Final Flashcards

(105 cards)

1
Q

How much of the european population did the black death kill?

A

50%

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2
Q

What was responsible for the plaque??

A

Yersinia
A gram-negative, rod-shaped, non-motile facultative anaerobe. There are 3 human pathogens among 11 species. Causes zoonotic disease.

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3
Q

What are the three types of yersinia that affect humans? Name and compare.

A

Y. enterocolitica: enteric pathogen acquired by the consumption of contaminated food or water, causing inflammation of the intestinal tract
Y. pseudotuberculosis: enteric pathogen but causes less severe inflammation of the intestines
Y. pestis: more virulent of the three but not enteric.

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4
Q

Describe Y. pestis.

A

It is a nonmotile, coccobacillus, facultative anaerobe, non-enteric pathogen. It is one of the most virulent bacteria known with an infectious dose of 1-10 cells. Disease progresses very quickly, within a few days, and has caused more than 75 million deaths.

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5
Q

What are the different diseases caused by Y. pestis?

A
Bubonic plague (50-70% fatal)
Septicaemic plague (~95% fatal)
Pneumonic plague (100% fatal)
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6
Q

How is Y. pestis transmitted?

A

Rodents are hosts for the natural endemic cycle with fleas as the vector for spread. The bacteria in the fleas blocks the esophagus, causing them to starve and feed more aggressively, jumping from host to host. Humans can get it through both rodent sand fleas as well as through airborne transmission in the case of pneumonic.

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7
Q

Describe the bubonic plague (transmission, signs, symptoms).

A

Most common form of the plague (80% of cases)
Transmitted through bites of infected fleas or direct contact with an infected host. It incubates for 2-6 days then causes fever, chills, headache, and very swollen, painful lymph nodes called bubo.

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8
Q

Describe the pneumonic plague (transmission, signs, symptoms).

A

A rare, highly contagious version with aerosol transmission. It is the most rapidly developing and life threatening form of the plague, with an incubation period of 1-4 days. Symptoms include fever, cough, headache, bleeding in the lungs, etc., and difficulty breathing that can develop into respiratory failure.

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9
Q

What are the two types of pneumonic plague?

A

Primary: direct inhalation
Secondary: spread of bacteria from the bubo to the lungs, more common

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10
Q

Describe the septicaemia plague (transmission, signs, symptoms).

A

Occurs when Y. pestis enters the bloodstream and causes septicaemia. Results in fever, chills, extreme weakness, abdominal shock, and possibly bleeding into the skin and other organs. Although it can occur as the first symptom of the plague, this is relatively rare and more often develops from untreated bubonic. Known as the black death due to appearance of dead infected tissue.

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11
Q

Describe the virulence factors of Y. pestis.

A

The bacteria has 3 plasmids with important virulence factors. pPCP is a pla protease causing organ destruction. pMT1 codes for Ymt causing flea toxicity and envelope F1 antigen causing antiphagocytic properties. pCD1 codes for a type III secretion system.

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12
Q

Describe the pCD1 plasmid in Y. pestis.

A

It codes for T3SS and is essential for virulence in the species. It allows for the injection of Yersinia outer proteins (Yops) into target host cells. These have antiphagocytic and/or anti-inflammatory effects.

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13
Q

Describe the evolution of Yersinia species.

A

Non-pathogenic environmental yersiniae split into Y. enterocolitica and y.pseudotuberculosis when it picked up the pCD1 plasmid. After this, the y. pseudoteberculosis gained the pPCP and pMT1 plasmids developing into ancestral Y. pestis. A series of gene mutations, genome rearrangements, gene inactivation, and gene gains resulted in the modern Y. pestis.

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14
Q

Discuss the diagnosis and treatment of Y. pestis.

A

The diagnosis and treatment must be rapid due to the progression and deadliness of the plague, usually looking for the characteristic symptoms (bubo). Treatment includes antibacterial drugs such as gentamicin, ciprofloxacin, doxycycline, and streptomycin.

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15
Q

How has the distribution of the plague changed since 1954?

A

See somewhat regular spikes int he number of cases, mainly among Asian and African countries.

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16
Q

What were the three major plague pandemics?

A
Plague of justinian (541-750)
Black plague (1347-1352)
Third Pandemic (1855-1896)
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17
Q

What are the three main causes of the increased rate of the plague in the 21st century?

A

Increased international trade
Rising urban population
Lack of medical knowledge

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18
Q

Describe the measles virus (MeV).

A

It is a non-segments, -ssRNA virus with an envelop and a helical capsid. It is in the genus morbillivirus and family paramyxoviridiae. The natural host is humans and can cause measles as well as subacute sclerosing pan encephalitis. (SSPE).

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19
Q

Describe the transmission of MeV.

A

It is highly infectious and airborne, spread through respiratory droplets and contact with infected secretions. It can exist for hours outside outside the body as aerosols.

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20
Q

Describe the genome of MeV.

A

Contains 6 genes: fusion protein, large protein, hemagglutinin protein, phosphoprotein, metric protein, and nucleocapsid protein.

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21
Q

Describe the state of measles prior to the introduction of the vaccine.

A

It was estimated that prior to 1963, there were 30 million cases per year with more than 2 million deaths. Overall, it has resulted in around 200 million deaths.

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22
Q

How and why has the rate of measles changed?

A

After the introduction of the vaccine, case numbers began to drop but they dropped more sharply in 2001 after the global measles and rubella initiative, with a 79% decrease and 17.1 million deaths prevented from 2001 to 2014.

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23
Q

Describe the state of measles globally today.

A

In 2017, 110 000 people died from measles, mostly children under the age of 5. It has a fatality ration of less than 0.01% in industrialized countries and greater than 5% in developing countries.

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24
Q

What caused the decrease in measles mortality seen in industrialized countries in the early 1900s?

A

Economic development combined with improved nutrition statue and better supportive care, in particular antibiotic therapy for measles associated bacterial pneumonia, helped improve the survival rate of measles prior to the vaccine.

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25
Describe the coverage and efficacy of the measles vaccine.
In 2000, prior to the initiative, 72% of children received one dose, where as 85% received 1 dose in 2017. Currently, 15% of children fail to develop immunity from one dose. In 2017, 67% of children received the 2nd dose. However 20.8 million infants are still not vaccinated, 40% in india, nigeria, and pakistan alone.
26
What is the treatment for measles?
There is no treatment for measles. When diagnosed, kids get two doses of vit. A supplements across 2 hours to help prevent eye damage and blindness. Often, anti-measles immunoglobulin is given within 6 days of exposure. These combined with good nutrition, adequate fluid intake, and antibiotics to treat secondary infections help reduce the chance of death.
27
Describe the mechanism of MeV.
F protein and H proteins on the envelope mine to SLAM on the cell surface. This causes the envelope to fuse with the cell membrane, releasing RNP into the cell. This RNP is then used to synthesize viral mRNA. The newly translated M proteins and RNP travel to the cell membrane while the F and H proteins are transported first to the golgi complex for further modification. Once everything is at the cell membrane, the virus assembles and the cell membrane pinches off to form the new membrane.
28
How are measles diagnosed?
Look for the signs of measles (Kolpick spots, rash) plus serological tests to confirm the presence of measles antigens in respiratory and blood specimen.
29
What are some challenges to the global eradication of measles?
In order to eradicate it, it would require 95% two-dose vaccine coverage which would require a global effort, funding, and leadership. It would also require a novel delivery system and new vaccine strategies to help deal with minimally trained volunteers. Vaccine hesitance requires outreach to improve parents' knowledge and confidence in benefits. We also must improve access, demand and use of immunization services along with strategies to improve immunization among hard to reach populations.
30
What are the 4 main subtypes of the influenza virus?
Influenza A, B - 8 RNA segments | Influenza C, D - 7 RNA segments
31
Describe influenza A and B.
The RNA segments code for glycoproteins. Hemagglutinin (HA) allows viral entry and Neuraminidase (NA) allows viral release. The segmented nature of the viral genome allows for reassortment.
32
Describe the epidemiology of influenza virus.
3-5 million cases of severe (seasonal) influenza per year with children being the main human transmitters but zoonotic human infections do (rarely) occur. The seasonal epidemics of A and B result in around 500000 deaths annually globally.
33
Describe the transmission of influenza.
Transmission occurs through the respiratory route with cell entry occurring in the epithelial cells of the respiratory tract by the binding of HA.
34
What virulence factors does influenza have?
HA is stable among various pH (allows transmission between hosts) Antigenic drift of HA and NA glycoproteins.
35
What are the risk factors for influenza?
Very young or old Pregnant women Chronic cardiopulmonary conditions Immunocompromising conditions
36
What are the the symptoms of the seasonal flu?
Caused by A H1N1 and H3N2 currently, it results in mild respiratory disease causing a fever, sore throat, runny nose, cough, headache, muscle pain, and lethal pneumonia.
37
What is antigenic drift? Talk about it with respect to influenza.
The gradual accumulation of mutations allows the virus to develop the capacity for evading antibodies and immune responses. Means that the flu vaccine requires yearly updates and surveillance programs to monitor the virus' evolution.
38
What is antigenic shift? Talk about it with respect to influenza.
They are drastic changes in the antigenicity of circulating viruses. This is often associated with influenza pandemics and cannot be predicted as it is caused by the acquisition of animal strains into human strains.
39
How do you diagnose influenza?
Typically it is based on symptoms but you can also use a culture, RT-PCR, a rapid antigen test, or rapid molecular assay. Most people stay home so a vast majority of cases go unreported.
40
How do you treat influenza?
Antivirals are provided for the extremely ill or immunocompromised, otherwise, treatment includes remaining at home until symptoms disappear, controlling fever and treating the symptoms.
41
What are the two types of antivirals used for influenza?
NA inhibitors | Adamantanes
42
What are the issues with the use of antivirals in the treatment of influenza?
There is now widespread resistance among the circulating A viruses. The seasonal H1N1 is resistant to adamantanes now. No longer recommended for treatment.
43
What factors influence the viral selection for the flue vaccine?
1) the degree of similarity between the circulating virus and produced vaccine virus 2) validity and quality of the vaccine virus for protection
44
Who develops the influenza vaccine?
100 national influenza centres in over 100 countries conduct year round surveillance. These labs send representative viruses to WHO collaborating centres for references and research on influenza.
45
Describe mycobacterium tuberculosis.
It is a gram (+), non-motile, slow-growing, rod-shaped bacteria that lacks endospores. The cell wall contains mycolic acid (a waxy lipid). The cell envelope is made up of strong hydrophobic molecules creating a lipid shell. These are C60-C90 long chain fatty acids that contribute to virulence. Make up 50% of the dry weight of the cell envelop.
46
What properties are mycolic acids associated with in M. tuberculosis?
``` Impermeability to stains and dyes Resistance to many antibiotics Resistance to killing by acidic and alkaline compounds Resistance to desiccation Resistance to lethal oxidations Protection from lysis after phagocytosis Survival inside of macrophages ```
47
How do you stain M. tuberculosis?
Acid-fast stain. | Involves carbolfuchsin, heating, decolorization with HCl, then counterstaining with methylene blue.
48
How is TB transmitted?
Airborne droplets and inhalation
49
What are the three types of TB?
Primary TB: results from the initial infection with M. tuberculosis Secondary, reactivated, activate TB: reestablishment of active infection after period of dormancy Systemic, miliary TB: results when infection spreads throughout the body with symptoms arising due to complications at the various sites involved
50
Describe the pathogenesis of TB.
Infects the respiratory tract in the alveolus. Macrophages phagocytize mycobacteria but cannot digest them due to bacterium inhibiting fusion of lysosomes to endocytic vesicles. Bacteria replicate freely within macrophages, gradually killing them. They are then released and phagocytized by more macrophages. The infected macrophages present antigens to T lymphocytes, causing lymphokines to be attracted and activate more macrophages, triggering inflammation.
51
Describe the formation of a a tubercle.
Tightly packed macrophages surround the infection, forming a tubercle over 2-3 mo. Other cells deposit collagen fibres, enclosing the tubercle. Cells in the centre die, releasing M.tuberculosis producing necrosis. Enters stalemate with body's defences.
52
What occurs in secondary TB?
M. Tuberculosis breaks the stalemate, ruptures the tubercle, and establishes an active infection. Occurs in about 10% of patients.
53
What is disseminated TB?
Results when macrophages carry the pathogen via blood and lymph nodes to other sites, including bone marrow, spleen, kidneys, spinal cord, and brain.
54
What does the distribution of TB look like today?
250-fold higher in South Africa than the US. From 1900-1980, TB related deaths in Western Europe and US fell by 100 fold. 10% of all new cases worldwide occur in children with an untreated fatality rate of 50%.
55
What are some risk factors for TB?
HIV Type 2 diabetes Excessive alcohol use Smoking
56
What are some signs and symptoms of TB?
25% of cases are without symptoms. These include bloody cough, fever, chest pain, chills, weight loss, night sweats, no appetite, and fatigue.
57
How do we diagnose TB??
Choice depends of purpose of testing. Tuberculin test, IGRA, X-ray/CT scan, or lab testing (staining, culture, PCR, etc.).
58
Describe the tuberculin test.
A purified protein deritavide is introduced to the skin. A positive tests means they were exposed at some point, whether latent or active TB. This works because tuberculin is a component of TB and therefore it you have been exposed it will result in an immune reaction, causing a red, raised, hard area.
59
Describe the Interferon gamma release assay.
Find evidence in the blood and is more specific to TB.
60
What is the treatment for TB?
Most antimicrobials are ineffective therefore combination therapies are often required for months to treat it, using drugs such as Isoniazid, Rifampicin, Pyrazinamide, or ethambutol.
61
What are some prevention strategies for TB?
The BCG vaccine is commonly used now, with more than 90% of infants vaccinated. It has an efficacy of up to 80%. Made of attenuated live bovine tuberculosis bacillus M. bovis, it protects for up to 10 years. Several new drugs and vaccines are currently in development.
62
What is WHO's strategy to end TB?
1. Interventions in diagnosis, treatment, management, and prevention 2. Broad health systems and policies 3. Research and development of new tools
63
What are some developments that facilitate the spread of infectious diseases?
``` Commercial air travel Global trade Urbanization Unchecked population growth Climate Change ```
64
What are some advances that are helping control infectious disease transmission?
Genome sequencing to identify emerging viruses Global communication networks Rapid diagnostics New approaches to vaccine and therapeutic design.
65
What are the different biosafety levels?
BSL1: non disease in immmunocompeted adults = standard biological practices BSL2: associated with human disease = limited access with biohazard warnings BSL3: indigenous or exotic agent with potential for aerosol transmission, causing high personal risk but low public risk = controlled access and decontamination of all wastes and lab clothing BSL4: agents which pose high risk of life threatening disease with high personal and public risk = controlled access with a positive pressure suit.
66
What is required to be a member of the filoviridae family?
Infect primates, bats, or pigs Cause viral hemorrhagic fever in some primates Replicates exclusively in cytoplasm
67
What virus causes ebola?
Genus: ebolavirus Species: Reston ebolavirus (reston virus)
68
How many genes does ebola have and what are they?
1. Glycoproteins (full length GP, secreted GP, and ssGPNP) 2. VP24 3. VP30 4. VP35 5. VP40 6. NP 7. L
69
What is the reservoir of the ebola virus?
Believed to be hosted by bats although there has never been any direct evidence. It is believed that it replicates below the levels of detection in bats, specifically fruit bats.
70
Describe the transmission cycle of ebolavirus.
In the wet season there is very little transmission. In the dry season, animals are much more condensed. Bats eat fruit which falls and is eaten by primates, infecting them. Human to human transmission occurs once early clinical symptoms appear.
71
How is the ebola virus transmitted to humans?
Transmitted by virus coming into contact with open wounds on skin or coming into contact with the mucous membrane. Also spread via sex.
72
Describe the clinical course of the ebolavirus.
The virus will replicate under the radar of the immune system by traveling to the lymph nodes. During this, you see fever, chills, headache, diarrhea, abdominal pain, etc. After 6-7 days, the virus erupts, entering the blood stream and traveling to the major organs. Begin to see bleeding signs, anuria, shock, etc. The virus causes a lot of damage very quickly, causing high levels of inflammation that persists even after the viral load has decreased.
73
Who dies from ebola?
We have not clue, but people will generally die 9 days after onset of symptoms and those with bloody diarrhea are more likely to die.
74
Why can ebola be transmitted via sex?
It has been found that the virus can survive and replicate in the testes without causing symptoms and not being detected through normal testing. During sexual intercourse, it can still be transmitted and actually exists at a higher viral load than during disease. This makes treating outbreaks very challenging.
75
What caused the bottleneck in ebola research?
1. Sample acquisition from human patients - cultural and societal norms 2. Sporadic outbreaks 3. Biocontainment requirements - virtually impossible outside developed countries 4. Animal models do not fully recapitulate human disease
76
Why was the treatment of ebola in liberia so hard?
Liberia was colonized by freed US slaves in the early 1820s, who quickly established a slave culture with the locals. This created strain as well as anti-western sentiment, leading to civil wars in the 1990s and 2000s. With a population of around 4mil, 1 million live in the Monrovia and 85% live below the international poverty line, the country having the third lowest GDP in the world.
77
Describe the 2014 Ebola outbreak.
The disease emerged in December 2013 in New Guinea and spread slowly to Sierra Leone and Liberia in early 2014. By early summer, researchers knew it would be large and began recruiting volunteers in August. Case numbers exploded around September, 2014. Overall, the outbreak resulted in 12 000 deaths and 28 000 infections.
78
What happened in west point during the ebola epidemic?
Westpoint is a slum in Monrovia. When the outbreak occurs, several cases hit this area. However, local militant groups believed this was a lie and physically removed patients as well as blankets and bedding from treatment centres. In response, the government quarantined the slum and the virus spread like wildfire.
79
What is ELWA3?
The largest treatment centre operating in Liberia during the 2014 epidemic, run by Medecin Sans Frontieres.
80
What was the issue with research facilities during the ebola outbreak?
Every night, labs would have to call the ministry of health with their results. This makes it hard to reach outlying communities with results. Labs also differed greatly in their rules and methods. Finally, the rest of the world got involved too late, sending funds and equipment over as the virus was already declining.
81
What factors contributed to the severity of west african ebola epidemic?
1. Old disease but new region 2. National infrastructure 3. Severe shortage of healthcare workers 4. Cultural beliefs and societal norms 5. Traditional healers and/or self-medication 6. Community resistance 7. Social and/or mass media coverage 8. Additional endemic infectious disease
82
What is hindering aid in the current ebola outbreak in the congo?
Violence and civil unrest | Burning down treatment centres as they believe the illness is fake.
83
What are some ways we could control and prevent infectious diseases?
``` Immunization Screenings Health laws Hygiene Antimicrobial chemotherapy Awareness Diagnostic tools ```
84
What is chemotherapy?
The use of drugs/chemicals to treat a disease.
85
What are the different types of chemotherapy?
Antibacterial Antiviral Antifungal Antiprotozoal
86
Give a brief history of antibiotics.
Late 1800s: Paul ehrlich searched for antimicrobial agents and discovered that arsenic compounds work against syphilis. 1928: discovery of penicillin by Alexander fleming (development in 1939) 1932: discovery of sulphanilamide (first practical antimicrobial agent) by gerhard domagk.
87
Why are tetracyclines different from other antibiotics?
Get incorporated into skeletons.
88
What are some commonly used antibiotics and their modes of action?
Inhibitor of cell wall synthesis: beta lactams (penicillin), glycopeptides (vancomycin) Inhibitors of nucleic acid synthesis: quinolones (ciprofloxacin) Inhibitors of metabolic pathways: sulphonamides Inhibitors of protein synthesis: macrolides (Azithromycin), tetracycline, aminoglycosides (gentamicin) Disruption of cytoplasmic membrane: peptide antibiotics (polymyxin B)
89
Describe the development of antibiotic resistance in S. aureus.
1940: penicillin-resistance identified 1960: 80% penicillin-resistant isolates, introduction of methicillin Mid 1960s: first MRSA-isolates Late 1960s: introduction of gentamicin 1970: gentamicin resistance Late 1980s: Start of MRSA spread`
90
What are some mechanisms of antibiotic resistance?
1. Impermeable barrier 2. Efflux pumps 3. Resistance mutation 4. Drug inactivation 5. Overproduction of target
91
What are some different approaches currently being used to discover new antibiotics?
``` Rationally improve existing antibiotics Repurpose old drugs Discover untested new chemical diversity (synthesis or natural) Target-based approaches Rediscover old antibiotics ```
92
Describe the drug discovery process.
Academic and industry discovery (min 3 years) Preclinical (1 year) - on animals Phase I (1 year) - on animals Phase II (1 year) - on healthy humans Phase III (3-4 years) - on sick humans Government review (2-4 years) Overall takes around 15 years and costs around $1 billion/drug
93
What are some reasons for the low availability of new antibiotics?
Used for a relatively short period of time Newer antibiotics are priced at max $1-3 per course Availability, ease of use, and generally low cost has led to a perception of low value among prayers and the public New antibiotics are now saved for resistant infections
94
What are some novel approaches to treat resistant bacterial infections?
``` Phage therapy Repurposing old drugs Targeting bacterial virulence Metagenome analysis Quorum Quenching Bioinformatics - modelling Combination therapy ```
95
Why are there only a few antiviral drugs?
Drugs that interfere with viral growth can also hurt the host cell as replication engages host function, resulting in side effects. In other viruses, there are no animal models to grow them in. Many acute infections are also short, leaving little time for diagnosis and treatment and antivirals must be given early in infections. There are also no broad spectrum antivirals on the market. Finally, they must block replication entirely otherwise resistance will arise quickly, therefore the drug must be potent.
96
Give a brief history of antivirals.
Initial search began in 1950s with chemists looking at derivatives of sulphonamide antibiotics and managed to synthesize an agent active against smallpox. In the 1960s and 70s, several high throughput/blind screening programs were running to find new antivirals. Random chemical and natural product libraries were screened for the ability to block replication requiring considerable effort with very little success. The one exception was symmetrel (amantadine) to treat influenza A.
97
Describe the mechanism of amatandine.
Blocks the uncaring of viruses in endosomes.
98
What are some approaches to antiviral discovery today?
Recombinant DNA technology and sophisticated chemistry make targeted discovery possible Essential viral genes cloned, expressed in genetically tractable organisms, purified, analyzed in atomic detail Life cycle of most viruses known, targets for intervention can be generalized Modern technology allows inhibitors to be found even for viruses that cannot be propagated in cell culture Blind screening procedures are dead
99
What are some targets for antiviral drug discovery?
``` Fusion inhibitors (HIV) Early inhibitor (influenza) Interferon (hep C) NA inhibitors (influenza) Protease inhibitors (HIV, HCV) Nucleoside, non-nucleoside analogs (HIV, HCV, herpesvirus) ```
100
How does resistance to antiviral drugs occur?
Resistance occurs in most due to modest to high mutation frequencies. Resistance to every antiviral drug has been found.
101
Describe the HIV virus.
Family: retroviridae, retrovirus Genus: lentivirus Genome: ssRNA, reverse transcribed into HIV DNA and integrated into the host DNA, polyhedral capsid with spiked envelope Humans are host with the first documented HIV infection recorded in 1951 with the discovery of the virus in 1983. Currently infects more than 75 million people worldwide.
102
What is the treatment for HIV?
``` Antiretroviral therapy (ART) Composed of a variety of antiviral drugs, such as nucleoside analogs, protease inhibitors, and inhibitors of reverse transcriptase. ```
103
How is HIV prevented?
Sexual abstinence, refrain from sharing intravenous needles, condom use (only reduces risk)
104
Describe the life cycle of HIV.
Attachment: HIV enters and Env on the surface binds to CD4 and CCR5 or CXCR4 on cell surface Fusion: virus fuses with the cell membrane and is uncoated once inside the cell. Reverse transcription: viral components are transcribed and assembled into a circular piece of DNA Integration: DNA is imported into the nucleus and is incorporated into the host DNA. Transcription: Host DNA is transcribed in mRNA and exported from nucleus Translation: mRNA is translated into proteins Budding and maturation: proteins travels to cell wall and buds off, gaining envelope. Once free of cell, virus matures and assembles inside envelope. REPEAT
105
What are some potential targets for antiretroviral drugs in HIV?
``` Attachment inhibitors Fusion inhibitors NRTIs and NNRTIs (reverse transcription) INSTIs (DNA integration) Maturation inhibitors Protease inhibitors (assembly) ```