Lesson 1: Introduction to the study of viruses Flashcards
General description of a virus
> obligatory intracellular infectious agents, ranging in size from 20 to 400 nanometer (nm)
> filterable agents
> cannot be seen by light microscope except poxviruses. They are seen only with the aid of an electron microscope.
> no cellular organization and do not have organelles
> contain only one type of nucleic acid, either DNA or RNA
> cannot replicate on inert media; viable host cells are required for replication
> unaffected by antibiotics
size of a virus
20 to 400 nanometer (nm)
example of specific picornavirus
Foot and Mouth-Disease virus
are the smallest viruses (size?)
picornaviruses (20nm)
the largest viruses (size?)
poxviruses (300nm)
These viruses cannot be seen by light microscope because of their small size except of this virus.
poxviruses
Viruses are seen only by the aid of what?
electron microscope
Viruses are composed of what?
nucleic acid surrounded by a protein coat
2 types of nucleic acid
DNA or RNA
Viruses multiply by a complex process involving what?
protein synthesis and nucleic acid production
Viruses are unaffected by these drugs
antibiotics
Three categories of viruses
DNA viruses
RNA viruses
Viruses that utilize both DNA
and RNA for replication
The viruses that infect bacteria
Bacteriophages or Phages
an infectious extracellular virus particle consists of nucleic acid (DNA or RNA) that is covered by a protein coat called capsid
Virion
Virion is an infectious extracellular virus particle consists of nucleic acid (DNA or
RNA) that is covered by a protein coat called __________.
capsid
a shell of subunits of proteins called capsomere that encloses the genome of vertebrate viruses
Capsid
capsid vs capsomere
capsid is the protective protein coat of viruses, whereas capsomere is the smallest subunit of viral capsid
subunits of proteins
capsomere
4 Functions of a Capsid
> offers protection for the nucleic acid against adverse
conditions
> it facilitates attachment and entry of the virus into host cell
> it possesses antigens used for virus identification in serological tests
> it determines the symmetry of the virus
2 types of capsid symmetry
described in viruses
Icosahedral and Helical Symmetries
the term used to refer to the combined nucleic acid and capsid which can either be naked or covered with a membrane termed an envelope
Nucleocapsid
the proteins that make up the subunit of capsid
Structural proteins
The viral genome also codes for important enzymes called__________ required for viral replication but are not incorporated in the virion.
non-structural proteins
are generally assembled in the host cell prior to incorporation of the viral nucleic acid.
Icosahedral capsids
are formed by the insertion of protein units between each turn of the nucleic acid helix, incorporating the RNA in the tubular package.
Helical capsids
a lipid bilayer and associated glycoproteins that cover a nucleocapsid
Envelope
Envelope composition
lipid bilayer and glycoproteins
are usually susceptible to detergent and are rendered non
infectious following damage to the envelope
Enveloped viruses
the proteins encoded by viral nucleic acid for binding to receptors on host cells, membrane fusion, uncoating of the virion and destruction
of receptors on host cells
Glycoproteins
knob-like projections from the envelope formed from the oligomers of glycoproteins.
Peplomers or Spikes
Peplomers or spikes are formed from what?
oligomers of glycoproteins
Present in certain viruses including coronaviruses, retroviruses, orthomyxoviruses, rhabdoviruses and
paramyxoviruses
Peplomers or spikes
Peplomers or spikes are present in certain viruses including such as the ff:
> coronaviruses
retroviruses
rhabdoviruses
orthomyxoviruses
paramyxoviruses
used to bind to cell receptors or may have enzymatic activity
Peplomers or spikes
a layer of protein present between the nucleocapsid and the
envelope in some enveloped viruses that provides additional rigidity to the virion
Matrix protein
Components of an enveloped virus
> Membrane
Lipids
Proteins
Glycoprotein
Properties of an enveloped virus
> Environmentally labile; disrupted by acid, detergents, drying, and heat
> Modifies cell membrane
during replication
> Released by budding and cell lysis
enveloped viruses are released through?
budding and cell lysis
Biological functions of an enveloped virus
> Must stay wet
> Cannot survive in the
gastrointestinal tract
> Spreads in large droplets, secretions, organ transplants, and blood transfusion
> Does not need to kill the cell to spread
> May need antibody and cell-mediated immune response for protection and control
> Elicits hypersensitivity and inflammation to cause immunopathogenesis
Component of a non-enveloped/naked virus
Protein
non-enveloped/naked viruses are released from cell by?
lysis
Properties of a non-enveloped/naked virus
> Environmentally stable to temperature, acid, proteases, detergents, and drying
> Is released from cell by lysis
Biological functions of a non-enveloped/naked virus
> Can be spread easily through fomites, from hand to hand, by dust, and by small droplets
> Can dry out and retain infectivity
> Can survive the adverse
conditions of the gut
> Can be resistant to detergents and poor sewage treatment
> Antibody may be sufficient for immunoprotection
viruses are named according to what? give examples
> type of disease they cause
Examples
include poxviruses, herpesviruses (creeping lesions)
> based on acronyms of disease
** (papovavirus-papilloma; polyoma–vacuolating)** or acronym of observable characteristics (picornavirus - pico/small–rna–virus)
> based on morphology Coronaviruses (halo or corona/crown of spikes), Togavirus (Toga/cloak), Rhabdovirus (Rhabdo/Rod-shaped), Calicivirus (Calix/cup-shaped depression)
> after geographical regions where they were first isolated ** (E. g. Coxsackie-, Marburg-, Gumboro-, Mokola- virus)**
> after individual discoverer (Epstein-Barr virus)
Someviruses are named according to the type of disease they cause. Give examples.
poxviruses, herpesviruses (creeping lesions)
Other are named based on acronyms of disease or acronym of observable characteristics . Give examples.
papovavirus-papilloma
polyoma–vacuolating)
(picornavirus
pico/small–rna–virus)
herpesviruses also known as what?
creeping lesions
papovavirus meaning?
papilloma
polyoma meaning?
vacuolating
picornavirus meaning?
pico/small–rna–virus)
Viruse are also named based on morphology as revealed by electron microscopy. Give examples.
> Coronaviruses (halo or corona/crown of spikes)
> Togavirus (Toga/cloak), Rhabdovirus
> (Rhabdo/Rod-shaped),
> Calicivirus (Calix/cup-shaped depression)
Coronaviruses meaning?
halo or corona/crown of spikes
Togavirus meaning?
Toga/cloak
Rhabdovirus meaning?
Rhabdo/Rod-shaped
Calicivirus
Calix/cup-shaped depression
Some viruses are named after geographical regions where they were first isolated. Give examples
Coxsackie-virus
Marburg-virus
Gumboro-virus
Mokola-virus
Occasionally, viruses are named after individual discoverer. Give example.
Epstein-Barr virus
five hierarchical levels
order
family
subfamily
genus
species
established in 1973, developed and expanded the universal scheme in which characteristics of
virions are used to assign them to five hierarchical levels (order, family, subfamily, genus and species)
International Committee on Taxonomy of Viruses (ICTV)
The hierarchical levels are denoted with the following suffixes:
Order: -virale
Family: -viridae
Genus: -virus
Species:- virus
Order suffix
-virale
Four orders containing viruses of animals
Mononegavirale
Herpesvirales
Picornavirales
Nidovirales
Genus suffix
-virus
Family suffix
-viridae
Species suffix
-virus
Order Mononegavirale families
(PaRaBeFore)
Paramyxoviridae, Rhabdoviridae, Bornaviridae and Filoviridae
Members of this order have common attributes
including a single stranded, non-segmented, negative sense RNA genome, similar replication strategies
Mononegavirale
Order Herpesvirales families
(HAM)
Herpesviridae, Alloherpesviridae and Malacoherpesviridae
Order Picornavirales families
(PIDMS)
Picornaviridae, Iflaviridae,
Dicistroviridae, Marnaviridae and Secoviridae
Order Nidovirales families
(CAR)
Coronaviridae, Arteriviridae and
Roniviridae
are infectious particles, which can transmit a disease, composed mainly of a protein without any detectable nucleic acid
Prions
apparently have no virion structure or genomes and evoke no immune response in the infected host.
Prions
These are extremely resistant to inactivation by heat, disinfectants, and radiation
Prions
causative agents of slow viral infections, such as subacute spongiform encephalopathy
prions
slow viral infections
subacute spongiform encephalopathy
After long incubation period of years, they produce a progressive disease that causes damage to the central nervous system, leading to subacute spongiform encephalopathy.
Prions
True or False
Viruses are more resistant than bacteria to chemical disinfectants such as phenol.
True
Active virucidal agents
formaldehyde and betapropiolactone
most active antiviral disinfectants
> hydrogen peroxide
potassium permanganate
hypochlorite
organic iodine compounds
Most of the viruses with few exceptions are highly heat labile. They are inactivated within seconds at _____, within minutes at _____, and within days at _____.
56°C
37°C
4°C
The viruses usually remain viable in a pH range of ______, but are sensitive to extremes of acidity and alkalinity
5–9
active against enveloped
viruses but are not active against non-enveloped/naked viruses
Ether, chloroform, and detergents
the viruses are readily inactivated by these radiations
sunlight, ultraviolet (UV) radiations, and ionizing radiations
Viruses rely completely on what for their replication.
living host cells
it carries the genetic information of the virus
viral nucleic acid
The replicative cycle of a virus may range from how many hours?
6-40 hours
Within hours of infection, this phase occurs.
eclipse phase
It is the initial stage of virus replication whereby the infecting virus loses its physical identity and most or all of its infectivity. At this time, no virus is detectable in the infected host by methods such as virus
assay or electron microscopy.
eclipse
new viral particles are formed and released from the cell wherein the number of viral particles increases exponentially
productive stage
The Virus Replication Cycle
- Inoculation: inoculum of virus binds to cell
- Eclipse: virions penetrate the cells
- Burst: host cells release many viral particles
- Burst size: number of virions released per bacterium
Steps in virus replication
1. Attachment
2. Entry
Mechanism of entry:
A. Endocytosis
B. Fusion
C. Direct introduction of viral genome into the cytoplasm (injection) through
channels in the plasma membrane.
3. Uncoating
4. Biosynthesis or Replication of nucleic acid
5. Maturation/Assembly of virus
6. Release of the daughter virion
Virus receptors on cells
glycoproteins or glycolipids, proteoglycans
following attachment, the virus gains access to the host cell internal environment where replication takes place
Entry
an active process by which nutrients and other molecules are brought into a cell
Endocytosis
Example of Endocytosis which is used by cells to internalize receptor-bound ligands, fluid, lipids and membrane proteins
clathrin-mediated endocytic pathway
receptor-based endocytosis also known as?
viropexis
enveloped viruses enter the cell by an alternate method called ________ in which the viral envelope fuses with the plasma
membrane and releases the capsid into the cell cytoplasm
Fusion
Fusion can be seen in these viruses
retroviruses, paramyxoviruses, and herpesviruses
Direct introduction of viral genome into the cytoplasm (injection) through channels in the plasma membrane. This is seen in some non envelope viruses such as
picornaviruses
It is the process of separation of viral nucleic acid from its protein core for transcription to take place.
Uncoating
However, in certain viruses, transcription may proceed without complete release of the viral genome. Example?
reoviruses
Uncoating may occur here
cell membrane, cytoplasm, or nucleus
Uncoating may lead to what?
loss of virus infectivity
Some viruses (most DNA viruses) makes use of the host cells enzymes called _______ to synthesize mRNA,
transcriptases
Most RNA viruses generate its own enzyme called _______ to transcribe and replicate mRNA
polymerase
DNA viruses replicate their DNA in the _______ of the host cell by using _______ enzymes
nucleus
viral enzymes
DNA viruses synthesize their capsid and other proteins in the _______ by using ______ enzymes.
cytoplasm
host cell
the complete, infective form of a virus outside a host cell
virions
DNA viruses
(HAPH)
herpesvirus, adenovirus, and papovavirus, hepadnavirus
Poxvirus is an exception, because all of its components are synthesized in the _______.
cytoplasm
Most of the DNA viruses synthesize their nucleic acid in the host cell _______.
nucleus
The RNA viruses replicate in the ________
cytoplasm
The RNA viruses replicate in the cytoplasm except these viruses
Orthomyxoviruses and Borna disease virus
have a non-obligatory
nuclear phase of replication
paramyxoviruses
these viruses which replicate via a DNA
intermediate (provirus)
retroviruses
During the Replication of RNA viruses, transcription occurs in the ________ under the direction of a viral transcriptase.
cytoplasm
RNA viruses
paramyxoviruses, retroviruses, orthomyxoviruses, Borna disease virus
It is the first step in viral maturation.
assembly of the protein capsid
are present in the host cell as fully developed virion
Non-envelope viruses
acquire their envelope from plasma membrane during their release
envelope viruses
The envelope develops around the capsid by a process called ________.
budding
The assembly of
various viral components into virions may take place in the nucleus. Give examples
herpesvirus and adenoviruses
The assembly of various viral components into virions may take place in the cytoplasm. Give examples
picornaviruses and
poxviruses
It is surrounded by an envelope, which is derived from the host cell membrane during the process of budding.
nucleocapsid
enveloped viruses are released through what process?
exocytosis
Abnormal replicative cycles may occur in four ways
- Incomplete viruses
- Pseudovirions
- Abortive infections
- Defective viruses
Due to defect during assembly of viral components, some of the daughter virions that are produced may not be infective.
Incomplete viruses
are the viruses that occasionally enclose host cell nucleic acid instead of viral nucleic acid, therefore, are non infective and lack the capability to replicate
Pseudovirions
In this type of infection, the virus components may be synthesized but the maturation is defective maybe due to infection of the wrong host cells by the virus.
Abortive infections
These are viruses that produce fully mature virions only in the presence of helper viruses which supplement the genetic deficiency in the defective viruses.
Defective viruses
Example of a Defective virus
Hepatitis D virus
It replicate only in the presence of hepatitis B virus (helper viruses).
Hepatitis D virus (defective virus)
The viruses show variation in their genomic structure by two principal methods
mutations and recombination
Spontaneous and random errors in the copying of viral nucleic acid
Mutations
Mutation may be induced by what?
mutagens
Mutation may be induced by mutagens like?
X-rays, UV irradiation or chemical agents, or may occur spontaneously
resulting from single nucleotide substitutions, are the most common type of mutation
Point mutations
Less common types of mutation
deletion or insertion of
one or more nucleotides
a new area of antiviral research wherein those RNA viruses with inherently high mutation rates are administered with mutagenic agents to drive viral extinction through violation of the error threshold and error catastrophe
Lethal mutagenesis
is the extinction of an organism as a result of excessive mutations
Error catastrophe
a virus mutant which can replicate only under defined permissive conditions
Conditional-lethal mutants
rendering a virus towards low viral load and low viral fitness by subjecting it to a combination of mutagenic agents and antiviral compounds
Viral suppression
variant strains showing differences in the tissue type and species of target cells affected by viruses
Host-range mutants
viruses that replicate in the presence of antibody. Because of altered antigenic surface determinants, the mutants are unaffected by neutralizing antibodies induced by the wild-type virus. Such a selection process may facilitate persistent or recurring infections
Antibody escape mutants
a virus with decreased infectious titer despite a high number of viral particles. This mutant promote the establishment and maintain persistent infections
Defective-interfering mutants
variant strains that cause less serious infections in human and animals.
Attenuated mutants
the exchange or transfer of genetic material between different but closely related viruses infecting the same cell simultaneously, or between virus and host cell
Recombination
occurs between two closely related DNA or RNA viruses
Intramolecular recombination
a recombination between positive-sense single stranded RNA viruses and occurs through a template switching mechanism; RNA polymerase switches between template strands during synthesis of the complementary negative-sense strand
Copy-choice (template switching)
Copy-choice (template switching) can occur in these viruses
picornaviruses, togaviruses and coronaviruses
An exchange of segments occurs between these viruses, resulting in production of new hybrid strains
Reassortment
infectious progeny are produced from parental viruses, of which one or both are non-infectious, following mixed infection of a cell
Reactivation
when infectious progeny are produced from related viruses inactivated by lethal mutations at different loci in their genomes
Multiplicity reactivation
It occurs when an inactivated virus becomes capable of replicating after acquiring genetic material from an infective virus
Cross-reactivation or genome rescue
widely used for virus propagation
Tissue culture
It is employed for the isolation and production of particular viruses
inoculation of chick
embryos and experimental animals
It is required for the isolation and identification of viruses involved in disease, for the titration of viruses for vaccine production and for the provision of stocks for research purposes
Propagation
2 types of tissue culture
A. Explant cultures
B. Cell cultures
Three types of cell
culture
a) Primary cell culture
b) Semi-continuous
c) Continuous cell cell culture
a tissue fragment is used to isolate viruses from animals with persistent infection
Explant cultures
the tissues are digested into individual cells by mechanical cutting followed by digestion with enzymes such as trypsin
Cell cultures
type of cell culture derived directly from tissues and contain many cell types such as epithelial cells, fibroblasts, keratinocytes, melanocytes, endothelial cells, muscle cells, hematopoietic cells, mesenchymal stem cells, etc.
Primary cell culture
type of cell culture where cells of semi-continuous or diploid cell lines retain their characteristic diploid chromosomal constitution and can support the growth of a wide range of viruses. However, such cell lines, tend to die out between the 30th and 50th passage
Semi-continuous
type of cell culture which are derived from either normal or neoplastic tissue and can be passaged indefinitely
Continuous cell cell culture or immortal cell lines
How to detect viral growth in cell cultures
> light microscopy
Serological tests using fluorescein-labeled antibody
Two types of virus according to cytopathic effect (CPE) production
a) Burster (lytic) virus
b) Creeper virus
these induce formation of multinucleated giant cells
Creeper virus
induce cell lysis and cellular transformation in cell culture
Burster (lytic) virus
Serological tests
> Inoculation on embryos
Use of experimental animals
though no longer extensively used, this remains the preferred method for isolation of influenza A viruses and for many avian viruses
Inoculation on embryos
Inoculation on embryos modes of inoculation
via the:
> allantoic cavity
> amniotic cavity or the
yolk sac
> chorioallantoic membrane (CAM), or intravascularly
Inoculum of virus binds to cellls
Inoculation
Virions penetrate the cells
Eclipse
Host cells release many viral particles
Burst
Number of virions released per bacterium
Burst size
Mechanism of entry of a Virus
A. Endocytosis
B. Fusion
C. Direct introduction of viral genome into the cytoplasm (injection) through
channels in the plasma membrane
This is seen in some non-envelope viruses such as picornaviruses
Direct introduction of viral genome into the cytoplasm (injection) through channels in the plasma membrane.
Define the 3 Mechanism of Entry
a. Endocytosis - an active process by which nutrients and other molecules are
brought into a cell
b. Fusion - enveloped viruses enter the cell by an alternate method
c. Direct introduction of viral genome into the cytoplasm (injection) through channels in the plasma membrane. - This is seen in some non-envelope viruses such as picornaviruses
It is where naked viruses or non-enveloped viruses undergo a
receptor-based endocytosis
Endocytosis
in these viruses, transcription may proceed without the complete release of the viral genome
reoviruses
In some viruses it is facilitated by lysosomal enzymes present inside the phagocytic vacuoles and
Golgi vesicles of the host cell that degrade the protein of the viral capsid
Uncoating
it leads to loss of virus infectivity
Uncoating
Difference between negative-sense strand and positive-sense strand
The negative-sense strand of each segment is transcribed to produce individual mRNA molecules. In contrast, the genomes of positive-sense, single-stranded RNA viruses can act directly as mRNA following infection.
