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Send Out the Search Party for New Covid Strains

Caitlin Rivers, PhD, MPH

By WWSG exclusive speakers Scott Gottlieb & Caitlin Rivers

Many are expecting vaccinations, rising levels of immunity and warmer weather to help control the Covid-19 pandemic and make spring and summer more bearable. But new viral variants threaten these prospects. The U.S. is struggling to estimate how prevalent these strains are and how fast they’re spreading. The infrastructure for dealing with a pandemic is still incomplete a year into the crisis.

At issue are mutated strains: one identified in the U.K., another first spotted in South Africa, and a third strain in Brazil that is similar to the South African one. The mutations speckling these new strains appear to make the virus spread more easily. New waves have swamped places where these variants have become prevalent across Europe, Africa and Latin America.

There is new research that the U.K. variant may also cause more serious illness. The strain found in South Africa may have mutated parts of its protein structure to help it defeat some antibody drugs and could render vaccines less effective. A lot is unknown, but the variants pose a serious threat.

Americans are wondering: Are these new variants spreading around my city? The U.K. variant, known as B.1.1.7, has been discovered in as many as 20 U.S. cities, although many of the cases are localized in Florida and San Diego. The variant circulating in South Africa and Brazil hasn’t been detected in the U.S., but the search only started recently. It is almost certainly circulating somewhere.

Until recently, there wasn’t a systematic effort to look for these variants. Such an effort involves sampling positive Covid cases to determine their genetic makeup. Much of the sequencing in the U.S. is academic work and not devoted to public-health surveillance.

The U.K. has put substantial resources behind such an effort and was able to detect the new variant relatively early. The U.S. is late to this game, and is only now organizing a nascent effort. The Centers for Disease Control and Prevention has focused much of its relatively small sequencing operation on other priorities and is only now starting to aim more of it at Covid.

One of us serves on the board of Illumina, a company that manufactures machines used in such sequencing work. Illumina has been working with the Helix genetic-testing company and the CDC to develop a more organized effort at routine surveillance for troubling new mutations. Illumina estimates that detecting a new variant when it represents about 0.1% to 1.0% of all cases—when containing spread is still manageable—requires sequencing about 5% of positive Covid cases. Right now, the U.S. is sequencing less than 0.3% of cases. Yet there are enough sequencing machines and other infrastructure in the U.S. to reach the 5% goal.

It’s also important to invest in research that examines the behavior of new variants, and the outcomes in patients who contract it. Congress can dedicate more funding to the National Institutes of Health for this purpose.

The experience so far with these new variants is that when they gain a foothold, they quickly become the dominant strain. In cities such as San Diego or Miami, where prevalence may already be 1% or 2%, these new strains could represent 30% of all infections in six weeks. Cities such as New York or Boston, where they may only represent 0.1% or 0.2% of infections, have more time.

With Covid continuing to spread, it was inevitable that new strains would emerge. The country will need more-efficient drug regulation that makes it easier to update antibody drugs and vaccines to target these mutations. But America can do better at stopping the spread of the new variants—if it first focuses on uncovering them.

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