Viruses
* Latin word meaning "Poison".
* Obligate intracellular parasites.
* They only demonstrate characteristics of life while "inside" a host cells like Bacteria, animal or plant cells.
* Outside a host cell, viruses are inert i.e. they do not show any activity.
Definition of viruses
"Viruses may be defined as a cellular organisms whose genomes consist of nucleic acid and which obligately replicate inside host cells using host metabolic machinery".
* Virology is the bioscience for study if viral nature and the relationship between and hosts.
Viral Properties
* Viruses are inert (nucleoprotein) filterable agents.
* Viruses are obligate intracellular parasites.
* Viral genome are RNA or DNA but not both.
* Viruses have a naked capsid or envelope with attached proteins.
* Viruses do not have the genetic capability to multiply by division.
Size of viruses
* Their size varies.
* A small virus has a diameter of about 20nm.
Example: Parvovirus
* A large virus have a diameter of up to 400nm.
Example : Poxviruses
Shape of Viruses
* Spherical
* Rod-shaped
* Brick-shaped
* Tadpole-shaped
* Bullet-shaped
* Filament
Rod-shaped or helical E.g. Tabacco Mosaic viru (TMV)
Brick-shaped viruses E.g. Poxviruses
Tadpole-shaped viruses E.g. Bacteriophages
Bullet-shaped viruses E.g. Rhabdoviruses
Filament shaped viruses E.g. Ebolaviruses
Structure of viruses
Virion
* The complete infections unit of virus particle.
* Structurally mature, extracellular virus particles.
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| Virion |
1. Core of genetic material (nucleic acid).
2. Protein coat or capsid.
- Protects viral genes from inactivation by adverse environmental factors.
- Core + Capsid = nucleocapsid
- In many viruses important in attachment of viruses to specific receptors on host cells.
- Composed of a large number of subunits capsomeres.
3. Many animal virus particles are surrounded by a lipoprotein envelope.
The nucleic acid genome plus the protective protein coat is called the nucleocapsid, helical or complex symmetry.
Viral core
* It contains the viral nucleic acid genome.
* In the center of the virion: Controls the viral heredity and variation, responsible for the infectivity.
Genome
*The genome of a virus can be either DNA or RNA
* DNA-double stranded (ds): linear or circular
Single stranded (ss) : linear or circular
* RNA- ss: segmented or non-segmented
ds: linear (only reovirus family)
Viral Capsid
* The protein shell, or coat, that encloses the nucleic acid genome.
* It is an outer covering of protein that protects the genetic material of a virus.
* The capsomere is a subunit of the capsid
* Capsomeres self-assemble to form the capsid.
* Subunits called protomers aggregate to form capsomeres.
Functions of capsid:
a. Protect the viral nucleic acid.
b. Participate in the viral infection.
c. Share the antigenicity.
Nucleocapsid
The core of a virus particle consisting of the genome plus a complex of proteins.
Symmetry of Nucleocapsid
* Helical
* Cubic / Icosahedral
* Complex
Helical Capsid
* The icosahedral capsid structure of adenovirus is made up of three proteins, hexon, penton base and fiber.
* Helical morphology is seen in nucleocapsids of many filamentous and pleomorphic viruses.
* Helical nucleocapsids are characterized by length, width, pitch of the helix and number of protomers per helical turn.
Icosahedral Capsid
* Icosahedral morphology is characteristic of the nucleocapsids of many "spherical" viruses.
* The icosahedral capsid structure of adenovirus is made up of three proteins hexon, penton base and fiber.
* Some proteins are associated with viral DNA, whereas others are associated with hexon and are involved in the formation of the capsid.
Envelope
* A lipid-containing membrane that surrounds some viral particles.
* It is acquired during viral maturation by a budding process through a cellular membrane
* Not all viruses have the envelope, and viruses can be divided into 2 kinds: Enveloped Virus and Naked Virus.
The Envelope
* Enveloped viruses obtain their envelope by budding through a host cell membrane.
* In some cases, the virus buds through the plasma membrane but in other cases the envelope may be derived from internal cell membranes such as those of the Golgi body of the nucleus.
* Enveloped viruses do not necessarily have to kill their host cell in order to be released, since they can bud out of the cell - a process that is not necessarily lethal to the cell - hence some budding viruses can set up persistent infections.
Functions of envelope
* Antigenicity. Some viruses possess neuraminidase
* Infectivity
* Resistance
Bacterial viruses (Bacteriophages)
* Bacteriophages, also called phages, are viruses that infect bacteria.
* They have the most complex capsids found among viruses.
* Phages have an elongated capsid head that encloses their DNA.
* They have a protein tail piece which helps in attachment of the phage to the host and injecting the phage DNA inside the host cell.
* Bacteriophage (bacterial viruses), as the name suggests, are the viruses that infect and replicate within bacteria.
* They are commonly called a phage.
* They are found everywhere.
* They contain DNA or RNA in their genome, which is encapsulated in a protein coat.
* They also infect archaea.
* Bactericidal activity of bacteriophage was first observed in 1896 by Ernest Hanbury Hankin in the water of river Ganges, which could kill cholera bacteria.
* William Twort discovered bacteriophage in 1915.
* D’Hérelle termed them as ‘bacteriophage’ in 1917, as they showed the ability to kill bacteria.
* There are several types of phage virus, which infect only certain bacteria specifically.
* They act in the same way as antibiotics by disrupting the cell wall of bacteria and have been used for the same. They have the potential to be used against antibiotic-resistant pathogenic bacteria.
* Significance
– Models for animal cell viruses
– Gene transfer in bacteria
– Medical applications
Composition of Structure
* A bacteriophage is made up of a protein coat known as a capsid, which encapsulates the genome.
* It consists of a polyhedral head.
* It may be enveloped or nonenveloped and have different shapes such as rod-shaped, filamentous, isometric, etc.
* The capsid is made up of many capsomeres.
* The size and shape vary in different species.
Morphology
* Tadpole shaped
*Hexagonal head (ds DNA)
* Tail: hollow core with contractile sheath
* Base plate: tail fibers
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.
Classification and Examples
* Bacteriophages are classified based on their nucleic acid content and morphological characteristics.
* There are 19 families of bacteriophages found, of which two families are of RNA bacteriophages.
* The main families and characteristics of bacteriophages are-
Replicative Cycles of Phages
* Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle.
1. Lytic cycle i.e. Virulent infection
2. Lysogenic cycle i.e. Temperate infection
Multiplication of Virulent phage: The lytic cycle
* The lytic cycle is a phage replicative cycle that culminates in the death of the host cell
* The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses
* A phage that reproduces only by the lytic cycle is called a virulent phage
* Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA.
The lytic cycle has the following steps:
* Adsorption- Anchoring of bacteriophage to the bacterial cell wall with the help of tails fibres.
* Penetration- The phage DNA gets injected into bacteria.
* Replication and synthesis- The bacterial DNA is disrupted and the viral genome takes charge of bacterial machinery. It starts making proteins required for replication and other structural proteins.
* Assembly- Phage components are assembled into new viral particles.
* Lysis and release- Bacterial cells are lysed and new viral particles are liberated to infect other cells.
The development of temperate phages: Lysogeny
* The lysogenic cycle replicates the phage genome without destroying the host
* The viral DNA molecule is incorporated into the host cell’s chromosome
*This integrated viral DNA is known as a prophage
* Every time the host divides, it copies the phage DNA and passes the copies to daughter cells
* It is relatively harmless and continues to remain in the position until the lytic cycle is triggered.
* It may be spontaneous or due to certain external conditions such as radiation exposure.
* Then the prophage becomes active and a lytic cycle initiates resulting in the lysis of the cell wall.
* After penetration, the phage DNA gets integrated into bacterial DNA and gets replicated along with the bacterial genome.
* As the bacterial genome is inserted into the bacterial genome and bacteria continue to perform the normal activities, the viral genome gets transferred to the progenies as well.
* Bacterial cells containing a prophage are called lysogenic cells.
* The lysogenic cells (having a prophage) may exhibit new properties, e.g. Corynebacterium diphtheriae and Clostridium botulinum, when containing certain prophage DNAs, synthesize toxins, which are harmful.
* Examples of lysogenic phage include lambda (λ) phage.
* Due to the ability to insert their genome specifically and replicate, they are used in genetic recombination.
Classification of viruses
Basis of viral Classification
1. Virion morphology
*Size
* Shape
* Type of symmetry
* Presence or absence of peplomers
* Presence or absence of membranes
2. Virus genome properties
* Type of nucleic acid (DNA or RNA)
* Size of genome in kilobases (kb)
* Strandedness (single or double)
* Linear or circular
* Sense (positive, negative)
* Segments (number, size)
* Nucleotide sequence
* G + C content
3. Physicochemical properties of the virion
* Molecular mass
* pH stability
* Thermal stability
* Susceptibility to physical and chemical agents especially ether and detergents
4. Virus protein properties
* Number, size, and functional activities of structural and nonstructural proteins
* Amino acid sequence
* Modifications (glycosylation, phosphorylation)
5. Genome organization and replication
* Gene order
* Number and position of open reading frames
* Strategy of replication (patterns of transcription, translation)
* Cellular sites (accumulation of proteins, virion assembly, virion release)
6. Antigenic properties.
7. Biologic properties
*Natural host range
* Mode of transmission
* Vector relationships
* Pathogenicity
* Tissue tropisms
* Pathology
DIFFERENT SYSTEMS USED FOR THE CLASSIFICATION OF VIRUSES
* ICTV classification
* Baltimore classification
* Holmes classification
* LHT System of virus classification
* Casjens and Kings classification of virus
ICTV Classification
* The International Committee on Taxonomy of Viruses (ICTV) developed the current classification system and put a greater certain virus properties to maintain family uniformity.
* Viral classification starts at the level of order and follows as thus, with the taxon suffixes given in italics:
- Order (-virales)
- Family (-viridae)
- Subfamily (-virinae)
- Genus (-virus)
- Species (-virus)
* So far, six orders have been established by the ICTV:
1-Caudovirales
2-Herpesvirales
3-Mononegavirales
4-Nidovirales
5-Picornavirales
6-Tymovirales
Currently (2012) 7 orders, 96 families, 22 subfamilies, 420 genera, and 2,618 species of virus have been defined.
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.
*As per Baltimore classification there are 7 classes of viruses
HOLMES CLASSIFICATION
* Holmes (1948) used Carolus Linnaeus system of binomial nomenclature classification system for viruses to group them into 3 groups under one order, Virales.
* They are placed as follows:
* Group I: Phaginae (attacks bacteria)
* Group II: Phytophaginae (attacks plants)
* Group III: Zoophaginae (attacks animals)
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.
* Andre Loff, Robert Horne, and Paul Tournier (1962)
* This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962).
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| LHT System of Virus Classification |
CASJENS AND KINGS CLASSIFICATION OF VIRUS
* Casjens and Kings (1975) classified virus into 4 groups based on type of nucleic acid, presence of envelope, symmetry and site of assembly.
* It is as follows:
1. Single Stranded RNA Viruses
2. Double Stranded RNA Viruses
3. Single Stranded DNA Viruses
4. Double Stranded DNA Viruses
Distribution and Structure of HIV
Scientific Classification
Kingdom : Pararnavirae
Phylum : Artverviricota
Class : Revtraviricetes
Order : Ortervirales
Family : Retroviridae
Subfamily : Orthoretrovirinae
Genus : Lentivirus
Species : HIV 1 /HIV 2
HIV v/s AIDS
HIV : Human Immuno-deficiency Virus
Human : Infecting human beings
Immunodeficiency : Decrease or weakness in the body's ability to fight off infections and illnesses.
Virus : A pathogen having the ability to replicate only inside a living cell
AIDS : Acquired Immuno Deficiency Syndrome
A = not inherited
I = immune system
D = deficiency - inability to protect against illness
S = syndrome, a group of symptoms or illnesses that occur as a result of HIV infection.
* HIV is the virus the causes AIDS.
* Not everyone who is infected with HIV has AIDS.
* Everyone with AIDS is infected with HIV.
* AIDS is result of the progression of HIV Infection.
* Anyone infected with HIV, although healthy, can still transmit the virus to another person.
[ AIDS is the final stage of the disease caused by infection with a type of virus called HIV ]
Global History
* 1981 - beginning of the epidemic in united states.
- Centers for Disease control and prevention (CDC) published a report about five previously healthy homosexual men becoming infected with pneumocystis pneumonia.
- Because the disease appeared to affect mostly homosexual men, officials initially called it Gay-related immune deficiency or GRID.
- CDC noted that this type of pneumonia had never affected people with uncompromised immune systems.
* 1983 - Lymphadenopathy - Associated virus (or LAC ) retrovirus was discovered.
* 1984 - National cancer Institute found the cause of AIDS to be retrovirus HTLV-III.
* 1985 - Food and Drug Administration licensed the first Commercial blood test of HIV.
* 1986 - The International Committee on the Taxonomy of viruses officially named the virus as HIV (human immunodeficiency virus).
* 1988 - The World Health organization declared December 1st to be World AIDS day .
* 1991 - The red ribbon became an international symbol of AIDS awareness.
* 2008 - Luc Antoine Montagnier was awarded Nobel prize in physiology and medicine for his discovery of the human immunodeficiency virus (HIV).
INDIA
* Suniti solomon - first AIDS case was diagnosed in Chennai in 1986.
* In 2009, she was awarded, "National Women Bioscientist Award" by ministry of science and Technology, Govt. of India.
* On 25th January 2017, Govt. of India announced "Padma Shri" award for her contribution towards Medicine.
* "What has been killing people with AIDS more is the stigma and discrimination".
The HIV infection spreads through the following :
* Unprotected sexual interaction with an already infected person.
* Reusing needles used by an infected person.
* From an infected mother to the baby through the placenta.
* Blood transfusion from an infected person.
* This virus has a long incubation period before it starts to attack the immune system (10 years).
* The immune system is the human body's natural defense mechanism, hence HIV can make it harder for the patient to fight off infections and diseases.
* HIV demolishes a particular type of WBC (White Blood Cells) and the T-helper cells T.
* His virus also makes copies of itself inside these cells.
* T-helper cells are also known as CD4 cells.
Types of HIV
* The two major types of HIV strains are -
* HIV-1 : The most common types of virus found Worldwide.
* Group M - 'M' stands for ' major' implies that 90% of HIV AIDS all over the World are caused by this group of HIV.
* Group N - 'N' stands for "non-M, non-O".
* Group O - 'O' implies 'outlier' group of HIV.
* Group P - This type of virus is recently diagnosed in 2009.
HIV- 2
* This is found primarily in Western Africa, with some cases in India and Europe.
* There are 8 known HIV- 2 groups (A to H).
* HIV-2 is closely related to simian immunodeficiency virus endemic in a monkey species (sooty mangabeys).
Structure
HIV
* Enveloped ssRNA virus,
* Genus : Lentivirus, Family Retroviridae
* Lentivirus (HIV 1 and 2)
* Attack CD4 + cells
* Replicates in actively dividing T4 lymphocytes.
* The virus can remain in lymphoid tissues in latent phase until it is activated.
* Unique ability to destroy T4 Helper cells.
* Once a person gets infected, HIV remains in his body lifelong.
* The person is a symptomless carrier for years before the symptoms actually appear.
Core
* HIV is roughly spherical with a diameter of about 120 nm, around 60 times smaller than a red blood cell.
* It is composed of two copies of positive-sense single-stranded RNA that codes for the viruses nine genes.
* The single-stranded RNA is tightly bound to nucleocapsid proteins, P7 and enzymes needed for the development of the virion such as reverse transcriptase, proteases, ribonuclease and integrase.
Capsid
* It is enclosed by a conical capsid composed of 2,000 copies of the viral protein P24.
* A matrix composed of the viral protein P17 surrounds the capsid ensuring the integrity of the virion particle.
Envelope
* HIV has envelope, composed of the lipid bilayer taken from the membrane of a human host cell when the newly formed virus particle buds from the cell.
* The viral envelope contains proteins from the host cell and relatively few copies of HIV envelope protein.
* It consists of a cap made of three molecules known as glycoproteins (gp) 120, and a stem consisting of three gp41 molecules that anchor the structure into the viral envelope.
* The envelope protein, enclosed by the HIV env gene, allows the virus to attach to target cells and fuse the viral envelope with the largest cell's membrane releasing the viral contents into the cell and initiating the infectious cycle.
* As the sole viral protein on the surface of the virus, the envelope protein is a major target for HIV vaccine efforts.
Plant viral diseases
* Plant viruses and viruses that affect plants.
* Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host.
* Plant viruses can be pathogenic to higher plants.
* Most plant viruses are rod-shaped.
* They rarely have an envelope.
* The great majority have an RNA genome, which is usually small and single stranded (ss), but some viruses have double-stranded (ds)RNA, ssDNA or dsDNA genomes.
* To transmit from one plant to another and from one plant cell to another; plant viruses must use strategies that are usually different from animal viruses.
* Plant-to-plant transmission usually involves vectors (such as insects).
* Plant cells are surrounded by solid cell walls, therefore transport through plasmodesmata is the perferred path for virions to move between plant cells.
* The discovery of plant viruses causing disease is often accredited to A. Mayer (1886).