Download Lecture GuideViruses(Ch13)–7e

Lecture Guide
Viruses (CH13)
This chapter is on the general characteristics of viruses and focuses on both
bacterial and animal viruses and their life cycles. Let’s start with a quick look at the
history behind their discovery and then look at the general structure of viruses.
In the late 1800’s (1890) there were scientists working on understanding the
disease agent of plants, specifically tobacco plants. Aldolf Mayer showed that the
infectious agent was transmissible between plants and Iwanowski identified that this
infectious agent was capable of passing through a porcelain filter. These experiments
contributed to a better understanding of a new kind of infectious agent, one that was
capable of passing through filters and was called a filterable virus. In 1914/1915 Twort
and d’Herelle identified the first bacterial viruses and called them bacteriophages.
The basic structure of all viruses consist of a protein coat, called a capsid, made of
individual protein subunits known as capsomeres. Inside the capsid region is the nucleic
acid material, either DNA or RNA. Viruses that have this general structure of a capsid
and nucleic acid core are called naked viruses. Some viruses have an additional layer
around them known as an envelope, which is composed of a phospholipid bilayer. These
are known as enveloped viruses. Both types of viruses can have spikes, proteins used to
attach the virus to a specific marker or target cell. The shapes of viruses can be either
isometric (having 20 equilateral sides) and appear like a sphere, helical and appear rodlike, or complex (a combination of the two).
Review the rest of the general characteristics of viruses mentioned in the
powerpoint slides such as…they are obligate intracellular parasites and are very very
small.
Now let’s look at bacterial viruses. Phages infect bacterial cells and either
generate a productive infection, in which case the virus replicates and releases new
virions, or a latent state, where the virus integrates into the genome of the host cell and
does not generate new virions.
Productive infections can either be the result of the virus replicating in the cell
and then lysing the host cell to escape, this is called a lytic life cycle, or the virus
replicates slowly inside the host cell and is extruded or shed from the host cell.
The virus T4 is a virulent phage which participates in the lytic life cycle. The host
cell for this phage is E. coli and it binds to the cell wall of these cells using specific
receptors. There are six steps in the lytic life cycle, they are
1. attachment
2. penetration
3. transcription/translation
4. replication of DNA and protein synthesis
5. assembly
6. release
Review the figure in the text Fig 13.5 as a nice visual for the steps in the lytic infection
and the key points of each step. Most important idea to recognize in this chapter is that
the only form of the virus that enters host cells (bacterial) is the nucleic acid.
The virus lambda is a temperate virus that participates in the latent or lysogenic
life cycle. Notice that it has the same host cell as T4, E. coli. This virus can enter the host
cell and immediately circularizes its DNA material. At this point one of two things can
occur, either 1) the virus enters the lysogenic cycle by integrating its DNA into the host
cell chromosome and remains dormant (meaning that no new viruses are made) as a
prophage, replicating as the host cell replicates, or 2) the virus enters the lytic cycle,
produces more virions, and lyses the cell as new virions burst from the inside. To enter
the lysogenic life cycle the virus must integrate into the bacterial chromosome. Phage that
are integrated into the bacterial DNA are now referred to as prophage. In the lysogenic
phage the bacterial cell may have new characteristics that are due to the integration of the
phage DNA. There are toxins, such as the cholera toxin and botulinum toxin that are
acquired from phages. When a various signals from the environment (like DNA damage
from UV light) are sensed, the viral DNA then is “cut” out of the chromosomal DNA and
enters the lytic life cycle.
Part 2: Focus on Animal Viruses
So let’s begin with a look at the general structure of animal viruses. They are very
similar to bacterial viruses with a protein coat (called a capsid), nucleic acid, and some
animal viruses have envelopes. Enveloped viruses are more commonly found with animal
viruses than plant or bacterial viruses. Infection with an enveloped virus usually results
in shedding or budding of the virus from the host cell (so it can acquire the envelope).
Naked viruses tend to exit the host cells by cell lysis. The shape of animal viruses are
either isometric, helical, or pleomorphic (referring to an irregular shape). Note that the
complex tailed form seen with phage does not occur with animal viruses.
There are many ways to classify viruses. I want to use the nomenclature of the
virus family as a way to classify the viruses. The names of viral families all end in –
viridae, so watch for that to indicate a family designation. Use the tables on pages 308
and 309 as references to the different viral families and the general characteristics seen in
them.
There are two different types of interactions that viruses may have with host cells,
either they promote an acute infection or a persistent infection.
An acute infection is of short duration and the host may develop long lasting
immunity. (How does long lasting immunity develop? Look to the memory cells that
develop after an adaptive immune response in Chapter 15!) There are several key steps in
the reproductive cycle of an animal virus that produces an acute infection and they are
very similar to the steps found in the reproductive (life cycle) of virulent phages. Please
review the key stages listed on page 319-321. Figure 13.14 can be daunting to look at, but
can be made easier to read by understanding the following key concepts:
1) Understanding ss and ds
a. “ss” means single-stranded
b. “ds” means double-stranded
c. We often talk about double-stranded DNA or dsDNA because the DNA
structure for cellular chromosomes has two antiparallel polynucleotide
strands. mRNA only has one polynucleotide strand and so can be
described as single-stranded RNA or ssRNA.
2) Understanding (+) and (-) strands:
a. (+) RNA is mRNA. You can read the mRNA directly in order to translate
a protein. Therefore, (+) RNA  protein.
b. (-) DNA or (-) RNA are used as templates to make complementary (+)
DNA or (+) RNA and vice versa. Therefore, (-) DNA or (-) RNA 
(+) DNA or (+) RNA.
3) To make a new virus, it needs to make lots of viral proteins to make the capsid,
and multiple copies of its genetic material.
a. To make viral proteins, the virus needs to make (+) RNA to make protein
b. To make more genetic material, the virus needs to make a template.
Here is an example of how to understand Figure 13.14:
1. Viral genetic material: ss (+) DNA
a. To make viral proteins, need to make (+) RNA:
i. To make (+) RNA, I need a (-) DNA strand to use as a template.
ii. To make a (-) DNA strand, I can use the (+) DNA strand.
1. So, (+) DNA  (-) DNA (this makes dsDNA)  (+) RNA
 protein
b. To make more ss (+) DNA genetic material, need to make a (-) DNA
template.
i. So (+) DNA  (-) DNA (this makes dsDNA).
Can you make viral proteins and more genetic material from the following types of
viruses?
 ss (-) DNA
 ss (+) RNA
 ss (-) RNA
 ds (+/-) RNA
With all of these viruses, we have been following the flow of information in the
following manner: DNA  RNA  protein
This flow of information is called the “central dogma” where it was believed that
information ALWAYS went in that direction, never backwards. However, in 1970,
Howard Temin and David Baltimore both, independently, discovered that DNA could be
made from an RNA template by an enzyme called reverse transcriptase. The discovery
was, at first, very widely denied, but over time was accepted and these two shared the
Nobel Prize for their discovery. Thus, the central dogma was forever changed to
DNA  RNA  protein. Reverse transcriptase enzyme is made by some viruses like
HIV and Hepatitis B Virus (HBV) called reverse-transcribing viruses and is responsible
for DNA  RNA. Read more about reverse-transcribing viruses below.
Pay attention to how the infection of an animal virus is similar to a bacterial virus. How
do they differ??
A persistent infection is one where there is a constant presence of the virus, or
the genome in the host cell. There are three further sub-categories of persistent infection,
latent infection, chronic infections, and slow infections. As we define each of these
different types of persistent infections, think of an example of each.
Latent infections are infections which have a characteristic symptomless period
followed by a reactivation of the virus and symptoms. The virus is detected when it is
reactivated. The symptoms of the virus may be different when it is reactivated, for
example chicken pox and shingles. Some good examples of viruses that are latent are the
viruses in the Herpesviridae family.
We will talk more about this section for our final exam when we discuss viral
pathogenesis (not on Exam 2):
The Herpesviridae family is composed of double-stranded DNA viruses that have
an envelope. The most common viruses in this family are the Herpes simplex virus-1
(oral herpes) and Herpes simplex virus-2 (genital herpes). Both of these viruses cause
blisters or lesions to form in the skin and remain latent in sensory neurons. Treatment
with drugs such as Acyclovir, which is a purine analog shorten the duration of the
infection by inhibiting the formation of new viral particles. It is important to note that the
virus is never completely eliminated from the body.
The chicken pox virus (also known as human herpes simplex-3) is also a member
of the Herpesviridae family. It is transmitted by respiratory droplets and incubates about
10-20 days before skin lesions begin to appear over a 24 hour period. The skin blisters
last about a week and it is during this time that patients are infectious (as long as the
blisters have fluid they have live virus). Patients that recover from the chicken pox virus
will always have the potential to develop shingles, a reactivation of the chicken pox virus.
Such things as stress, treatment with chemotherapy or radiation therapy can reactivate the
chicken pox virus.
The last Herpesviridae virus in this family is the Epstein-Barr virus. This virus is
responsible for infectious mononucleosis (AKA “mono”) and can also cause Burkitt’s
lymphoma. This virus is transmitted from contact with the saliva of a patient who has the
virus and takes about 4 weeks to incubate before symptoms appear.
Chronic infections are characterized by a viral infection where there is virus
present at all times. This does not mean that the patient will necessarily also have
symptoms. Symptoms may be absent or appear late in the infection. A good example of a
virus that is responsible for chronic infections is Hepatitis B virus. It is in a family known
as Hepadnaviridae, dsDNA virus with an envelope. This virus is transmitted by contact
with blood and bodily fluids and has an incubation period of about 12 weeks. There are
an estimated 300 million people who are carriers of the virus worldwide. Anyone who is
a carrier may not have symptoms but can transmit the virus to someone else. While only
10% of those infected become carriers, carriers are considered to have chronic Hep B.
These individuals are more likely to develop liver cirrhosis or liver cancer as a result of
the viral infection. Hep B has an interesting pattern of replication in that it requires the
enzyme reverse transcriptase to replicate its DNA. Also of interest is that the virus may
replicate in liver cells generating three different forms of the Hep B virus, a Dane
particle, spherical particle, and filamentous particle. All three of these forms can be
detected in the blood of an infected individual but only the Dane particle is infectious.
We will talk amore about this section for our final exam when we discuss viral
pathogenesis (not on Exam 2):
Since we are talking about Hepatitis viruses let’s also include the other two types
of Hepatitis virus, Hep A and Hep C. Hepatitis type A is in the Picornaviridae family, and
is a (+) ssRNA viruse without an envelope. It is transmitted through the fecal-oral route,
meaning that you have to come in contact with contaminated fecal material to be
exposed. The incubation period is about 4 weeks with symptoms of fatigue, loss of
apetite, abdominal discomfort, fever, chills and jaundice lasting anywhere from 2-21
days. Patients with Hep A recover from this type of Hepatitis and establish long lasting
immunity. There is a vaccine for this virus, a good idea if you think you may be in a
situation to be exposed.
Hepatitis type C is in the Flaviviridae family and is also a (+)ssRNA virus with an
envelope. This virus is transmitted through blood and bodily fluids. It has a long
incubation period of about 6 weeks and causes symptoms similar to Hep A and Hep B but
often much milder. More than 80% of individuals with Hep C develop a chronic disease
where the virus infects the liver cells and promotes an inflammatory response. Over time
the liver cells are replaced with scar tissue and liver cirrhosis develops. In 2005 the virus
was cultured in a lab which was a huge accomplishment. There are new tests to screen
blood samples for the presence of virus and the risk of contracting Hep C from a blood
transfusion is reduced to 0.001%. Patients with chronic Hep C are often treated with
interferon. There is currently no vaccine for this virus.
Want more information about hepatitis viruses?
Review the text for more information on the Hepatitis viruses from p 597-601.
Also note that there is an excellent summary table on p 598, Table 24.14 which compares
all the different types of Hepatitis viruses.
Slow infections are characterized by a period where the infectious agent increases
over time and symptoms appear after a long period with the virus. An excellent example
of a slow virus is HIV. This virus is in the family Retroviridae, a family of (+)ssRNA
(actually two identical ssRNA strands) viruses with envelopes. The HIV virus infects
cells that have a CD4 receptor, majority of which are helper T cells. The replication of
HIV is unique in that it converts the ssRNA to ssDNA using the enzyme reverse
transcriptase. (Remember this is similar to Hep B replication except that Hep B is a
dsDNA virus and HIV is a ssRNA virus). Another key point with HIV is that when it
transfers its ssRNA to ssDNA, the ssDNA becomes dsDNA and then can integrate into
the host cell chromosome. The virus is now called a provirus when integrated. While
integrated the virus can synthesize new virions that are shed from the host cell. An
interesting feature is that the virus will make one long ssRNA that functions as mRNA
and codes for many viral proteins. This long strand forms a polyprotein, many proteins
which are cleaved by a special protease. Some drugs used to slow down the replication
process of HIV inhibit this necessary protease enzyme.
We will talk more about this section for our final exam when we discuss viral
pathogenesis (not on Exam 2):
The last family of viruses that I want to cover in this section is the family
Orthomyxoviridae. This is family of (-)ssRNA viruses which have many segments of
their genome and also an envelope. The influenza virus is a virus in this family with 8
segments of ssRNA that make up its genome. There are two key spikes found on the
envelope, an H spike and an N spike. The H spike (hemagglutinin) is used by the virus to
enter/bind to target host cells. The N spike (neuraminidase) is used by the virus to escape
the host cells. Since the genome consists of these 8 strands, there is a “mixing” of strands
that can occur if there are two types or variants of the virus that infect one cell. This
“mixing’ leads to gene reassortment and promotes variability in the types of virus made.
If the changes that occur result in a new protein from acquiring a new segment of ssRNA
such as a new spike, these are called antigenetic shifts. An antigenic shift is responsible
for the strain of Influenza known as the bird flu (H5N1). This virus also needs RNAdependent RNA polymerase to replicate the ssRNA. This enzyme does not have the
proof-reading ability of DNA polymerase so it is common that mistakes in the sequence
are made. If the sequence changes due to mistakes or point mutations, this often results in
a subtle change in the protein and are called antigenetic drifts.
The influenza virus is transferred from one person to another through respiratory
droplets, with an incubation period of 1-3 days. Symptoms include a fever, chills,
headache, muscle aches, and lead into cold-like symptoms. There are approximately 1040,000 deaths each year from this virus, death often due to the secondary bacterial
infections that occur. There is an annual flu vaccine available to protect individuals
against the flu. What type of virus is found in the vaccine? There are antiviral treatments
that can slow down the replication of the virus. The drugs zanamivir and oseltamivir are
neuraminidase inhibitors, basically prevent the virus from escaping the infected host cell.
Review the influenza virus information in chapter 21 p508-511
Viruses have been found to play a role in the development of human tumors. How
is this possible? There are a few mechanisms thought to lead to this outcome. One
mechanism is seen with the insertion of the virus genome into the host cell chromosome.
When the viral genes are expressed, they promote cellular responses that lead to cancer.
In other words, the expression of these cancer genes carried by the viral genome is what
promotes the development of cancer. These cancer-causing genes are known as
oncogenes and were found to have originated in host cells from proto-oncogenes. Protooncogenes are the “normal” functioning form of a gene found in a host cell and have the
potential to become oncogenes, or cancer causing genes. It was found that viruses that
integrate into the host chromosome can “pick up” some of the host cell DNA when they
excise themselves out of the chromosome. (This is similar to what lambda phage does.)
Another mechanism is seen with papillomavirus and herpesviruses where the DNA of the
virus replicates as a plasmid inside of cells or may integrate in the host cell chromosome
and express genes that may cause the cell to become cancerous.