Retroviruses Flashcards
1
Q
What are retroviruses and why are they particularly interesting?
A
Retroviruses are important human and animal pathogens and are particularly interesting because of their unusual replication cycle.
Retrovirus are enveloped viruses with a single stranded RNA genome.
2
Q
What do retroviruses package and why?
A
Retroviruses package reverse transcriptase enzyme in the particle to copy their RNA genome into double stranded DNA.
Retroviruses also package an integrase enzyme and integrate their DNA into the host cell’s DNA.
This allows the retroviral genome to be transmitted to both daughter cells when the infected cell divides.
3
Q
When does the host cell RNA polymerase transcribe the virus’ genome?
A
During its replication cycle (and also produces the genome for the new virus particles).
4
Q
Give an example of a retrovirus that belongs tothe genera of Lentiviruses?
A
Human Immunodeficiency Virus (HIV)
5
Q
Where did HIV originate?
A
HIV is very similar to a virus called SIV (simian immunodeficiency virus), which is found in monkeys.
SIV likely jumped species to humans in the late 19th or early 20th century.
HIV-1 evolved from a SIV that infected chimpanzees whereas HIV-2 evolved from a SIV that infected sooty mangabeys.
6
Q
How many types of HIV are there?
A
There are two major types of HIV, namely HIV-1 and HIV-2.
HIV-1 and HIV-2 are genetically distinct, sharing only a 55% sequence identity.
7
Q
What are the subtypes of HIV-1 and HIV-2?
A
Each type of HIV can be further broken down into groups, which themselves can be subdivided into clades (i.e., subtypes).
HIV-1 comprises groups M (main), O (outlier), and N (non-M or O).
There are two main HIV-2 subtypes, A and B.
8
Q
What is the most common form of HIV?
A
HIV-1 is the most common type of HIV; 95% of people living with HIV globally have HIV-1.
9
Q
Describe the structure of HIV.
A
HIV is an enveloped virus that has a complex structure.
The genome is in the form of a nucleocapsid, and is packaged within the virus capsid along with reverse transcriptase and integrase.
The matrix protein lies between the capsid and the viral envelope.
Two viral envelope proteins are present; SU (gp120) binds to the CD4 receptor and a chemokine receptor, and TM (gp41) is the fusion peptide that results in the viral envelope fusing with the cell’s plasma membrane, thus releasing the capsid into the cell’s cytoplasm.
10
Q
What does the HIV virus envelope contain?
A
The virus envelope contains a trans-membrane glycoprotein (TM, gp41) that is joined to a second virus glycoprotein (SU, gp120) by a di-sulphide bond.
11
Q
What part of HIV binds to the host cell protein CD4?
A
The gp120 binds to the host cell protein CD4 and the gp41 is the fusion protein.
12
Q
What lines the inner surface of the envelope in HIV?
A
The matrix (MA, p17) protein
13
Q
What is inside the HIV envelope?
A
A conical capsid made from the virus protein p24 (CA).
14
Q
What does the HIV capsid contain?
A
Two (+) sense RNA molecules that are covered with nucleocapsid (NC, p7) proteins, and the enzymes involved in the early stages of genome replication, reverse transcriptase (RT) and integrase (IN).
Protease proteins can be found inside and outside of the capsid.
Vpr is a regulatory protein.
15
Q
The genome of HIV has several features that are common to retroviruses and distinct from other RNA viruses.
What are they?
A
The genome is diploid: it consists of two, usually identical molecules of single-stranded RNA.
Both RNA strands are (+) sense with a 5’ cap and a 3’ polyA tail, but it does not serve as a mRNA immediately upon entry into the host cell cytoplasm.
The genome is associated with a specific tRNA (derived from the host cell) that is used to prime the synthesis of DNA.
Finally, the genome is synthesized and processed by the host cell mRNA “handling machinery” after the virus has integrated its DNA into the host cell chromosome in the previous round of infection
16
Q
What are the three major genes that HIV has that are common to all retroviruses?
A
HIV has three major genes (gag, pol and env) that are common to all retroviruses.
17
Q
What are the genes that HIV has that code for regulatory and accessory proteins?
A
HIV has six genes that code for regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) proteins.
18
Q
What is the gene order in all Retroviruses?
A
The gene order in all Retroviruses is invariant:
5’ – gag– pol– env– 3’.
19
Q
Describe the HIV genome.
A
The genome of a HIV consists of two identical (+) RNA molecules.
Although these resemble mRNA molecules, they are not translated by the ribosomes when the virus infects the cell.
The gene order for all retroviruses is 5’ – gag – pol – env – 3’.
The gag gene encodes structural proteins, the pol gene encodes the enzymes needed in genome replication, and the env gene encodes the envelope proteins needed to bind to host cells.
Note: This diagram is showing the DNA structure after the process of reverse transcription
20
Q
What does the gag gene encode?
A
The gag gene encodes the Gag polyprotein, that when cleaved yields the CA, MA and NC proteins.
21
Q
What does the pol gene encode?
A
The pol gene encodes the Pol portion of the Gag/Pol polyprotein, that when cleaved yields the enzymes PR, RT and IN.
The PR becomes activated after the assembly of the virus particle and cleaves the Gag and Gag/Pol polyproteins at specific sites.
22
Q
What does the env gene encode?
A
The env gene encodes the Env polyprotein, that when cleaved yields the gp120 and gp41 proteins.
23
Q
Reverse transcriptase is an enzyme unique to Retroviruses and has at least three different enzymatic activities.
What are they?
A
- an RNA dependent DNA polymerase,
- RNase (an enzyme to degrade RNA), and
- a DNA dependent DNA polymerase.
24
Q
What are the key points in the process of reverse transcription of the RNA genome in HIV?
A
- RT uses a tRNA as a primer to synthesize a DNA copy of the RNA genome. This creates a DNA:RNA hybrid molecule,
- RNase H removes most of the RNA strand (this particular form of RNase can digest the RNA in hybrid molecules),
- the remaining RNA is then used as a primer for synthesis of the complementary strand of DNA,
- the RNA has been copied to yield a double stranded DNA molecule.
25
When does the process of reverse transcription occur?
In the capsid after the capsid has been released into the cytoplasm.
26
What is the primer binding site?
Part of the tRNA molecule hybridizes to a complementary site on the RNA genome called the primer binding site (PBS).
27
What direction does reverse transcriptase read the sequence of genomic RNA?
What direction does it add the complementary DNA nucleotides?
The RT reads the sequence of the genomic RNA in a 3’ to 5’ direction, adding the complementary DNA nucleotides in a 5’ to 3’ direction.
28
What happens when the RT reaches the end of the RNA strand?
RNase H activity digests this portion of the RNA template.
The DNA product is transferred to a site near the 3’ end of the RNA template.
The newly made minus-strand of DNA binds to the repeat (R) sequence on the RNA template.
RT reads the sequence of the genomic RNA in a 3’ to 5’ direction, adding the complementary DNA nucleotides in a 5’ to 3’ direction to complete the synthesis of the minus-strand of DNA.
29
What is the poly-purine tract?
What is it used for?
Most of the RNA is digested, except for a small region called the poly-purine tract (PPT).
Using the PPT on the RNA strand as a primer, the RT reads the minus-strand DNA as a template in a 3’ to 5’ direction, adding the complementary DNA nucleotides in a 5’ to 3’ direction.
RNase H activity digests this PPR region of the RNA template.
The newly made fragment of plus-strand DNA is transferred to the 3’ end of the minus-strand DNA, and the RT then completes the synthesis of the double stranded DNA
30
How are the long terminal repeats generated?
The long terminal repeats (LTRs) are generated as a consequence of the reverse transcription process.
31
What is the end result of reverse transcription of the HIV genome?
The R-U5 (repeat sequence unique sequence 5' end) and U3-R (unique sequence 3' end repeat sequence) from the genomic RNA have now both become U3-R-U5 in the viral DNA, giving it the required LTR at each end.
The R site in the 3′ LTR contains a cleavage site and a polyadenylation site used for the transcription of viral mRNA.
32
Describe the process of reverse transcription.
* The tRNA binds to a complementary sequence in the viral genome and is used as a primer by the RNA dependent DNA polymerase (RDDP) activity of reverse transcriptase (RT) to synthesize complementary DNA (the (–) strand).
* The RNase H activity of RT removes the short stretch of the 5’ end of the viral RNA.
* The short DNA sequence can bind to the 3’ end of the other strand of the RNA.
* The RDDP of RT uses this RNA strand as a template to continue DNA synthesis.
* The RNase H continues to remove RNA leaving short segments to be used as primers for DNA synthesis.
* The DNA dependent DNA polymerase (DDDP) of RT then uses the RNA primers to synthesize the (+) sense DNA strand.
* **The key point in this process is that the single stranded RNA molecule is used as a template to synthesize double stranded DNA molecules.**
33
Where does the HIV DNA synthesis take place?
In a protein-coated core inserted into the cytoplasm of the host cell.
34
Where does HIV get the primer needed to synthesize the first strand of DNA?
How about the primer for the second strand?
The primer for the first strand of DNA is a packed tRNA molecule, and the primer for the second strand of DNA is a small piece of RNA left behind after the RNase action of the RT degrades the RNA part of the RNA:DNA hybrid.
35
The genome of the HIV particle is composed of a double stranded RNA – one strand is positive sense and one strand is negative sense.
True or false?
False.
36
HIV is an enveloped virus.
True or false?
True.
37
Human immunodeficiency viruses have a dsRNA genome.
True or false?
False.
38
HIV requires a co-receptor to infect cells.
True or false?
True
39
The genome of the HIV is reverse transcribed in the particle before it enters into the host cell.
True or false?
False.
40
In reverse transcription the first strand of DNA synthesized is a plus strand.
True or false?
False.
41
RNAse H is used to degrade host cell RNA such that translation of viral mRNA transcripts is priority for the cytoplasmic ribosomes.
True or false?
False.
42
Reverse transcriptase is an RNA dependent DNA polymerase.
True or false?
True.
43
Retroviruses package a positive ssRNA genome, which resembles an mRNA and is immediately translated upon entry into the host cell.
True or false?
False.
44
Unlike most other viruses, retroviruses package two identical copies of their genome in the virion.
True or false?
True.
45
HIV has 3 main genes; gag, pol and env.
True or false?
True.
46
Retroviruses package reverse transcriptase enzyme and integrase in the virus particle.
True or false?
True
47
Reverse transcription results in a single strand of (+) RNA being copied into a double stranded DNA structure.
True or false?
True.
48
Reverse transcriptase has two distinct polymerase activities: RNA dependent DNA polymerase and DNA dependent DNA polymerase.
True or false?
True.
49
RNase H is a nuclease that degrades all of the RNA in the cell.
True or false?
False.
50
RNase H is one of the functional active sites in reverse transcriptase.
True or false?
True.
51
The reverse transcriptase uses a cellular mRNA as a primer to make the first strand of DNA.
True or false?
False.
52
The reverse transcriptase does not require a primer to make a DNA strand.
True or false?
False.
53
What are lentiviruses?
Slow virus
Infections with lentiviruses are characterized by a long interval between the initial infection and the onset of serious clinical symptoms.
eg - HIV
54
What is AIDS?
Acquired Immune Deficiency Syndrome
**AIDS is the final stage of the HIV infection**
**Acquired** – means that the disease is not hereditary but develops after birth from contact with a disease-causing agent (in this case, HIV).
**Immunodeficiency** – means that the disease is characterized by a weakening of the immune system.
**Syndrome** – refers to a group of symptoms that indicate or characterize a disease.
55
How does HIV damage a person's immune system?
Both types of HIV damage a person’s immune system by destroying the CD4 T cells.
Recall how crucial T helper cells were to the adaptive immune responses.
56
When will a person that has HIV+ status be diagnosed with AIDS?
When they have one or more opportunistic infections (or certain cancers) and a CD4 T cell count of less than 200 cells per µl of blood.
57
Where does HIV get the tRNA that associates with the two strands of positive sense RNA?
Acquired from the host cell of the previous infection
58
After infecting the cell, the first step in the HIV replication cycle involves translation of the RNA on a ribosome.
True or false?
False
When HIV first enters into the cytoplasm, it is not completely uncoated.
The reverse transcription occurs in the core of the virus, and the core delivers the dsDNA to the nucleus.
59
What is the group specific antigen gene?
gag
Encodes capsid, nucleocapsid, matrix, protease
60
What is the polymerase gene?
pol
Encodes reverse transcriptase, integrase
61
What does the env gene encode?
encodes the viral envelope glycoproteins - gp120 and gp41
62
What mediates the conversion of the RNA genome into a ds DNA genome?
The reverse transcriptase (RT) enzyme.
63
The resulting dsDNA product from reverse transcription is slightly longer in length than the original RNA due to the RT process.
This produces a promoter and transcription terminator in the DNA sequence.
True or false?
True
64
What are the main steps of reverse transcriptase that Dr. Kion wants you to know?
1. RNA dependent DNA polymerase activity of reverse transcriptase (Reads the RNA template and synthesizes a complementary DNA strand)
2. RNase activity of reverse transcriptase (degrades the RNA strand)
3. DNA dependent DNA polymerase activity of reverse transcriptase (Reads the DNA template and synthesizes a complementary DNA strand to make dsDNA)
65
Reverse Transcriptase has 3 distinct enzymatic activities, each catalyzed at a different site in the enzyme.
Which of the three activities in the Reverse Transcriptase enzyme is the most suitable for targeting for an anti-viral therapy and why?
RNA dependent DNA polymerase
RNA-dependent DNA polymerase is a unique virus activity that makes it ideal for anti-viral therapy.
Something that targets the other enzymatic functions of RT would be terrible – it would impact non-infected cells too (and interfere with DNA synthesis).
66
How do retroviruses leave the host cell permanently infected?
Retroviruses copy their RNA genome into double stranded DNA and then integrate the DNA into the host cell’s DNA, leaving the host cell permanently infected.
The virus uses the host cell’s RNA polymerase II and splicing enzymes to produce its mRNAs and its genome.
67
How does the replication cycle begin for HIV?
The viral glycoprotein gp120 binds to the CD4 cell surface marker of susceptible cells (usually T helper cells, but macrophages and dendritic cells are usually the first cells infected).
## Footnote
*The binding to CD4 alone is not sufficient for the virus to infect the cell.*
68
What happens after the gp120 of HIV binds CD4?
gp120 undergoes a conformational change.
The co-receptor molecule, CXCR4 or CCR5 is recruited to the site and also binds to the virus.
69
What causes the fusion of the HIV virus envelope with the host cell membrane?
After the binding of gp120 to the co-receptor molecule, the virus glycoprotein gp41 undergoes a conformation change and inserts its fusion peptide into the host cell membrane.
After the fusion of the envelope with the plasma membrane, the virus’ capsid is released into the cell’s cytoplasm.
70
Describe HIV attachment and entry of the virus capsid.
HIV requires a receptor and a co-receptor.
The binding of gp120 to the CD4 protein induces a conformation change in both gp120 and gp41 that ultimately results in the fusion of the virus envelope with the host cell plasma membrane and result of the capsid into the cytoplasm.
71
What happens while the reverse transcription process is occuring in the capsid?
The capsid structure uses the microtubule network to traffic towards the nucleus of the cell.
The pre-integration complex consisting of the virus DNA (also called the provirus) and the integrase protein traffic through the nuclear pore complex.
72
Describe the delivery of the HIV genome to the cell nucleus.
The virus reverse transcribes its RNA genome into the double stranded DNA genome.
Following arrival at the nucleus, the pre-integration complex (PIC, which contains the provirus and integrase) traffics through the nuclear pore complex (NPC).
73
What happens after nuclear import?
Following nuclear import, the integrase catalyzes the integration of the provirus into the host cell DNA at random sites.
The process of integration is specific (i.e.,it requires site-specific insertion sequences that are recognized by the integrase protein) but the sites of integration into the host cell genome are not specific (i.e.,there are multiple copies of this insertion sequence in the genome).
The process of integrating the proviral DNA is irreversible (i.e., the host cell is now permanently infected).
74
The process of integrating the proviral HIV DNA is irreversible (i.e., the host cell is now permanently infected).
True or false?
True
75
Describe the integration of proviral DNA into the host cell genome.
The integrases recognizes specific sequences and uses its endonuclease activity to make a staggered cut into the host cell DNA.
The integrase transfers the proviral DNA so that it is joined to the host cell DNA.
Host cell DNA polymerases repair the single stranded DNA of the target site.
The process of integration results in the duplication of the target site.
76
Where is HIV transcription initiated?
At a promoter site in the 5’ long terminal repeat (LTR) of the virus’ DNA integrated in the genome.
Transcription begins at the first base of the R region and polyadenylation occurs immediately after the last base of R.
77
What composes each LTR?
Each LTR is composed of three sub-regions designated as U3 (unique 3’ sequence), R (repeated sequence) and U5 (unique 5’ sequence).
The U3 region contains the binding sites for the cellular transcription factors.
78
What are the three types of RNAs produced, depending on the splicing site used?
**Unspliced RNA.**
**Incompletely spliced RNA.**
**Fully spliced RNA.**
79
What is unspliced RNA?
This RNA can be used as mRNA that are translated by cytoplasmic ribosomes to generate the Gag and Gag-Pol polyproteins.
Alternatively, the RNA transcripts can be packaged into new virus particles to serve the genomic RNA.
80
What is incompletely spliced RNA?
These mRNAs use the splice donor site located nearest the 5' end of the HIV RNA genome in combination with any of the splice acceptors located in the central region of the virus.
These RNAs can be translated to generate the Env polyprotein or some of the accessory or regulatory proteins.
81
What is fully spliced RNA?
These RNAs can be translated to generate some of the accessory or regulatory proteins.
82
What happens to the fully spliced viral mRNAs?
Exit the nucleus by using the export pathway followed by the majority of cellular mRNAs.
83
Describe the mRNA of HIV.
The integrated provirus DNA is transcribed and processed by host cell enzymes to at least seven different mRNA.
The thin lines in the diagram represent the RNA that was spliced out of the primary RNA.
The thicker purple lines represent the remaining RNA.
The blue dot represents the 5’ cap.
84
What is unspliced mRNA translated to synthesize?
Two polyproteins: the Gag polyprotein and the Gag-Pol polyprotein.
Most of the time (~95%), the ribosome stops translation at the stop codon in the Gag open reading frame.
85
What are the products of the Gag polyprotein after cleavage?
The capsid protein (CA), nucleocapsid protein (NC), matrix protein (MA).
86
What is required in order to express the pol gene?
A programmed −1 ribosomal frameshift (–1 PRF) is required to induce the ribosome to skip over the gag stop codon and entering into the reading frame of the pol gene.
87
Where does the -1 PRF site lie?
Between the gag and pol open reading frames (ORFs), with pol in the −1 reading frame relative to gag.
88
Where does the programmed change in reading frame occur?
At the heptanucleotide slippery sequence (UUUUUUA) that is followed by a spacer region and a downstream RNA stem–loop structure.
The structure causes the ribosome to stall during translation and slip back one nucleotide and continue translation in the –1 reading frame
89
Describe the HIV-1 frameshift site.
Two cis-acting RNA elements (i.e., they are on the same strand) are separated by a single-stranded spacer.
These act with trans-acting factors to regulate post-transcriptional gene expression.
90
Describe the mechanism of translation to merge proteins encoded by two overlapping open reading frames.
Ribosome frameshifting
For HIV, the frameshift occurs at low frequency and consists of ribosomes slipping by one base in either the 5'(-1) direction during translation.
Other virus species may have the ribosome slips in the 3'(+1) direction, and some virus species contains both a +1 and a -1 ribosomal frameshifts.
91
What gene products come from the pol gene?
The pol gene products include reverse transcriptase (RT), integrase (IN) proteins and protease (PR) proteins.
92
What does the Gag-Pol polyprotein contain?
All of the gag gene produces as well as the polgene products.
It makes sense that most of the time no frame shift occurs: for each new virus particle, many structural proteins are needed as opposed to only one copy of the polymerase enzymes.
93
Some of the spliced mRNAs serve as the mRNA for the envelope proteins. How are these processed?
These mRNA molecules are translated by ribosomes bound to the endoplasmic reticulum.
During transit through the Golgi, the Env polyprotein glycosylated and is cleaved by the host cell enzyme furin to form the gp120 and gp41 proteins.
gp41 is anchored in the host cell membrane, and gp120 is attached to gp41 by a di-sulphide bond.
The mRNA for the accessory and regulatory proteins would be translated by cytoplasmic ribosomes.
94
What are the multiple functions of the Gag polyprotein?
The Gag polyprotein has multiple functions in the assembly of the HIV particle.
Gag forms dimers (and other oligomers) and can interact with the plasma membrane at the sites where the envelope proteins gp120/gp41 are present.
Gag oligomers can also selectively captures the HIV genomic RNA and serve as the nucleation point for HIV assembly at the plasma membrane.
Additional Gag polyproteins are recruited to the plasma membrane and induce a curvature into the plasma membrane, resulting in HIV particle bud formation.
Gag also recruits the ESCRT (endosomal sorting complex required for transport)machinery needed for membrane fission.
95
What results in the release of the HIV virus particle from the host cell?
Membrane fission
96
Describe HIV assembly and egress.
HIV Gag protein drives virus assembly and recruits the ESCRT proteins for facilitate virus egress.
The ESCRT pathway is used in cellular processes such as endocytosis where the membrane constricts away from the cytoplasm and membrane fission is catalyzed by cytoplasmic dynamin, which acts from the outside of the bud neck.
When the viruses bud, the membrane must be constricted toward the cytoplasm, and cytoplasmic host factors that catalyze membrane fission must work from within the bud neck.
The ESCRT pathway can perform such “reverse topology” membrane fission events.
97
When does the HIV virus undergo maturation?
During or shortly after budding
98
What mediates HIV virus maturation?
A viral-encoded protease that is part of the Gag-Pol polyprotein.
99
What does the protease cleave in HIV virus maturation?
Specific sites in the Gag and Gag-Pol polyprotein.
The CA protein reassembles to form the capsid of the virus structure and the MA protein remains associated with the envelope.
100
Describe the maturation of HIV.
The maturation of HIV to form an infectious particle involves cleavage of the polyprotein and several conformational changes.
Note the morphologically distinct capsid.
The cleavage of the Gag-Pol protein results in the production of a functional reverse transcriptase and integrase.
The enzymes, however, remain inactive until the virus enters the cytoplasm of a host cell and gains access to nucleotides to allow for the process of reverse transcription followed by integration.
101
What is the cellular receptor for HIV?
The surface protein CD4 found on T helper cells (and macrophages and dendritic cells).
102
What are the two co-receptors required by HIV?
CCR5 and CXCR4.
103
What is the function of CCR5 and CXCR4?
The function of the co-receptor is to cause a conformation change in the surface viral protein gp41, allowing it to insert itself into the host cell membrane, fusing the two membranes, and allowing the core to enter the host cytoplasm.
104
When do retroviruses transcribe their RNA genome to DNA?
During microtubule trafficking towards the nucleus.
105
What is the role of integrase?
Catalyzes the integration of the viral DNA into the host cell DNA at random sites but by a specific process.
106
What mediates HIV gene expression and genomic RNA production?
By the host cell RNA polymerase.
107
What are some HIV mRNA spliced to yield?
mRNA for the envelope, accessory and regulatory proteins.
108
Where are the mRNA for the envelope proteins translated, processed, then integrated?
The mRNA for the envelope proteins are translated by endoplasmic reticulum associated ribosomes and the envelope protein is processed in the Golgi, and integrated into the plasma membrane of the cell.
109
What is programmed ribosome frameshifting required to produce?
The Gag and Gag-Pol polyproteins from the unspliced mRNA transcripts.
110
What drives virus particle assembly?
The Gag polyprotein drives virus particle assembly at the sites of the envelope protein in the plasma membrane.
111
What is exploited to facilitate virus budding from the plasma membrane?
The cell’s ESCRT machinery is exploited to facilitate virus budding from the plasma membrane.
112
What does HIV virus maturation involve?
Cleavage of the Gag and Gag-Pol polyproteins by the virus encoded protease protein into the individual components.
113
A pH change is needed to get the fusion peptide (gp41) to be revealed so that the envelope of HIV fuses with the plasma membrane.
True or false?
False.
114
The gp120 envelope protein of HIV binds to the CD4 protein of T helper cells.
True or false?
True.
115
Cellular DNA polymerase replicates the HIV genome for new virus particles.
True or false?
False
116
The host cell integrase enzyme integrates HIV’s DNA into the host cell DNA.
True or false?
False
117
The virus uses the host cell RNA polymerase to transcribe the virus DNA.
True or false?
True.
118
HIV produces several types of mRNA – spliced and unspliced.
True or false?
True.
119
HIV utilizes the polyprotein strategy to make some of its proteins.
True or false?
True.
120
HIV uses cap-dependent translation.
True or false?
True.
121
The Gag/Pol polyprotein is produced as a result of a programmed ribosomal shift on the mRNA.
True or false?
True.
122
The Env polyprotein is made by ribosomes associated with the endoplasmic reticulum.
True or false?
True.
123
The Env polyprotein is cleaved by a host cell enzyme in the Golgi apparatus.
True or false?
True.
124
The Gag and Gag-Pol proteins of retroviruses are translated from viral mRNA the same length as the virus genome.
True or false?
True.
125
Ribosomal frame-shifting is responsible for the synthesis of gene product from env gene.
True or false?
False.
126
Retroviruses only integrate into a few very sequence specific sites within the host cell genome.
True or false?
False.
127
When retroviruses integrate their provirus into germ line cells they can be vertically transmitted.
True or false?
True.
128
HIV matures after the virus egresses from the host cell.
True or false?
True.
129
How is HIV-1 transmitted?
Through the direct contact of a mucus membrane or the bloodstream with a biological fluid containing HIV-1.
These biological fluids include blood, semen, vaginal fluid, pre-ejaculate fluid and breast milk.
130
What does HIV-1 primarily infect?
CD4 T cells, macrophages and dendritic cells, but infection can extend to microglia cells in the brain.
Recall that T cells with the CD4 marker are helper T cells.
These cells are required for the activation of macrophages (to kill intracellular pathogens) and to activate B cells for antibody production (to neutralize viruses, opsonize or kill bacteria).
131
What is HIV not transmitted by?
air, water, sweat, tears, insects, pets, contact with toilet seats.
132
What are the four stanges of HIV-1 infection?
How may the stage of infection be determined?
**Incubation period**
**acute infection**
**latency stage**
**AIDS**
The stage of infection can be determined by measuring the patients CD4 T cell count and the level of HIV-1 in the blood
133
Describe the incubation period of HIV.
This stage usually lasts between two and four weeks.
The infected individual is usually asymptomatic.
There may be a slight decline in the number of circulating CD4 T lymphocytes.
134
Describe the acute stage of HIV infection.
This stage lasts on average about four weeks.
The symptoms of infection are non-specific and therefore are often not recognized as signs of HIV-1 infection.
Patients are frequently misdiagnosed with a more common illness such as Influenza.
During this time, there is an abundance of virus in the blood and its dissemination to lymphoid organs.
The acute infection stage is also marked by a drop in the number of circulating CD4 T lymphocytes.
The body’s immune system activates CTLs that kill some virally infected cells (resulting in the decline in CD4 T cells), as well as activates some B cells resulting in antibody production.
Antibodies against several HIV protein can be detected (i.e., anti-gp120 antibodies).
135
What is seroconversion?
Seroconversion is the term used to describe the production of antibodies to the virus and marks the start of the latency stage.
136
What marks the start of the latency stage of HIV infection?
Seroconversion
137
Describe the latency stage of HIV infection.
This stage can vary from as little as 2 weeks to many decades.
During this stage, HIV-1 is actively replicating within the lymphoid organs (e.g., lymph nodes).
Low levels of virus are usually found in the blood stream (the immune response may be controlling the amount of circulating virus).
138
Describe the AIDS stage of HIV infection.
The definition of AIDS has changed over time as the understanding of the virus and its relationship with the immune system increases.
When CD4 T cell numbers decline below a critical level (~200/mm3), HIV-1-positive individuals become highly susceptible to infections with a variety of opportunistic bacteria, viruses, fungi and parasites that are normally controlled by the elements of the immune system that HIV-1 has damaged.
In this stage, the amount of virus circulating in the blood is usually very high
139
HIV infection is the same as AIDS.
True or false?
False
140
What does an HIV virus load test measure?
The amount of HIV in the bloodstream.
The tests are done on a blood sample and measure the amount of virus nucleic acid by employing various hybridization methods with or without RNA amplification (e.g., reverse transcriptase polymerase chain reaction, RT-PCR, branched DNA test).
The patient may have their HIV viral loads measured several times during a year.
141
Describe current efforts for control and prevention of HIV.
Current efforts at prevention of HIV-1 infection are directed at limiting the spread of HIV-1 from individual to individual.
142
Describe problems associated with developing a vaccine for HIV.
The immune system produces antibodies and CTL responses during the acute phase of HIV-1 infection, but these immune responses do not offer protection (that is, the immune responses do not eliminate the virus).
Other problems include the lack of an animal model for testing the effectiveness of a vaccine and the logistics of conducting clinical trials.
Chimpanzees can be immunized with HIV and develop antibodies to the virus, but they do not develop AIDS.
Therefore, it is difficult to know if the anti-HIV antibodies that result from vaccination would be protective.
Human volunteers could be immunized with potential HIV vaccines, however, they cannot be challenged with “live” HIV to measure the efficacy of the vaccine.
Attenuated, live virus would not be a suitable candidate for vaccine because of the potential reversion to the virulent form.
Inactivated viruses may also not be suitable for vaccines if the inactivation procedure denatures the epitope on the glycoprotein that would need to be neutralized by the antibodies to prevent viral attachment.
There would also be safety concerns regarding the complete inactivation of the virus.
143
Why is it more difficult to develop medications that target virus infections compared to bacterial infections?
This is because the virus is using the host cell for is replication.
The medications would have to enter into the host cell cytoplasm and selectively interfere with the virus replication cycle without harming uninfected host cells.
For example, a medication that targets the ribosomes would not be suitable because protein synthesis is essential for life.
Therefore, the goal is to try to identify virus-specific molecules or processes (i.e., proteins, enzymes etc.) that can be the targets of these antiviral compounds.
144
How do antiretroviral medications work?
By preventing HIV from multiplying thus reducing the amount of HIV in the body.
Some antiviral medications work early in the replication cycle (e.g., reverse transcriptase inhibitors, integrase inhibitors) and prevent the virus from permanently infecting the cell.
Other antiviral medications work later in the replication cycle (e.g., protease inhibitors) and prevent the virus from maturing into an infectious particle.
145
What is antiretroviral therapy?
The treatment for HIV is called antiretroviral therapy (ART) and consists of taking a combination of antiviral medications every day.
The goal of antiviral therapy is the suppression of plasma HIV-1 RNA levels to \<50 copies/millilitre (this is monitored as described above).
146
What are the three main categories of antiviral medications currently in use against HIV-1?
**reverse transcriptase inhibitors, integrase inhibitors and protease inhibitors.**
Other categories of antiviral medications include fusion inhibitors, CCR5 antagonists and post-attachment inhibitors.
Many of the drugs are used as “combination therapeutics” to elicit a synergistic response – the choice would depend on the individual patient’ needs.
A regiment may consist of two nucleoside analogue reverse transcriptase inhibitors plus a protease inhibitor, but other combinations are possible.
147
Reverse transcriptase has unique enzyme activity that makes it an obvious target for anti-viral therapy.
What are two types of approaches that have been used in affecting RT function?
nucleoside analogs and non-nucleoside analogs.
148
How do reverse transcriptase inhibitors work?
RT inhibitors work early in the HIV cycle to prevent the virus from copying its RNA genome into a double stranded DNA copy.
## Footnote
**As a result, the cell does not become permanently infected with HIV.**
149
How do protease inhibitors work?
The protease enzyme is required for HIV maturity, allowing the virion to become infective.
These drugs competitively inhibit the HIV-1 protease, preventing maturation of the viruses by blocking the cleavage of the Gag-Pol polyprotein to release RT and integrase.
This results in a non-infectious virus particle.
The virus may be able to bind to another host cell, but the process of reverse transcription will not occur when the capsid enters into the cytoplasm.
These drugs are transition state analogues and can be considered as “plug” drugs
**Protease inhibitors work in infected cells and result in the production of defective virus particles.**
150
How do integrase inhibitors work?
Integration of the virus DNA into the host cell genome is a crucial step in the HIV life cycle.
The part of the replication cycle can be blocked by integrase inhibitors.
Integrase inhibitors work early in the HIV cycle to prevent the DNA copy of the genome from inserting itself into the host cell genome.
**As a result, the cell does not become permanently infected with HIV.**
151
What is prophylaxis?
The antiretroviral medications can also be used to prevent infection in a person that is not yet infected with HIV.
The use of a medicine to protect against infectious disease is called prophylaxis
152
What is pre-exposure prophylaxis?
Pre-exposure prophylaxis (PrEP) is used for prevent infection in people that are at high risk for contracting the virus.
PrEP involves taking anti-HIV medicines, usually daily, as well as other options to reduce the risk of HIV infection.
153
What is post-exposure prophylaxis?
Post-exposure prophylaxis (PEP) is for someone that may have been exposed to the virus.
PEP is initiated as soon as possible (within 72 hours) after possible exposure to HIV.
A course of PEP lasts for 28 consecutive days.
154
Compare pre and post exposure prophylaxis.
Individuals that are not currently infected with HIV may take antiretroviral medications to prevent infection if exposed to the virus.
155
What is essential in monitoring the efficacy of antiviral medications?
Monitoring of virus load and CD4 T cell counts
156
There is currently a vaccine that will induce protective immunity against infection of HIV.
True or false?
False
There is currently no vaccine to induce protective immunity against infection with HIV.
157
HIV+ individuals must use a cocktail of several antiviral drugs, rather than just a single drug, in order to slow the replication of HIV.
True or false?
True.
158
Reverse transcriptase inhibitors are effective after the virus has integrated its genome into the host cell.
True or false?
False.
159
Protease inhibitors prevent the HIV polyprotein from cleavage as the virus is assembled inside the host cell.
True or false?
False.
160
Worldwide, the percentage of HIV infections among men and women are equal.
True or false?
True
161
There are individuals who have had repeated exposures to HIV and remain uninfected.
True or false?
True.
162
During the first two to six weeks after infection with HIV, most people do not have any symptoms of infection.
True or false?
False.
Only during the first 2-4 weeks
163
The majority of individuals infected with HIV develop AIDS 8-10 years after the initial infection even if they are on antiretoviral therapy.
True or false?
False.
164
During the clinical latency period of an HIV infection, the virus is not replicating and no virus particles are produced any where in the body.
True or false?
False.
165
All positive HIV-ELISA tests must be confirmed by another independent test, usually the HIV Western blot.
True or false?
True.
166
In the ELISA test for HIV infection, the microtiter plate is coated with disrupted HIV particles.
True or false?
True.
167
When using the EIA test for HIV screening, both false negative and false positive results are possible.
True or false?
True.
168
Individuals that have severe mutations in the genes encoding the CXCR4 and CCR5 proteins may be immune to HIV infection.
True or false?
True.
169
The use of highly active anti-retroviral therapy (HAART), which involves a combination of nucleoside analogs and protease inhibitors, will eliminate HIV from a patient’s body.
True or false?
False.
