Viruses

Black, J.G.. Microbiology: principles

and explorations, latest edition
Chap 10
• Viruses: infectious agents that are too small to be seen
by light microscope & are not cells. They have no cell
nucleus, organelles or cytoplasm. When they invade
host cells they display properties of living organism.

• Viruses replicate only inside living host (obligate

intracellular parasite)

• Prokaryotes & eukaryotes have DNA & RNA, virus

particles contain only one kind of nucleic acid DNA or
RNA.

• Viruses don’t grow or replicate alone, they infect host cell

& program it to synthesize the components of new virus
Components of viruses

 Nucleic acid core surrounded by protein coat

(capsid), some viruses have surrounding lipid
bilayer membrane (envelope). All of these called
virion
 Viral genome (genetic material) is either DNA or RNA,
either single stranded or double stranded, linear or
circular or segmented

 Capsid: most viruses have capsid to protect nucleic

acid & determine the shape of virus, in some
viruses help in attachment to host cells. Capsid
composed of protein subunits called capsomers.
The no. of proteins & the arrangement of
capsomers are characteristics of specific viruses→
useful in virus identification & classification
 Envelope: enveloped viruses have bilayer
membrane outside the capsid. Envelop is acquired
after the virus is assembled in a host & when it
buds or move through the membranes

• Virus with nucleocapsid (viral genome+ capsid) &

without envelope are called naked or nonenveloped
virus.

• Composition of envelope is determined by viral

genome & by substances derived from host
membrane, lipids, proteins & CHO

• Some viruses have spikes on the envelope (glycoprotein

projections may extend outside the envelope). They attach
virus to host receptors, some spikes causes RBC to clump
(hemagglutinate) used to identify viruses
• Envelope:
– Advantages to viruses
• Because derived from host cell membrane, virus
maybe hidden from attack by host immune system
• Helps virus infect new cells by fusion of envelope with
host cell membrane

– Disadvantages
• Enveloped viruses are damaged easily by any
environmental condition that destroys membrane:
increase in temp, freezing, thawing, pH below 6 above
8, lipid solvents, chemical disinfectant

• Size & shapes

Viruses have range of sizes, the largest is about 1/10 of
RBC
Most viruses have specific shape determined by the
capsomer or the envelope
•Helical capsid: composed of
ribbon like protein forms a
spiral around the nucleic acid

•Polyhedral: many-sided e.g

picornavirus, icosahedral
virus (have 20 triangular
faces)

•Complex capsid is a
combination of helical &
icosahedral shape
• Some have bullet shaped capsid

• Viruses with envelope have almost spherical shape

• Some viruses have thread like shape, complex viruses have more
elaborate coat or capsid (poxvirus). Bacteriophage have complex shape,
they have special structures like head, tail & tail fibers (to attach to host
bacteria)
• Host range & specificity of viruses
Viruses can infect all forms of life (algae, bacteria, fungi,
protozoa, plants , vertebrates, etc..) but for most viruses,
each virus is limited to one host & to one cell or tissue of the
host, e.g poliovirus: causes infection to only humans; while
rabies virus causes infection to many warm blooded
animals.

• Host range of a virus: the spectrum of host the virus can

infect.

• Viral specificity: the specific kind of cells a virus can infect.

E.g some papilloma viruses infect only skin cells, while
cytomegalovirus (have lethal effect) attacks salivary glands,
GIT, Liver, lungs, crosses placenta & attacks fetus

• “one virus one disease” is not true!

• Specificity is determined by

– The ability of virus to attach to cell (depends on presence of

specific receptor on host cell & specific attachment structure
on viral capsid or envelope)
– Presence of enzymes & proteins in the host that the virus
needs to replicate inside the cell
– Ability of viruses to be released from the cell

• Viruses can’t reproduce, they must infect host cells, uncoat their
genetic material & use the host’s machinery to replicate

• Debate: viruses are they living or non living chemical

aggregates?

– Non living: can’t reproduce, no metabolism

– Living: because they have genetic material that is active after
infection
Classification of viruses
 International committee on taxonomy of viruses (ICTV)
– The family is the highest taxonomic category
– Currently: the viral species (group of viruses that share
the same genome & the same relationship to organisms)
is written in English not Latin, e.g HIV virus: family
Retroviridae, genus Lentiviridae, sp Human
immunodeficiency virus
– Virus families are often distinguished based on nucleic
acid type, capsid symmetry (shape), envelope & size

Nucleic acid classification

– Major groups are classified first as DNA or RNA viruses

– Subdivisions are based on properties of nucleic acid,

single stranded (ss) or double stranded (ds)
 – ssRNA viruses contain either (+)sense RNA i.e RNA acts as
mRNA that can be translated by host ribosomes or (-)sense
RNA: RNA acts as template during transcription to make
complementary (+) sense mRNA which will be translated by
host ribosomes.

– Since eukaryotic cells don’t have enzymes to copy viral RNA

molecules, RNA viruses must have enzymes or genes for the
enzymes that are needed to copy viral RNA molecules

• (-) sense virus must carry RNA polymerase within virion

 RNA viruses
• Examples :
• Picornaviridae: e.g genus Enteroviruses (intestines) include
poliovirus. They are resistant to chemicals & can replicate in
& pass through GIT & spread to nervous system.
• Retroviridae: have two copies of (+)sense RNA, contains
the enzyme reverse transcriptase; uses RNA→DNA →
replicate → ds DNA → transcription → viral RNA → act as
mRNA → protein synthesis. To do so, viral DNA migrate to
host cell nucleus & incorporated into chromosomes of host
cell. The integrated viral DNA is known as provirus.
– Retroviruses causes tumors, leukemias & AIDS
 Corona viruses are enveloped nonsegmented positive-
sense single-strand RNA viruses. The current Pandemic
is caused by a virus known as Severe Acute Respiratory
Syndrome Coronavirus-2 (SARS-CoV2), family
Coronaviridae, genus Betacoronavirus.

 DNA viruses

Examples:
• Herpesviridae: widely distributed in nature & most
animals are infected with herpes, one or more of them
(table).

Cells infected with herpes virus, dsDNA can exist as

provirus → latency: ability to remain in host cells, usually
neurons for long time, e.g child chickenpox → stress or
other factors → shingles (zoster)
Emerging viruses
• Viruses caused infections since 1000s yrs ago

• Microbiologists believe that many recent unexpected viral diseases are

caused by emerging viruses: viruses that were endemic (low level of
infection in localized area), e.g poliovirus was endemic since ancient
times, 1900 →spread world wide, explanation: after industrial revolution
→ people emigration → non immune exposed to immune people who
carry the virus,
• or through vectors (insects) that transmitted the disease from carrier
animals.
• Through “crossing species barrier”, e.g SIV (simian immunodeficiency
virus) to……HIV?!

• Influenza virus: if a host cell is simultaneously infected by 2 different

viruses (e.g human, swine) they can swap parts of their genomes → new
mutant type occur → resulting in for e.g human flu virus covered by bird
or pig type capsid, that is a new virus that is not recognized by immune
system
 Bacteriophages (phage) eaters of bacteria
T-even phages (T=type) obligate parasite of E.coli has
capsid made from head, collar & tail. The DNA is packed
in the polyhedral head
Soviet union → phage therapy to treat bacterial disease,
was preferred over antibiotics because: Bacteriophages
are highly specific (attacking only targeted bacteria &
leaving the beneficial normal flora),

cheap, effective in
small doses
(cures in 48hrs),
used to treat
patients with long
term antibiotic
resistant bacterial
infections & rarely
cause side effects
 Viral replication

Replication cycle of viruses

• Adsorption: the attachment of viruses to host cells

• Penetration: the entry of virion or genome into host cells

• Synthesis: the synthesis of new nucleic acid molecules,

capsid proteins & other viral components using the cell’s
machinery

• Maturation: assembly of newly synthesized viral

components into complete virions

• Release: release of virions from host cells. Sometimes

this step causes lysis to the cell
Replication of bacteriophage

• Adsorption: the attachment of viruses to host cells. It is chemical

attraction. Specific proteins found in tail fibers bind to specific
receptor sites on host cells. Some bind to cell wall, others bind to
flagella or pili.

• Penetration: Lysozyme (present in phage tail) weakens bacterial cell

wall, tail contracts, the hollow tube (core) penetrates the cell wall &
contacts cell membrane. Viral DNA is injected & the capsid remains
outside

• Synthesis: Phage DNA controls host cell’s metabolic machinery,

bacterial DNA is disrupted & the resulting nucleotides are used to
build new phages. Phage DNA → transcribed mRNA → translated on
host ribosome → proteins (e.g capsid+enzymes)

• Maturation: assembly of newly synthesized viral components into

complete virions. In host cytoplasm, heads are assembled, ds DNA is
packed into each head, also phage tails, sheath & collar are
assembled,
• Release: Lysozyme (coded by phage gene) breaks down cell wall
allowing viruses to escape, i.e bacterial cell is lysed, phages infect
more cells again.
Phages that lyse & destroy the cell are called lytic phages e.g T-4,
this cycle is called lytic cycle.
Phage growth & estimation of
phage no.

Replication curve
•Eclipse period: from
penetration to biosynthesis, in
this period mature virions are
not detected in host cell
•Latent period: from
penetration up to phage
release. This period includes
eclipse period
•After eclipse period no. of
viruses/host cell rises & then
levels off
 Phage assay: a method to count no. of phages in a tube
1) Prepare plates containing susceptible bacterial lawn (layer of
bacteria)
2) Make serial dilution of phage suspension
3)From each tube take a
sample (small volume) &
inoculate onto a plate
containing susceptible
bacteria. Each phage will
infect a bacteria & the
phages produced from
each bacterium will lyse
the bacterium & the
surrounding bacteria.

4)Incubate, the bacterial lawn

will have clear zones
called plaques

5) Count the no. of plaques x

dilution factor=no. of
phages (plaques forming
units)
 Lysogeny

• Virulent phages: destroy their host cells.

• Temperate phages: for some time may undergo a lytic cycle but most of
the time exhibit lysogeny (stable long-term relationship between the
phage & its host where phage nucleic acid is incorporated into the host
nucleic acid, this bacteria is called lysogenic cell)

• Viral DNA within bacterial chromosome is called prophage, the

combination of bacteria+temperate phage is called a lysogen

• The virus remains dormant for a long time & when bacterium divides, the
prophage multiply as part of bacterial chromosome

• The inserted prophage has genes that repress virus replication& gene to
provide ‘immunity’ to infection by another phage of same type, a process
known as lysogenic conversion which prevents adsorption or
biosynthesis of phages whose DNA is present in lysogen
• Lysogenic conversion is medically important as some bacteria
release toxins due to prophages, e.g Corynebacterium diphtheria
& Clostridium botulinum, they don’t cause disease unless they
are infected by a phage→prophage has genes that codes for the
toxin →released by bacteria →tissue damage.

• Lysogenic cycle: the period of bacterial growth with a prophage in

it

• Due to outside stimulation (e.g lack of nutrients for bacteria, or

toxic chemicals to the lysogen) or spontaneously, the prophage
becomes active & starts lytic cycle, a process called induction. i.e
the provirus senses the unfavorable conditions.

• Through induction the provirus removes itself from the bacterial

chromosome, phage DNA codes for viral protein…etc & the cycle
is completed as lytic cycle

• The majority of bacteriophages undergo lysogeny

 Replication of animal viruses

1) Adsorption: naked viruses have attachment sites (proteins)

on the surfaces of their capsids e.g (canyon or depression)
that bind to specific receptors on host cells. Enveloped
viruses have spikes that recognize a membrane protein
receptor on the surface of host cell

2) Penetration: nucleic acid & capsid penetrate animal cell

(unlike phages only nucleic acid injected).

-Naked viruses enter cells by endocytosis (pitlike region on cell surface)

& enter the cell as vesicle
-Enveloped viruses either fuse with host plasma membrane or enter by
endocytosis
-Once inside cell cytoplasm, uncoating (release of viral genome) from
protein coat occurs by proteolytic enzymes .
3) Synthesis: depends on the nature of infecting virus
-DNA animal viruses: DNA replicates in host nucleus, capsid & other
proteins are synthesized in cytoplasm. The new viral proteins move
to nucleus & combine with new viral DNA to form virions.

-RNA viruses: synthesis undergoes in greater variety than DNA. (RNA &
RNA retroviruses).

4) Maturation: when virion components are available in abundant amount,

assembly starts (maturation). Envelope lipids & glycoproteins are
synthesized by host enzymes. If the virus is of enveloped type, the
virion is incomplete until it buds through host membrane e.g plasma
membrane, nuclear membrane, Golgi or endoplasmic reticulum
depending on the virus.

5) Release: the budding of new virions may or may not kill the host cell
(herpes & pox virus cause lyses to cells)

Latent viral infection

Herpes simplex virus causes cold sores, can exhibit lytic cycle & can remain
latent within the cell through out the individual’s life in the nerve cell.
When activated (cold, stress, fever) they replicate resulting in lysis
Another eg: Varicella-Zoster virus, remains dormant in nerve cells, once
activated , forms rash along the nerve (shingles)
 Culturing animal viruses

• Viruses have to be grown in living tissue, first were cultured in living

animals, later, in chick embryo, recently in cell culture (tissue culture)

• Cell culture: animal cells are taken freed from surrounding tissue by
enzymes, washed, counted & dispensed into plastic flasks, tubes or bottles
containing nutrients. Antibiotics are added to prevent microbial
contamination

• Cells will attach to plastic surface, multiply & spread to form sheets, one cell-
thick called monolayers.

• Monolayers can be subcultured ( a process where cells from a culture are

transferred to new container with fresh nutrient).

• Plaque assay similar to those of phages can be used on human cells.

• Cytopathic effect (CPE) is the visible effect viruses have on cells. The effect
differs according to the infecting virus. e.g change in shape of cells,
swelling, lysis, detachment from adjacent cells or the container.
 Viruses & teratogenesis

• Teratogenesis is the induction of defects during embryonic

development.

– Teratogen: an agent that induces such defect.

– Some viruses act as teratogen & can be transferred

through placenta & infect the fetus. The earlier the embryo
is infected, the more the damage, e.g cytomegalovirus,
herpes simplex & rubella cause teratogenic effect. If the
damage is severe may lead to death of fetus

– TORCH: series of tests to detect teratogenic diseases in

pregnant women & new born infants. The test detects
antibodies against Toxoplasma, other disease causing
viruses (usually hepatitis B, varicella) rubella virus,
cytomegalovirus & herpessimplex virus.
 Virus like agents
• Viruses usually have the genetic information to produce new
virions in a host cell. But there are some exceptions.
• There are smaller agents than viruses that can cause
diseases

 Satellites: small single stranded RNA molecules, which lack

genes required for their replication. In presence of helper
virus, they can replicate. They are not related to (different
from) the helper virus.

– called satellite as their reproduction “revolves around” a helper

virus.
– There are 2 types: satellite viruses code for their capsid
protein while the satellite nucleic acid (virusoid) whose
helper virus encodes their capsid.
– They are associated with plant viruses

 Viroids: An infectious RNA particle smaller than a virus &

Don’t require helper virus
 Causes plant diseases
 Delta hepatitis (hepatitis delta virus HDV): similar to
viroid & virusoid RNAs. It is a defective pathogen that
requires coinfection with hepatitis B virus to replicate.
– Can be prevented by vaccination against hepatitis B as it can’t
infect without its helper virus. It has the smallest genome of any
known animal virus.
– Causes more severe disease
– Transmitted by blood.

 Virophages
– It is not actually a phage but acts similarly in that it impairs its
host virus’s replication
– It doesn’t have the genes needed to replicate unless it coinfects
with the helper virus
– It differs from the other satellite viruses in that it is the only
satellite virus that negatively effects its virus host’s replication.
– E.g Sputnik virophage which infects mimivirus (a giant virus that
infects an amoeba & also causes pneumonia in humans)
 PRIONS
infective agents may be exceedingly small proteinaceous
infectious particle, that cause neurological degenerative
diseases eg mad cow disease.
https://www.youtube.com/watch?v=aP-ShyyHiIc

• characteristics:
– resistant to inactivation by heating to 90°C, which will
inactivate viruses.
– Prion infection is not sensitive to radiation treatment
that damages virus genomes.
– not destroyed by enzymes that digest DNA or RNA.
– sensitive to protein denaturing agents, such as phenol
and urea.
• prions are normal proteins that become folded incorrectly, possibly
as a result of a mutation.

• The harmless, normal proteins are found on the plasma

membrane of many mammalian cells, especially brain cells.

• The prion proteins (PrP) are thought to stick together inside cells,
forming small fibers, or fibrils. Because the fibrils cannot be
organized in the plasma membrane correctly, such aggregations
eventually kill the cell.

• Prions move easily from one species to another (injection or

ingestion of contaminated food like in cannibalism)

• How the disease spread? prions cause other copies of the normal
protein to fold improperly.

• Prions have now been newly associated with many diseases, such
as Alzheimer’s, Parkinson’s, some dementias, type II diabetes,
and cancer.
 Spongiform encephalopathy

Diseases: Bovine spongiform encephalophathy (Mad cow disease),

Creutzfeldt-Jacob diseases, Kuru (humans), scrapie (sheep)
 Viruses & cancer
• cancer is an uncontrolled & /or invasive growth of abnormal cells.

• Tumor or neoplasm (localized accumulation of cells) can be benign, a

noncancerous growth. But if the cells invade and interfere with the
functioning of surrounding normal tissue, the tumor is malignant.
Malignant tumors and their cells can metastasize, or spread, to other
tissues in the body.

• About 15% of human cancers are caused by viruses. At least 6 viruses

are associated with cancer, e.g human papilloma virus which causes
cervical cancer, Epstein-Bar virus (affects lymphocytes, causes
destruction to the jaw), Kaposi’s sarcoma (a cancer of the endothelial
cells of the blood vessels or lymphatic system) caused by Herpesvirus 8,
Hepatitis B virus a potential cause of liver cancer.

 ONCOGENES
The proteins produced by tumor viruses that cause uncontrolled host cell
division come from segments of DNA called oncogenes (onco, =mass).

• In DNA tumor-causing viruses, oncogenes cause neoplasm & also

contain the information for synthesizing viral proteins needed for viral
replication.