January 12, 2021

America is 'flying blind' in detecting new coronavirus variants, experts warn

Daily Briefing

    Officials have identified a new, more-contagious variant of the novel coronavirus in the United States and roughly 44 other countries, but experts worry that the United States and other countries have been slow to track the variant's spread—meaning they could be unaware of how widespread the variant already may be.

    The more infectious coronavirus strain has hit the US. Here's what you need to know.

    A lack of tracking

    Officials first discovered the new variant, called B 1.1.7, in the United Kingdom in December 2020. Since then, officials also have detected the new variant in a small handful of U.S. states.

    However, many public health experts have warned that the United States doesn't yet possess the robust surveillance program needed to determine how widespread the variant actually is in America, and therefore is "flying blind" when it comes to addressing it, the New York Times reports. That's because the United States currently lacks a nationwide system for tracking how coronavirus genomes mutate, with researchers doing genome sequencing on fewer than 3,000 samples a week. And sequencing is uneven by state, with California having sequenced 8,896 genomes so far, while North Dakota hasn't sequenced any, according to the Times.

    For its part, CDC in May put together the SARS-Cov-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance consortium (SPHERES), which brought together labs nationwide to share advice on sequencing genomes. But while participants in SPHERES have said the project marks a good start, it falls short of the nationwide system needed to adequately track new variants of the novel coronavirus.

    "As a country, we need genomic surveillance," Kristian Andersen, a virologist at Scripps Research Institute, said, and "[i]t needs to be a federal mandate."

    The United States isn't the only country that's underprepared, public health experts say. Other countries also lack the surveillance systems necessary to track coronavirus variants.

    In Brazil, for example, researchers discovered a mutation in the novel coronavirus as early as this past spring, the Times reports. However, not much is known about how quickly the variant spread or how widespread it is, according to the Times.

    "We just don't know because no one is either sequencing or sharing the data," Nuno Faria, from Imperial College and Oxford University, said. "Genomic surveillance is expensive."

    Michael Worobey, a professor of evolutionary biology at the University of Arizona, said the situation with tracking new variants of the novel coronavirus feels familiar to when the virus first emerged last year and started spreading throughout the world. "It feels a lot like that time between Jan. 19 or so when we had that first case in the Seattle area and six weeks later, when all of a sudden, it looks like we've got community transmission in California and Seattle and who knows where else," Worobey said.

    According to Worobey, the new variant likely has already been spreading throughout the United States unbeknownst to officials and researchers because of the country's dearth of genome sequencing. "We're a little behind the eight ball in terms of our genomic sequencing, both in terms of absolute number and the sort of delay between sampling and getting the sequences out there, compared to the [United Kingdom]," he said.

    According to the Times, the United Kingdom has implemented a fairly robust surveillance system, developing a scientific consortium throughout the country that's aimed at sending samples to labs that will sequence the virus and determining where each mutation fits on an evolutionary tree.

    "What the [United Kingdom] has done with sequencing is, to me, the moonshot of the pandemic," Emma Hodcroft, a molecular epidemiologist at the University of Bern in Switzerland, said. "They decided they were going to do sequencing and they just stood up an absolutely incredible program from scratch."

    Why more surveillance is needed

    Experts say implementing a national surveillance system in the United States would allow public health officials to warn people in areas affected by the new variant and quickly implement measures meant to stem the variant's spread, rather than waiting until hospitals are overrun by newly infected patients.

    "We need some sort of leadership," Charles Chiu, a researcher at the University of California-San Francisco, said. "This has to be a system that is implemented on a national level. Without that kind of dedicated support, it's simply not going to get done."

    Better surveillance of coronavirus mutations would allow experts not only to track B 1.1.7, but also any other new and potentially more-dangerous variants of the novel coronavirus that may arise.

    Hodcroft said constant surveillance is the only way to catch these variants. "They don't pop up on the first day and kind of introduce themselves and say, 'Hey, watch me!'" she said. "It takes us a while to figure that out. And it takes us longer if we're not looking."

    And "[j]ust because" the United States doesn't have a constant, coordinated surveillance system "set up" now, it "doesn't mean we can't do it," Hodcroft said. "We just have to really decide this is something we want."

    For its part, President-elect Joe Biden's transition team has signaled that Biden may be open to expanding national genomic surveillance for the novel coronavirus. Biden "supports a national testing program that can help stop the spread of Covid-19 and find variants," T.J. Ducklo, a spokesperson for the transition team, said. "That means more tests, increased lab capacity, and genome sequencing. This is vital to control Covid-19 and to prepare the United States to detect and stop future disease threats."

    In the meantime, Brian Katzowitz, a spokesperson for CDC, said the agency "is working with state public health, academic, and commercial laboratories to increase domestic strain surveillance capacity to sequence thousands of specimens every week."

    Greg Armstrong, who is leading the surveillance efforts at CDC, separately said the agency is "definitely taking this seriously, and we're assuming for now that this variant is more transmissible."

    But some experts fear that, by the time the United States could get to the level of surveillance needed to address the new variant's spread, it could be too late. "It might become the dominant [variant] [in the United States] in the next couple months," Nathan Grubaugh, a virologist at Yale University, said.

    And while it's currently too soon to tell how the variant will effect the United States' coronavirus epidemic, experts are concerned the more-contagious variant could accelerate the country's new case rate—as well as the country's totals of hospitalizations and deaths tied to the novel coronavirus.

    "Epidemiological models and Britain's experience indicate that, while only a few cases of the variant have been identified in the United States, it will likely become our dominant strain within a few months," Ashish Jha, a general internist and professor of global health at the Harvard T.H. Chan School of Public Health, and Robert Wachter, chair of the department of medicine at the University of California-San Francisco, wrote in an opinion piece recently published by the Washington Post. They added, "a more infectious virus means more cases, which means more hospitalizations and deaths" (Zimmer, New York Times, 1/6; Apuzzo et. al., New York Times, 1/9; Branswell, STAT News, 12/31/20; Achenbach/Guarino, Washington Post, 1/6).

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