FDA warns omicron variant can evade certain COVID-19 tests

We're two years into the COVID-19 pandemic and the original virus strain is old news. Delta remains the most common variant fueling infections around the world, but another variety of SARS-CoV-2 called omicron is raising alarm bells. Amid the potential for another wave of cases fueled by this new variant, the FDA has published an extensive analysis of COVID-19 tests and how the viral mutations may impact them.

Evolving virus and false negatives

The FDA has issued several Emergency Use Authorizations (EUAs) for COVID-19 tests from various manufacturers. These tests come in three different forms: serology (blood antibodies), antigen (virus proteins), and molecular (RT-PCR). Viral mutations, some of which are more significant than others, may impact the performance of any given COVID-19 test, potentially increasing the rate of false negatives, for example.

A web page dedicated to SARS-CoV-2 virus mutations and their known effects on COVID-19 tests has been published by the FDA, which continually updates the document with more information as it becomes available. Among other things, the FDA includes a list of COVID-19 tests that are known to be impacted by certain viral mutations — now including omicron.

Omicron hides from some COVID-19 tests

Of note, the FDA reports that the omicron SARS-CoV-2 variant may impact results from reverse transcription-polymerase chain reaction (RT-PCR) COVID-19 tests. Tide Laboratories is the only manufacturer currently on the list; its DTPM COVID-19 RT-PCR test "is expected to fail to detect" the omicron variant, the FDA says, due to some of the genetic mutations present in this version of the virus.

Tide Laboratories' product is a single target test, meaning it only looks at part of the virus's N-gene. This is unfortunate, as the specific part of the N-gene evaluated by the test is the same portion that experienced a nine-nucleotide deletion mutation. The resulting omicron variant, therefore, is able to evade detection with this particular type of test, potentially resulting in a false-negative result.

The FDA says it is working with the test maker "to address this issue," also noting that the test will likely still be suitable for detecting other known SARS-CoV-2 variants in circulation. Beyond that, the FDA explains that multiple SARS-CoV-2 mutants have presented "S-gene drop out," which refers to deletion in the virus's spike gene.

Many COVID-19 testing products evaluate multiple targets, not just a single target, meaning the mutation may not impact their ability to detect omicron and other similar variants. The agency goes on to explain the delta variant hasn't typically presented S-gene drop out and that detecting this drop out in test results may indicate the patient has contracted the omicron variant.

S-gene drop out isn't limited to the omicron variant, however, and therefore detecting it with one of these tests alone isn't enough to determine whether omicron is behind any given infection.

Wave after wave

COVID-19 infections are once again rising in the US, with the most recent seven-day daily average sitting at more than 118,000 new cases. The growing spike, which is expected to get worse as colder weather forces more people indoors and holiday gatherings resume, has arrived following the October lull, which itself followed the big August and September wave (via Google).

Public health officials continue to urge vaccination, as it remains the most effective way to substantially reduce hospitalizations and death from COVID-19. The delta variant has proven more infectious than the original virus strain, according to the CDC, but concerns are now turning to omicron. Infections involving this still largely unknown SARS-CoV-2 variant have popped up around the world, including in the US — though, fortunately, early data indicates it may result in less severe infections (via NYT).