It's Almost Impossible to Find Out Which Covid Variant You Got

(Bloomberg) -- Last month, shortly after returning home from a bachelorette party, I tested positive for Covid. Twelve of us spent a weekend packed together in carefree revelry, including a night of drinking and dancing at a Connecticut casino; four of us got the virus within 72 hours. The point of origin seemed obvious. The bigger question: Which variant did we catch? 

I was mostly just curious. But in some cases, knowing which variant you have could help dictate treatment – certain monoclonal antibody drugs, for instance, are less effective against omicron. It might also help inform your personal risk calculus: We know that while an omicron infection provides immune protection against prior variants, those other variants don’t necessarily put your immune system in a position to defend against omicron. 

As part of public health officials’ efforts to monitor and track the virus, Covid samples are randomly and routinely sent to laboratories for genetic sequencing. New York State, where I live, has sequenced about 3.5% of reported positive cases, amounting to viral samples from some 46,000 New Yorkers. 

But none of those people will ever find out exactly which version of the virus they had, because accessing this information in the U.S., it turns out, is next to impossible.

The argument is that sequencing done in the interest of public health surveillance isn’t accurate enough at an individual level to have people base health decisions on. In the case of Covid viral surveillance, often the labs doing the sequencing don’t even receive identifying data alongside samples.

Labs that run tests to help doctors make medical decisions must undergo certification by the Centers for Medicare & Medicaid Services to ensure that results are consistent and accurate every time a particular test is run. Research labs worry less about the veracity of individual results and focus more on the big picture.

The virus is also constantly changing, making accuracy harder to achieve in the first place. “Whenever you have a new variant, you have to verify and accredit your processes again,” said Kelly Wroblewski, the director of infectious disease programs at the Association for Public Health Laboratories.

Labs that aren’t certified can’t perform tests for “the purposes of diagnosing stuff,” said Jacob Sherkow, a law professor and bioethics expert at University of Illinois. There is, however, technically nothing to stop any lab from doing so in a non-medical context. Anyone, he said, could technically hire a lab to sequence their snot. 

I thought I would give it a shot. Friends who had caught Covid during the winter omicron wave said they experienced a version of the virus that wasn’t much worse than a cold. But even with three doses of Moderna, I had a 104-degree fever, chills I couldn’t seem to shake and no energy or appetite. Was I particularly susceptible to omicron, or was this another variant altogether? 

Opentrons, a laboratory technology company with a pandemic response lab that contracts with government entities and businesses to handle surveillance sequencing efforts, agreed to help me in my quest so long as I promised the results would only be used for educational purposes.

So a lab like Opentrons might know my identity. In some cases, sequencing labs might even report what they find when they sequence my variant back to public health authorities for purposes such as contact tracing. But neither entity is allowed to report that information back to me.

Sharing this information is so frowned upon that, a few days after the director for Opentrons’ Queens lab watched me stick a swab so far up my nose that my eyes watered, a company attorney suggested it would probably be best to not sequence my sample after all.

The state of Oregon is the exception. There, a combination of patient health record access laws and Covid surveillance reporting rules mean that if an identified sample is sequenced, patients are allowed to request access to their results. A spokesperson for the Oregon State Public Health Laboratory said that they do not get such direct requests often. (He also emphasized that much of their sequencing efforts are not on identified data, except in the case when they are investigating specific outbreaks.)

Jeremy Kamil, a microbiologist and immunologist at Louisiana State University Health Shreveport, advocates for making this information more widely available to the public. More widespread viral sequencing, he said, would help better prepare us for future outbreaks of the virus.

And sharing sequencing information with the public would help bolster those efforts by encouraging people to participate in viral surveillance. Right now, he said, most people who test positive on an at-home test never report their results, leaving a huge blindspot in our ability to monitor the virus.

“A decent chunk of the public is curious to know what variant they have,” he said. “I really strongly believe that there is no benefit to not rewarding public curiosity.”

As I waited for my sequencing results, Bloomberg’s health team took bets on which variant I had. The timing of my illness led most to wager it was omicron — BA 1.1 or BA 2. The severity made one bet on delta. Another joked it might be the yet-to-be identified Star Wars-themed variant R2.D2.

A few days later, I got an email from Opentrons. While my sample had enough virus DNA to result in a positive test nearly three weeks after that first positive rapid test, there wasn’t quite enough of it to reconstruct the DNA of my particular breed of Covid.

Like everyone else, it turned out I would be stuck simply guessing which variant had finally gotten me. My money is on R2.D2.  

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