Interpreting a Negative

No, this is not a recap about reporting negatives in CDA (or in FHIR for that matter), instead, this is about how to interpret (or fail to interpret or explain how to interpret a negative test result).

If you haven't been on a call with me recently, it might be because I've had a flu.  What type of flu remains to be determined, though I'm fairly sure it's NOT COVID-19.  How do I know?  Well, I got tested.  Why am I not sure?  Because negative test results don't necessarily mean I don't have COVID-19, it just means that what I have is not detectable as SARS COV-2.

Wednesday morning I woke up fuzzy, feeling feverish (but no temp), and generally out of sorts, after having trouble sleeping.  I contacted my doctor (to apologize for missing a work related meeting), and he suggested I get tested (even though my symptoms were not specific to COVID-19).  So, I went and got tested at a drive up testing site at a nearby mall. Here's what it looks like.

It takes all of five minutes to take the sample.  It's not pleasant to have a swab that far back in your nasal cavity, but it's not really that painful either, just uncomfortable.  I wouldn't do it for fun.  I also got about 10 printed (full color) pages of stuff about the test, COVID-19, what to do if positive, et cetera, in three languages (looked like Spanish and Portuguese to me), reproducing two different information packets from CDC with overlapping information.  Stuff which I've already seen a dozen times or more.

I got a very nice recorded phone call the next morning after my test, telling me the result came back negative, and how I should treat that information.  But it was the usual, extremely digested baby-food level of information that is normally given to patients.

What I basically wanted to understand was, given the test reported that I was negative, what was the likelihood that result was wrong (a false negative).  So I went looking for more information.

So after the phone call, I looked at my personal e-mail.  I had received an e-mail from Quest (the lab) telling me that I had a new result that morning.  The e-mail showed up at 5am, about 4 hours before the phone call.  I checked the lab result, on Quest's portal, and felt not much more educated.  

It could have been from one of two different testing systems, Aptima and Panther (both from Hologic).  There were four different links (one for physicians and one for patients) to data about the testing system.  It was a typical reproduction of what is reported to FDA, so NOT that useful.  And the reported test result in the portal was again, standard pap (as in food for children).

Of course, being done by Quest, and having signed up, it was also available in my iPhone's Apple Health app, in FHIR format. The sad thing there is that the only value given for code was a string (SARS COV 2 RNA(COVID 19), QUALITATIVE NAAT), no LOINC code, nothing telling me much about the test itself.

Eventually, I determined from Quest (by zip code and lab) what the right LOINC code might be (I think the test was from Aptima), but am still uncertain, because it's reported based on where the test was sent, and I honestly am not certain (it could have been performed in MA or NY), because nothing in the lab report tells me that.  

There's data also available in MyChart, with actual links.  Though I cannot copy and past links from MyChart, nor can I click through them (it's a stupid s**t safety restriction that makes sense ONLY when you don't know how to implement a whitelist for websites).

So, next up I start looking at studies around false negatives for COVID-19, and actual sensitivity/specificity values for the test equipment in use based on real-world testing.  And honestly, I'm still feeling uninformed.  What I really want to know is the NPV, given that I have a negative result, what's the likelihood it's a true negative.  You cannot actually compute the NPV from Sensitivity or Specificity, you have to have the raw data to get that (or an estimate of disease prevalence).  Here's a good diagram showing all the details 

Unfortunately, none of the studies I dig into can really give me these details at a level that makes me feel comfortable interpreting an answer.

So, I asked my doctor the following two questions:

A) What's the NPV for this particular test (Hologic Aptima)?

B) What's your assessment of my pre-test probability, and how did you come up with that value?

We'll see how he answers and where I go from here.  Basically, my assumption based on symptoms is that I had a gastro-intestinal sort of flu infection rather than COVID-19.  Oh yeah, I'm still feeling icky, so trying to figure this stuff out while unwell is not my favorite past-time, nor the best time for me to figure it out.

   Keith