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This content is taken from the Lancaster University's online course, Influenza: How the Flu Spreads and Evolves. Join the course to learn more.

Skip to 0 minutes and 9 seconds Hello. Today I’m joined by Kate Atkinson, who’s a medical student at Lancaster Medical School. And Kate’s doing a Masters level project on influenza. And she’s going to be demonstrating today how to take a swab from the back of my nasopharynx. So what is the purpose of taking the swab from the nasopharynx of the patient? OK, so the aim is to get one of these swabs, and we want to get some of the lining of the epithelium. So some of the cells in the nasopharynx– we want to get some of those onto the end of the swab. So what, then, happens to the swab sample once it’s been taken from the patient?

Skip to 0 minutes and 44 seconds OK, so once we’ve got the sample on the end of the swab, then it goes into this solution here. And this contains viral transport medium. So that just preserves the RNA that’s in the virus. So that goes into the solution. Once the sample’s in the preservation fluid, what’s the next stage in the process? So once the virus is, as you said, in the viral transport medium, then what we need to do is we need to extract the viral RNA from the solution. So after you’ve obtained RNA from the sample, what are the next processes that are carried out on it?

Skip to 1 minute and 21 seconds So once we’ve got the RNA, we convert it to cDNA so that we can do something called PCR on it. And PCR stands for Polymerase Chain Reaction. So some samples will have a positive PCR result. And what does that mean? So any samples that come up positive, that means that they’ve got the live virus in the sample. So what we can do then is we can send any positive samples off for deep sequencing. So what do we obtain from deep sequencing that we didn’t get from the PCR reaction? So the deep sequencing gives us back the whole genome sequence for the virus. So Kate’s going to be demonstrating the nasopharyngeal swabbing on me now.

Skip to 2 minutes and 0 seconds She’s going to be wearing gloves, as you see. And prior to putting on the gloves, she also washed her hands using the full clinical Ayliffe technique for hand washing. OK, ready? Yep. Ready.

Taking a nasopharyngeal swab

In the second of our clinical demonstration videos, Kate Atkinson, a medical student at Lancaster University, demonstrates the technique for scraping a tiny quantity of cells from the nasopharynx. This is the modern way to retrieve material for diagnosis of influenza.

In this, and the next few videos, our theme is diagnostic techniques. The nasal swab that Kate takes from Derek, can be used to diagnose the presence of flu virus in the nasal passages using Polymerase Chain Reaction (or PCR, this is not demonstrated).

In the following video, Martin will take a blood sample from Derek, which could be used to detect viral antigen in Derek’s blood, using Western Blotting, or the presence of anti-influenza antibodies in Derek’s blood, using ELISA. Western Blotting and ELISA are demonstrated in the final video in this section, by Katharina and Lisa.

The nasopharyngeal swab taken by Kate contains a small scraping of cells from the back wall of Derek’s nasal cavity. These cells are then placed by Kate in a preservative solution. Later, RNA can be isolated from them, which will include flu virus genomes if any are present. This RNA can then be deep sequenced, which will reveal all the viruses present in the back of the subject’s nasal cavity. Later in the course, we discuss the new science of metagenomics which produces catalogues of pathogens in clinical samples, like the nasal cells Kate has collected in this video.


Unlike the Ayliffe handwashing technique, this requires specialist equipment and training, and is only for professionals.

The sound on this video is a little fainter than the others, so if you are having problems, please try switching on the subtitles. Using headphones could also help.

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This video is from the free online course:

Influenza: How the Flu Spreads and Evolves

Lancaster University