DNA Viruses Flashcards
1
Q
Are Viruses Alive?
A
No viruses are not considered alive:
1) They can’t reproduce on their own
2) They can’t make their own energy
2
Q
Key Components of a Virus
A
- Genome - Necessary for replication and give instructions for proteins
- Capsid - protein that protects the genome from the environment
- +/- (Polymerase) - protein that replicates the genome; very often a target of medications
- +/- (Envelope) - not all viruses have them, often involved in virus attachment and entry to host cells
- +/- (Some other proteins) - Down-regulate or evade immune response; cut polyproteins
3
Q
General concepts in medical virology
- Host tropism
- Susceptibility
- Permissiveness
A
- Viruses “target” specific cell types and organs
- Host tropism: the infection specificity of certain viruses to particular hosts and host tissues. (e.g., for influenza host tropism is to humans, birds, pigs, etc and host tissue is generally nasal pharynx and epithelial tissue in face/mouth).
- Viral host tropism is determined by a combination of:
- Susceptibility: possess the receptor needed for viral entry
- Permissiveness: allow viral replication (e.g., viruses wouldn’t be able to infect RBCs)
- Most are diagnosed using molecular or serology tests (not culture)
- High genomic diversity is a challenge for treatment and vaccines
4
Q
Virus classification: “families”
A
5
Q
Some Medically Important DNA Viruses
A
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Skin:
- HSV (herpesvirus)
- HPV (papillomavirus)
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Nerve/Brain:
- HSV (herpesvirus)
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Liver:
- Hepatitis B (hepadnavirus)
6
Q
What to know for each virus discussed:
A
- Genome type (e.g., DNA, RNA) and general structure (enveloped or non-enveloped)
- Important features of its life cycle and reproduction
- Target cells and organs
- Symptoms and clinical features
- Transmission route
- Diagnosis
- Treatment
- Prevention
7
Q
Herpesviruses (HSV)
A
-
Genome type and general structure
- Double-stranded DNA genome
- 150,000 base pairs; forms close to 100 proteins. Much larger genome than most viruses
- 100-200 nm in diameter
- Enveloped
-
Important features of its life cycle and reproduction
- Two lifecycles: lytic and latent
- Lytic lifecycle - leads to generation of new virions (also leads to clinical disease)
- 1) Virus binds receptor and enters cell
- 2) Tegument proteins facilitate transport of virus capsid to cell nucleus, where genome is then injected.
- 3) Immediate early genes (alpha) - encode transcription factors. So makes the proteins it needs in order to begin replication of its own genome.
- 4) Early genes (beta) - encode proteins required for DNA replication.
- 5) Late genes (gamma) - encode structural proteins (e.g., to make capsid)
- 6) Virus assembles in the golgi body and buds through the membrane to form envelope. Takes the host cell’s cell membrane to form the envelope.
- Latent lifecycle - Non-replicating part of life cycle that helps virus evade immune response
- Non-replicating viral genome persists (unlike chronic infection)
- Viruses produced in epithelial cells are picked up by neurons, and travel along the axon of the neuron to its cell body in the ganglia (collection of neuron cell bodies). Viral genome is inserted into the nucleus of the nerve cell body.
- Viral DNA is silent except for the latency-associated transcript (LAT)
- LAT helps suppress the lytic viral life cycle and evade the immune response
- At some point there is a trigger for the virus to reactivate, and the lytic life cycle begins with the production of virus in the nerve, which travels back down the axon and into the epithelial cell, where it again begins to replicate.
- Separately, HSV can evade immune response through HSV proteins interfering with MHC class 1 antigen presentation on the cell surface, by blocking TAP (transporter associated with antigen processing)
- Also, part of the cellular immune response to HSV is wrapping the viral DNA around histones and condensing it into chromatin, causing the virus to be latent. If the chromatin is loosely bundled, the viral DNA will be accessible, starting a lytic infection.
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Target cells and organs
- Infects epithelial cells and neurons
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Symptoms and clinical features
-
Causes vesicle, then ulcer
- HSV-1: cold sores
- HSV-2: genital sores
- Often preceded by pain (prodrome)
- Rarely: brain infection, pneumonia, acute liver injury, or disseminated disease. These would tend to happen in immunocompromised people.
- Causes lifelong, latent infection. In a latent infection, the virus is not continuously replicating, but is in a dormant/sleeping state. In contrast, in a chronic infection (e.g., HIV, HCV, and HBV) the virus is continuously replicating
- Episodes of reactivation cause disease
- Recurrent sores with pain/prodrome
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Causes vesicle, then ulcer
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Transmission route
- Direct mucosal contact; does NOT require open sores
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Diagnosis
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Direct detection
- Direct Immunofluorescence Assay (DFA) - stain for viral proteins and looking for them under a microscope.
- PCR - amplifying viral DNA and if it’s able to be amplified then it indicates the virus is present. PCR is primarily used to diagnose HSV.
- (Tzanck smear for cytopathic effects) - no longer used in US.
- Culture - you can culture but it’s incredibly difficult and time intensive and so is not normally done.
- (Serology) - NOT Helpful
- IgG: many of use have been exposed to HSV at some point in our lives, so IgG will be positive regardless if we have an acute infection
- IgM: Disease can relapse throughout life, and there is no guarantee you are going to have an IgM spike with each relapse
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Direct detection
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Treatment
- Can treat episodes, or chronically suppress it
- Most common treatment is Acyclovir or Valacyclovir. Acyclovir tends to have better oral absorption.
- Are nucleoside analogues, so they are incorporated into the replicating viral genome, and prevents another base of DNA from being added on next to it so causes chain termination.
- It’s a prodrug - It needs to be activated (via phosphorylation) by our liver to work and as a result it does not have many side effects. Some variants are resistance to these compounds and can be isolated from immonosuppressed individuals
- Can treat both HSV-1, HSV-2, and VZV (Varicella-zoster virus).
- Ganciclovir: also a nucleoside analogue, treats all of above: HSV-1, HSV-2, and VSV, plus HHV-5 or CMV (cytomegalovirus)
- Foscarnet: non-nucleoside polymerase inhibitor, “broad spectrum”
- To date, there is no antiviral drug that can rid an infected body of a herpesvirus.
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Prevention
- No vaccine is available
8
Q
Herpesvirus Epidemiology
A
WHO (2012):
- HSV-1
- An estimated 3.7 billion people, or 67% of the world population, had an HSV-1 infection
- HSV-2
- An estimated 417 million people, or 6% of the world population, had an HSV-2 infection
- In the US:
- About half of human adolescents and adults under the age of 50 are infected with HSV-1, and about one in eight are infected with HSV-2
9
Q
Other medically-important herspesviruses
A
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HSV-3: Varicella-zoster virus
- Causes chicken pox
- Characteristic skin rash that forms small, itchy blisters
- Easily spreads easily through the coughs and sneezes of an infected person
- Can be reactivated later in life and cause shingles (also known as herpes zoster)
- When it reactivates, it travels from the nerve body to the endings in the skin, producing blisters. Because it only infects one nerves root, so the rash would not cross midline.
- Prevention:
- In 1995, a vaccine (live attenuated virus) was introduced to prevent against chickenpox
- In 2006, a zoster vaccine was approved for adults who were exposed to chickenpox as children and reduces shingles by 51%
- HHV-4: Epstein-Barr virus – the virus that causes infectious mononucleosis or mono
- HHV-5: Human cytomegalovirus (tends to infect only people who are immunocompromised)
- HHV-8: Kaposi’s sarcoma virus (opportunistic disease seen in patient’s with AIDS)
- Monkey B virus: can be transmitted to humans (e.g. lab workers), highly lethal, but can give medication for prophylaxis
10
Q
Hepatitis B Virus (HBV)
A
-
Genome type (e.g., DNA, RNA) and general structure (enveloped or non-enveloped)
- Circular, (partly) double standed (as shown in the picture). The single-stranded DNA gets “filled in” after infecting the host cell.
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DNA genome
- Very small (only 3,200 kb genome)
- It gets away with such a small genome because every kilobase of its genome “count” twice by using different reading frames. So know overlapping reading frames.
- Very small (only 3,200 kb genome)
- Life-cycle includes RNA intermediate
- Contains polymerase, Core, and Envelope
- Polymerase (3 Functions) :
- Reverse transcriptase: copies genomic RNA into DNA - incredibly error prone! When it incorporates errors it helps the virus evade the immune response and develop resistance to antivirals
- RNAse - degrades RNA in RNA-DNA hybrid
- DNA polymerase - synthesizes the second strand of DNA
- Core (core antigen + e antigen).
- Know the core is the main capsule and the names HBcAg (HBV core antigen) and HBeAg (HBV e antigen) because these are important when we talk about tests to diagnose HBV infection.
- These core proteins are transcribed and translated using the viral partially double stranded DNA.
- Envelope (surface antigen)
- HBsAg - also important when we talk about HBV diagnostic tests.
- The envelope is actually acquired through budding of the virus off the host’s endoplasmic reticulum.
- Polymerase (3 Functions) :
- Important features of its life cycle and reproduction
Has a partially double stranded DNA genome to start, which gets completed to a full double stranded DNA genome, which then forms the cccDNA, which then is transcribed into mRNA, and the RNA is reverse transcribed back into single stranded DNA, which is then replicated to form the viral partial double stranded DNA.
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Target cells and organs
- Infects liver cells
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Symptoms and clinical features
-
Acute infection:
- often asymptomatic
- can have fever, nausea, abdominal pain, jaundice
-
Chronic infection:
- Develops in only 5% of infected adults but 90% of children infected perinatally. In contrast Hepatitis C infection will go on to cause chronic infection in 85% of adults.
- Cirrhosis, liver cancer
-
Acute infection:
-
Transmission route
- Bloodborne (needlestick, transfusions), mother-to-child, sexual
- Needlestick from an HBV-infected source leads to transmission in 30% of cases! (compared to 3% for HCV and 0.3% for HIV). So very infectious.
- High rate of mother-to-child transmission in West Africa, Asia
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Diagnosis
- In active infection, the virus is replicating: so you can detect viral DNA (via PCR), surface antigen and core protein (e antigen secretion) both via serology.
- In early infection, we make IgM to the core protein; later we make IgG to the core protein – helpful for diagnosis but not clearing infection!
- The only antibody that is protective against HBV protection is to have an antibody response to the surface (envelope) protein. This is because the antibodies can only get to the surface antigens to be able to attack, not the core antigens. So when people are immunized, they generate antibodies to the surface proteins.
- KNOW THIS BELOW:
- Ever infected?
- Core antibody IgG
- Recently infected?
- Core antibody IgM
- Still actively infected?
- DNA (PCR); surface antigen; “core” e antigen
- Cleared infection? (or immunized)
- Surface antibody (the only antibody that is protective)
- Ever infected?
-
Treatment
- Indications for treatment:
- Clinical: liver function abnormality; liver fibrosis or cirrhosis +
- Viral: e antigen detection; DNA level above a threshold
- Treatment options:
- Entecavir
- Tenofovir (good if prior treatment or resistance; good if HIV co-infection)
- Both are nucleoside analogues
- Are incorporated into viral genome by error-prone polymerases, leading to chain termination
- Indications for treatment:
-
Prevention
- Subunit Vaccine:
- Derived from HBsAg
- 3-dose series now administered with routine childhood vaccines
- Immune globulin (HBIG):
- Passive immunity
- Given to exposed individuals
- If the source is HBV positive and the recipient is non-immune
- Subunit Vaccine:
11
Q
HBV genomic replication cycle
A
Step 1: HBV enters the cell. Enters hepatocytes (liver cells).
Step 2: the HBV capsid is dissembled and the partially double stranded DNA enters the nucleus. Using viral DNA polymerase, the sequence is completed to make full dsDNA. Host proteins then “repair” the dsDNA and in doing so generate cccDNA or covalently closed circular DNA.
Step 3: Using host DNA dependent RNA polymerase, the cccDNA is transcribed into mRNA.
Step 4: Using host machinery, some of this mRNA is translated into proteins to form the viral capsid. Using viral polymerase, the RNA is also reverse transcribed into single stranded DNA, which creates a RNA-DNA hybrid.
Step 5: the single stranded RNA and single stranded DNA hybrid molecule is degraded using viral RNAse H into a single stranded DNA molecule
Step 6: using the viral DNA polymerase again, the + strand of the DNA is replicated to once again form partial double stranded DNA.
She says the key things to know are:
Has a partially double stranded DNA genome to start, which gets completed to a full double stranded DNA genome, which then forms the cccDNA, which then is transcribed into mRNA, and the RNA is reverse transcribed back into single stranded DNA, which is then replicated to form the viral partial double stranded DNA.
12
Q
HBV Diagnosis Quiz
A
13
Q
Hepatitis D
A
- Circular -ssRNA genome (1600bp)
- Envelope (takes it from HBV)
- Occurs as a superinfection of HBV
- Can lead to fulminant liver failure
- Found in Mediterranean, Eastern Europe, Amazon
- People who are immunized against HBV also are immune to HDV because they have the surface antibodies that are protective against the envelope.
14
Q
Recap/Summary of HBV and HSV
A
15
Q
Human Papilloma virus (HPV)
A
-
Genome type (e.g., DNA, RNA) and general structure (enveloped or non-enveloped)
- Papovavirus
- Circulas dsDNA genome
- 7,900 bp (Relatively small)
- Non-enveloped
- Early genes: encode proteins for viral DNA replication
- Late genes: encode structural proteins
- Important features of its life cycle and reproduction
HPV life cycle
- Infection begins with a break in the skin surface that allows the virus to travel all the way down to the bottom, basal layer of skin epithelium
- Viruses infect basal epithelial cells, where it forms episomes (circular pieces of viral DNA) that replicate at the same time as the host cell is replicating (replicate along with cell division). At this stage, early genes are expressed.
- Some early genes (E6 and E7) stimulate the host’s epithelial cells to differentiate, and when skin differentiates they move up the layers of the epidermis. At this stage, late genes, which encode for the virus’ structural proteins, begin to be expressed.
- Late genes generate virus in superficial epithelial cells.
HPV life cycle in cancer
- Viral genome can integrate into the host genome (this is a “dead end” for the virus… why?). It’s a dead end because the integrated DNA can only produce RNA (doesn’t bring reverse transcriptase with it so it can’t turn the RNA back into DNA to make more viral particles).
- Integration can lead to increased expression of E6 and E7 portions of the viral DNA, which are oncogenes:
- E6 encodes a protein that degrades p53, a critical gatekeeper of the cellular replication cycle.
- E7 encodes a protein that inactivates Rb
- By degrading p53 and Rb, the cell is allowed to move on in the division on lifecycle when not all the requirements have been met, meaning it can move on and replicate with mutations or incomplete genomes.
- Leads to cell cycle dysregulation and proliferation and over time leads to cancer.
- Target cells and organs
-
Symptoms and clinical features
- Infects epithelial cells
- Warts
- Skin
- Genital (types 6, 11)
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Cancer (HPV types 16,18) - alpha
- Cervical cancer
- Penile cancer
- Anal cancer
- Head and neck cancer
-
Transmission route
- Skin to skin contact
- HPV is the most common sexually transmitted infection; not prevented by condoms
- Most people acquire HPV at onset of sexual activity; many will clear the infection
-
Diagnosis
- Detected in screening tests for cervical cancer and anal cancer:
- Pap smear: changes in cell appearance/structure
- PCR testing for high-risk HPV types and “other” HPV types
- Detected in screening tests for cervical cancer and anal cancer:
-
Treatment
- Warts:
- Topical salicylic acid (exfoliation; stimulates immune response)
- Cryotherapy (freeze the warts)
- Imiquimod: stimulates immune response
- Cancer: surgery, chemotherapy, radiation
- UNLIKE HSV and HBV there is no treatment for the virus itself, only can treat the symptoms
- Warts:
-
Prevention
- Two vaccines, which are formed of virus-like particles.
- Quadrivalent vaccine: types 6, 11, 16, 18 (cause cancer).
- 9-valent vaccine: additional oncogenic types 31, 33, 45, 52, and 58 (less common strains, but can potentially cause cancer.
- Recommended for males and females at 11-12 years of age.
16
Q
HPV Life Cycle and Life Cycle in Cancer
A
HPV life cycle
- Infection begins with a break in the skin surface that allows the virus to travel all the way down to the bottom, basal layer of skin epithelium
- Viruses infect basal epithelial cells, where it forms episomes (circular pieces of viral DNA) that replicate at the same time as the host cell is replicating (replicate along with cell division). At this stage, early genes are expressed.
- Some early genes (E6 and E7) stimulate the host’s epithelial cells to differentiate, and when skin differentiates they move up the layers of the epidermis. At this stage, late genes, which encode for the virus’ structural proteins, begin to be expressed.
- Late genes generate virus in superficial epithelial cells.
HPV life cycle in cancer
- Viral genome can integrate into the host genome (this is a “dead end” for the virus… why?). It’s a dead end because the integrated DNA can only produce RNA (doesn’t bring reverse transcriptase with it so it can’t turn the RNA back into DNA to make more viral particles).
- Integration can lead to increased expression of E6 and E7 portions of the viral DNA, which are oncogenes:
- E6 encodes a protein that degrades p53, a critical gatekeeper of the cellular replication cycle.
- E7 encodes a protein that inactivates Rb
- By degrading p53 and Rb, the cell is allowed to move on in the division on lifecycle when not all the requirements have been met, meaning it can move on and replicate with mutations or incomplete genomes.
- Leads to cell cycle dysregulation, not just proliferation
- Leads to cancer
