Lecture 10 - Viruses Flashcards
what are some types of viral diseases?
flu, ebola, HIV
what is the size of a virus relative to a bacteria?
it is smaller than bacteria
is a virus a virion? what is a virion? and an example
yes, it is non-living and non-replicating outside the host cell. example: on a door-knob or in blood
are viruses obligate intracellular pathogens?
yes, they can’t survive outside of a cell and they cause diseases
can you see a virus with a light microscope?
no
can viruses infect all forms/domains of life?
yes
what are the domains that viruses infect?
-Bacterial (bacteriophages)
-Archaeal
-Eukaryotic (animal and plant viruses, etc)
is the host range that viruses infect specific or broad? is there an exception?
the host range is usually specific. One exception is Rabies, it has a broad host range
what are the two parts of the virus structure that is always present?
- Genome (nucleic acid core)
- Capsid
what is one part of the virus structure that is not always present?
The envelope
what is within the viruses’ genome/nucleic acid core? does it have DNA or RNA, and is it single-stranded or double-stranded?
-it has either DNA or RNA
-it can be ss or ds
how does the virus being ss or ds help us to detect a virus?
it helps to detect a virus because it we see a ds RNA, we know its a virus
how many genes are present within the genome of viruses? what do they code for?
only a few genes - they code for the viral structure
within the genome of the virus, how does it replicate?
it replicates using the metabolic machinery of the host, because the virus only has a few genes. So they use the genes of the host (our ribosomes, glycolysis, etc.) to replicate.
why are the genome’s within a virus an exception?
Every living cell has DNA as its genome. A virus is an exception because it can have DNA or RNA. All viruses have a genome.
within the capsid of the virus, what is present?
it has a protein coat that is always present with protein spikes that are not always present
what are the protein spikes on the capsid?
they are proteins of the surface
what does the capsid of the virus serve to do?
it protects and attaches
is the viral shape based on the capsid? what are the three shapes?
yes
1. icosahedral: flu, polio, norovirus
2. Helical (filamentous): ebola, rabies
3. Complex: bacteriophage
what is the macromolecule that the capsid is made up of?
protein
what is the envelope made out of in viruses?
a lipid bilayer with protein spikes (that help with attachment)
where is the lipid bilayer of the envelope taken from?
it is taken from the plasma membrane of their host cell
what does the envelope serve to do?
protects and attaches
what are examples of viruses that are enveloped?
HIV, SARS-CoV-2
what is a naked virus?
a virus without an envelope
why are enveloped viruses easier to kill?
because the lipids can be dissolved easier with alcohol, etc.
what does the envelope surround?
it surrounds the protein coat
what is the classification of viruses based on?
on their structure, for example do they have DNA, or RNA, are they ss or ds, etc.
do the viruses species name use binomial nomenclature?
no
what are the viruses named based on?
-Appearance: Coronavirus
-Location: Ebola
-Disease it causes: HIV
in SARS-CoV-2, what is the genome?
ss RNA
what types of proteins are present in SARS-CoV-2?
Nucleocapsid protein (N)
Spike protein (S)
Envelope protein (E)
Membrane protein (M)
does SARS-CoV-2 have an envelope? What is it made out of?
yes:
-lipid bilayer
-Spike protein (S) - corona (crown) of spikes
what is the spike protein?
it is a protein that binds to our cells and helps to attach to our cells
what vaccine is the spike protein present in?
in the mRNA vaccine
how does a typical DNA virus replicate?
- Attachment (attaches to the surface of a host cell to get inside via spike proteins).
- Penetration (gets inside the cell)
- Uncoating (the genome gets outside of its capsid coat).
- Synthesis (makes more genome and proteins for the capsid*. the viral DNA/RNA is replicated, and some viral proteins are made).
a. DNA to DNA (DNA -dependent DNA polymerase).
b. DNA to RNA to proteins using RNA polymerase. - Assembly (takes the genome and covers it with the capsid*? coat).
- Release
If the following are templates and products for virus replication, what are the enzymes used?
1. DNA to DNA
2. DNA to RNA
3. RNA to RNA
4. RNA to DNA
- DNA-dependent DNA polymerase.
- DNA-dependent RNA polymerase.
- RNA-dependent RNA polymerase. (Replicase - the virus has these enzymes NOT the host).
- RNA-dependent DNA polymerase (reverse transcriptase - ONLY in retroviruses).
what are the two types of penetration (the two types of ways viruses enter the host cell)?
- Fusion
- Endocytosis
what happens in fusion?
The envelope of the virus fuses with the plasma membrane of the host cell.
This ONLY happens if the virus has an envelope.
Both of the bilayers fuse together.
Examples of viruses that perform fusion: enveloped viruses such as HIV
what happens in endocytosis?
Both enveloped and naked viruses perform this. Example: the flu virus.
The virus comes into the host cell through membrane pockets and is engulfed. The spike proteins firstly attach.
what are the two types of releases (two ways that the virus is released from the host cell)?
- Lysis
- Budding
what happens in lysis?
The virus cell bursts.
This only happens in naked viruses.
Example: the common cold virus
what happens in budding?
The envelope layer is gained during the release, and the capsid wraps itself in the host cell membrane and pinches off. The virus gets its enveloped layer as they are released.
This only happens in enveloped viruses such as HIV.
how does SARS-CoV-2 replicate?
- Attachment: the S protein (the spike proteins) binds to the ACE2 receptor on the host cell membrane.
- Penetration: Fusion of the viral envelope occurs with the host cell membrane.
- Uncoating: the viral RNA is released in the host cell cytoplasm.
- Synthesis:
- Translation: the ss RNA is used to make viral proteins.
- Replication: RNA-dependent RNA polymerase (RdRP) or Replicase is used. It starts with RNA and makes more RNA. - Assembly: the production of viral proteins and RNA.
- Release: through exocytosis
which of the following in NOT a unique characteristic of viruses?
1. Viral nucleic acid is either DNA or RNA.
2. Virus spikes attach to the host cell receptors.
3. Viral release can occur through lysis or budding.
4. Viruses can replicate on doorknobs.
- Viruses can replicate on doorknobs
What are 3 ways that viruses can interact with host cells? AKA what are the 3 types of infections that viruses can cause in host cells?
- Acute infection
- Chronic (persistent) infection.
- Latent infection.
what is an acute infection?
It is a short-term infection such as the flu, cold, etc. You end up being fine in the end.
-It has a short duration.
-It can have long-lasting immunity.
-Symptoms are the host cell death.
-The virus usually disappears afterward.
what is the chronic (persistent) infection?
The number of viruses is gone after the acute infection period, but they come back.
- t is a long-term infection.
-It is continuous but usually has low numbers.
-The virus can be detected at all times.
-It may or may not cause disease in the chronic phase.
-No symptoms
-You are considered a carrier if you spread the virus. Sometimes you cannot shed the virus (spread the virus).
-Examples: Hepatitis B and C, HIV
in chronic infections, what do you initially have?
you initially have an acute infection, then the viral numbers go down, but we don’t completely get rid of the virus and it resurfaces later.
what is a latent infection?
It is when all the viruses are gone after the acute phase, but the viruses hide in the host cells. It comes back later and the patient experiences different symptoms.
(finish latent infections later).
do all types of infections have an acute phase?
YES
what is an example of a retrovirus?
HIV
do retroviruses have a unique RNA virus replication cycle? what is it the replication cycle?
yes:
1. RNA to DNA via reverse transcriptase (RNA-dependent DNA polymerase).
2. The DNA integrates into the host genome as a provirus via integrase.
what is the HIV genome structure? What 3 enzymes does it have and why are they important? What two proteins does it have? Is it enveloped?
The genome is a ss RNA, with 2 copies.
The 3 enymes are:
-Reverse transcriptase (RT)
-Integrase (IN)
-Protease (PR)
These 3 enzymes are really important in the replication cycle of HIV, so HIV treatment targets these 3 enzymes.
The proteins:
-Capsid protein (CA)
-Matrix protein (MA).
Yes, HIV is an enveloped virus with spike proteins (gp120 and gp41).
One way to treat HIV is to block the 3 important enzymes. What is another way?
To block the spike proteins so that they don’t attach
what are the stages of HIV replication?
- Attachment: The spike proteins gp120 bind to the CD4 receptor on the host cell membrane, and onto the TH cells.
- Penetration: gp41 facilitates the fusion of the viral envelope with the host cell membrane.
- Uncoating: the viral RNA and enzymes are released into the host cell cytoplasm.
- Synthesis:
-Reverse transcription: the ss RNA is reversed and transcribed into a ds DNA by RT (RNA-dependent DNA polymerase).
-Integration: the ds DNA is integrated as a provirus into the host genome by IN (this step is irreversible. If the virus goes into the DNA chromosome, it is there forever).
-Transcription: the provirus is transcribed into a ss RNA by the host’s RNA polymerase.
Translation: the mRNA is translated to form viral proteins.
SO ss RNA to ss DNA to ds DNA. - Assembly: the viral proteins and RNA are made, this is facilitated by PR.
- Release: budding occurs.
what is the result of HIV replication?
The result is death of the infected cells, which lower the immune cell numbers
what is HIV pathogenesis?
the process of the disease developing
HIV pathogenesis:
how long is the incubation period? are there any symptoms?
6 days to 6 weeks with no symptoms
HIV pathogenesis:
what is the acute illness period?
It is about 1 month.
It is asymptomatic or flu-like symptoms.
This is the most infectious stage.
The virus levels drop down to a stable “set point”.
HIV pathogenesis:
What is the Latent/Chronic illness period?
It is about 10 years.
The viral numbers slowly increase.
The TH numbers slowly decrease.
You can’t be protected in this stage against opportunistic infections.
HIV pathogenesis:
what happens in the AIDS stage?
This is when the TH levels drop to less than 200 cells/ul.
Immunodeficiency causes opportunistic infections.
in HIV pathogenesis, which is the most infectious stage?
The acute illness period
what is HIV treatment used to treat?
it is used to control HIV but not cure the infection
what is a provirus?
the HIV once is enters into our genome
the host cells that contain the provirus of HIV as a reservoir, meaning what?
Meaning they can’t be cleared up by drugs or our immune system.
drugs against HIV lead to what?
Drugs lead to viral suppression - which is when the viral load is less than 200 copes/ml of blood.
what does viral suppression prevent and reduce?
Viral suppression:
-Prevents progression to AIDS
-Reduces the risk of transmission - allows safe sexual contact and the delivery of a healthy baby
in HIV treatment, what are antiretrovirals (ARVs)?
They are entry inhibitors - they bind to gp120, gp41, or CCR5 coreceptor, which prevents the entry of HIV.
They are also:
RT inhibitors
IN inhibitors
Protease inhibitors
how is HIV transmitted?
It is transmitted by body fluids coming in contact with:
-a mucous membrane (in the rectum, vagina, tip of penis, and mouth)
OR
-blood
what are examples of how HIV is transmitted?
-Sexual contact (anal or vaginal sex).
-Blood and blood products (sharing needles, or blood transfusion/organ transplants).
-Vertical transmission (during pregnancy, birth, or breastfeeding).
is there a vaccine currently for HIV prevention?
no, but it is in development
how can HIV be prevented through sexual contact, blood, and pregnancy?
Sexual contact:
-Abstinence
-Condoms
-Oral sex is less risky
-Reduce # of sexual partners
Blood:
-Never share needles
Pregnancy:
-Continue treatment through child-birth and avoid breastfeeding
if you are HIV+, what should you do?
Get tested frequently and encourage sexual partner to be in treatment
what are the two main ways of HIV prevention?
- Pre-exposure prophylaxis (PrEP)
- Post-exposure prophylaxis (PEP)
what is PrEP for? how much does it reduce transmission? What is an example?
It is for high-risk individuals:
-If you have an HIV+ partner
-If you have an STD
-If you share needles
It reduces transmission in sex by 99% and in needles by 74%.
Example of a PrEP: Truvada (RTIs - reverse transcription inhibitors).
what is PEP for? when do you take it?
It is given after a possible exposure like a workplace accident, a condom broke, a needle shared, or sexual assault.
You start the PEP medication within 72 hours post-exposure and you continue taking it for 28 days.
explain the latent infection stage -
It occurs after the acute stage, but the viruses hide, so we cannot detect them. But later, it will come back. When the virus comes back, it is a reactivation. This causes a different type of infection/virus.
when is the virus non-infectious in the latent stage?
after the acute stage but before the virus reactivation
what is an example of a latent infection?
Human herpes viruses (HHV)
what does the word latent mean?
hidden
what are the four sub-viruses of HHV?
HHV-1, HHV-2, HHV-3, HHV-4
what is HHV-1 and HHV-2? what do they cause?
Herpes simplex viruses (HSV-1 and 2) which cause oral/genital herpes
what is HHV-3? What does it cause?
Varicella-zoster virus (VSV) causes chickenpox-shingles
what is HHV-4? What does it cause?
Epstein-Barr virus (EBV) causes infectious mononucleosis (kissing disease)
during the latent infection: after the initial infection, is the virus detected?
no, after the initial infection, the virus is not detected unless the disease is reactivated.
where can latency occur?
latency can be in nerves or immune cells
what can trigger the latent infection to reactivate?
a decreased immune system
in latent infections, can reactivation symptoms be similar or different?
they can be similar or different
oral/genital herpes simplex sores have periodic outbreaks. Are they similar to the initial infection?
yes
what percent of people get shingles who’ve had chickenpox?
30%
in patients with EBV and AIDS, what are their latent infections?
hairy leukoplakia
what is transformation?
when viruses can cause cancers
what percentage of cancers are caused by viruses?
up to 20%
can viruses ever cause cancers?
yes
what viruses cause cancers?
viruses that integrate into the host genome and activate cell division leading to uncontrolled growth
what are 3 examples of viruses that cause cancers?
-Hepatitis B and C virus: causes liver cancer.
-Human papilloma virus: causes cervical, vaginal, vulvar, penile, anal, or oropharyngeal cancer.
-EBV: causes lymphomas, and nasopharyngeal cancer.
which of the following is a unique feature of the HIV virus (compared to other viruses)?
1. It can go latent.
2. It uses the metabolic machinery of the host cell.
3. It has reverse transcriptase.
4. It uses fusion to enter the host cell.
- It has reverse transcriptase.
what is the full name of prions?
Proteinaceous Infectious Particles
what are prions made of?
only proteins
do prions have nucleic acid?
no
what are prions?
proteins causing infections
prions are similar to what normal protein?
PrPc
why are prions and PrPc similar?
their neuroprotective functions
what is the abnormal version of PrPc?
PrPsc, it is missfolded verson for srapie
what is one similarity and one difference between PrPc and PrPsc?
they have the same amino acid sequence, but different folding properties
how do prions replicate?
Prions replicate by a catalyzing conversion of normal to an abnormal prion protein
what are the steps of prion replication?
- Both the normal (PrPc) and abnormal (PrPsc) proteins are present.
- PrPsc interacts with PrPc.
- PrPc is converted into PrPsc.
- Conversion continues and PrPsc accumulates.
Overtime, what happens with the build-up of abnormal proteins? is it fatal?
It creates holes and plaques in the brain tissue, which is fatal.
what does TSE stand for? what is it?
Transmissible spongiform encephalopathy, it is a disease in the brain. It is a blanket term for all prion diseases
how is TSE transmitted? why is it called TSE?
it is transmitted between hosts. It makes the brain look like a sponge with holes
T/F: prions are hard to kill
yes, very
what are the three types of prions?
-Sporadic
-Inherited
-Acquired
what are sporadic prions?
they are due to random spontaneous protein misfolding. It is rare, and shows up in older people
what are inherited prions?
Fatal Familial Insomnia (FFI):
It is due to genetic mutations. It is fatal and shows up in people older than 50 years old.
what are acquired prions?
From contaminated sources. Kuru is an example and was transmitted in the Fore Tribe of New Guinea because of cannibalism.
What are three examples of prion diseases?
- Scrapie (in sheep)
- Bovine spongiform encephalopathy (mad cow disease)
- Creutxfeldt-Jakob disease (CJD): sporadic - in old people.
What is Creutzfeldt-Jakob disease’s variant?
Variant CJD (vCJD) - in young people
which of the following represents a prion disease?
1. Hepatitis B
2. vCJD
3. HIV
4. EBV
- vCJD
A public health physician isolated large numbers of phages from rivers used as a source of drinking water in western Africa. The physician is very concerned about humans becoming ill from drinking this water although she knows that phages specifically attack bacteria. Why is she concerned?
Humans carry intestinal bacteria as part of their normal flora. These bacteria have various functions including protection from pathogenic organisms. The phages in the water may harm/kill the beneficial bacteria in the intestine. This could lead to susceptibility to intestinal pathogens. Infection with such a pathogen could result in diarrhea, similar to that caused by giving a broad-spectrum antibiotic. In certain areas of the world where there is already malnutrition present, an additional intestinal insult could kill vulnerable members of the population.
A patient presents with small, painful fluid-filled blisters in the genital area. He complains that this is the third time this year that he has had these. The last two times they went away on their own so he did not seek medical treatment. Using your knowledge of viral infections, explain what is going on with this patient.
The patient likely has a genital herpes virus infection. This type of infection is life-long and goes into a latent period between outbreaks. During this time, the virus “hides” in the nerves. It can be reactivated during periods of stress, hormonal changes, etc. While the outbreaks can be managed with antiviral medications, the virus never leaves the body and can be transmitted even if no signs are visible.
Viruses that infect bacteria are called:
Bacteriophages
Which of the following is true about viral structure?
1. Viruses use spikes for reverse transcription
2. Virus shape is based on capsid structure
3. Viruses have DNA as their core nucleic acid
4. Virus genes code for the lipid bilayer of an envelope
5. Viruses always carry their own enzyme
- Virus shape is based on capsid structure
Enveloped animal viruses contain a lipid bilayer which is acquired during viral:
release
Retroviruses are unique in that they:
Use RNA as a template to make DNA
The enveloped viruses obtain their envelope from:
the host cytoplasmic membrane as they exit the host
