catalyze the synthesis of complementary mRNA from the virion genomic RNA before viral protein synthesis can occur.

Capsid (Protein coat)

  • The capsid surrounds the nucleic acid and is composed of identical repeating protein subunits known as capsomeres.It is called the nucleocapsid.
  • Capsomeres form highly symmetrical structure which can be crystallised.Tobacco mosaic virus, which was crystallized by Wendell Stanley in 1935. This makes possible their x-ray crystallography and electron microscopy.
  • There are two major classes of viruses based on the protein capsid:
    1. Helical:- In some viruses like TMV, the capsid formes a helical coil around a single (or segmented) linear nucleic acid with two free ends is essentially completely extended or somewhat coiled (a helix)
    2. Isometric:-A number of virses like adenovirus, polio virus, tomato bushy stunt virus are nearly spherical (isometric) Those in which the nucleic acid, which may or may not be a covalently closed circle, is wound tightly into a condensed configuration, like a ball of yarn.
  • The number of capsomeres varies greatly among different viruses.
  • Two virus groups have more complex structure :-
  1. Poxviruses are large brick-shaped (or ovoid)viruses.
  2. In many bacteriophages, capsid is composed of a polyhedral head connected to a helical tail (Tadpole-shaped). Such combined structure is called binal.

Function of Capsid:- The capsid has three functions:-

  1. It protects the nucleic acid from digestion by enzymes.
  2. Contains special sites on its surface that allow the virion to attach to a host cell.
  3. Provides proteins that enable the virion to penetrate the host cell membrane and, in some cases, to inject the infectious nucleic acid into the cell's cytoplasm.

Under the right conditions, viral RNA in a liquid suspension of protein molecules will self-assemble a capsid to become a functional and infectious virus.

Envelope:-

  • Some viruses have lipoprotein (called peplomers) envelope surrounding the nucleocapsid.
  • The envelope is composed of two lipid layers interspersed with protein molecules (lipoprotein bilayer) and may contain material from the membrane of a host cell as well as that of viral origin.
  • The virus obtains the lipid molecules from the host cell membrane during the viral budding process.
  • However, the virus replaces the proteins in the host cell membrane with its own proteins, creating a hybrid structure of host cell-derived lipids and virus-derived proteins.
  • Some types of virus have a glycoprotein envelope surrounding the nucleocapsid.
  • Many viruses also develop spikes made of glycoprotein on their envelopes that help them to attach to specific cell surfaces.
  • Non-enveloped viruses are known as naked.
  • Nearly all plant viruses and phages are naked.

Tobacco mosaic virus (TMV)

  • Tobacco mosaic virus is an RNA virus.That causes stunted plant growth and mottled, discolored plant leaves, especially in tobacco and other members of the tomato family (Solanceae).
  • TMV is a elongated, rod-shaped virus of 3000 Å long, 180 Å in diameter. Proteins and RNA are interwined to form helical, grooved cylindrical rods of uniform diameter with hollow channel (40 Å wide).
  • The walls of the cylinder are 70Å thick
  • A single TMV particle is composed of 2,130 copies of the coat protein (CP) that envelope the RNA molecule of about 6,400 nucleotides .
  • Its capsid is made from a single protein that assembles itself around the viral RNA in a helical structure (16.3 proteins per helix turn) and 130 turns in complete virus capsid.
  • Each capsomere has a molecular weight of 17,400 and is formed by condensation of 158 aminoacids.
  • This single-stranded RNA encodes four genes: two replicase-associated proteins that are directly translated from the TMV RNA, and the movement protein and a coat protein that are translated from subgenomic RNAs.

Bacteriophage (The Virus that Infect Bacteria)

  • Bacteriophage (phage) are obligate intracellular parasites that infect bacteria.
  • Almost every group of bacteria is subject to infection by one or more viruses or "bacteriophages" as they are known "phage" for short, from Gr. "phagein" meaning "to eat" or "to nibble".
  • Bacteriophages attacking E.coli are called Coliphages and are designated T type.
  • These were numbered T1, T2, T3.........T17 by Max Delbruck (1938)
  • T-even phages are T2, T4, and T6 and T3, T5,.. are called T-odd phages.

Morphological 7 types of bacteiophages

 

Type A Type B Type C Type D Type E Type F Type G
Hexagonal head, rigid tail with a contractile sheath and tail fibres. Hexagonal head, flexible tail contractile sheath absent. Tail fibres present or absent Hexagonal head, Tail shorter than head, contractile sheath absent. Tail fibres present or absent Only head made up of large cashmeres. No tail. Only head made up of small cashmeres no tail. Filamentous Pleomorphic, no detectable capsid, envelop contains lipid.
ds DNA ds DNA ds DNA. ss DNA ss DNA ss DNA ds DNA
e.g. coliphages like T2, T4, T6 (T-even) e.g. -coliphages like T1 and T5. e.g. coliphages T3 and T7. e.g. coliphages f x 174, S 13. e.g. coliphages f2, MS2. e.g. coliphages fd, fl. e.g. MV-L2.

Size:- T4 is among the largest phages; it is approximately 200 nm long and 80-100 nm wide. Other phages are smaller. Most phages range in size from 24-200 nm in length.

Structure: - Bacteriophage are of different shapes. The basic structural features of bacteriophages T4:-

  • Head or Capsid - All phages contain a head structure which can vary in size and shape. Some are icosahedral (20 sides) others are filamentous. The head or capsid is composed of nucleic acid molecule (usually DNA) coiled within a protein coat or capsid (made of capsomeres).

 

  • Tail - Many but not all phages have tails attached to the phage head. The tail is a hollow tube through which the nucleic acid passes during infection. The tail includes a core, a tail sheath, base plate, tail pins, and tail fibers, all of which are composed of different proteins. In the more complex phages like T4 the tail is surrounded by a contractile sheath which contracts during infection of the bacterium. At the end of the tail phages T4 have a base plate and one or more tail fibers attached to it. The base plate and tail fibers are involved in the binding of the phage to the bacterial cell. Not all phages have base plates and tail fibers.

Replication of viruses

Five steps are typical in viral reproduction:-

  • Absorption (or Attachment)- The virus attaches to receptors on the host cell wall.
  • Penetration- The nucleic acid of the virus moves through the plasma membrane and into the cytoplasm of the host cell.
  • Replication- The viral genome contains all the information necessary to produce new viruses. Once inside, the virus induces the host cell to synthesize the necessary components for its replication.
  • Assembly- The newly synthesized viral components are assembled into new viruses.
  • Release- Assembled viruses are released from the cell.

Reproductive cycle of Bacteriophages

  • Bacteriophages can undergo two alternative life cycles: -
    1. Virulent or Lytic infections:- Lytic infection ends in lysis (the virus destroys the host cell) and death of host cell. In E. coli, lytic infections are caused by a group seven phages known as the T-phages.
    2. Lysogenic infections.:-The phage reproduces without killing its host.

Lytic cycle of a bacterial virus, e.g. bacteriophage T4.

  1. Absorption (or Attachment):- The tail fibers of Phage or by some analogous structure on those phages that lack tail fibers attach to specific receptors on the bacterial cell. The host specificity of the phage (i.e. the bacteria that it is able to infect) is usually determined by the type of tail fibers that a phage has. Tail fibres bend to anchor the pins and base plate of the cell surface
  2. Penetration:- Tail sheath contracts and the hollow tail fiber is pushed through the bacterial envelope . Phages that don't have contractile sheaths use other mechanisms to get the phage particle through the bacterial envelope. Some phages have enzymes that digest various components of the bacterial envelope.

  1. Replication :-The phage nucleic acid takes over the host biosynthetic machinery and phage specified m-RNA's and proteins are made.Phage utilizes the host cell’s nucleotides to make copies of its genetic material and the cell’s amino acids to make proteins. Early m-RNA's code for early proteins which are needed for phage DNA synthesis and for shutting off host DNA, RNA and protein biosynthesis.After phage DNA is made late m-RNA's and late proteins are made.
  2. Assembly:-Finally, the nucleic acid and protein components are synthesized, the virus particle is assembled with the protein capsid surrounding the phage DNA. Enzyme lysosyzme is synthesised.
  3. Release:-Bacterial cell wall is weakened by lysozyme action leading to lysis of bacteria and the release of the mature viruses, which spread to nearby cells, infect them, and complete the cycle.The life cycle of a T-phage takes about 25-35 minutes to complete.

Eclipse period:-The time between infection and assembly of new phages is called eclipse period.

latent period- The time between infection and release of viral particles by destruction of host cells is called latent period.

Lysogenic cycle bacteriophage

The first two steps of this process are exactly the same as the first two steps of the lytic cycle (attachment and penetration). Those steps are then followed by integration and replication. In the case of some bacterial viruses, the phage DNA becomes incorporated into the host bacterial DNA and is referred to as a prophage or temperate phage.

When the bacterial DNA replicates, the prophage also replicates. Bacterial cells carrying prophages are called lysogenic cells. Certain external conditions, such as ultraviolet light and x-rays, can cause temperate viruses to revert to a lytic cycle and then destroy their host cell.

Name of Some viral disease of plants

Name of Disease Causal Virus Name of Disease Causal Virus
Tobacco mosaic. Tobacco Mosaic virus Abutilon mosaic Abutilon mosaic virus
Papaya mosaic Papaya mosaic virus Tomato leaf curl Tobacco leaf curl virus
Potato leaf roll Potato leaf roll virus Sugarcane mosaic Sugarcane(or Saccharum)Virus I