Can you tell which COVID variant you have?

At-home COVID-19 rapid test kits are flying off the shelves, and appointments for PCR tests are hard to come by in many parts of the country. With the omicron variant now accounting for a majority of COVID-19 cases in the US, mixing with an already-abundant number of cases from the delta variant, you may be wondering: If I test positive, which coronavirus variant do I blame? 

Through the process of elimination and a little intuition hard-earned by living two years through a global pandemic, you may be able to guess based on where you live (in New York City, for example, omicron is estimated to account for more than 90% of cases). Scientists also believe omicron is causing more breakthrough cases in fully vaccinated (and boosted) individuals compared to delta, and also causing more reinfections and people getting sick with COVID-19 a second time. 

But scientifically speaking, people working in labs who process positive COVID-19 tests will be able to pinpoint cases that indicate omicron is the likely variant that caused the infection. That information is unlikely to get back to you, however. Here's why.

How PCR tests can detect omicron

Dr. Manoj Gandhi is the senior medical director at Thermo Fisher Scientific. He explains that the PCR tests widely used in the US (polymerase chain reaction tests that pick up the virus' genetic material) have three signals or genes to be detected – a signal from two of the three genes means the sample is positive for COVID-19. While the delta variant causes all three gene signals to show up on a PCR test, the omicron variant causes one to drop off in what's also called an S gene target failure. 

When scientists in South Africa noticed a change in the PCR test signals (which was also found in cases caused by the alpha variant), they alerted virologists and sent the newer samples in for additional tests, which revealed a new variant with many mutations – omicron. 

"It all depends on what is the dominant variant at the time," Gandhi says. "So in the background of delta, now when you see this, that basically tells you that this is omicron." According to Centers for Disease Control and Prevention data projected for the week ending Dec. 18, about 73% of US COVID-19 cases were omicron, about 26% were delta and a small fraction were caused by another variant. 

To confirm a COVID-19-positive sample is the omicron variant, the sample needs to be sent in for genomic sequencing. Through sequencing, scientists can discover new variants and learn more about their mutations, which is important for surveillance and public health. 

At the end of November, US CDC Director Dr. Rochelle Walensky said that the CDC had increased the number of samples it was sequencing – about 80,000 positive COVID-19 samples per week (or one in seven positive tests), up from 8,000 per week earlier this year. 

Can I tell if it's omicron by the symptoms? 

Based on symptoms alone, it's probably difficult to discern between delta and omicron. Zoe, a UK-based company that contributed to initial reports last summer that delta caused slightly different COVID-19 symptoms, compiled the top five symptoms of COVID-19 from omicron so far: runny nose, headache, fatigue, sneezing and sore throat. These were the same symptoms as the ones collected during a period when delta was dominant, Zoe said. 

According to a December report from the CDC based on 43 of the early cases of omicron in the US, most people had a cough, were fatigued and congested or had a runny nose. Muscle and lower-back pain has also been reported as a symptom of COVID-19 now. 

Loss of taste and smell, a symptom that continues to haunt many people who were infected with earlier variants of the virus that causes COVID-19, doesn't appear to be common with omicron and also wasn't as common with delta. 

In general, it's difficult to make definitive claims about symptoms now, as many adults around the world who've had omicron and reported their symptoms were fully vaccinated, which typically leads to much milder symptoms.

Can I call my doctor and ask which variant I have? 

It's not likely. Not only is the US swimming in COVID-19 cases with many people struggling to even get a test, the sequencing of COVID-19 samples is meant for tracking and surveillance purposes – it's not tied to the identity of the person taking the test. Indicators of omicron would also be seen in a lab where PCR tests are processed (even if you send in a sample from home). 

"There's a little bit of decision making to be done as to what this information really means to the patient, and also from a public health measure," Gandhi says. "Most of the variant information comes down to some further testing that needs to be done."

Can a rapid test tell me which variant I have? 

No. And although they're helpful and being encouraged by health officials prior to people gathering indoors for the holidays, rapid antigen tests are less sensitive than PCR tests because they look for proteins of the virus. This means if a person is asymptomatic or has a really low viral load – thanks to the COVID-19 vaccines and/or prior COVID-19 infection – Gandhi says their rapid test may show up as negative when they actually have the virus. 

Most popular at-home tests can detect COVID-19 caused by omicron, though not all rapid tests, Dr. Anthony Fauci told the US Chamber of Commerce Foundation last week. The US Food and Drug Administration is keeping tabs on the tests.

"Vaccination doesn't really prevent you from getting infected – it prevents you from getting the disease," Gandhi says. On the flip side, if someone is symptomatic with COVID-19 and has a lot of the virus in their system, the rapid tests are very accurate. But this makes other public health measures like masking and social distancing all the more important, especially during the holidays, according to Gandhi. 

"It's always better to take a test than not to take a test," he says, but take it with a grain of salt. "You've got to take this in the totality in how your body responds to the virus as well, not just the behavior of the virus by itself."