Tag: testing

You are going to stick *what* up my nose? [Update with TikTok links!]

These are not your grandmother’s nasal swabs.

To continue our recent discussions on disease testing, today we’re talking about swabbing and swabs. 

Perhaps you’ve been lucky enough to experience a swab test firsthand. As testing becomes more widespread, we are all likely to have a nasopharyngeal swab taken for a  COVID-19 test. When I was a child, maybe around seven, I remember going to the doctor’s office to be tested for influenza, another virus that replicates in the nasopharynx. When the nurse first pulled the slim, wire swab out of the packaging, I thought no way. No way that daunting, 5-cm long wire will fit up my nose. Sadly, I was mistaken. I won’t lie – it wasn’t the most pleasant experience. The tickling sensation lingered in my throat long after the swab had been removed. I still felt it even after my results had come back – negative, luckily for me. Just a common cold! 

This kind of swab is referred to as a nasopharyngeal swab, which I learned many years later. Nasopharyngeal swabs are used to collect samples from the back wall of the nasopharynx (hence the name), which is where the nasal passages meet the throat. Other common swab tests include nasal swabs and oropharyngeal (throat) swabs.

Nasal swabbing vs. nasopharyngeal swabbing from link.

Swabs are made out of a number of different materials. Since the nasopharynx is much farther back in the nasal passage, the swab needed to get there must be longer and somewhat bendable. The swabs used for sampling the nostrils and throat are generally stiffer and shaped like long Q-tips. The materials that comprise the tips of these swabs are different, too. If you are trying to get material out of the oral or nasal cavities for testing, you need a surface at the tip that is good at grabbing that material. It is also important to be able to wash the material off and into the testing solution when needed. Thus, regular cotton is often not suitable. 

In terms of COVID-19 testing, the swabs you’re most likely to encounter are nasopharyngeal and nasal swabs. Nasal swabs are less invasive. The swab only needs to be inserted 1 cm into the nostril and rubbed along the septum for a few seconds. Nasopharyngeal swabs, on the other hand, require a longer swab, which is inserted about 4-6 cm back into the nostrils (about half-way between the entrance to the nares and the base of the ear). The swab is then rotated inside the nasal passages and left in place for a few seconds to absorb the sample. 

Check out Dr. Klapperich demonstrating anterior nares swabbing (AN) here and here on TikTok!

Swabs made to sample the nasopharynx usually have a tip made of plastic foam, or another material with lots of surface area. These are called “flocked” swabs. Only a few factories in the world make these swabs, which is why you regularly hear about swab shortages for testing. Sadly, using a version of a regular Q-tip would not be a suitable replacement. There are a number of innovative groups around the world looking for ways around this shortage. Some of them include 3D printing swabs made from medical grade plastics. All swabs that are used to apply topical medications or collect fluid samples are considered Class I medical devices by the FDA. 

In studies comparing the sensitivity of nasal vs nasopharyngeal swabs for influenza, nasopharyngeal swabs were found to be slightly more sensitive (94% vs. 89% sensitivity). This means that for the flu, a nasal swab sample will lead to a false-negative test result more often than a nasopharyngeal swab. But despite their inferior sensitivity, nasal swabs are simpler and useful for “self-swabbing”- taking your own sample to send or have delivered to a testing facility. According to the most recent update to the CDC’s COVID-19 specimen collection guidelines, nasal swabs taken by a healthcare worker or via self-swabbing are acceptable if taking a nasopharyngeal swab is not possible. But these guidelines are sure to change as more information comes out about how swab type affects false-negative rates for COVID-19. Early indications are that nostril swabs are not as good as nasopharyngeal swabs for this new virus. 

Building a COVID-19 Test Lab (1/n)

When the president of the university asked me to put together a plan for what an on campus testing site would look like for our large campus community, I said yes.

Initially, this was going to be a short little post about my experiences the past couple of months. Turns out this experience has been the most complicated and rewarding time in my career, and it will require installments! Also, in this manner I can make sure that all the info I am providing is fact-checked and that I don’t get out ahead of guidance we are giving to our campus community. 

I hope you decide to follow along. 

Back in late April, a couple of emails popped into my inbox about what I thought about the possibility of building an on-site COVID-19 testing lab at my university. I had watched colleagues do this at our medical school to expand their ability to test patients and healthcare workers during the early surge in Boston. Colleagues at UC Berkeley, my alma mater, were also doing the same for their campus. From afar I had admired their resourcefulness and ability to pull together these complicated undertakings in a few weeks, and even faster at Boston Medical Center!

Stock image of a large scale laboratory.

Yeah, I thought, we can do this, but we need either a lot of people to pipette, or robots. Graduate students, much to the chagrin of many in the academy, are not an infinite resource! Besides, like everyone else, they wanted to get back to their own disrupted lives and research.

I’ve always been into outbreaks. For me, they are like the true crime of science. I’ve read all the books. The villain is the microorganism. Sometimes the causative agent is a mystery or comes from a mysterious source. Sometimes we know exactly who the serial killer is, and we have to try and stop it. SARS-CoV-2 is a virus we are getting to know quite well. 

One of my favorite colleagues is an honest-to-goodness card-carrying Ebola researcher. On my last sabbatical, I expressed my fascination with BSL-4 work, and how cool I thought it would be to just quit my job and train up with him to do this work. Leave everything behind and chase these mysterious villains. His immediate response was, “You are exactly the kind of person who should NOT be doing this work!” Hopes dashed, I went back to the relative safety of working on point of care (POC) tests for sexually transmitted infections.

Then COVID-19 emerged. The world seemed to start noticing POC diagnostics, or tests that can be done quickly and close to a patient. Journalists were calling to ask my opinion on how fast something like that could get to the mass market for COVID-19. The federal government started throwing money (billions of dollars, with a B) at my area of research. The little obscure molecular test system I work on was suddenly on the tips of the tongues of every Super Fancy Research University scientist. 

What I worked 20 years to make myself an expert in was finally interesting to someone other than my mother! But designing and developing new tests takes time, and we do not have a lot of time with this virus. Perhaps for the next one, and there will be a next one, quick POC tests will be widely available and cost effective. For now, we have to go with the systems we have, and the fastest way to get a lot of people tested efficiently is to scale up existing molecular tests and make sample collection as easy as possible. 

So, when the president of the university asked me to put together a plan for what an on campus testing site would look like for our large campus community (35 – 50,000 people, depending on how you count), I said yes. 

Next time I’ll talk about steps one and two in every big engineering project: defining the problem space and consulting the experts. 

What we talk about when we talk about diagnostics.

After spending the last few weeks talking with students, journalists, neighbors and family members, I’ve decided that there might be some value in discussing some of the terminology that we use when talking about diagnostic testing.

Science communication and media relations folks always discourage “jargon” when describing scientific concepts to laypeople. However, technical terminology can be a key part of scientific discussions, especially when it’s important to be precise. Now, in the setting of a global pandemic, precision is particularly important, and I believe people can handle more complexity than the scientific community often gives them credit for. Increasing scientific literacy can empower people to better understand and digest current events. So, here are some of those definitions.

First off, is reagent. In general, a reagent is any substance that is a starting material for a chemical reaction. Do you remember finding the “limiting reagent” in high school chemistry class? That’s the chemical that runs out first; thus, limiting the amount of product that can be made by the reaction. Many outlets have reported that one of the reagents failed in the initial test that the CDC distributed for COVID-19. It is still unclear which reagent did not perform as expected, but the reagent was one of the parts of the test reaction that the CDC shipped out to labs around the country. This problem has now been fixed, and all of the CDC test components are working well. 

Negative and positive screening test cassette strips.

The next term is assay. Assay is just the word we use for “test.” Anytime you hear someone say they are running an assay or assaying for something, they are simply running a test. 

Controls and control material also come up often when discussing test design. Controls are needed to make sure that the test you are running is valid. Basically, controls are parallel experiments that you run alongside your testing to make sure that you didn’t make a mistake while running the test. We science folks are always skeptical and are always checking to make sure we didn’t make a mistake! A positive control, in the context of COVID-19 testing, is when we put some material in the reaction that we know will make the test come up positive. If that reaction does not come up positive, we know that we made a mistake someplace, or that some of our other reagents are not working properly. A negative control is when we set up a test that does not contain a sample or additional material, that we expect to come up negative. If a negative control comes up positive, then we know that we have some kind of contamination, or that something we did not expect is happening in our reaction. If this happens, we need to start over, and figure out what went wrong. In both cases, controls that do not work as expected render any test result invalid. These results are not reliable and should not be reported. 

Now, we need to cover sensitivity and specificity. These guys are a bit more complex. Sensitivity measures how little of the virus you can detect using a particular test in a particular sample. A super-sensitive test can detect very small amounts of the virus. Sensitivity goes hand in hand with the concept of a false negative. A test that is not sensitive enough might come out negative for someone who is infected with the virus, but does not have a viral load high enough to make the test read positive. It is also possible that a false negative can arise from a swab being taken improperly. 

Specificity is a measure of how well the test detects the COVID-19 virus, and not other things that might confuse the test. A very specific test is good at detecting COVID-19 and will not detect other closely related viruses. Specificity goes hand in hand with false positive rates. If a test is not very specific, it might show a positive result when someone is not infected with COVID-19, but with something else like a flu virus. 

Both false positives and false negatives make it difficult for healthcare providers to interpret test results in the context of care. Low rates of false positives and false negatives make a test more trustworthy. 

Now you know the basics of test design and metrics! We hope that this makes reading some of the science reporting a little more clear.