INTRODUCTION TO VIROLOGY

PROPERTIES OF A VIRUS
A virus is an obligate intracellular parasite because a virus cannot replicate on
its own. A virus must enter a cell in order to replicate because the virus
cannot produce energy or proteins on its own. The virus needs the
mechanisms of replication and protein synthesis of the host cell.
The viral genome will determine the life cycle of the virus. The genome may
either be of RNA or DNA but not both.
There are two types of morphology. There is the capsid which is a protein
covering the genome; this capsid may be naked. Or there may be a lipid
envelope surrounding the capsid.
Viral components do not replicate by division. When it comes to viruses each
of the components of a virus are produced and then they are assembled.
Enveloped viruses will have a lipid bilayer surrounding the capsid.

Some viruses will only have a capsid surrounding them meanwhile other
viruses such as Poxiviridae will have a lipid envelope surrounding them.
Inclusive, the largest lipid envelope will be the one surrounding the Pox virus.

In RNA viruses the capsid may be helical. Remember that the typical capsid
shape in DNA viruses is the icosahedral shape.

NAKED CAPSID VIRUSES

These will lack the lipid envelope. These viruses will be stable in the
environment; making them resistant to temperature, acid, proteases,
detergents and drying. This is important because when these viruses are in
the environment then they will maintain themselves active. These viruses are
usually released by cell lysis. A prime example of this is the virus of the
cough, also known as a Rhinovirus which is a naked capsid virus with high
infectivity.

These naked capsid viruses can be spread easily from host to host. These
viruses can dry out and retain infectivity. They may also survive the adverse
conditions of the gut at a pH of 3 (all viruses that cause diarrhea will be naked
capsid viruses).
In order to inactivate these viruses, an antibody response (humoral) may be
sufficient for protection.

ENVELOPED VIRUS
Enveloped viruses are much more susceptible in the environment. They will be
environmentally labile to temperature, acid, proteases, detergents and drying.
If the transport medium in which these viruses is transported becomes dried
out then this virus will be inactivated.
During replication these viruses modify the cell membrane. This is because
the lipid envelop was originally part of the host cell membrane. It is this
reason that these enveloped viruses may evade the immune system due to
the similarities in phospholipid composition between host and virus. For this
reason protection against enveloped viruses may require antibody or cellmediated immune responses.

As a consequence of their enveloped nature these viruses must remain humid

or wet within their transport medium. Enveloped viruses cannot survive in the
GI tract. These enveloped viruses are typically spread in large droplets,
secretions or blood. In order to be spread the enveloped viruses do not need
to kill the host cell.

VIRAL GENOMES
Some viruses may have a linear, circular, double stranded, single stranded
genomes. The majority of the DNA viruses will have double stranded
genomes. The only member of the DNA genome virus family to have a single
stranded genome is PARVOVIRUS. Meanwhile the majority of the RNA viruses
will have a single strand. Also, in the majority of viruses the genome is only
one molecule.

There are 4 families who have a segmented genome. An example of this is

Rotaviruses, Influenza (has 8 molecules of RNA).
In RNA viruses there are those that are RNA (+) which are going to be
identical to the mRNA. Meanwhile the RNA (-) viruses will be complementary
to the mRNA.
In RNA viruses the only virus to have a double stranded genome (RNA +/-) is
going to be the Reoviruses. Reoviruses lack a lipid envelope, instead they
have a double capsid.
There is an RNA (+) that has a DNA intermediary for replication. This is going
to be the retroviruses.
All RNA (-) viruses will have a lipid envelope.
Influenza is a member of the Orthomyxoviruses.

STEPS OF VIRAL REPLICATION

The majority of the steps of viral replication will be the same in DNA and RNA
viruses. Differences will arise in the process of macromolecular synthesis.
1) Recognition the virus recognizes the host cell in which the virus will
replicate. The recognition depends on the host cell receptors and the
Viral Attachment Protein (VAP) within the virus. An important example is
if the VAP of HIV which is known gp120 which makes an important
contact with the CD4 receptor. The VAP cell receptor interaction will be
specific for each different virus.
2) Attachment
3) Penetration in order for the virus to replicate, it must be inside the cell.
In order to penetrate the virus has two options. The virus may make a
hole in the membrane and enter the cell within an endosome. This is
known as receptor mediated endocytosis. This mechanism is
commonly used by naked capsid viruses.
The alternate form of viral penetration is for lipid enveloped viruses. This
process consists of a membrane fusion.
4) Uncoating this will occur once the virus is inside the cell. The process of
uncoating involves the breaking of the capsid in order to release the
capsid. Once the genome is released it must head to the site of
replication which will depend on if it is a DNA or RNA virus. DNA viruses

will replicate within the nucleus (except the Pox viruses which replicate in
the cytoplasm).
RNA viruses will replicate in the cytoplasm of the cell. The exceptions to
this are retroviruses (which use DNA as an intermediary) and the
orthomyxoviruses (Influenza enters the nucleus during its process of
replication).

5) Macromolecular synthesis
During macromolecular synthesis the virus will produce the essential
components of its structure and those particles which are necessary for
replication.
In DNA viruses there will be transcription and translation of early genes.
These early genes are those that the virus needs in order to replicate the
viral genome. The next step involves replication of the viral genome.
The last step involves the transcription and translation of the late
genes. The late genes will codify for all the structural components such
as the capsid, proteins within the lipid envelope. The late genes will
codify for all the particles that form the viral particle.
6) Assembly of the Virus this involves putting each part together in order
to form the viral particle. The assembly process also involves the
entering of the genome into the capsid.
7) Release of the virus the virus may be released by cell lysis which is
caused by naked capsid viruses, remember that these viruses lack a
lipid envelope.
Those viruses which have a lipid enveloped may be released from the
cell by budding. Budding does not cause cell lysis.
When there is cell lysis by way of DNA viruses there will be lysis of the
nuclear membrane and the cellular membrane. This is essential for the
exit of the DNA virus.
Most viruses that undergo the process of budding will receive their lipid
envelop from the cell membrane but some viruses (Example Herpes
viruses) will receive their lipid envelope from the nuclear membrane.

STEPS OF REPLICATION IN (+) RNA VIRUSES

1) Recognition

2) Attachment
3) Penetration
4) Uncoating there is a rupture of the viral capsid. Since it is an RNA virus
then it will remain in the cytoplasm.
5) Macromolecular synthesis remember that RNA (+) genome is similar to
the mRNA. The first step of macromolecular synthesis will involve using
their genome as the mRNA for the synthesis of proteins. There is the
synthesis of a polyprotein which is the translation of the entire genome
within the same protein (proteins in chain!). In order for the proteins
within the polyprotein to be functional they must be cleaved.
Now the replication of the genome occurs last. This occurs last because
the polymerase (that uses RNA as a template) had to be synthesized
earlier (in the giant polypeptide). Once this polymerase is made then we
can continue with the replication of the genome.
Replication of an RNA (+) will involve the synthesis of a complementary
(RNA -) strand. This will then be transcribed into an RNA (+) strand. Keep
in mind that the produced RNA (-) strands are destroyed and are not
incorporated into the virus. The RNA + particles are incorporated into the
viral particle. The RNA (-) particles only serve as intermediaries of
replication that do not incorporate into the viral particle.
Keep in mind that naked RNA (+) is infectious. This means that
RNA (+) that lacks capsid can be injected inside an organism and the entire
cycle of viral replication and viral particle synthesis may occur. For this reason
purified RNA (+) can initiate replication if it is introduced within a cell in a
naked form.

STEPS OF REPLICATION IN RNA (-) VIRUSES

Remember that RNA (-) viruses genomes is complementary to the
messenger RNA. This means that an RNA (-) genome cannot be used as the
messenger for the synthesis of proteins. A differentiating factor of these
viruses is that they already bring the RNA polymerase made.
1) Recognition
2) Attachment
3) Penetration
4) Uncoating in this process the genome is being released and well as the
RNA polymerase is being released.

5) Macromolecula synthesis since the RNA polymerase is already made

(due to the fact that it was brought inside the virion) then the first
process involves the synthesis of a complementary RNA (+) strand from
the RNA (-) genome.
The newly synthesized RNA (+) strand will be used for protein synthesis.
After this then the RNA (+) strand will be used as a template for the
replication of the genome. So in this case we go from RNA (-) to (+) then
back to (-).
So, the intermediary RNA (+) strand will be used for protein synthesis
and then form replication of the genome.
6) Assembly of Virus
7) Release of Virus can be done by budding or by cell lysis
The naked RNA (-) is not infectious because if one were to nude the RNA (-)
virus then we would also be removing the RNA polymerase. For this reason
injection of RNA (-) will not cause anything
The genome of RNA (-) viruses is not infectious. Remember that the RNA
polymerase of the viruses will be dependent on RNA. This is a differentiation
factor from the eukaryote RNA polymerase which is dependent on DNA.

STEPS OF REPLICATION IN RETROVIRUSES

1) Recognition
2) Attachment
3) Penetration in this case penetration occurs by membrane fusion.
4) Uncoating once the membranes fuse the capsid is released into the
cytoplasm. A peculiarity of this virus is that it has two copies of its
genomes but it IS NOT SEGMENTATED.
Once the retroviral genome is in the cytoplasm it will initiate the process
of retrotranscription. It will be using a reverse transcriptase which was
included (prepackaged) in the virion. From here the virus will pass from a
single stranded RNA to a double stranded DNA molecule.
5) Macromolecular synthesis a double stranded DNA molecule is
synthesized. This then travels into the nucleus and it integrates itself into
the DNA of the host cell. Once the retroviral dsDNA integrates itself into
the DNA of the host cell (in HIV this would be inside the CD4 genome)
then it cannot be removed.
Once the retroviral dsDNA is integrated it will begin to act as any DNA
and there will be transcription of a mRNA. This messenger RNA will have
two functions. The mRNA will produce proteins and it will also act as the

retroviral genome. This means that the host cells polymerases will be
in charge of synthesizing the retroviral genome.
6) Assembly remember that the synthesized mRNA will act to produce
proteins and it will also be used as future retroviral genome. The
assembly of the virus will then occur at the level of the cellular
membrane.
7) Release of the virus the release of the virus will occur by budding.

When the virus exits the cell it is NOT infectious. This is because the protein is
still in polyprotein form. The process of retroviral maturation must occur in
which there will be cleavage of the retroviral proteins in order for the
retrovirus to become active. This cleavage is done by a viral protease. For this
reason HIV therapy consists of 3 therapies : antivirals against the reverse
transcriptase(2) ; and protease inhibitors (1) (that inhibit retroviral activation).
REMEMBER that RNA (+) and RNA (-) viruses will have an intermediary that is
a double stranded RNA.

VIRAL GENETICS

VIRAL MUTATIONS
The DNA viruses can undergo errors in the process of replication but these
viruses have effective repair mechanisms (proof reading). Now, RNA viruses
lack effective mechanisms of repair in order to correct mutations that occur
during viral replication. This is important because RNA viruses will accumulate
more mutations than DNA viruses.
Viral mutations result from errors in copying the viral genome during virus
replication. These mutations are usually not detrimental for the virus. Viral
mutations may cause resistance to antiviral drugs. Viral mutations may also
cause changes in the antigenicity of the virus in order to help it evade the
immune system. Both these mechanisms can act to increase the
pathogenicity of the virus.

As viruses become more evolved and gain more mutations they will become
more pathogenic.

Apart from mutations, other mechanisms can quickly form viral variants. In
order for these mechanisms to occur; both viruses must be infecting the same
cell in order for the genetic exchange to occur. For example if Herpes simplex
viruses I and II were infecting the same cell then there can be recombination
during the replication of these viruses. When this recombination occurs we
would then be mixing both genomes in order to create a chimera. Basically
the virus will have portions of type I herpes and type II herpes.

Reassortment this is a mechanism that commonly occurs in Influenza.

Remember that influenza has 8 segments. This means that there is a great
amount of reassortment of segments; leading to endless combinations of
Influenza strains. For this reason, influenza vaccines must be developed every
year. Due to this mechanism of rearrangement H1N1 was developed.
Reassortment has to occur between two viruses from the same family.
Reassortment involves the exchange of complete viral segments.
Reassortment is one of the most common mechanism.

Marker rescue - this is a similar process of recombination between two

viruses. The only exception is that the virus has a lethal mutation. When the
recombination occurs the virus with the lethal mutation is rescued and it
recombines with the other virus and replication is able to occur. In marker
rescue one of the viruses is unable to replicate but a new variant is created.
So in the next round of replication the previously lethally mutated virus will be
able to replicate.
Transcapsidation in this process there is no genetic recombination. In this
process there are two viruses entering the same cell and one of the viruses
will enter the other virus. In this process one virus changes its external
structure (capsid). In transcapsidation the genome is preserved; the external
structure is switched. If the virus were to undergo replication again then the
produced capsid will be the original one. Basically transcapsidation is a

temporary change that will only last one round of replication. Transcapsidation
allows a virus to infect a cell that it was unable to infect.
Complementation this process is similar to marker rescue but there is no
genetic exchange. Once again in this process there is a virus with a lethal
mutation that encounters a normal virus. The normal virus will not exchange
genes, instead it will donate the needed protein. So if the missing protein is
the polymerase, then the polymerase will aid the lethally mutated virus. Now
in the next round of replication the lethally mutated virus will remain affected
and in need of the missing protein. The change is only temporary.

VIRAL PATHOGENESIS

Viral pathogenesis is the process by which viruses cause disease, including

the effects of virus replication and the immune response. Viral pathogenesis
refers to the way that the virus will cause damage either by the effects of its
replication or by the effects of the subsequent immune response.

IN ORDER FOR THERE TO BE VIRAL INFECTION

1) There must be a sufficient amount of virus to initiate infection. There
needs to be an appropiate amount of viruses in order to overcome
physical barriers. A threshold must be surpassed in order to initiate the
process of replication. High numbers of viruses are also needed because
during the process of viral replication many defective particles are
produced.
2) The host cells must be susceptible and permissive to the infecting virus.
In order for the cell to be susceptible it must have the receptor that the
virus will recognize. The cell must also be permissive where it can
provide all the requirements for gene expression. For this reason viruses
will have tropism for certain tissues.
3) There must be an absence of host antiviral responses basically there
must be an absent immune response. This can be due to mutations in

the virus that help the virus evade the immune response. There are other
viruses that block specific immune defenses.

PATTERNS OF VIRAL INFECTIONS

1) Abortive infection if one of the previous three requisites does not occur
then we will have an abortive infection. In this case the infection is not
completed.
2) Acute infections in this case the virus enters the host and there is
rapid replication followed by rapid resolution due to the hosts
immune defenses. The infection may be asymptomatic if there is not
enough virus to produce symptoms. Eventually the immune defenses will
be developed for clearance of the virus. Once the virus is eliminated by
the immune system, it will never reappear BUT KEEP IN MIND that a virus
may have various serotypes and these can appear instead!.
3) Persistent infections in this case the virus persists and the immune
system cannot eliminate it. The virus does not need to persist in an
active form; it may persist in a latent form. In the latent form the viral
genome is present but it is only reactivated under certain stimuli
(as in the case of Herpes).
Chronic persistent viral infections mean that the virus is constantly
replicating.
A slow persistent replication means that the virus is replicating at a
slow rate. In slow replication there may be no clinical symptoms initially.
Transforming replication means that the replicating virus is
transforming the host cell (into a cancerous one?). Examples of this are
Epstein barr and Papilloma virus which can both cause cancer.

VIRAL DETERMINANTS OF PATHOGENESIS

The type of tissue that the virus infects will determine the specific clinical
symptoms that the virs is going to cause. The stability of the virus in the body
is another viral determinant of pathogenesis (lipid envelope vs nude capsid).
The ability to establish a viremia is also an important determinant of viral
pathogenicity. The ability of the virus to cause cell lysis is also an important
determining factor of viral pathogenicity.

STEPS IN VIRAL PATHOGENESIS

The portal entry points of viral entry are also important factors of viral
pathogenesis. One of the most common portal entry points of viruses is the
respiratory tract.
The skin is another entry point that serves as a barrier unless there are
scratches or bites.
The GI tract is another portal in the case of contaminated food and water.
Urogenital tract
Conjunctiva
Blood is another portal point but the virus must be carried into it by insects or
needles.

Once the virus enters through a portal entry point it can then become a
localized or systemic infection. The virus can spread by the circulatory
system, causing viremias; but another route of spreading is by way of the
neuronal system (Example: Rabies polio, herpes simplex).
In localized infections there will not be any viremia.

Once the virus reaches the organ where there will be the most replication we
can begin to observe the damage. The damage may be due to the infection
process or due to viral production of toxins. Some viruses may inhibit the
synthesis of proteins by the host cell (example poliovirus). Other viruses can
create accumulations of viral proteins and inclusion bodies (seen in Rabies).
Other viruses can alter cell metabolism and turn a normal host cell into a
cancerous one (this is seen in Papilloma cell cycle activation).
The hosts immune response may cause a complete recovery in acute
infections. Or the immune system may create an immunopathogenesis.
Instead of helping; the immune system contributes to the pathogenesis.
Antibodies may also be involved in the immunopathogenesis. Sometimes they
may recognize the serotypes of other viruses but instead they will aid in the

infection. This is seen in dengue. The antibodies for dengue I will aid in the
entry of dengue II into the host cells.

The papilloma virus vaccine is an inactivated vaccine

Rotavirus vaccine is the live attenuated vaccine
The Varicella zoster vaccine (shingles) is also a live attenuated vaccine.

DNA VIRUSES
PARVOVIRUSES
Parvoviruses are the only DNA viruses that have a single stranded genome
(DNA + or -).
Parvoviruses lack a lipid envelope and their genome is linear. This virus
requires growing cells.
The major replication site of Parvoviruses is within the RBCs; which in this
case the parvovirus will replicate within the bone marrow or fetal liver which
are the major sites of early hematopoiesis.
The major diseases that parvovirus B19 causes is:
1) Erythema Infectiosum this is a disease in children. This is also known
as slapped cheek disease. The symptoms consist of flu like symptos
such as fever, myalgia, chills or athralgias (these are non-specific
symptoms). The slapped cheek rash is a specific symptom for
parvoviruses. In adults there will be no inflammation of the face,
instead they will experience a strong arthritis.

2) Aplastic anemia this may be caused in patients who are

immunocompromised, or acquired anemias. What occurs is that since
the parvovirus lacks a lipid envelope then the RBCs will be lysed. In

normal people this infection will not reach the level of anemia (there
will be RBC lysis but it will not be too serious).
3) Hydrops fetalis this is the most severe condition in which there is
vertical transmission from mother to fetus. This may cause a severe
anemia and it wcould eventually kill the fetus.
The main forms of transmission of this virus is by way of respiratory secretions
which could cause the non-specific symptoms. This could eventually lead to
viremia and the possibility for vertical transmission is increased.
Parvovirus is a virus that is difficult to diagnose. This is because with this virus
it is difficult to do a tissue culture. For this reason the methods of diagnosis
will be molecular; involving hybridization, PCR or IgM (this is the first antibody
to activate and be present for 2-3 months).

The virological events that occur in this infection from early to late are. First
there is a viremia and the virus may also be present in the throat. This means
that early on the virus may be transmissible through particle expectoration.
There is an initially transitory IgM response which is then followed by an
increase in IgM.
In children by the time the specific symptoms appear in children then the
virus would have already been eliminated. This means that when the non
specific symptoms appear that will be the time in which the virus is present
but when the specific symptoms appear the virus will have already been
eliminated (this is because the specific symptoms are caused and mediated
by the response of the immune system).
There are no specific therapies against Parvoviruses. Treatment is supportive
and symptomatic.

PAPILLOMA VIRUSES
These viruses will cause warts. There are more than 70 papillomavirus
serotypes. Some papillomaviruses cause benign warts meanwhile others may
cause more severe outbreaks of warts. They may be sexually transmitted or
they may cause cancer.
The papilloma virus lacks a lipid envelope; it is basically a naked icosahedral
capsid.
The papillomavirus genome is circular and composed of double stranded
DNA.
The papillomavirus will replicate in the squamous epithelium of the skin. It is
here that it will be causing the formation of warts. The papilloma virus codes
for eight early proteins and two structural proteins
a) The E1 proteins will promote DNA replication.
b) When E1 acts together with E6 and E7 these will be critical
for the transformation mechanism of this virusor its ability
to cause cancer. This is because E6 will bind to p53 and
destroy it. Meanwhile E7 will bind to RB. Once these proteins
exert their function then the cell will have undergone
transformation and now the cell will become cancerous.
c) E1 + E2 will activate RNA synthesis and replication.
This virus becomes important when it can cause different types of cancer.
Papilloma viruses may cause cervical or penile cancer. More than 50% of
secually active men or women may be infected with HPV at some point in
their lives.
The Papillomavirus serotypes that can cause cervical cancer are 16 (50% of
cases) and 18 (14.4% of cases). These serotypes represent more than 60%
of viruses that can cause cervical cancer.
The Papillomaviruses that commonly cause genital warts are the 6 and 11
serotypes. The four previously mentioned serotypes 6,11, 16 and 18 are
those which are included in the vaccine (Gardasil).
Not all papillomaviruses are sexually transmitted. There is no specific antiviral
therapy. Therapy usually involves REMOVAL of the wart.

Laryngeal papillomas are acquired in newborns. The newborn may aspire

some of the particles of the papilloma virus that are in the vagina. The
laryngeal papilloma must be removed since it grows as a small tumor.
Transmission is via sexual contact or by direct skin to skin contact or
transmission may also occur during birth. This virus cannot be cultivated,
making diagnosis difficult.
Diagnosis of papillomaviruses is by molecular methods such as PCR,
hybridization, Hydbrid capture. Treatment is via salicylic acid, cryotherapy and
deep surgical removal. The removal must involve the deep layers of the skin
because the virus usually infects the deep tissue.
Therapy can also involve interferon alpha which can work against most
viruses. Interferon alpha is not a specific antiviral agent.
Cervical cancer is the second biggest cause of female cancer mortality.
The HPV vaccine (Gardasil) is effective against four serotypes. This means that
the risk for infection with the virus is still high as ever.

POLYOMAVIRUSES
The Polyomaviruses lack a lipid envelope; they are basically a naked
icosahedral capsid. The polyomaviruses genome is circular and double
stranded. The two members
A polyomavirus can cause infections that occur during childhood. The two
members that are in this family are the BK virus and the JC virus.
Infection will begin at the respiratory level; with non-specific symptoms. A
critical fact is that these viruses may become latent; if reactivation occurs
then the consequences could be severe. These viruses establish latency in the
kidneys and reactivation occurs in immunocompromised patients and during
pregnancy.
If reactivated:
a) The BK virus will remain in the kidney and cause renal disease.
b) The JC virus can then produce viremia and move to the CNS. Within
the CNS this virus will replicate SLOWLY and it will infect
oligodendrocytes (myelin producing cells). The destruction of myelin
producing cells will cause a progressive multifocal

leukoencephalopathy. Basically this produces a demyelinating disease

of the CNS in which symptoms could be impaired speech/vision and
mental deterioration.
Polyomaviruses are transmitted via the respiratory route.
There is no treatment for Polyomaviruses. The JC virus is dangerous upon
reactivation. As a primary infection the JC virus is relatively harmless.
Polyomaviruses are transmitted by the respiratory route.
Diagnosis is difficult and is done by PCR, hybridization. Serology reveals that
50% of children already have antibodies against this virus. Serology is not
diagnostic. An ELISA analysis for antigens in the urine can be helpful to
identify the BK virus since it rests within the kidneys.
The polyomaviruses are contagious at the respiratory level. When BK
reactivates, no viremia is produced; it is the JC virus which upon reactivation
will cause viremia.

ADENOVIRUSES
The adenoviruses lack a lipid envelope; they are a naked icosahedral capsid.
The adenoviruses have 51 serotypes divided into 6 groups. The genome of the
adenovirus is a double stranded linear DNA.
An important thing to note about adenoviruses is the types of proteins they
produce. During replication they can express certain genes that produce
proteins that inactivate p53 and RB. Basically speaking adenoviruses have the
potential to cause cancer but no cancers have ever been associated with
them.
Adenoviruses will cause infections in the respiratory and GI tracts and the eye.
Some of the diseases that adenoviruses cause are:
a) Acute respiratory disease: this is caused by the 3,7 and 21
serotypes. Initially the respiratory infection starts with non
specific symptoms such as cough, nasal congestion, fever and
sore throat but if they remain untreated it could cause
pneumonia.

b) Pharyngoconjuctival fever this is caused by the 3 and 7

serotypes.
c) Epidemic keratoconjunctivitis this is caused by serotypes 8, 19
and 37. Remember that since this virus lacks a lipid envelope it
can remain easily active in the environment. This conjunctivitis
causes a lot of itching.
d) GI infections can be caused by serotypes 40 and 41.

Adenoviruses can establish latency in lymphoid tissues such as adenoids or

tonsils. The adenoviruses can then become reactivated in
immunocompromised patients. This is because the immune system generally
keeps these viruses under control. The incubation period for adenoviruses is
5-8 days.
Transmission of adenoviruses is via the respiratory routes; fecal oral routes
(40, 41 serotypes); infected water.
Adenoviruses can be easily cultured or their antigens may be identified by
prepackaged ELISA kits. Unless the virus produced severe symptoms;
diagnosis is rare.
Culture of adenoviruses reveals CPE grape like clusters at 2-5 days after
inoculation.
A vaccine did exist and it was given orally. It was used in specific populations
like in jails. The vaccine was administered in order to avoid respiratory
transmission of this virus. The vaccine consisted of a live attenuated virus
(serotypes 4 and 7).

POXVIRUSES
This virus does have a lipid envelope. Examples of Poxviruses are Variola,
Molluscum contagiosum or Vaccinia. These viruses may have brick shaped
structures with a double envelope.
Poxviruses have a lipid envelope and they are the only DNA viruses that
replicate within the cytoplasm of the cell. The genome of poxviruses
consists of a linear double stranded molecule of DNA.

Vaccinia was the virus that was used as the vaccine in order to eliminate
smallpox; it can be pathogenic in persons that are immunocompromised.
Smallpox is the only virus that was eradicated by the use of a vaccine.
There are only two of the Poxviruses that are pathogenic:
a) Molluscum contagiosum consists of pink-wart like tumors. They
may appear at the back of the head. These are usually benign
and they are spread by close-sexual contact.
b) Variola this is commonly known as smallpox. Variola is
transmitted by the respiratory route. Transmission may occur via
direct contact when the pustules rupture. Variola is the ideal
biological weapon. Variola initially causes non specific respiratory
symptoms; eventually it will cause viremia. Small pox will cause a
great spanning vesicular rash and it may cause 5 days of fever.
Treatment is via methinasone.
Mortality usually occurs because the vesicles rupture and they
leave a great amount of skin exposed for secondary bacterial
infections.
Monkeypox is a directly transmitted virus which is similar to smallpox.
When the vaccinia vaccine was used; small lesion on the fingers may appear;
this is known as ORF. In this small lesion there may be transmission; for this
reason the ORF lesion must be covered initially. If one were to examine your
parents arms; most likely one could see a remnant lesion of the vaccinia
vaccine against smallpox.
Vaccinia cannot be used because in immunocompromised patients it could
cause a lethal infection. A modified vaccinia vaccine known as MVA (modified
vaccinia ancara) is being developed.

REPLICATION OF POXVIRUSES
Since the Poxviruses replicate in the cytoplasm there are some variations in
the way it replicates.
The virus is going to enter the cell via endocytosis. The outer membrane is
removed in the endosome. In this case the capsid is not removed.
Transcription will begin to occur thanks to enzymes within the capsid (the
capsid has not been destroyed). The early genes are encoded in order to

produce an enzyme known as uncoatase which will be in charge of breaking

the capsid. Another early encoded gene is the one that creates DNA
polymerase.
Since DNA replication will occur in the cytoplasm then there will be the
production of inclusion bodies known as Guarnieris inclusion bodies.
Even though this virus has a lipid envelope; it WILL BE RELEASED BY CELL
LYSIS. This will cause a lot of the associated pathogenesis.
For Diagnosis the poxviruses can be easily cultured but the quickest way is by
H & E staining in order to identify those Guarnieris inclusion bodies.

HERPESVIRUSES
The Herpesvirus family includes various genus and subfamilies (alpha,
gamma, beta).
The Herpesvirus family includes:
a
b
c
d
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Herpes simplex virus Type I and II

Varicella Zoster (alpha)
Epstein barr (gamma)
Cytomegalovirus (beta)
Human herpesvirus 6 and 7(beta)
Human Herpesvirus Type 8 (gamma)

The Herpesvirus is a virus that has a lipid envelope and an icosahedral capsid.
Between the envelope and the capsid there is a space known as the
tegument. This tegument has different viral proteins that are necessary for
viral replication.
The Herpesvirus has a double stranded DNA genome. Within this genome
there are large unique segments (known as UL) and small unique segments
(US). Between these segments are going to be areas of identical repeats.
These areas of identical repeats are important because here there can be

internal recombination. This internal recombination is important for producing

additional viral variants but it has no effect on the pathogenicity
These viruses have a large tissue tropism. They can infect various cells.
Herpesviruses can cause lytic, persistent and latent infections. In the case of
EBV these infections may be immortalizing.

REPLICATION OF HERPESVIRUSES
When the herpesvirus is assembled; there is going to be budding from the
nuclear membrane and subsequent exocytosis or cellular membrane
lysis. This is an important key factor that differentiates the replication of
Herpesviruses from other viruses. The herpesvirus can be released from the
cell by lysis or exocytosis (by a normal cell secretory route). Due to the fact
that the envelope of the virus is assembled from the nuclear membrane this
virus DOES NOT ACQUIRE A DOUBLE ENVELOPE.

HERPES SIMPLEX VIRUSES 1 AND 2

Generally speaking herpes simplex 1 virus occurs from the waist up and
herpes simplex 2 virus occurs from the waist downwards. This is a general
pattern but it is not exclusive.
Oral herpes is frequently caused by herpes simplex 1 virus meanwhile genital
herpes is frequently caused by herpes simplex 2 virus.
Neonatal herpes may be caused by both viruses. Neonatal herpes occurs
when the baby is born from a Herpes (+) woman who has an active infection.
The HSV 1 and 2 infect skin, eye, genitourinary tract and it can reach the CNS.
In the CNS it may cause meningitis or encephalitis in some cases. This virus
has the ability to move along the nervous system. This virus does not cause
viremia, its spread is by way of the nervous system.

HSV Type I will establish latency in the trigeminal ganglia. Meanwhile HSV 2
will establish latency in the sacral ganglia. Once the HSV establishes latency it
will be inactive; not undergoing replication. Some conditions that

reactivate HSV is fever, sunburns, stress. Upon reactivation the HSV will
reinitiate replication and the lesions will reappear.
HSV is treated by acyclovir, valacyclovir, famciclovir, foscarnet and
vidarabine.
Transmission of HSV is by direct contact and sexual contact. Transmission may
also occur in the saliva (type I) and there may be vertical transmission to a
fetus in which most of the transmission will occur at the moment of
parturition. For this reason those children are typically extracted by cessarian.
When babies are born exposed to herpes there is a common eye infection.
Diagnosis of HSV is easyit can be cultured in the laboratory (primary). The
HSV can be diagnosed via PCR, hybridization, or ELISA.
Serology of HSV is not important because HSV is a common virus. Almost
everyone will have antibodies against HSV. Even still, when there is a
reactivation of HSV; the titers of antibodies will not increase or vary much.
Antibody detection is not the best way to make a diagnosis.
Keep in mind that genital herpes can be caused by HSV type 1 and 2 although
there is an increased incidence of genital herpes caused by HSV type 2.
HSV may cause Bells Palsy.
Disseminated herpes is seen in immunocompromised patients and it may
be lethal.
Acyclovir is actually an inactive drug that is known as a prodrug. This drug
can only become activated in presence of the HSV. Acyclovir will then be
activated by way of phosphorylation. This phosphorylation is by way of a viral
Thymidine kinase and cellular kinases. Acyclovir will only exert its function
once it becomes triphosphated. Acyclovir will cause a termination in the
replication of the viral DNA. REMEMBER that the HSV must be present in order
for Acyclovir to function. If the virus is latent, then the thymidine kinase is not
present and Acyclovir is not activated.
A person who is sexually active should be on chronic acyclovir therapy in
order to impede the viral replication.

There are different manifestation of HSV. The HSV type I can manifest itself in
the form of a stomatitis or a gingivostomatitis. This is a primary manifestation
of HSV.
Once the virus enters latency and becomes reactivated then there will usually
be a lesion on one side of the mouth. This lesion will resemble a cold sore.
Herpetic whitlow was an occupational sickness seen in dentists. If the
patient had active herpes lesions then the virus could be transmitted and it
can cause herpetic whitlow. For this reason there was mandatory glove usage
by dentists.

CYTOMEGALOVIRUS
This is known as one of the principal viruses of congenital sickness. CMV is
an hetrophile (-) agent that can cause mononucleosis.
CMV can cause hepatitis, pneumonia, Guillain-Barre syndrome,
arteriosclerosis.
CMV is a virus with high tropism that can infect various tissues such as liver,
pancreas, bile ducts, salivary glands, gut epithelium and lung and others. CMV
can also infect monocytes, lymphocytes and endothelial cells. It is in
these three cells that CMV can establish latency.
Immunocompromised patients who receive organ transplants are at risk of
complications by CMV. During the organ transplant there may be
reactivation of CMV or the received organ may have had latent CMV.
Treatment can be by administration of ganciclovir. If resistance is established
then patient can receive instead, foscarnet or cidofovir.
Transmission of CMV can be by direct contract or sexual contact. There may
also be transmission by saliva or by vertical transmission between mother and
fetus. A distinguishing factor of CMV is that it CAN CAUSE VIREMIA.
This is one of the differences between CMV and HSV.
Diagnosis can be difficult due to the long time it takes to culture this virus.
Even so, the time it takes for this virus to do the cytopathic response we are
looking for may also be long.

An alternative for diagnosis is by histological examination. This is

because the histology of CMV will resemble a owls eye. This is because CMV
will produce intranuclear inclusion bodies. The cell that is infected with CMV
will be much larger and they will resemble a syncitium of various cells.
Another method of CMV diagnosis is by shell vial which is a combination of
immunofluorescence and other techniques.

CONDITIONS ASSOCIATED WITH CMV

Congenital infection with CMV may occur at any moment of the pregnancy.
Infection may occur postnatal in maternal milk. If the virus is transmitted early
to the fetus the effects may be even more severe. If the baby receives the
virus post-partum then the effects may be less severe.
For this reason pregnant women may receive a TORCHHS test. This test does
not say if the virus is active; it merely looks for the presence of
antibodies. These tests should be done in the first trimester of pregnancy.

Complications may arise during gestation due to the reduction in the maternal
immune defenses. This could cause a reactivation of CMV.

When CMV is transmitted in children it is typically an asymptomatic infection.

When the CMV is transmitted in younger adults and adolescents the
symptoms become more symptomatic: for example mononucleosis.
Mononucleosis may be caused by CMV which is heterophile negative or by
Epstein Barr virus which is hetrophile positive.
CMV may be transmitted in the hospital as a nosocomial infection. It used to
occur when persons received blood samples that were contaminated with
CMV.
In an immunosupressed patient we will see serious symptoms associated
with CMV. In patients who are HIV positive it is common to see retinitis due to
CMV.
Babies who are born with CMV will produce a rash. These babies may have
mental retardation, deafness.

VARICELLA ZOSTER VIRUS

This is the virus that causes varicella. Chicken pox used to be a common
infection in children up until the vaccine was developed. If the VZV
reactivates, it can produce shingles in adults.
Shingles can be associated with other conditions such as Reyes syndrome
which is an acute encephalopathy or liver degeneration ; and encephalitis.
The varicella zoster virus is of oral transmission which then causes a primary
and secondary viremia. In the first viremia the virus heads to the liver and the
spleen. .. meanwhile in the second viremia the VZV will more to the skin. It
uses the blood as its means of transport in order to infect other tissues. For
this reason VZV can have up to a two week incubation period.
VZV will establish latency in sensory ganglia. For this reason when there is a
reactivation of VZV patients remark that it is extremely painful.
Therapy for VZV is acyclovir, famcyclovir, valacyclovir (valtrex) and foscarnet.

Transmission of VZV is via the respiratory route; it has an incubation period of

2 weeks. Transmission can then continue by a disseminated viremia.
After the lesions appear there can be transmission by direct contact. The
lesion contains a liquid that has many viral particles that can be transmitted
by skin to skin contact. Diagnosis is not needed due to the fact that the lesion
is typical and easily identifiable.
The VZV is an attenuated virus known as Varivax.
Varivax is also used to avoid the reactivations of VZV and shingles. This is
used in patients that are above 60 years old. This is because these patients
have frail immune systems.

The Varicella Zoster Virus is characterized by the presence of vesicles in

differing stages of growth. Typically the pattern of growth is from macula to

papula and then to vesicle. The vesicle then becomes filled with liquid
this is the stage in which the virus may be transmissible by direct contact.
When the lesions reach the crust stage that is when they shed their scabs.
Once in the crust stage, the VZV is no longer transmissible.
When there is reactivation of the VZV there is no dissemination over the
skin and there is NO VIREMIA. The reactivation of VZV will only be within the
nervous system, there is no viremia. This means that the reactivation of VZV
is localized.
Typically the reactivation of VZV is in the stomach but it can invade the eye in
order to cause Herpes Zoster ophtalmicus. VZV reactivation is typically seen
in the elderly which have a reduced immune system.

EBSTEIN-BARR VIRUS
This is the virus that is said to cause mononucleosis. The transmission of
EBV is by way of saliva.
The EBV will produce a heterophile positive mononucleosis. Remember that
CMV can cause a heterophile negative mononucleosis.
The reason the antibodies produced by an EBV mononucleosis are heterophile
positive is because the EBV infects the B lymphocytes. When the EBV infects B
lymphocytes it will subsequently activate them in order to produce antibodies
that have no particular specificity. The antibodies produced by an EBV induced
mononucleosis will not be specific for the virushence these are known as
heterophile (+) antibodies. This is only seen when the mononucleosis is
produced by the EBV.

The mono test looks for these heterophile antibodies that will agglutinate
goat, sheep or horse RBC. The mono test will be positive for EBV but negative
for CMV induced mononucleosis.

The Ebstein Barr Virus is associated with many types of cancer such as
Burkitts lymphoma or nasopharyngeal carcinoma. These cancers are
not usual in the US because they require coinfection. This is seen in Burkitts

lymphoma which requires a coinfection with the parasite that causes malaria
(Plasmodium).
It is thought that nasopharyngeal carcinoma also requires certain cofactors
that have not yet been identified. Nasopharyngeal carcinomas are typical of
China.

In immunocompromised the Ebstein Barr Virus may manifest itself in the form
of oral hairy leukoplakia which produces white crusty lesions on the lateral
sides of the tongue.
The transmission of the Ebstein Barr virus is by way of saliva and the
incubation period can be in excess of one month. This means that the person
could be transmitting the virus way before he begins to manifest the
symptoms.

Symptoms of an Epstein barr virus mononucleosis include tiredness. The

person cannot swallow well since the virus is actively replicating in the
pharynx.
Diagnosis can be by way of a mono test. Another form of diagnosis is by a
CBC which should show development of atypical lymphocytosis. Some
alternative antigens can be identified such as the viral capsid antigen (VCA);
early antigen (EA) or the ebstein barr nuclear antigen (EBNA). The
identification of these antigens can help identify EBV. First we will be able to
see antibodies against VCA. These IgGs that target VCA will be permanent.
We can also see IgGs against early antigen (EA) but this response will
decrease. For this reason it is said that antibodies for EA are potential markers
of the active phase of this infection.
There is no treatment for Epstein barr virus. Treatment is usually
supportive.
Presentation of EBV mononucleosis can be with a pharingitis or
adenopathy. There may be inflammation in the liver or spleen. There can
also be virus shedding which will allow the virus to be transmitted even before
the clinical symptoms are noticeable.

There may also be T-cell activation which can produce atypical

lymphocytes. It is said that the T-cell activation will be what produces the
lymph node inflammation or spleen inflammation.

If the EBV becomes latent and then reactivates; the antibodies for EA antigen
will also increase. The antibodies against VCA are not effective for
identification since they will persist even after the virus becomes latent. The
antibodies for VCA do not indicate if the EBV is active.
The last antibodies to arise will be those against the EBNA antigen.
These antibodies are associated with the transformation abilities of the virus.
This means that if the patient develops antibodies against EBNA he shall be
protected from potential cancers that can be caused by the transformation
abilities of the EBV.

HUMAN HERPES VIRUS 6 AND 7

The most common clinical presentation of these viruses is the childhood
manifestation of roseola infantum. Roseola infantum is a typical rash in
children which is usually preceded by a fever.
Treatment is usually unnecessary because by the time the rash presents; the
virus is usually reducing in number.
In adults the clinical manifestations of HHV 6 and 7 will resemble that of a
mononucleosis infection.
By the ages of 7 or 8 most children have been in contact with this virus.
There is a rash which is typical of HHV 7 which is known as pitiriasis
rosea. Which is in the shape of a rose.

The HHV 6 and 7 will be infecting T-lymphocytes; specifically those that are
CD4+. They may also infect monocytes, CNS and lung. Since these viruses
infect the same cells the HIV infects (CD4) if both infections were to occur
concurrently; then the symptoms would be even more severe.

Treatment of HHV 6 and 7 involves foscarnet and cidofovir.

Transmission of these viruses is by saliva (both), direct contact or congenital
transmission. The Human herpes virus type 6 can be transmitted
sexually.
Diagnosis is difficult because culture must be done with primary cells; this
means that there needs to be cocultivation with umbilical cord blood
lymphocytes. Diagnosis can be done by molecular methods such as PCR
(serum or plasma).
Serology is not useful since most children between 7 or 8 have antibodies
against this virus due to its high prevalence.

HUMAN HERPES VIRUS TYPE 8

This is the virus that can cause Kaposi Sarcoma. The Kaposi sarcoma if a
form of cancer that is commonly associated with HIV patients. When the
immune system is greatly weakened this can lead to the formation of the
Kaposi Sarcoma cancer.
HHV type 8 may also cause less frequent diseases such as Castlemans
disease or primary effusion lymphomas.
The primary infection with HHV 8 does not cause Kaposi sarcoma. It is the
reactivation of HHV type 8 which is responsible for causing Kaposi
sarcoma.

Transmission of HHV8 is by way of vertical and sexual transmission. Patients

who have AIDS can have a much higher viral replication; allowing the virus to
be transmitted in saliva, nasal secretions or semen.

Diagnosis of HHV8 is difficult. HHV8 can be diagnosed by molecular methods

such as PCR, hybridization, IFA (serology). Virus culture of HHV8 is difficult.
Treatment of human herpes virus 8 is by way of cidofovir, foscarnet and
ganciclovir.

RNA VIRUSES PART I

Those viruses which have an RNA (+) genome will have a genome that is
identical to the mRNA. This means that the RNA (+) genome is ready for
replication. Meanwhile in the genome of an RNA (-) virus; there must be the
synthesis of a complementary strand which will then be the true initiator of
replication and protein synthesis.

The Reovirus family is the only family to have a double strand of RNA (+/-).
They will also have a double capsid.
The Retrovirus family is RNA (+) but its intermediary in transcription is DNA.
The retroviruses will have a lipid envelope as their covering.
All RNA (-) viruses have lipid envelopes as their covering.

PICORNAVIRIDIAE FAMILY (RNA+)

Members of the Picornaviridae family will lack an envelope. These viruses

have a naked icosahedral capsid. Picornaviruses have a linear, single
stranded (RNA+) genome.

ENTEROVIRUSES these viruses are stable at acidic pH. For this reason they
can pass from the stomach to the intestine in order to cause viral GI problems.
The enteroviruses are Polioviruses, Coxsackieviruses and Echoviruses.
RHINOVIRUSES these viruses are unstable at acidic pH and they prefer to
grow in colder areas of the body like the nose (near 33 degrees C).
HERPENAVIRUSES these cause Hepatitis A.

When Picornaviruses infect their host cell they will bind to it via specific
receptors (attachment). This is then followed by the liberation of the RNA (+)
genome into the cytoplasm. The (+) RNA is translated into a polyprotein
within the cytoplasm. This polyprotein will then be cleaved in order to aid in
the structural assembly of the virus and to also aid in the transcription of RNA
into more copies of the genome. The viral particles will then be assembled in
the cytoplasm where the will be released from the cell by lysis.

Picornaviruses will form a polyprotein which is then fragmented in order to

produce many little proteins.

ENTEROVIRUSES EPIDEMIOLOGY
The enteroviruses are acid stable, resistant to ether, ethanol and various
detergents. This is typical of viruses that lack a lipid envelope and a merely
naked capsid.
Enteroviruses are inactivated by UV light, formalin and chlorine at 10%
Transmission of enteroviruses is by the fecal-oral route. They can also be
acquired by ingesting contaminated water.

Enterovirus epidemics commonly occur during the summer but in the tropics
the disease can occur all year.

POLIOVIRUS PATHOGENESIS
The Poliovirus can cause intestinal infection. It is commonly acquired by the
oral route. The Poliovirus is also secreted in feces.
Poliovirus has the ability to cause viremia. When the virus is passing through
the intestine it can enter the blood stream because it will invade the lymph
nodes and Peyers patches.
After the poliovirus invades the bloodstream it may then invade Nerve cells
and cause paralysis. The paralysis caused by the Poliovirus is not due to the
viruss effects on muscles but its effect on the Nervous system.
The infection by poliovirus may be asymptomatic in some patients. Other
patients may experience a mild illness characterized by fever, malaise,
headache, drowsiness or vomiting.
Other patients may have an asceptic meningitis caused by the poliovirus.
In the worst cases some patients may have paralytic poliomyelitis. This is
characterized by a flaccid paralysis from lower motor neuron damage. This
flaccid paralysis may persist for 6 months.

Diagnosis of Poliovirus depends on the stage that the virus is in. In response
to the poliovirus there will be antibodies synthesized which can last for the
rest of the patients life. The first antibody is IgM, then IgG and finally followed
by IgA. The synthesis of IgA is important since the virus may be present in the
mucosa. This developed immunity will be permanent.
Diagnosis of poliovirus may be by: throat swab (in the beginning of the
infection); CSF sample(if the patients has meningitis symptoms). The
Poliovirus can be cultured in MKC. The virus may also be typed by antibody
antigen tests. Molecular methods such as PCR are also effective in the
diagnosis of Poliovirus.

POLIOVIRUS PREVENTION

Poliovirus is rare in industrialized countries.

There are effective vaccines such as the Salk vaccine which is made up of
the inactivated virus. This is the vaccine that is most commonly being
administered in the US. This is because the Sabin vaccine caused
symptoms in immunocompromised persons (since it is an attenuated virus).
There is also a Sabin vaccine which consists of live attenuated virus. This is
also known as the oral polio vaccine (OPV). The OPV should not be given to
immunosupressed patients.

COXSACKIEVIRUS PATHOGENESIS this is another enterovirus.

COXSACKIEVIRUS GROUP A
In the Group A coxsackievirus group there may be up to 23 immunological
types. Their infections may cause herpangia (fever, sore throat, vomiting,
pain). This virus may also cause the hand/foot/mouth disease which is
characterized by a vesicular rash or ulcers on hands, feet and toes. Another
possible symptom by this virus is acute hemorrhagic conjunctivitis. All of
these are extremely contagious.

COXSACKIEVIRUS GROUP B
In this group of viruses there are only 6 immunological types. The group B
Coxsackievirus affects internal organs and may cause: myocarditis,
pericarditis, pleurodynia (fever/chest pain), pancreatitis or
meningoencephalitis.

Both Coxsackievirus A & B may cause asceptic meningitis or perinatal

heart damage. Perinatal heart damage may occur when the mother
becomes infected with Coxsackievirus in the last trimester of the
pregnancy.

COXSACKIEVIRUS DIAGNOSIS

Depending on the stage of the infection will depend the method in which
specimens are acquired. This may be by throat washings, stools, conjunctival
swabs or others.

An identification of a virus infection by antibody production is only

possible if there is a 4-fold increase in the titer of antibodies. This
means if the amount of antibodies quadrupled; then we can be sure
that the patient did have a viral infection.

ECHO VIRUSES
These are known as Enteric cytopathogenic Human Orphan Viruses
(ECHO).
Echo viruses infect the human enteric tract. There are more than 30 serotypes
of echoviruses.
Echo viruses can only be recovered in certain tissue cultures. Some serotypes
of echoviruses can cause an asceptic meningitis with rash, infantile
diarrhea or colds.

Enteroviruses typically cause infections in the summertime.

OTHER ENTEROVIRUSES
Enterovirus 68 can cause bronchiolitis or pneumonia in children.
Enterovirus 70 may also cause acute hemorrhagic encephalitis.
Enterovirus 71 may cause meningitis, encephalitis or paralysis.

RHINOVIRUSES these viruses are also members of the Picornaviridae

family.
RHINOVIRUSES
These are the agents of the common cold. Rhinoviruses may be isolated from
the nasal, oral and throat secretions. The Rhinoviruses typically cause upper
respiratory tract infections since they grow best at cool temperatures such as
33 degrees C.
Rhinoviruses are acid labile; for this reason they cannot pass through the
intestine.
There are more than 100 serotypes of Rhinoviruses. This means that there are
over 100 viruses that can cause cough. Some of these infections may descend
to the lower respiratory tract if their defenses or weak or if they are
susceptible to diseases such as athsma.
The virus can bind to receptors on the ciliated epithelial cells of the
respiratory tract. The virus will then enter these cells and commence
replication. It is in this process that the patient will develop a cough until
these cells recover.

The viral replication of Rhinoviruses typically occurs in the nose.

There is synthesis of IgA and IgG but there are too many serotypes.
There is an innate immune response that involves the production of
interferon. Interferon will help prevent infection of nearby cells.
Sadly there may be the release of cytokines that further promote the spread
of viral infection. What these cytokines do is that they will increase the
expression of the receptor that Rinovirus uses, being ICAM-1. The produced
cytokines by the cells will help upregulate the amount of ICAM-1
receptors that are expressed.
So in the case of Rhinovirus; interferon will help protect the organism
meanwhile cytokines will have a counterproductive effect on the immune
response of the organism.

EPIDEMIOLOGY OF RHINOVIRUS

Transmission of Rhinovirus is by direct contact and fomites. Everybody is at

risk for contracting Rhinovirus. Prevention is by washing hands and
disinfection of all surfaces.
Currently there are no vaccines against Rhinovirus.

CALICIVIRIDAE these are RNA (+) viruses that lack a lipid envelope.
There are two members of the Calciviridae family:
a) Sapovirus this is known as the Sapporo like virus or Calicivirus.
The Sapovirus is an agent of gastroenteritis in children. It is
located in the areas of Asia, Japan, United Kingdom. The
Sapovirus cannot be grown in cell cultures.
b) Norovirus this virus was isolated from Norwalk Ohio. It is usually
found in contaminated water, food and shellfish. The Norovirus
also produces an associated gastroenteritis. The
gastroenteritis is 24 to 48 hours and is usually due to ingestion of
contaminated food. The Norovirus is grown in cell cultures.

PATHOGENESIS OF SAPOVIRUS AND NOROVIRUS

The incubation period is of 16-48 hrs. Symptoms may last 24-48 hrs. The
symptoms associated with infection by Sapovirus and Norovirus are diarrhea,
fever, abdominal cramps, headache and malaise.

CORONAVIRUSES
These are viruses that have a lipid enveloped helical capsid. These
viruses, under EM, appear to have a crown around them.

Viruses that have a lipid envelope usually contain glycoproteins that project
into the membrane; as spikes. These glycoproteins will be known as the viral
attachment proteins. This means that these glycoproteins will bind to the
receptor of the cell that the virus is to infect. These glycoproteins may have
hemagglutinin and neuraminidase. Hemagglutinin will cause agglutination
of the RBCs.
Coronaviruses are also able to cause the common cold. Coronaviruses are
also associated with the SARS virus.

REPLICATION OF CORONAVIRUSES
The coronaviruses will attach to the epithelial cells and they will enter the
cytoplasm with their capsid by way of endocytosis or fusion. This is
different from Picornaviruses in which only the RNA enters.
All of the Coronavirus replication occurs in the cytoplasm. Initially there is the
production of early proteins such as RNA polymerase. This is then followed by
the RNA replication. And finally there is production of late proteins which are
then exert a function as structural proteins.
The viruses are then assembled in the cytoplasm and they will exit via
exocytosis.

SEVERE ACUTE RESPIRATORY SYNDROME (SARS)

There were worldwide outbreaks in China and Canada. The SARS virus is
caused by a new strain of Coronavirus which is distinctly related from the
coronaviruses that cause the common cold.
SYMPTOMS OF SARS
SARS usually begins with a high fever, headache, body aches, mild respiratory
symptoms. Diarrhea was only seen in 10-20% of cases. MOST OF THE
PATIENTS developed pneumonia.

HOW SARS SPREADS

SARS disseminates by close person person contact. SARS is transmitted by
respiratory droplets from cough or sneezes.
Virus can enter into the nose, mouth, eyes or contaminated surfaces.
Currently there have been no current SARS transmissions worldwide.

TOGAVIRUSES AND FLAVIVIRUSES these are also RNA (+) viruses that
contain a lipid envelope.
Arboviruses are viruses that are arthropod born; they are transmitted by
arthropods form one vertebrate host to another. Insects will propagate the
virus, so, vertebrates end up becoming accidental hosts.
The lifecycle usually alternates between insects and humans which are the
accidental hosts. Arboviruses may amplify their replication in small mammals
or birds. This mechanism allows the virus to migrate quickly from area to
another and it can disseminate easier also.

Roboviruses - are found in ruminant animals and they may also have ticks
as their vehicles of transmission.

TOGAVIRUSES
Within the Togaviruses we can find the equine, western, and venezuelan
encephalitis virus. All these are encephalitis viruses that will affect horses.

FLAVIVIRIDAE
Members of the Flaviviruses are Dengue, Japanese Omsk, West nile virus,
Yellow fever.

TOGAVIRIDAE
These are enveloped icosahedral viruses composed of single stranded
RNA. They have two glycoproteins which aid in adherence to target cells.
These glycoproteins will be hemagglutinins.
There are two genera of viruses:
1) Alphavirus all of the alpha viruses are transmitted by arthropods
and they cause infection in horses.
2) Rubivirus Rubella. This is the only exception of the Togaviruses
because it is NOT transmitted by an arthropod.

FLAVIVIRUSES these are RNA (+) lipid enveloped viruses.

Flaviviruses also contain hemagglutinins.
In this family there are other viruses such as :
a) Dengue this may cause dengue fever, dengue hemorrhagic
fever or dengue shock syndrome.
b) St. Louis virus this virus causes encephalitis.
c) West Nile Virus this virus also causes encephalitis
d) Yellow Fever

FLAVIVIRUSES DENGUE
When a person has been infected with more than one dengue serotype then
the next infections tend to cause dengue hemorrhagic fever or dengue shock
syndrome. There are four dengue serotypes in PR; these are DEN 1,2,3,4.
Patients will develop a lifetime immunity for each serotype. The severity of
DHF infectio: DEN 2>3>4>1.
The neutralizing antibodies produced against one serotype of virus
will only protect the persons against that serotype. This leaves the person
susceptible to disease and infection produced by the other dengue virus
serotypes.

Dengue is endemic of the Carribean and Asia.

DENGUE CLINICAL DESCRIPTION
Dengue fever the person has headache, fever, generalized, rash, myalgia
and thrombocytopenia
Dengue hemorrhagic fever and dengue shock syndrome this is a much more
severe form. Due to the thrombocytopenia the person is at a higher risk for
hemorrhages. The vessels may become leaky and increased in permeability.
This may cause extreme shock and possibly death.
The current epidemic of dengue has been said by the CDC to be due to the
climate shift and ever increasing temperatures. A strong El Nino effect is
occurring in PR at 2010. The increase in temperature and rain has caused an
increase in dengue cases.
With dengue there may be antibody dependent enhancement upon
reinfection. In the first infection antibodies are produced against dengue.
Upon reinfection these antibodies may aid the virus in penetration into the
host cells.

FLAVIVIRUS WEST NILE VIRUS

The West Nile Virus was first isolated in Uganda (1937). The virus has spread
to the USA.
Some symptoms of the West Nile Virus are a mild dengue-like illness (20%) or
the infection may be asymptomatic (80%). In 1% of cases an encephalitis,
meningitis, acute flaccid paralysis and anterior myelitis may be caused.
Infants, elderly and the immunocompromised are at risk for infection by the
West Nile Virus.

RNA (+/-) VIRUSES

REOVIRIDAE
The reoviruses have a double icosahedral capsid. Their genome is composed
of double stranded RNA with about 10-11 segments (segmented). Since the
Reovirus genome is segmented; these may undergo genetic reassortment
in order to increase the genetic variability of the Reoviruses.
Reoviruses are stable to heat, pH, lipid solvents but they may be
inactivated by 70% ethanol.

REPLICATION OF REOVIRUSES the reovirus replication occurs in the

cytoplasm of the cell
1) First there is the loss of the outer capsid.
2) Then there is cleavage of the infectious subviral particle (ISVP);
this means that it will lose the second capsid.
3) Binding and endocytosis
4) In the cytoplasm the virus undergoes replication, transcription
and translation.
5) The virus then buds into the ER to acquire the outer capsid.
6) The virus will lose the envelope and it is released by cell lysis.

REOVIRUS FAMILY
Includes 8 genera; four of which affect humans:
A) Rotavirus - this is a major agent of diarrhea in children.
B) Orbivirus/Coltivirus this infects insects and causes mild fevers in
humans. An example if the Colorado tick fever.

ROTAVIRUS

Rotavirus is the single most important cause of diarrhea and gastroenteritis in

children around the world. Up to 50-60% of hospitalized children with acute
gastroenteritis, will be due to Rotavirus. In developing countries 3.5million
deaths of preschool children has been due to severe Rotavirus induced
infection.
Rotavirus predominates in the winter and it has an incubation time of 1-4
days. Rotavirus usually produces symptomatic infections at 6months-2 years
of age. Rotavirus infections can be picked up in day care centers and it is
highly contagious. The symptoms of a Rotavirus infection are diarrhea, fever,
abdominal pain, and vomitingall leading up to inevitable dehydration.

ROTAVIRUS PATHOGENESIS
Rotavirus has the ability to multiply in the cytoplasm of cells of the small
intestine. The symptoms of Rotavirus are caused by the non-structural 4
protein (NSP4) which is a viral enterotoxin that induces the secretion of water
and electrolytes.
The Rotavirus may also damage transport mechanisms and it may also cause
glucose and sodium malabsorption.
The child may be secreting contagious viral particles for 2-12 days. The
Rotavirus may be acquired by inhalation or by oral-fecal contact with
contaminated surfaces.

ROTAVIRUS DIAGNOSIS
Rotavirus can be isolated from the stool. Other techniques such as electron
microscopy, ELISA, latex agglutination, gel electrophoresis, Rotavirus-PCR.
Serology is also effective for Rotavirus diagnosis during the acute and
convalescent phases.

ROTAVIRUS TREATMENT
Treatment for Rotavirus is by replacement of fluids as soon as possible in
order to prevent infant mortality. A new vaccine has been developed, known
as Rotateq, which consists of an attenuated version of the virus. The Rotateq

can protect the person against the 5 most common virus strains. The Rotateq
virus can be given by mouth at 2,4, and 6 months.

ORTHOMYXOVIRUSES these are RNA (-), enveloped, single stranded RNA

viruses, they also have a segmented genome.
The only member of the Orthomyxovirus family is Influenza.
There are three serotypes of influenza: A, B, C.
Within the lipid envelope, Influenza has two glycoproteins:
1) Hemagglutinin
2) Neuraminidase
Influenza is an interesting Orthomyxovirus because it replicates in the cell
nucleus.
Influenza is one of the most prevalent and significant viral infections.

ORTHOMYXOVIRUS REPLICATION
1) Influenza, by way of the hemagglutinin in its lipid envelope will bind
to the receptor (sialic acid) on the membrane of the cell that it is going
to infect.
2) The virus then enters the cytoplasm completely by budding.
3) Once the pH in the vesicle drops then the virus is uncoated in the
cytoplasm and the RNA (-) genome is subsequently released.
4) The RNA(-) genome will migrate and enter the nucleus. Once in the
nucleus it will transcribe into RNA(+).
5) The RNA (+) will then exit the nucleus in order for it to be translated in
the ribosomes. There is going to be subsequent production of
important proteins.

6) The virus is then assembled in the cytoplasm and it buds off from the
plasma membrane in order to exit the cell.

INFLUENZA ENVELOPE PROTEINS

A) Hemagglutinin (HA) : this is a trimmer viral attachment protein that
binds to the sialic acid receptor on the epithelial cells that it is going to
affect. The attachment is then followed by a fusion effect. HA has the
ability to hemagglutinate human, chicken and guinea pig RBCs.
Hemagglutinin is antigenic; for this reason HA will be responsible for
eliciting the protective neutralizing antibody response. HA is used as an
antigen in vaccines.

B) Neuraminidase (NA) : this is a dimmer that acts at the end of the

replicatory life cycle of the virus. Neuraminidase will prevent virus
aggregation. NA is also antigenic, this means it will elicit a protective
neutralizing antibody response. The neuraminidase is the target of the
antivirals zanamivir (Relenza) and ostealmivir (Tamiflu).

THREE INFLUENZA SEROTYPES

Type A this serotype is the only one that can infect humans and animals.
This type is the one serotype that causes most epidemics and pandemics.
Type A influenza can undergo reassortment or antigenic shift. Once there is
antigens are changed, then the previously produced antibodies are
ineffective.
Type B this serotype only infects humans. Type B influenza has caused
epidemics and it only undergoes antigenic drift.
Type C this serotype of influenza infects humans but it a relatively mild
fashion. It may cause minor respiratory illness and it is genetically stable.
Since the infection by the Influenza Type C is mildit is not included in the
vaccine.

Reassortment of genes in Type A influenza can create new strains of influenza

that may be transmitted from animals to humans. This is the case of last

years H1N1 outbreak. Due to the genetic reassortment, all previously

produced vaccines are rendered ineffective.
Up to the moment there have been reported 14 different types of
Hemagglutinin and 9 types of Neuraminidase.

INFLUENZA PATHOGENESIS
Influenza is transmitted by aerosols. The incubation period of Influenza is 1-4
days. Influenza may cause headache, fever and myalgias. These are nonspecific symptoms.
The influenza infection may become complicated with bacterial infections
such as Streptococcus pneumonia, S. pyogenes and Hamophilus influenza.
Influenza may also cause Reyes syndrome, and is associated with aspirin
usage. The syndrome of Guillan Barre may also occurrarely causing
damage to the CNS.
The influenza virus may be excreted for 1-2 days but the weakness may
persist for 1-2 weeks.
INFLUENZA PNEUMONIA
The influenza virus may target and destroy the mucus-ciliated and other
epithelial cells of the respiratory tract. This is due to the fact that they all
contain the sialic acid receptor.
Neuraminidase facilitates access to tissues. The Influenza virus may cause
severe desquamation of bronchial alveolar epithelium. The virus may
also promote bacterial adhesion to epithelial cells.
Influenza pneumonia arises as a result of viral pathogenesis or from
secondary bacterial infections.

DIAGNOSIS OF INFLUENZA
The virus can be recovered from specimens containing respiratory secretions.

Diagnosis can be done by rapid antigen detection tests either by

immunofluorescence.
Serology may also be done for epidemiologic purposes samples should be
taken in the acute and convalescent phases.
Molecular methods of diagnosis include RT-PCR.

INFLUENZA PREVENTION TREATMENT

The vaccine is revised each year and it should be used. The vaccines are
composed of subunits of hemagglutinin and neuraminidase. These
vaccines are highly effective in adults and less effective in elderly.
The influenza vaccine may be given inactivated, intramuscular,
attenuated or nasal.
Seasonal Flu Vaccines / H1N1 Vaccine

ANTIVIRALS
Amantidine and Rimantadine will inhibit the replication of Influenza A viruses
by preventing their replication. The mechanism of these antivirals involves the
prevention of RNA entry into the nucleus.
Neuraminidase inhibitors act at the end of infection (examples zanamavir and
oseltamivir). The neuraminidase inhibitors will prevent virus disaggregation
which is necessary for all the particles to become infectious.

PARAMYXOVIRUSES these are enveloped Viruses that have a helical capsid.

Their genome is linear and non-segmented.
The paroxamyxovirus has two glycoproteins:

A) Hemagglutinin
B) G-proteins this glycoprotein is important in the
respiratory syncitial virus.

There are many members of this family: Mumps (4 serotypes); Measles,

Respiratory Syncitial Virus (RSV) and the Metapneumovirus is also included in
the Paramyxovirus family.
All viruses in the Paramyxovirus family will cause cell fusion; thus creating a
large cell composed of many cells. This is also known as a sincytium.
All viruses contain hemolysin and hemagglutinin except RSV. Only the
Mumps virus has neuraminidase.
Additionally all viruses cause cytoplasmic inclusions except measles which
causes inclusions in the cytoplasm of the nucleus.

REPLICATION OF PARAMYXOVIRUSES
1) These viruses use the viral attachment protein in order to
bind to the sialic acid of the host cell.
2) The virus penetrates the cell by fusion.
3) RNA replication occurs in the cytoplasm
4) After replication the viruses will exit the cell by budding.

PARAINFLUENZA VIRUS (PIV)

There are four serotypes of the Parainfluenza virus.
PIV type I can cause laryngotracehobronchitis or croup.
PIV type II causes milder lower respiratory tract disease.
PIV type III this serotype of the parainfluenza virus can cause pneumonia
and broncheolitis in children that are less than 6 months of age.

MUMPS
MUMPS virus is an acute and very contagious disease. MUMPS is highly
contagious and spread by respiratory transmission.
The MUMPS virus can cause bilateral parotid gland enlargement but it may
also be unilateral. There may be involvement of submaxillary and sublingual
glands. The parotid glands are not affected by the MUMPS virus.
Complications of Mumps arise when there is CNS involvement. Once the CNS
is involved there may be manifestations such as meningoencephalitis,
fever, headache, vomitins, nucchal rigidity and irritability.
Before specific symptoms arise the virus replicates and may be in the
contagious transmission phase. Transmission is by the respiratory route. The
virus may be also secreted in the urine 14 days after the infection.

MUMPS PATHOGENESIS
Some 30% males can develop a testicular infection (orchitis) that may result
in atrophy. Sterility is rare but it may occur as a result of bilateral orchitis.
Other rare manifestations include ovarian involvement, pancreatitis, nephritis,
thyroiditis, myocarditis and deafness. Meanwhile, 30% of infected person will
not demonstrate any apparent symptoms.

MUMPS DIAGNOSIS AND PREVENTION

Diagnosis of a Mumps infection may be by serology during the acute and
convalescent phases. Serology must indicate a 4X increase in antibody titer in
order to indicate an acute infectious process.
A vaccine has been available since 1967. The vaccine consists of an
attenuated virus which is 85% effective. The mumps vaccine is given in
combination with measles and rubella (MMR).

MORBILLIVIRUS: MEASLES
The Measles is a dermotropic virus. Measles causes respiratory symptoms,
rash, fever. Complications become reduced by vaccination. Measles is still a
major cause of death in children within developing countries.

MEASLES PATHOGENESIS
When there is a Measles infection there is an incubation phase that may last 2
weeks. During the incubation phase the patient has a respiratory infection and
he may be spreading the virus (contagious).
About one day before the rash occurs; there will be the appearance of
lesions in the mouth known as Koplik spots. The Koplik spots are an
immunologic Rx to the virus.
During the recovery phase (7 days after rash outbreak) , encephalitis may
occur. Years after infection there may also be the occurrence of a subacutesclerosing-pan-encephalitis. This can occur due to an immunologic defect in
which the virus is not completely removed.
The virus can be recovered from the WBCs several days before the rash
appears and thereafter.
The pathology of the CNS includes edema, congestion and petechial
hemorrhages. Giant cells form with inclusions; in the lymphatic tissue. This is
due to the fact that these viruses tend to create syncitiums of cells.
Koplik spots are viral aggregates that appear in the mouth a day or two
before the onset of the rash. Keep in mind that the Measles rash is an
inflammatory response; so that there are no viral particles within the rash. The
rash merely reflects one of the effects of cell mediated immunity.

MEASLES COMPLICATIONS

There is a complication known as subacute sclerosing panencephalitis

(SSPE). This is a degenerative disease of the brain that occurs in children and
predominantly in boys.
This SSPE occurs because there was a defect in the removal of the measles
virus by the immune system. This means that the measles virus persisted in
these patients following initial infection in infancy or childhood. SSPE is
not common.

MEASLES DIAGNOSIS
The diagnosis of measles is made based upon symptoms and clinical grounds.
Serologic tests may be done early and after (7-14 days of infection). The
serologic tests must show a 4X increased antibody production.

MEASLES VACCINATION
An attenuated virus vaccine is given along with mumps and rubella (MMR). At
15-24 months and 4-6 years.

RESPIRATORY SYNCITIAL VIRUS

The RSV does not have neuraminidase or hemagglutinin activity. The
incubation period of RSV is of 4-5 days. Infection may begin as an upper
respiratory tract infection (nasal congestion, pharyngitis, cough, fever). The
RSV may replicate in the mucosal epithelial cells and macrophages.
In adults, infection with RSV is contained in the upper respiratory tract. In
children RSV is the most important cause of lower respiratory tract
infection (bronchiolitis and pneumonia) in infants from 6-weeks to 6
months of age.

Metapneumovirus this is a new pneumovirus that causes 15% of common

colds. It is complicated by otitis media.
RSV makes cells fuse in order to create a syncitium. When the RSV virus
replicates it will cause cellular membrane fusion.

RSV DIAGNOSIS
The virus may be isolated; but usually serology is used for diagnosis.
Diagnosis may also involve RNA detection. Most labs use antigen detection in
order to diagnose infection

TREATMENT
There are no vaccines available. No specific treatment is available except
antipyrogenics.
Children may require oxygen therapy and mechanical ventilation.
In patients with a severe disease; the aerolized form of RIbavirin may be
used for treatment.
In patients who are immunocompromised; these may receive preformed
antibodies as a mechanism for therapy.

PREVENTION
Development of RSV vaccine is a high priority. Prevention by way of hygiene
and usage of preformed antibodies are the only ways we can lidiate with this
infection.

TOGAVIRUS FAMILY : RUBELLA

Rubella is not transmitted by interactions with arthropod vectors. Rubella
may clinically resemble the measles virus and it may cause German
measles.
Rubella is regarded as a benign childhood rash disease. In 1941 Rubella was
found to cause congenital malformations resulting from maternal Rubella

during the first 4 months of pregnancy. If the mother is infected within the first
4 months of pregnancy then the fetus cannot be born because the virus
upsets the mitosis.

RUBELLA PATHOGENESIS
Rubella is spread by respiratory tract transmission. It may spread to
lymphatics and then to the blood.
There may be Viremia and respiratory shedding of the virus that precede
the viral rash by 1 week. The incubation period of Rubella is 2 weeks with
minimal symptoms.
Rubella may cause fever and respiratory symptoms. There is a mild rash
known as an exanthema which consists of pink macules and papules first on
the face and then on the neck, trunk and extremities. These which last 3 days.
Bone involvement is a rare complication that may occur in women.

CONGENITAL RUBELLA SYNDROME

The Rubella virus can pass the placenta. The infection may occur in the first 4
months of pregnancy.
The Rubella infection in human embryonic cells is associated with
chromosomal breakage and inhibition of normal mitosis.
The congenital rubella syndrome may cause fetal death, abortion or neonatal
death.
The defects that rubella may cause in a fetus include: deafness, congenital
heart disease, eye defects, growth retardation, thrombocytopenic purpura,
osteitis, encephalitis, pneumonitis, mental retardation and diabetes mellitus.
The infected neonate may continue to harbor the replicating virus and
excretion of such virus may persist throughout the first year of life.
RUBELLA PREVENTION
A vaccine for Rubella has been available since 1969. Thevaccine consists of
an attenuated live rubella virus that will stimulate IgA, IgM and IgG
production.

Rubella vaccine is available as a single antigen or it may be given in

combination with measles and mumps vaccines (MMR). Immunity lasts for
10 years. This means that boosters should be given in the reproductive age.

RHABDOVIRUSES
This is an RNA (-) virus that is lipid enveloped and wrapped in a bullet shaped
helical capsid. A common rhabdovirus is the virus of rabies.
The genome of Rhabdoviruses consists of a linear RNA(-) non segmented
genome.
Rhabdoviruses contain a G-protein which is a Viral Attachment Protein
(VAP). The diseases that are commonly caused by Rhabdoviruses are rabies
and less commonly the foot and mouth disease.

RHABDOVIRUS REPLICATION
The receptor to which the Rhabdovirus VAP binds to will be the acetylcholine
receptors of nerve cells. This means that the rhabdovirus will have to reach
the brain in order to cause infection and damage.
Rhabdovirus replication occurs in the cytoplasm of the infected cell. The
virus will then assemble in the cytoplasm and it will bud off from the cell
membrane.

RABIES
Rabies consists of an acute infection of the CNS that is always fatal.
Transmission of Rabies to humans is usually by a bite from a rabid animal.
Rabies can spread through animal reservoirs.

RABIES PATHOGENESIS

Due to rabies there is demyelinization of the white matter; leasing to axon

degeneration as well as degeneration of the myelin sheaths.
Infected cells may present with eosinophilic cytoplasmic inclusions;
known as Negri bodies. The presence of Negri bodies occurs in 20% of the
cases. But if the Negri bodies are observed this is then diagnostic for
rabies.

RABIES INFECTION
The incubation period of rabies varies from 2-16 weeks. This is usually
determined by the time it takes to reach the CNS. The incubation period may
be as short as 10 days or may be a year long.

FOUR PHASES OF RABIES DISEASE

Prodromal phase (2-4 days) with malaise, anorexia, headache, nausea,
vomiting, sore throat and fever. There may be overactivity with
lacrimation/papillary dilatation, increased salivation and perspiration.
Additional symptoms of a rabies infection are hallucinations, muscle
spasms, drooling due to painful swallowing. The patient may also have
convulsions, seizures or coma and death by respiratory paralysis.
Recovery and survival from a rabies infection is rare.

RABIES PREVENTION
There are vaccines of inactivated viruses such as the Human Diploid Cell
Vaccine; or the Rabies Vaccine Absorbed with aluminum phosphate &
inactivated.
There are also mechanisms of passive immunity that may be used for
prevention. This consists of administering preformed antibodies. Such
treatments are known as the Human Rabies Immunoglobulin (HRIG). This
is given around the bite and intramuscularly.

ARENAVIRUSES
Arenaviruses under EM appear to have sand in them. This morphology is due
to the presence of ribosomes within the capsid. Arenaviruses are viruses
that contain an envelope with RNA (-).
The genome of Arenaviruses is circular and consists on 2 segments. One
segment is RNA (-) and the other is ambisense.

Arenaviruses can cause:

A) Hemorraghic fevers
B) Lymphocytic choriomeningitis influenza like disease with
meningitis.

Examples of Arenaviruses are Lassa fevervirus which can cause hemorrhages.

Lassa fever is found in Africa. Other viruses may be found all throughout
South America.

SYMPTOMS OF ARENAVIRUS HEMORRHAGIC FEVERS

Lassa Fever is endemic to West Africa. Symptoms consists of fever,
coagulopathy, petechia, hemorrhages, necrosis. There is also pharyngitis,
diarrhea and vomiting.
ARENAVIRUSES ARE TRANSMITTED BY THE RESPIRATORY ROUTE this means
that they must be isolated in biolabs with a phase 3 or phase 4 security.

FILOVIRUSES
Symptoms of Filoviruses resemble the arenaviruses.
Filovirus genome consists of a linear RNA (-) genome.
Important examples of filoviruses are the: Marburg and Ebola viruses.

Filoviruses are enveloped filaments that have a helical capsid.

Filoviruses can cause severe hemorrhagic fevers and death.

MARBURG AND EBOLA

These viruses are endemic to Africa. These viruses cause extensive necrosis of
the liver, spleen, lymph nodes and lungs.
Death is by edema and shock.
Marburg and Ebola viruses are associated with animals (monkeys) to human
transmission. They are very contagious. Virus handling requires a BL4 facility.

BUNYAVIRIDAE
These are spherical, enveloped, and they have an RNA (-) genome.
Bunyaviruses may also replicate in the cytoplasm.
There are four genera in the Bunyavirus family but the most important are the
Bunyaviruses and the Hantaviruses.

BUNYAVIRUS
These are arboviruses because they are transmitted by arthropods. The
Bunyaviruses may cause encephalitis and meningitis.

HANTAVIRUS
Hantavirus is a Robovirus that is transmitted by way of aerosols and
excretions of rodents. The Hantavirus is associated with hemorrhagic fever
and hantavirus pulmonary syndrome (which is of high mortality).

RETROVIRUSES (RNA+) THAT HAVE A DNA INTERMEDIARY

RETROVIRUSES
These are enveloped viruses that have a capsid and two identical copies of
RNA (+) genome. Retroviruses also have a special RNA-dependent DNA
polymerase; this enzyme is also known as the reverse transcriptase.
Retroviruses also carry integrase enzymes with them in the virion. These
integrase enzymes help the retrovirus integrate its genome into the
chromosome of the cell.

Replication of retroviruses is through a DNA intermediate (provirus) that

integrates itself into the host chromosome and it will become a cellular gene.

There are simple retroviruses such as the Avian Leukemia Virus that contain
the basic components of a retrovirus. They have LTR genes which are
repetitive sequences that help with the integration of the genes into the DNA.
There is also gog genes that will code for the core proteins. There is a pol
gene that will code for reverse transcriptases and the integrase. And finally
there is also envelope proteins that code for the synthesis of the viral lipid
envelope.

Complex Retroviruses these viruses will contain most of the genes that
simple retroviruses have; but they will also include other genes that will help
the infection. These extra genes will help the infection escape the immune
response.

RETROVIRUS SUBFAMILIES

Oncovirinae this viruses have the ability to cause cancer and other
neurological disorders. In this family there is the HTLV-1 and HTLV-2 (human Tcell leukemia virus) viruses.
Lentivirinae these are slow growing viruses. These are associated with
neurological disorders and immunosupression. In this family we can find
HIV-1 and the HIV-2 viruses.
Spumavirinae a member is the Human Foamy Virus. This does not cause
human disease.
Endogenous Viruses examples of endogenous viruses are the human
placenta virus.

RETROVIRUS REPLICATION
1) Recognition
2) Attachment the virus attaches via its glycoproteins to the host cell.
3) The virus will then fuse its membrane with that of the host cell
4) Penetration
5) In the cytoplasm the retroviruses (+RNA) will synthesize a molecule of
DNA using the reverse transcriptase. This is then followed by a drop in
pH which will destroy the capsid.
6) The newly formed DNA will then become transcripted into a double
stranded DNA molecule. This molecule of dsDNA will then proceed to
the nucleus.
7) Using the LTR sequences, this will help the dsDNA integrate itself into
the genome of the host cell. Here the retroviral dsDNA sequence may
be quiescent (latent) or it may become activated due to changing
cellular factors. Once it becomes activated, the viral replication will
begin.
8) After this there will be viral assembly and exit from the cell by
budding.

HTLV-1 AND HTLV-2

These viruses are members of the Oncoviridae family.

HTLV-1 virus has affinity for T-cells. This virus can cause a cutaneous
lymphoma and Tropical Spastic paraparesis which is a CNS disease. The LTR
gene of the HTLV-1 virus will induce T-cell proliferation.
HTLV-2 virus this virus is not associated to a specific disease.

LENTIVIRIDAE
The members of this family are HIV-1 and HIV-2. These are surrounded by a
lipid envelope and they have an icosahedral capsid. The HIV-1 and HIV-2
viruses have nuclear replication and assembly in the cytoplasm.

PROPERTIES OF LENTIVIRIDAE
Lentiviruses tend to persist lifelong. The Lentiviruses also have high mutation
rates.
Depending on the illness there is a high degree of variation in disease
presentation. There will also be a variation in the time of disease onset (this
may be due to genetics, age, stress or viral factors.
The infection proceeds through 3 stages. These being the Acute Infection, the
latent period, and the period of a high level of viral replication.
There is a high degree of phylogenetic relationship between the HIV and
the Simian Immunodeficency Virus.

There are different varieties of HIV virus. In USA, South America and Europe;
the B HIV subtype predominates. In ASIA the B and C recombinant forms of
HIV predominate. There is a higher incidence of HIV associated
dementia in persons who are infected with the B- variant of HIV than
with the C-variant of HIV.
The C-variant of HIV has a high incidence in INDIA.

The HIV glycoprotein (gp120) will be the one that helps the virus bind to the
host CD4 cell that it will infect. The p24 protein will be the important
component of the capsid. This is important because when using antibodies in
Western Blot; the antigens the antibodies look for will be gp120, p24,
integrases, reverse transcriptase and other antigens.

Complex retroviruses will have additional auxiliary genes. An important

auxiliary gene seen in HIV is the tat gene which is a transactivator of
transcription. The tat gene helps the virus transcribe itself quickly, the tat
gene will also activate replication. The tat gene is also secreted from the cell
and it may cause neuron death. The nef and rev proteins also function
as negative regulatory factors and they also regulate the expression of
virion proteins.

HIV-1 is said to have many different co-receptors apart from the CD4 receptor.
There are other receptors involved that are necessary for an effective
infection. The most common coreceptors are the CXCR4 receptor (chemokine
receptor). If one blocks the CRXC4 then the infection cannot proceed; this is
seen when the CD4 is bound to stromal derived factor.
In macrophages HIV uses CD4 receptors and the CCr5 receptor
(chemoreceptor). If one adds the chemokines for the CCr5 receptor which are
Mip-1alpha and Mip-1beta then the virus cannot infect the macrophage.
Persons with a high amount of chemokines, a component of innate immunity
will be less susceptible to become infected by HIV. Some persons in Europe
have a delta-32 mutation in which they do not produce the CCr5 receptor.
These persons are resistant to infection by way of HIV. This is because the
initial strains of HIV will use the CCr5 receptor.

HIV-1 is transmitted mainly by sexual transmission or by infected needles

(drug users). HIV-1 also has vertical transmission from mother to fetus.

HIV-1 PATHOGENESIS
The HIV-1 virus primarily infects CD4 cells and macrophages. The virus causes
lytic death of CD4 cells and it becomes a persistent low-level productive
infection of macrophage lineage cells. Macrophages serve as reservoirs
for the HIV-1 virus. Keep in mind that in lymphocytes the virus replicates
rapidly and it will cause their lytic death.
Macrophages are responsible for taking the virus to the CNS. HIV-1 alters
lymphocyte and macrophage function.
HIV-1 may cause syncitia formation with cells expressing large amounts of
CD4 antigen.

THE COURSE OF THE HIV DISEASE

First there is an acute infection which occurs 1-2 months after transmission.
There is an increase in p24 which is an indicator of HIV viral replication.
Remember that p24 is the capsid protein. Initially CD4 levels are normalize
because the macrophages will be initially infected. Throughout the course of
the infection the CD4 levels will decrease until the person has AIDS.
After the p24 protein decreases; this means that the acute phase of the
infection is subsiding, then the gp120 antibodies will increase. These are the
anti-HIV antibodies. These anti-HIV antibodies will eventually decrease in the
end stages of this disease.
There is a latent phase in the HIV disease. This latent phase is known as the
chronic lymphadenopathy phase. In this phase it is difficult to detect
viruses in the blood. The virus at this point is replicating within the lymphatic
nodules.
Also in the acute phase there is an increase in CD8 cells which will fight the
HIV virus in the latent phase. In the end stage of HIV the levels of CD8 will
decrease cytotoxic cells wear out.

After the acute phase there is a phase where there is a strong immune
response. During this phase there is production of antibodies against gp120.

During this phase the virus enters a latent period and it is difficultly
identifiable in the bloodstream (virologic set point). During the acute phase
there is a good CD8 response. Also antibodies may appear against surface
and internal proteins but THESE ARE NOT PROTECTIVE. The virus in the strong
immune response phase originates from recently activated and infected CD4
cells. The HIV test will be positive in this period because the immune system
is producing antibodies

LATENT PHASE in the latent phase there is no observable viruses in the

blood. This is because the virus is actively replicating in the lymphatic system.

The beginning of the disease- this is the end point of the HIV virus because
it is the point in which we will begin to observe all the symptoms of
immunodeficiency. The person will fall prey to opportunistic fungi, neoplasm
etc. At the beginning of this stage there is a massive loss of CD4 cells. There is
also increased antigenic variation which will contribute to the virus evading
the immune system. There is also CD4 cell apoptosis. Patients with high levels
of CD4 will NOT develop AIDS.
In the ADVANCED STAGE of the disease the CD8 cells will destroy more
infected CD4 cells. Loss of CD4 cells means that the virus and the infected
cells are no longer controlled. When CD4 cells fall below 200cells/mL the virus
titer increases rapidly and the remaining immune response collapses. In the
advanced stage the CD8 cell number will also collapse. There will also be
opportunistic infections and death may occur within 2 years without
intervention.

There is a good correlation between the measured amount of HIV particles

(measured by PCR) and the progression to disease. The viral load will
predict survival time. A person with a low viral load will be more likely to
last more years. A CD4 count is not a good predictor of the
progression of the disease.

HIV-1 may induce cancers (transformations). This is because other viruses

such as EBV may cause lymphoma in B-cells. The HHV-8 can also cause Kaposi
Sarcoma. The HPV may also cause sarcoma.
Not all cases of Kaposi sarcoma are associated with HIV!

HIV NEUROPATHOGENESIS
HIV may cause subacute encephalitis with dementia (AIDS dementia
complex). Dementia is observed when CD4 levels go below 500. There is an
alteration of the BBB. There is also increased migration of macrophages and
inflammatory cells to the brain. There is astrocyte activation and this can
culminate with neuronal apoptosis.

HIV can be diagnosed by ELISA and this is usually confirmed by Western Blot.
In order for the Western Blot to be reactive (positive) there had to have been
two or more products reacting with the antigens provided in the blott.
Diagnosis by ELISA cannot be done during the acute phase because the
antibodies against HIV will have not been produced yet.

HIV ANTIRETROVIRAL THERAPY therapy consists of reverse transcriptase

inhibitors and protease inhibitors. These protease inhibitors act at the end of
the replication cycle; they will not allow for the maturation of the viral particle.
HAART Highly active retroviral therapy antiretroviral cocktail? This is
combination of two nucleoside analogs and 1 protease inhibitor.
Persons undergoing antiretroviral therapy will have resistant and sensitive
viruses. For this reason antiretroviral therapy compliance is critical in order to
preserve a balance so that there may be no increase in resistant viruses.
There are some new integrase inhibitors that inhibit the integration of the
DNA particle into the genome of the host cell.

HIV-1 Vaccine an ideal vaccine must be able to stimulate the cellular and
humeral immune responses. Vaccine development is attempting to develop a
recombinant virus therapy. These recombinant viruses may not always
stimulate the immune response; this is a problem with current vaccine
development.

PRIONS these are not viruses; they lack a genome but they produce
abnormal proteins. Prions replicate very slowly and the prion proteins are
resistant to heat, chemical agents, irradiation, boiling or formalin. These are
usually transmissible to rodents or primated
The infected brain may appear spongiform and may form vacuoles.
These have little
or no inflammatory response.
Prion disease is restricted to CNS and lymphoid tissues.

Creutzfeld Jakob disease the natural mode of transmission is unknown. It can

be transmitted by contaminated food, medical equipment; 10% of cases have
a mutation that codes for the prion protein.
Kuru this is a fatal prion associated neurological disease in tribes of Papua
New Guinea. It is associated with ritual cannibalism and consumption of dead
family members. Kuru may have a 4-20 year incubation period.

SEROLOGIC AND MOLECULAR DIAGNOSIS

The most common form of viral diagnosis is done by viral culture.

Sequence amplification is also known as PCR.

VIRAL CULTURE
Viral culture is known as the gold standard for viral diagnosis. In a viral culture
we will be looking for the cytopathic effects that the virus causes. Cytopathic

are the specific changes that the virus will produce in the host cell when the
virus undergoes replication. Cytopathic effects will be specific and
distinguishing for each type of virus.
Cytopathic effects such as syncytium formation are very common in the many
families of viruses. This may be caused by herpes, CMV, HIV it is a highly
common cytopathic effect.
Inclusion bodies are proteins or genome accumulations that occur during viral
replication. The size and location of these will depend on the nature of the
infecting virus. Adenoviruses may cause inclusion bodies in the nucleus;
meanwhile the rabies virus causes inclusion bodies in the cytoplasm known
as Guarneri bodies.
The influenza, parainfluenza, mumps, coronaviruses and measles viruses will
cause hemadsorption of erythrocytes to cells. The hemadsorption test is
specific for viruses that cause hemagglutinin.

SEROLOGICAL METHODS
One of the most common and quickest methods is immunofluorescence.
Immunofluorescence is used for detection of specific viral antibodies in a
patients serum or it may also be used to detect specific antigens on the
surface of the hosts cells.
There is a direct from of immunofluorescence: the direct
immunofluorescence is used to detect viral antigens on the cell surfaceusing
an antiviral antibody that has been conjugated with fluorochrome.
The indirect form of immunofluorescence is used to detect specific viral
antibodies in patient serum using a fluorochrome conjugated anti-human
antibody.
SHELL VIAL
This method of diagnosis is useful for CMV. The SHELL vial involves a
combination of viral culture with direct immunofluorescence. The direct
immunofluorescence will involve the usage of antibodies that are specific for
the virus we are looking to identify and diagnose. This methodology is highly
specific.

This technique is highly useful for CMV and the also fore Respiratory Sincytial
Virus (which is important in prematurely born babies).

ELISA
This is another useful test that can be used for antibody detection and
antigen detection.

In serologic methods it is important to have two samples from the patient

one sample during the acute phase and one sample taken during the
convalescent phase. In order for serological methods to result positive for a
viral infection; there must be a minimal increase in antibody concentration
of 4X from the acute phase to the convalescent phase. In ELISA we must
establish cutoff values that allow us to determine that values above these
will be a positive response to a virus and hence a positive diagnosis.

Another effective method for serology involves looking for IgM. Remember
that IgM is an acute phase antibody and its presence would hint at the
presence of an acute viral infection. This would allow us to administer the
appropriate therapy at an adequate time.

HIV-1 ELISA
The ELISA of HIV will be looking for p24 protein. In order to diagnose HIV
effectively we must use the OD which will quantitatively measure the amount
of viral particles in the serum.

Influenza Rapid tests these tests will be looking for the antigen. The tests
consist of units that contain the specific antibody. If the antigenic RX occurs
then various lines will form on the testing trip.
WESTERN BLOT this may be also used in the detection of antibodies and
antigens. Western Blot is used in order to confirm the diagnosis of HIV.

MOLECULAR TESTS HYBRIDIZATION

Steps:
A) Hybridization will be specific
B) DNA/RNA isolation
C) The sample of the genome must be fixed to a support system
D) The genome must be denatured by way of heat or chemicals.
This allows is to become a single strand in order to make it ideal
for hybridization.
E) Hybridization
F) Detection
Hybridization may occur by DOT PLOT.
The Southern Blot is used to identify specific sequences of DNA. Meanwhile
the northern blot is used for identification of RNA sequences.
Hybridization in situ may be used for possible identification of viruses in
organ transplants.

PCR this is a specific method that is used to amplify a certain region of the
DNA or RNA virus. The results of this may be ambiguous.
Nested PCR this adds specificity to PCR.

If a PCR were to be used it should be combined with hybridization or with a

nested PCR. These methods have higher specificity than normal PCR.

MOLECULAR DIAGNOSTIC KITS

Hybrid Capture this is a method that is commonly used for the detection of
Papillomaviruses. Hybrid capture seeks to create a DNA/RNA hybrid. This
hybrid is then captured in tubes covered with an antibody.
These methods can aid in determining the viral load in these patients.

BRANCHED DNA
The branched DNA method is used to measure viral load. There will be
probes that will hybridize with the capture molecule and the DNA or RNA from
the sample.

ANTIRETROVIRAL DRUGS AND THERAPY

Viruses are obligate intracellular parasites that do not carry the metabolic
machinery for normal life processes.