micro chapter 25 (RNA viruses) Flashcards
(107 cards)
1
Q
4 types of viruses
A
- +ssRNA (ex. coronavirus)
- retroviruses (ex. HIV)
- -ssRNA (ex. influenza)
- dsRNA (ex. rotavirus)
2
Q
Retroviridae
A
- contain reverse transcriptase
- have a polyhedral capsid
- genome contains two IDENTICAL molecules of +ssRNA
3
Q
What is the function of reverse transcriptase?
A
- transcribe +ssRNA into dsDNA
4
Q
HIV characteristics
A
- contains a polyhedral capsid with 2 identical strands of +ssRNA
- carries enzymes in capsid
5
Q
What three enzymes does HIV carry in its capsid at all times?
A
- integrase
- protease
- reverse transcriptase
6
Q
Proofreading of rev. transcriptase
A
- LACKS proofreading
- makes it very error prone and causes many mutation in DNA sequence
- nicks RNA strand to expose OH group to synthesize DNA strand
7
Q
What is the significance of the mutations due to lack of proofreading by rev. transcriptase?
A
It creates mutations in the sequence which causes protein to fold uniquely. This may prevent previous antibodies made from being able to detect HIV viruses.
8
Q
Initial attachment of HIV?
A
- gp120 attaches to CD4
THEN - gp41 attaches to CCR5 and initiates fusion of HIV into the T-helper cell
- BOTH attachments are needed for HIV to do anything
- envelope spike proteins remain on outside of host cell
9
Q
After fusion of HIV
A
- capsid degrades because it is made of proteins
- RNA and associated enzymes are released into T-helper cell
10
Q
Function of integrase
A
Integrate viral DNA into our DNA
11
Q
Function of protease
A
Cleave polycistronic genes into functional subunits
12
Q
Function of rev. transcriptase
A
transcribe RNA into DNA
13
Q
AIDS
A
- not a disease but a disorder
- a progression of HIV
- acquired immunodeficiency syndrome
14
Q
What are the two types of HIV?
A
- HIV-1: prevalent in US and Europe
- HIV-2: prevalent in west Africa
15
Q
Glycoproteins of HIV
A
- gp160 is cleaved into gp120 and gp41
16
Q
HIV genes
A
- gag
- pol
- vif
- vpr
- tat
- rev
- vpu
- env
- nef
17
Q
gag gene
A
- codes for p17, p24, and p7
- p17: matrix proteins that help with envelope stability
- p24: capsid proteins
- p7: bind to ssRNA and enzymes in capsid to anchor them in place
18
Q
pol gene
A
- a polycistronic gene that codes for protease, rev. transcriptase, RNAse H, and integrase
- genes result in one big blob that has to be cleaved by protease to function
- protease: cleaved genes into functional subunits
- rev. transcriptase: transcribe RNA into DNA
- RNAse H: degrade RNA that is part of hybrid and creates nicks in RNA strand to copy DNA strand from open OH groups on RNA
- integrase: integrate viral DNA into out DNA sequence
19
Q
Integration of viral genome
A
If viral DNA is integrated into out DNA it enters a latent phase where it is a pro-virus.
- virus is not actively made
- viral DNA is passed through generations of t-helper cells
20
Q
vif gene
A
- counteract APOBECs in T-helper cells
- APOBEC’s are upregulated as a response to interferons binding to receptors
- chew up APOBEC’s so they cannot modify virus RNA
- ubiquitin tagging leads to rapid degradation
21
Q
What is the function of APOBEC’s?
A
- they modify nucleic acid sequences
- when HIV enters a cell APOBEC’s can modify the RNA and make mutations that are unsustainable for the virus
22
Q
vpr gene
A
- helps guide hybrid RNA-DNA strand into the nucleus of out cells so it can be integrated into our DNA
23
Q
tat gene
A
- released by HIV and results in upregulation of gene transcription
- T-helper cells enter lytic phase and virus is actively being made
24
Q
rev gene
A
- helps transcribe pieces of viral genome out of nucleus and into cytoplasm
- gets viral genome to ribosomes so it can be translated into proteins
25
vpu gene
- degrades CD4 on T-helper cells to prevent multiple HIV viruses from attacking same cell
- instead HIV can attach to a different T-helper cell
- increases the population of HIV
26
env gene
- envelope protein
- gp160 cleaved into gp120 and gp41
27
nef gene
- functions of gene regions to downregulate T-helper cells production of CD4
28
What does HIV bind to?
HIV binds specifically to CD4 receptors on T-helper cells
- this limits MHC2 response which lowers cytokine production and memory B cell production
29
HIV budding
- as HIV leaves host cell, it buds off host cell and picks up its spike proteins (gp120 and gp41)
- if too many bud off it can decrease the integrity of host cells membrane
- causes cell to lyse
30
HIV's effect on the immune system
- HIV population levels increase by killing out T-helper cells
- this decreases cytokine levels and thus, plasma/memory B cells
31
How does HIV lead to death?
- lack of T-helper cells DOES NOT kill you
- if a secondary infection is apparent, lack of immune response from T-helper cells can lead to death
- HIV knocks out our immune system and when a second infection is introduced, our body cannot fight it
32
Why does HIV stay as a life-long disease?
1. it is integrated into out DNA
2. reverse transcriptase lacks proofreading and leads to mutations
- each cell has a chance of making a variant
33
Significance of mutations in HIV
- mutations make it so that memory B cells cannot recognize mutated strains of HIV
- because rev. transcriptase is SO error prone mutations occur over and over
- for each mutated strand, our body has to make new antibodies and mem B cells
- we lose T-helper cells at each section of this process which suppresses our immune system
34
Where is HIV found?
- it is found in semen, blood, saliva, vaginal secretions, and breast milk
- blood and semen are the most infective
- infected lesions must contact a cut or lesion on skin or mucous membranes
- can also be injected into the body
- it is most prevalent in south Africa
35
Diagnosis of HIV
- serological diagnosis
- specifically ELISA sandwich test
36
ELISA sandwich test process
37
Why is a serological test used to diagnose HIV?
- because many times it can be in the latent phase in which HIV may not be physically present in body fluids
- present in body as a pro-virus
38
Treatment of HIV
- want to target something that viruses have that we don't
- HAART (highly active anti-retroviral therapy)
- a cocktail of drugs used to treat HIV
- targets reverse transcriptase enzyme
- 5 drugs used
39
What are the five drugs in HAART?
1. nucleotide analogs
2. non-nucleotide inhibitors
3. integrase inhibitors
4. fusion inhibitors
5. protease inhibitors s
40
Function of nucleotide analogs
- made to mimic bases of DNA
- rely on reverse transcriptase making mistakes and picking them up to interfere with viral genome
- some lack an OH group and stop DNA sequence completely
- some have and OH group and let sequence continue but rely on creating many errors in the strand so that it cannot code for proteins correctly
- better coverage than non-nucleotide inhibitors
41
Function of non-nucleotide inhibitors
- bind directly to reverse transcriptase to inhibit its function
- effective but the number of enzymes overpowers the use of this drugs
- that is why it is used in a cocktail
42
Do nucleotide analogs or non-nucleotide inhibitors have better coverage?
nucleotide analogs
43
Function of integrase inhibitors
- bind to the active site on integrase enzymes to prevent it from integrating viral DNA into our DNA
44
Function of fusion inhibitors
- interfere with gp41 and gp120
- mainly with gp41 to prevent fusion of virus to host cell
45
Function of protease inhibitors
- bind to HIV proteases enzymes to prevent cleaving
- polycistronic genes cannot be cleaved into functional subunits
46
HIV prevention
- TRUVADA for Pre-P
- to be taken by people at risk of contracting HIV
- can help prevent infection of HIV
- if infected, HIV levels are maintained relatively low
47
What two drugs are in TRUVADA and what are they?
- tenofovir
- emtricitabine
- both are nucleotide analogs
- also a cocktail drug
48
HIV prevention (other)
- behavior changes to slow progression of HIV and AIDS
- abstinence and safe sex
- administering AZT to pregnant women
49
HIV vaccination
- many problems in the development of a vaccine because of errors made by reverse transcriptase
- mutated strains continue to be made and antibodies cannot recognize all mutations
50
T-cell transplants
- can only work if individual also has leukemia
- NOT COMMON
- rare because finding a donor is very tough
- complete radiation of blood is done and ALL white cells are killed, new T-cells can be introduced
- donors need to have T-cells that lack CCR5 so HIV cannot infect T-cells
- lack of CCR5 receptors is found in 10% of Europeans
51
Why does 10% of the European population lack CCR5 on their T-cells?
- traced back to yersinia pestis
- Yop E and Yop H caused inflammation which lead to swelling lymph nodes
- CCR5 also triggers inflammation, so people who lacked it had a better chance at surviving the infection
- those people survived and passed that on to new generations
52
Cord blood case
- has only been done and worked on 1 person
- more versatile because this can be done to anyone with HIV
- cord blood cells have a lifespan of ~2 months and then die
- new cells made lack CCR5 and HIV cannot infect those cells
53
Rhinoviruses characteristics
- causes common colds
- naked (no envelope)
- +ss RNA
- attachment proteins are on capsid
54
Why do the number of common colds decrease with age?
- as mutations occur in viral genome throughout life, our body makes antibodies each time
- next time it infects body, antibodies are already present to fight infection
- mem B cells with different antibodies that correspond to different mutations of virus are stored in body
- common colds can be apparent again in older ages to due immune system compromising
55
Why do mutations occur in Rhinoviruses?
- the +ssRNA is transcribed into -ssRNA in order to produce more copies of +ssRNA for new cells made
- this is done by RNA dependent RNA polymerase which lacks proofreading
- this creates mutations in the viral sequence
56
Rhinovirus infection
- limited to the upper respiratory tract
- easily spread through coughing and sneezing
- only 1 virus is needed to cause a cold (usually thousands are needed for other viral infections)
- can be transmitted by aerosols, fomites, or hand-to-hand contact
- immunity can be acquired against serotypes infections from the past
57
How is Rhinovirus most commonly spread?
direct person-to-person contact
58
Rhinovirus lytic vs latent
- does NOT have a latent phase
- only lytic
- virus is actively being made in host cells
- causes host cell to lyse and release virus
59
What is the best preventative measure for Rhinovirus?
hand washing
60
Rabies characteristics
- enveloped
- unsegmented -ssRNA
- -ssRNA has to be transcribed into a +ssRNA strand to be translated
- rabies virus is causative agent
61
Where is rabies commonly found?
- zoonotic disease of mammals like racoons and dogs
- bats are the source of most cases of rabies in humans
62
How is rabies most commonly transmitted?
via a direct bite
- rabies attaches to nerve cells and travels to CNS
63
Diagnosis of rabies
- usually, people do not know they are infected
- if not treated quickly, person will sub come to virus
- it is too late to intervene
64
Treatment of rabies
- vaccination
- treatment of infection site
65
Prevention of rabies
- we vaccinate our pets to prevent spread
66
Influenza characteristics
- enveloped
- segmented -ssRNA
- has 8 unique -ssRNA
- needs RNA dependent RNA polymerase
- genome is highly variable due to error prone RNA dep RNA polymerase
- envelope has NA and HA spike proteins
67
Types of influenza?
- type 1: infects birds, pigs, and humans
- subject to antigenic shift and drift
- type 2: infects humans and seals
- subject to antigenic drift but not shift
68
Genes of influenza (list)
1. HA
2. NA
3. NP
4. M1
5. M2
6. PB1 and PB2
7. NS1
8. NS2
69
function of hemagglutinin (HA)
- a spike protein that functions in attachment of virus
- binds to sialic acid modified proteins on our lungs
70
function of neuraminidase (NA)
- a spike protein that functions in detachment of virus
- cleaves bond between NA and sialic acid as virus buds off which allows virus to be released from host cell
71
function of NP
- covers RNA
- basically, a capsid for RNA
72
function of M1
- matrix proteins
- line envelope and help stabilize it
73
function of M2
- porin protein through the matrix that allows for ion flow
- ion flow causes a change in pH levels
- change in pH levels leads to other processes that help virus reproduce and spread
74
PB1 and PB2
- form RNA dependent RNA polymerase complex
- ultimately allows conversion of -ssRNA into +ssRNA
75
function of NS1
- binds to poly A tail on our RNA in the nucleus to prevent it from exiting nucleus
- prevents out RNA from reaching ribosomes and being translated
- this allows for more translation of viral RNA
76
function of NS2
- plays a role in interacting with interferons to prevent them from binding to receptors on neighboring cells
- this limits upregulation of APOBEC's and other proteins so that influenza virus can infect those cells too
77
Antigenic drift
- subtle changes in proteins that occur over time
- changes in proteins can limit antibodies from binding
- a vaccine given for H1N1 sub C may not work for H1N1 sub D if protein structure has changed
- especially in spike proteins like NA and HA
78
Antigenic shift
- take 8 pieces of RNA and can leave with 8 different pieces of RNA
- only occurs if two viruses of different strains infect SAME cell
- RNA from both viruses is in cell and when a new virus is made it can pick up a combination of the RNA
- this can create completely new strand of virus
- virus needs strands of RNA that codes for all essential proteins to be infectious
- does not happen very often
79
Antigenic shift outcome
- does not happen often
- when it does happen, it causes really bad flu years
- new strand can jump into humans and spread very quickly
- vaccine for that strand may not be available yet
- example: spanish flu
80
spanish flu
- actually, began in Kansas because people would practice in pig skin
- strand that could infect pigs would then infect humans
- rapid spread occurred
- killed 40-100 million people
81
diagnosis of influenza
- sign and symptoms during community wide outbreaks
82
treatments of influenza
1. Amatadine drugs
2. Tamiflu and Relenza
-nucleotide analogs DO NOT work
83
Amatadine drugs
- work by blocking M2 ion channels of virus
- prevents pH change
- prevents uncoating of viral RNA
- prevents any other processes initiated by pH level change
84
Tamiflu and Relenza
- work by preventing the release of virus from host cell
- inhibit NA and prevents its function of cleaving HA from sialic acid
- need to be taken within 48 hrs of exposure to be effective
- usually taken if believed to have been exposed
85
Amatadine in feed
- drugs were put into poultry feed and led to high levels of resistance in H3H2
- to prevent increasing resistance, avoid using drugs in bird and pig feed
86
Vaccine preparation
1. virus is injected into embryonated chicken egg
2. virus grows rapidly
3. egg is cracked to separate out virus
- extremely expensive and hard to do
- usually not possible so virus may contain egg proteins
4. virus is purified and radiated
- virus is dead
5. virus is made into a vaccine and injected into body
6. immune system is turned on BUT virus cannot reproduce
- may feel sick due to activation of immune system
7. virus is presented on MHC receptors and memory B cells are made
- if virus infects body again, mem B cells are already made to fight virus
- cytotoxic T cells are activated but not triggered because other cells cannot express virus on MHC1 receptors because virus is dead
87
Why do vaccines work for smallpox but not influenza?
1. smallpox is a DNA virus and influenza is an RNA virus
- smallpox does not need error prone RNA dep RNA polymerase
- less mutations occur
2. smallpox can only infect humans, but influenza can infect birds, pigs, and humans
- no antigenic shift is possible because limited host range
3. if someone has smallpox it is visible
- if someone has smallpox they could be easily quarantined
- pigs and birds are not so easily quarantined
- even people may go out with flu
88
COVID mRNA vaccine
1. S2 gene is taken out of genome
2. PCR is used to amplify gene
3. copies of gene are placed into a fat bubble
4. fat bubble is injected into body
5. S2 is released and can enter our cells
6. it is engulfed by macrophages because it is foreign
7. It is presented on MHC receptors
8. mem B cells and mem cytotoxic T cells are made
- some of our other cells may be killed if MHC1 presents S2 gene because cytotoxic T cells release cytotoxins
9. if infected by virus again mem B cells and mem cytotoxins are ready to fight it off
- 90% effective
89
What happens if a new strain of Covid is made?
- mRNA vaccines can be made quickly rather than having to make vaccines in chicken eggs (a lot longer)
- if any new pandemic occurs and mRNA vaccine is the best shot
90
mRNA vaccine and influenza
- only 30% effective
- due to mutations caused by antigenic shift and drift
- many mutations occur, and the vaccine may not cover new mutated strands
91
Coronavirus characteristics
- +ssRNA, non-segmented
- enveloped (buds off host)
92
Coronavirus proteins
1. S protein
2. E protein
3. M protein
4. N protein
5. NSP
93
Function of S protein
- in coronavirus
- has to subunits S1 and S2
- has a bridge between the subunits
- a spike protein for attachment
- bridge breaks in entry phase
94
Function of E protein
- in coronavirus
- and envelope protein
- not much present
95
function of M protein
- in coronavirus
- main envelope protein
96
function of N protein
- in coronavirus
- binds to RNA to protect it
- basically a capsid to the RNA
97
Function of NSP
- binds to interferons to limit upregulation in neighboring cells
- prevents upregulation of APOBECs and RNAseL
98
function of RNAseL
- binds to dsRNA intermediate
- dsRNA is made by coronavirus as it is copying its +ssRNA into a -ssRNA
- the intermediate if not seen in our cells
99
What characteristic if significant of coronavirus RNA
- their RNA is capped and has a polyA tail
- this is NOT commonly seen in viral RNA but it is in our RNA
- this can confuse our cells because it looks more like our RNA
- gives coronavirus good translation from out ribosomes
100
Sick feeling caused by viruses?
- NOT caused by a viral toxin
- it is caused by out body's immune response to the viral infection
- if too many cells get infected in the lungs it can limit gas exchange and lead to death
101
Omicron variant
- has mutated spike proteins that only need to bind to ACE-2 receptor to get into host
- allowed this variant to enter cells above our lungs
- helped it spread quicker, but the older variant is more deadly because it binds to lung cells specifically
102
Mutations of viruses
- as mutations occur, they usually make a virus LESS pathogenic
- mutations hurt protein structure and function
- this is to keep host alive and spread more
- BUT viruses do have numbers on their side and so mutations will be beneficial to them sometimes
103
How does coronavirus avoid out immune system?
1. RNA is capped and has a polyA tail
2. NSP's bind to interferons and prevent upregulation of APOBEC's and RNAseL
3. proteins hide in endoplasmic reticulum as virus is being produced to prevent them from being target by out immune response
104
Treatment of coronavirus
1. mRNA vaccine
2. sub-unit vaccine
3. PAXLOVID
- targets protease in virus to prevent cleaving
-nucleotide analogs DO NOT work
105
Antibody harvest treatment
1. draw blood from a health individual that has had covid
2. add protein A to the blood so that the antibodies bind to it
3. separate antibodies after collection
- blood can be out back in
4. put antibodies into a sick person to help fight virus
- antibodies can stick to virus and trigger NKC or neutralize them
106
What is the concern about antibody harvest treatment?
AED- because antibodies also cause opsonization, there is a chance that it could help coronavirus into cells it normally would not be able to access
107
Biosafety level classification (BSL)
BSL 1: organisms are safe, no separate lab needed
BSL2: separate lab is needed
ex. salmonella and listeria
BSL3: hood and - air required
- - air prevents air flow out of hood and lab
ex. covid and flu
BSL4: hood, suit, and - air required
- suit is pressurized so air cannot flow into it
ex. ebola
