US CDC announces $265 million 'down payment' to track coronavirus variants

WASHINGTON (NYTIMES) – As lawmakers push for billions of dollars to fund the nation’s efforts to track coronavirus variants, the Biden administration announced Wednesday (Feb 17) a new effort to ramp up this work, pledging nearly US$200 million (S$265.62 million) to better identify the emerging threats.

Calling it a “down payment,” the White House said that the investment would result in a significant increase in the number of positive virus samples that labs could sequence.

Public health laboratories, universities and programs run by the Centres for Disease Control and Prevention (CDC) sequenced more than 9,000 genomes last week, according to the database GISAID. The agency hopes to increase its own contribution to 25,000 genomes a week.

“When we will get to 25,000 depends on the resources that we have at our fingertips and how quickly we can mobilie our partners,” Dr Rochelle Walensky, CDC director, said at a White House news conference Wednesday. “I don’t think this is going to be a light switch. I think it’s going to be a dial.”

The programme is the administration’s most significant effort to date to address the looming danger of more contagious variants of the virus. A concerning variant first identified in Britain has infected at least 1,277 people in 42 states, although scientists suspect the true number is vastly higher.

Doubling about every 10 days, the B117 variant that emerged in Britain threatens to slow or reverse the rapid drop of new coronavirus cases. What’s more, Dr Walensky said that the nation had seen its first case of B117 that had gained a particularly worrying mutation that has been shown in South Africa to blunt the effectiveness of vaccines. Other worrisome variants have also cropped up in the United States.

The FDA is preparing for a potential redesign of vaccines to better protect against the new variants, but those efforts will take months. In the short term, experts say, it is critical to increase sequencing efforts, which are too small and uncoordinated to adequately track where variants are spreading, and how quickly.

White House officials cast the sequencing ramp-up as part of a broader effort to test more Americans for the virus.

The Department of Health and Human Services and the Defence Department on Wednesday announced substantial new investments in testing, including US$650 million for elementary and middle schools and “underserved congregate settings,” like homeless shelters. The two departments are also investing US$815 million to speed the manufacturing of testing supplies.

The CDC’s US$200 million sequencing investment is dwarfed by a programme proposed by some lawmakers as part of an economic relief package that Democratic congressional leaders aim to pass before mid-March. Senator Tammy Baldwin introduced legislation to enhance its sequencing efforts. House lawmakers have allocated US$1.75 billion to the effort.

In an interview, the Biden administration’s new testing coordinator, Ms Carole Johnson, said that the US$200 million investment was a “down payment” and just the beginning of what would likely be a much more aggressive campaign to track the variants.

“This is us being able to look at: What are the resources that we have at the ready right now? What can we find to act quickly?” she said. “But know that we need larger investments going forward and a systemized way to do this work.”

Since 2014, the CDC’s Office of Advanced Molecular Detection has used genome sequencing to track diseases like influenza, HIV and food-borne diseases. But when the coronavirus pandemic struck the United States, the CDC was slow to adapt these tools to track the coronavirus. For weeks it struggled simply to establish a test for Covid.

In contrast, Britain started a widely praised sequencing programme last March, taking advantage of its nationalised healthcare system with a central genomics lab. It now sequences up to 10 per cent of all positive Covid tests and delivers deep, rapid analysis of the results.

The CDC began ramping up surveillance efforts over the course of 2020, helping academic labs, commercial sequencing companies and public health departments to collaborate and share insights.

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In November, it invested in a programme of its own, called NS3, to analyse coronavirus genomes. Every other week, the agency asks state health departments to send at least 10 samples to its lab for sequencing.

In December, it became clear those efforts would not be enough. Researchers in Britain found a new variant, called B117, that was up to 50 per cent more transmissible than other variants. Scientists now suspect it is also probably more lethal. In South Africa, another variant called B1351 proved not only more contagious, but less vulnerable to several vaccines.

CDC officials began to fear B117 had already been spreading widely in the United States, according to one senior federal health official. They began setting up new efforts, including contracts with lab testing companies that were running Covid tests.

In the early days of the administration, Dr Walensky spoke of an initial goal for the CDC of sequencing 7,000 genomes a month. Since then, the labs have not come close to that figure.

The agency’s National Genomic Surveillance Dashboard showed that they logged just 96 genomes in the week of Feb 6. The following week, the figure rose to 1,382 genomes. Dr Walensky’s new target of 25,000 genomes a week will require a significant increase.

Ms Caitlin Rivers, a public health researcher at Johns Hopkins Bloomberg School of Public Health, said putting US$200 million quickly into monitoring variants was a welcome development in advance of what she hoped would be longer-term improvements.

“Time is of the essence,” she said. “An initial investment to expand genomic surveillance while the supplemental funding package comes together is a smart move.”

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But she warned that the plan won’t be able to spring instantly into action. It may take a month just to get the basic improvements in place. By then, B117 may already dominate US cases and could jeopardise the current decline.

The larger programme in the stimulus package will be crucial to managing the pandemic in the long run, Ms Rivers said.

“We may not be able to get very far as relates to B117, but what’s the next one, three months from now, or six months, or next winter?” she asked. “It’s not always just the thing in front of you. It’s what’s coming around the corner.”

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