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MODULE 9 - Respiratory System > INFECTIOUS AGENTS - Influenza Virus and PCR > Flashcards

INFECTIOUS AGENTS - Influenza Virus and PCR Flashcards

1
Q

What is a viral quasispecies?

A

A group of closely related viruses that exist within a population

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2
Q

What encourages mutation and genetic variation in viruses?

A

Selection pressures

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3
Q

What causes genetic variation in viruses?

A

Spontaneous mutations
Genetic exchange

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4
Q

What are the two methods of genetic exchange used by viruses?

A

Recombination
Reassortment

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5
Q

What is viral recombination?

A

Viral recombination is the process in which two viruses infect the same host cell and exchange genetic material

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6
Q

What is viral reassortment?

A

Viral reassortment is the process in which viruses with segmented genomes infect the same host cell and exchange genetic segments

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7
Q

Outline four examples of how selection pressures can facilitate emergence of new viral strains

A
  1. Immunity of the target population drives the emergence of antigenic variation in viruses
  2. Changes in the physiological environment drives the emergence of antireceptor variation in viruses
  3. Altered dynamic in the host population drives the emergence of viruses with an altered pathogenicity
  4. Use of anti-viral drugs drives the emergence of drug-resistant viruses
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8
Q

What type of virus is the influenza virus?

A

Orthomyxovirus

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9
Q

Describe the structure of the influenza genome

A

Linear, segmented, RNA genome

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10
Q

How many genome segments does the influenza virus have?

A

Eight segments

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11
Q

What are the two major antigens present on the surface of the influenza virus?

A

Haemagglutinin
Neuraminidase

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12
Q

What is the main function of the haemagglitinin antigen?

A

Haemagglitinin facilitates the attachment and entrance of the influenza virus into the host cell

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13
Q

What is the main function of the neuraminidase antigen?

A

Neuraminidase facilitates the release of viral particles from infected cells

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14
Q

How many variations of haemagglitinin and neuraminidase antigens are there in the environment?

A

18 Haemagglitinin
11 Neuraminidase

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15
Q

Which two processes lead to antigenic variation in the influenza virus?

A

Antigenic drift
Antigenic shift

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16
Q

What is antigenic drift?

A

Spontaneous mutations which occur within surface antigens

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17
Q

What is antigenic shift?

A

Viral reassortment resulting in a major variation in antigenicity

18
Q

Which animals are reservoirs for the influenza virus?

A

Wild aquatic birds

19
Q

What are four methods that can be used to control the influenza virus?

A

Vaccination
Hygiene
Education/awareness
Culling/quarantine

20
Q

What is polymerase chain reaction (PCR)?

A

PCR is a diagnostic technique used to amplify specific regions of DNA sequences

21
Q

Which piece of equipment is used to carry out a PCR?

A

Thermocycler

22
Q

What are the three steps of PCR?

A

Denaturation
Annealing
Extending

23
Q

Describe the denaturing stage of PCR

A

Temperature is increased to 95°C which separates the double stranded DNA into two single strands which act as a template for amplification

24
Q

Describe the annealing stage of PCR

A

Temperature is decreased to 55-65°C to allow the primers to bind to the target region of the single DNA strands

25
Q

Describe the extending stage of PCR

A

Temperature is increased to 72°C to allow the Taq polymerase enzyme to bind to the primer to add nucleotide bases to form a complementary strand of DNA

26
Q

How many times is the PCR amplification cycle repeated?

A

20 to 40 times

27
Q

What is reverse transcriptase PCR (RT-PCR)?

A

RT-PCR is a technique used to amplify specific regions of RNA sequences. This involves the conversation of RNA into DNA using a reverse transcriptase enzyme followed by performing a traditional PCR

28
Q

Which technique can be used visualise and analyse the amplified DNA fragments following PCR?

A

Gel electrophoresis

29
Q

What is real time (quantitative) PCR (qPCR)?

A

Real time PCR is a PCR technique that allows for the real time monitoring of amplification of DNA. This is achieved through the use of fluorescent dyes or probes which emit signals proportional to the amount of target DNA that is present in the sample

30
Q

Give an example of a non-sequence specific fluorescent dye that can be used in real time (quantitative) PCR?

A

SYBR green dye

31
Q

What is Taqman PCR?

A

Taqman PCR is a type of real time (quantitative) PCR which uses Taqman probes which bind to the target regions of the DNA being amplified. During amplification, the probe will be cleaved by the Taq polymerase enzyme, resulting in the release of a fluorescent signal proportional to the amount of target DNA is present in that sample

32
Q

What is cycle threshold (Ct)?

A

Cycle threshold (Ct) is the measure of the real time PCR amplification cycles required for the fluorescent signal to reach a detectible level

33
Q

What is indicated by a low cycle threshold (Ct) value?

A

Low Ct value indicates that there is a higher amount of the target DNA present in the clinical sample

34
Q

What is indicated by a high cycle threshold (Ct) value?

A

High Ct value indicated there is a lower amount of the target DNA present in the clinical sample

35
Q

What is relative quantification?

A

Relative quantification compares the amount of target DNA present in a clinical sample to a reference or control sample

36
Q

What is absolute quantification?

A

Absolute quantification determines the exact quantity of target DNA present in a clinical sample

37
Q

What are the four main advantages of real time (quantitative) PCR compared to traditional PCR?

A

More sensitive
More quantitative
Faster process
Lower risk of contamination

38
Q

Why is there a lower risk of contamination in real-time PCR compared to traditional PCR?

A

Real-time PCR uses a closed system where the amplification and analysis of the target DNA occurs within the same tube, reducing the chances of contamination, however, traditional PCR requires gel electrophoresis to analyse the target DNA and thus the amplified DNA is going to be transferred between tubes and be at a higher risk for contamination

39
Q

What are the two main disadvantages of real time (quantitative) PCR compared to traditional PCR?

A

More expensive
Requires more specialised equipment

40
Q

What are the five main advantages of PCR as a diagnostic tool?

A

Identifies pathogens that can’t be cultured
Identifies early infection due to being so sensitive
Identifies carriers of the infection
Allows for strain-specific identification
Differentiates between vaccine and environmental infection

41
Q

Explain the three main disadvantages of PCR as a diagnostic tool

A
  • Very sensitive, so need to avoid contamination
  • Lower specificity: primers can bind elsewhere in target sequence leading to false negatives/positives
  • Sequence variation: genetic mutations can lead to variations in the target sequence that affect primer binding, leading to false negatives

MODULE 9 - Respiratory System (15 decks)

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