The United States has identified hundreds of cases of a more contagious strain first linked to the UK — but two others, linked to South Africa and Brazil, are much harder to find, according to Dr. James Lu, president of a company called Helix, whose Covid-19 tests have helped identify many of these cases.
It’s the latter two strains that may be more concerning when it comes to vaccine efficacy and reinfection, experts say.
Part of the reason why we’ve found so many cases of B.1.1.7 — the strain first detected in the UK — is because of a testing glitch that picks up one if its mutations.
Not all samples with this glitch are the B.1.1.7 strain, since this mutation can exist on its own. And not all brands of PCR tests show this glitch, called S gene dropout. But it has been used to screen for potential cases of the variant, which must then be confirmed through genetic sequencing.
“S gene dropout gives us a really good way to enrich for the samples of B.1.1.7,” Lu told CNN. “That said, if you were just sampling randomly across the country, it's much harder to detect.”
The mutation that causes this glitch is not present in the strains first spotted in South Africa and Brazil.
Beyond appearing more transmissible, these two strains also contain a different mutation that scientists worry could help the virus escape some of the antibody protection from vaccines or previous infection. Even so, experts say they expect vaccines will still work against the variants — especially when it comes to preventing severe disease and death.
“They're not detectable with our level of sampling today,” Lu said of variants linked to South Africa and Brazil. “So, most of the time, if we're finding it, it’s serendipity right now. But that will change if they become more prevalent.”
Last week, the first US cases of the strain linked to South Africa were found in South Carolina. According to a state health official, these two cases were found during routine sequencing, but “the predominant strain that we are still seeing in our surveillance sequencing is the standard, or normal,” version of the virus. Maryland has also reported a handful of cases.
At least two cases of the P.1 strain linked to Brazil have been found in the US, as well. Both cases live in the same household in Minnesota, and one had recently traveled to Brazil, according to the state’s health department.
In comparison, more than 540 cases of B.1.1.7 have been found in 33 states, according to the US Centers for Disease Control and Prevention.
The US has been ramping up efforts to sequence at least 7,000 samples per week, according to the CDC. But experts have said we should be aiming much higher — somewhere between 50,000 and 100,000 samples per week, given current case counts.