H1N1: How we test for it and why there’s no FDA-cleared test

Oink, oink. Yes, one of those ILIs has caught up with me and I’m currently stuck in bed sipping water and battling a fever that makes me wonder if I could fry eggs on my forehead.

The CDC has some nifty graphs and tables on their website. You can learn about everything from the number of illnesses reported by US region to Antiviral resistance. In case you thought that H1N1 was some kind of trumped-up wimp on the block, note that

all 2009 H1N1 viruses tested since April 2009 have been resistant to the adamantanes (amantadine and rimantadine).

Oh great, just what we need: more superbugs!

I got my seasonal flu short earlier in the season, but due to massive shortages in supply I didn’t get an H1N1 vaccine. I work at DHMC, but I don’t work directly with patients so I’m probably at lower risk. It’s entirely possible that I don’t actually have H1N1, but given the fact that I and a few of my friends are currently self-quarantined at home while the one person I know that got the vaccine is cheerily going about business as normal…well, it just makes me suspicious.

Ordinarily when I get suspicious I like do something about it. I’ll investigate, do some research — you know, basically not sit on my ass in bed for 3 days straight. But that seems to be precisely what the Powers That Be™ suggest that I do. So how am I supposed to figure out if I actually have H1N1? How does the CDC expect to generate reliable data on how many people are infected with this porker of a problem if most sick people are asked to stay home in bed?

Doing some searching took me to the CDC page for H1N1 Clinicians. Unlike some of the other materials on the CDC’s website, this page stops talking at a 5th grade level and starts to give us science geeks some answers. First, according to the CDC,

the rRT-PCR test… is the only test that can confirm infection specifically with the 2009 H1N1 virus. Tests such as rapid antigen detection assays and diagnoses based on symptoms alone without rRT-PCR testing, cannot specifically determine if a person has 2009 H1N1 influenza.

So you have to have this rRT-PCR test, otherwise known as Real-time reverse-transcription PCR. It sounds a bit complicated and is probably not something I can cook up in my basement. Aw, shucks.

Doing a bit more digging brings up some PDFs on the CDC’s website about their testkit. If you delve into the Fact sheet for healthcare providers you’ll find that

At this time, no FDA-approved/cleared tests that identify the existence of 2009 H1N1 influenza virus in clinical specimens are available in the United States. Therefore, the Centers for Disease Control and Prevention (CDC) has developed this test to detect novel influenza A (H1N1) infections.

Just to make sure you caught that, there are no FDA-cleared tests for H1N1. The CDC had to just make one up super fast. Why?

A public health emergency has been declared by the Secretary of Health and Human Services because of the outbreak of the 2009 novel influenza A (H1N1) virus…The Food and Drug Administration (FDA) has authorized the emergency use of the Swine Influenza rRT-PCR Detection Panel (rRT-PCR Swine Flu Panel) to test for the presumptive presence of novel influenza A (H1N1) virus in clinical specimens under an Emergency Use Authorization (EUA).

So basically they’re saying that because of the risk to the population the CDC and FDA have got to go whole hog on this one and bust out an EUA, skipping the normal process by which the FDA clears test procedures. Okay, my respect for the virility of H1N1 has just gone up a couple of notches.

Created in 2004, the first use of the EUA was in 2005 to authorize the use of Anthrax Vaccine Adsorbed for military personnel. Although in that case the authorization took 5 weeks, the CDC notes that depending upon circumstances, the EUA could be granted within days or even hours.

Side Note: I’ve been unable to track down how many EUAs have been issued in total. If you know where I can find that information, please leave a comment on this article!

Getting back to our test, there’s a copy of the Swine-Flu EUA [PDF] up on the CDC website. Unfortunately this is a scanned PDF so I can’t copy text out of it. Here’s the a short blurb on the test specifics:

The Swine Influenza Virus Real-time RT-PCR Detection Panel is a panel of oligonucleotide primers and dual-labeled hydrolysis (Taqman®) probes for use in the real-time RT-PCR assay on the ABI 7500 Fast Dx Real-Time PCR instrument for the in vitro qualitative detection of 2009 H1N1 influenza viral RNA in nasopharyngeal swabs etc…

But that’s not quite the test itself. We’re so close, but we’ll need to go to another website to find that information. The CDC links to the World Health Organization, who has an actual CDC step-by-step protocol up on their website. Interestingly, unlike the CDC document above, this CDC document mentions several suitable PCR instruments from different vendors and includes an explicit disclaimer that

Names of vendors or manufacturers are provided as examples of suitable product sources. Inclusion does not imply endorsement by the Centers for Disease Control and Prevention.

Although the protocol expects the user to have a working knowledge of rRT-PCR assays, it is quite detailed, including what type of swabs to use (synthetic tip, aluminum or plastic shaft), how cold and how long a sample may be kept (2-4°C for 4 days or less, or frozen at -70°C or below), equipment sanitization, when to change gloves, etc…etc. The instructions are detailed enough that I think that someone with a college degree could limp through them in a pinch. You might need to spend some time reading the manual for the PCR machine, but I think that non-laboratorians could follow the instructions in an emergency.

Before we all start doing our own tests at home, I should note that we still have a large number of healthy lab techs and the simplest Thermal Cyclers that you’ll need to carry out PCR cost about $2000 – $7000, quite a bit for an inquisitive person to drop on a personal medical toy.

Of course, this article is all about the do-it-yourself spirit, so I will note that Wikipedia points to a NewScientist article that says that thermocyclers can be had for as little as $59 on eBay. Indeed, at a quick glance I saw machines on eBay for $100 – $200, certainly within the budget of any eccentric person who wishes to test for H1N1 at home.

So hop on over to eBay, get that thermocycler, and then find a source to ship you the necessary H1N1 assay chemicals (that might take some doing). With a small sample of sputum (on a synthetic-tipped swab, natch!) you can, in the comfort of your own home, see if you have been touched by the Oink or if you have some other, less interesting, ILI.

Warning: If you have an immediate need for medical care, head on over to your Emergency Room.
If you’re crazy enough to try this at home then please remember that I am not a Laboratorian and you probably aren’t one either. We just like to geek out on medicine from time to time.

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3 thoughts on “H1N1: How we test for it and why there’s no FDA-cleared test

  1. qubit's status on Thursday, 05-Nov-09 14:04:41 UTC - Identi.ca

  2. “the one person I know that got the vaccine is cheerily going about business as normal”

    Bwahaha. Well, I wouldn’t say that I’m completely going about business as normal– I’m fatigued and get chills and my body temperature is a little higher than normal (I’m normally close to 97 but now I’m 98-99). But yes, I seem to be doing better than several people here. So maybe you do have the hamthrax after all.

  3. Motorola Droid vs. HTC Droid Eris: Side-by-side spec comparison of Verizon’s Android Phones « Things that have escaped from my mind

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