Past Papers 11 Flashcards
Oral station - 15 mins
A midwife calls you to say that a follow-up blood sample from a pregnant lady is clearly HIV negative, whereas the first blood sample taken a week before is HIV-1 positive.
Discuss.
2 possibilities -
patient is truly neg, and first result has a problem
patient is truly pos, and second result has a problem
Check patient records - ensure no patient identifier issues, or name changes
Check positive result + paperwork. Was this positive for 2x antibody tests, plus immunoblot? HIV RNA PCR positive? Any issues with controls that might mean this result is an error. Any other problems with run, that might suggest samples have been swapped with a known HIV positive patient. Does patient have a history of HIV infection?
Check negative result - ensure this was actually negative and not entered incorrectly onto computer. Check controls worked, and there are no issues with assay. Check sample has not been swapped with a patient who is known HIV neg
If no obvious patient sampling/ labelling issue, then retest both samples in parallel to understand if those samples contain virus/ antibody.
If discordant results, request a fresh sample for testing, to ensure it is the correct patient sampled.
Oral station - 15 mins
A terrorist bomb victim sustained a penetrative injury from a sharp piece of bone, which originated from a deceased terrorist.
The Emergency Department team is calling you for advice
Apply first aid
Were they wearing gloves?
Visible blood?
Risk of injury - high as penetrating injury
Source - unknown risk. Without knowing much about source, would presume high risk.
HBV - booster vaccine if last 10 years
HCV - follow up
HIV- PEP
HIV PEP - take baseline bloods- FBC/ UE/ LFT, pregnancy test, and send sample for BBV screening to ensure does not already have HIV
Ask staff member to contact occupational health
Oral station - 15 mins
A 32-year-old male sewerage engineer presents with a 1-day history of fever, abdominal pain, headache, myalgia and drowsiness. He had just completed a 3-month assignment in rural Nigeria and returned to UK two days prior to his onset of illness.
The Emergency Department registrar has called you to
discuss.
Risk of VHF - fever within 21 days of returning from VHF country. Nigeria endemic for Lassa, and has risk exposure as rural and sewage worked
More History - caves, unwell contacts, funerals, accommodation stayed in, rat/ mice exposure. Lassa outbreak information via ProMed. Anti-malarial prophylaxis
More clinical history - any bruising, bleeding, vomiting, diarrhoea
isolate as possible VHF - full PPE. Double glove, visor, FFP3 mask, gown, boots, negative pressure room. Inform IPC
Discuss case with imported fever service - consider transfer to Royal Free
Inform UKHSA
Start contact list form
Blood film for malaria
Bloods - FBC/ UE/ LFT/ Coag/ blood culture
VHF screen - blood
Consider leptospirosis - blood/ urine
Consider LP
What is rotavirus pathogenesis?
VP4 capsid protein binds to villus surface
rotavirus non-structural protien (NSP4) acts as an enterotoxin by causing changes in Na+ channels in cells
necrosis of epithelium - diarrhoea
What are benefits of enteric viruses not having an envelope?
Means can resist alcohol gel
Lipid envelope actually means that nucleocapsid is usually quite vulnerable, so once lipid envelope destroyed, virus is subsequently destroyed
Bleach is used to disinfect following norovirus ward outbreak
What concertation is required?
1000 - 5000 ppm
Enterovirus can cause wide variety of conditions
What are possible presentations?
Enterovirus D68 - acute respiratory outbreaks
enterovirus D70 haemorrhagic conjunctivitis
enterovirus 71 HFM, meningitis
Enterovirus A71 - flaccid paralysis
all can cause myocarditisand gastroenteritis
herpangina
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist.
What are the problems with this PCR run? Specify missing items (6 marks)
- ## no R2 coefficint of determination value
- no note of if IQC controls passed
- no date/ name of person who has performed the run
- no negative control - unclear if sample 2/6 have zero copies because they are truly neg, or because PCR failed. Use water instead of DNA as a negative control to detect contaminants in the reaction and to discriminate background amplification
- no positive control - used known patient sample/ IHC or external quality control
- standard curve analysis requires at least 5 data points. This only has 4
- lowest standard is at 1000 - and this doesn’t even have a measured CT value.
Need standard sample which will range from from limit of detection, to 1000 IU/ml
i.e sample 2 is record as having 0 iu/ml. However, it’s true value could be anywhere between 0 and 1000 - highest standard is at 1million.
Needs standard sample in 10m and 100m, as sample 1 is recorded at 86m iu/ml.
if result is above 1m, then result is recorded as “above range of testing”
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist.
Would you accept this standard curve? Please explain why?
Do not accept
No positive/ negative controls
to create a standard curve need a minimum of 5 data points - our graph only has 4
Also want to repeat standards in triplicate, so you are sures that those values are correct
Would like to know the R2 value - the coefficient of correlation and should be > 0.99 to provide a good confidence within the correlation.
This value lets you see if there is a good linear relationship between the values of each sample. A low value could indicate a poor serial dilution. To avoid this, when making your serial dilutions ensure you pipette accurately, using well-calibrated pipettes, and mix dilutions well.
https://bitesizebio.com/31470/obligate-qpcr-standard-curve/#:~:text=To%20perform%20a%20qPCR%20standard%20curve%2C%20you%20set%20up%20qPCR,a%20proportional%20dose%2Dresponse%20curve.
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist.
can any of the results be reported? Please explain
???
Samples 2, 3, 6 cannot be reported, as there values fall below our threshold for limit of detection. There unclear if truly neg, or just low level
Sample 1 - above threshold for testing. Do not report as cannot give an accurate value?
Sample 4 - could report, as result falls within controls
Sample 5 - could report, as result falls within controls
answers very unclear
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist
What do you recommend your lab staff do next?
Repeat run
Add negative control - Use water instead of DNA as a negative control to detect contaminants in the reaction and to discriminate background amplification
Add positive control - in house control - could be old patient sample of external sample
Add another positive standard - to have 5 minimum targets
Add spike porcine virus as positive spike control
Calculate R2
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist
Is this run valid and is the standard curve acceptable? Please explain. (7 marks)
unclear answer?
needs 5 standards
needs R2 calculation
needs standard deviation calculation. CMV IU/ml value should be within 0.2 SD units. As each diluted sample should be 1/10th of the previous sample
Ct values of internal control (spiked phocine herpes virus) - these need compared to know in house values. Because these Ct values seem quite late for an IHC
now has negative and positive controls
What is R2 value?
The coefficient of determination (R²) measures how well a statistical model predicts an outcome.
The outcome is represented by the model’s dependent variable. The lowest possible value of R² is 0 and the highest possible value is 1.
draw a line for CMV viral loads. This means we can estimate with a detected value, what the true value might be
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist
Lower limit of detection was previously determined to be 100 IU/mL
whereas the lower limit of quantification was 400 IU/mL
Define these two concepts and clarify how these are usually determined.
Explain how can a sample be positive but below the limit of quantification
Limit of detection - The limit of detection LOD is the lowest possible concentration at which the method can detect (but not quantify!) the analyte with certain degree of confidence - e.g 99% of the time it will detect <40 copies. It is also defined as the lowest concentration that can be separated from a background noise with some reliability
Limit of quantification -
the lowest concentration that can be quantified with an
acceptable level of repeatability precision and trueness.
e,g can reliably detect >100 copies 100% of the time
and <100 copies only 90% of the time
If LoD is 40 copies, and LoQ is 100 copies, then a value of 60 copies would be detected, but unqauntifiable
https://www.rcpath.org/static/80d54920-b6e2-45aa-bdb6c34026e99179/Part-2-Virology-sample-questions.pdf
You are provided with the following data for a quantitative CMV DNA assay run by your trainee biomedical scientist
How would report these samples:
Sample1
Sample2
Sample3
Sample1
CMV detected above limit of quantification?
Sample2
CMV not detected
Sample3
CMV detected - <400 iu/ml - result is above limit of detection, but below limit of quantification
