November 28, 2023

When lawmakers asked billions of dollars to fund the country’s efforts to prosecute coronavirus variants, the Biden government on Wednesday announced new efforts to advance that work, pledging nearly $ 200 million to help the emerging ones Better identify threats.

Calling it a “down payment,” the White House said the investment would result in a significant increase in the number of positive virus samples that labs could sequence. Laboratories, universities and public health programs run by the Centers for Disease Control and Prevention sequenced more than 9,000 genomes last week, according to the GISAID database. The agency hopes to increase its own contribution to 25,000 genomes per week.

“When we reach 25,000 depends on the resources we have and how quickly we can mobilize our partners,” said Dr. Rochelle Walensky, CDC director, at a press conference at the White House on Wednesday. “I don’t think this will be a light switch. I think it will be a dial. “

The program is the administration’s most significant effort to date to address the looming threat of more contagious variants of the virus. An affected variant, first identified in the UK, has infected at least 1,277 people in 42 states, though scientists suspect the actual number is significantly higher.

Variant B.1.1.7 developed in the UK, which doubles roughly every 10 days, threatens to slow down or reverse the rapid decline in new coronavirus cases. In addition, Dr. Walensky that the nation saw their first case of B.1.1.7, which received a particularly worrying mutation that was shown in South Africa to affect vaccine effectiveness.

Other worrisome variants have also surfaced in the US, including one first found in South Africa that weakens vaccines.

The FDA is preparing a possible redesign of vaccines to provide better protection against the new variants. However, this effort will take months. In the short term, experts say, it is important to increase the sequencing effort, which is too small and uncoordinated to adequately track where and how quickly variants are spreading.

Scientists welcomed the Biden administration’s new plans. “It’s a big step in the right direction,” said Bronwyn MacInnis, geneticist at the Broad Institute.

Dr. MacInnis said the “minimum gold standard” would sequence 5 percent of the virus samples. If cases continued to drop, 25,000 genomes per week would bring the country near that threshold, she said, “where we need to be to detect not only known threats but emerging threats as well.”

Trevor Bedford, evolutionary biologist at the Fred Hutchinson Cancer Research Center, said the national sequencing effort had made “significant gains” since December. Still, he said the CDC also needs to make improvements in collecting data about the genomes – for example, to tie it to contact tracing information – and then support the large-scale analysis on computers that is needed to quickly understand everything .

“There’s too much focus on the raw count that we’re sequencing rather than the turnaround time,” he said.

White House officials occupied the sequencing attempt as part of a wider effort to test more Americans for the virus. The Department of Health and Human Services and the Department of Defense on Wednesday announced significant new investments in testing, including $ 650 million for elementary and middle schools and “underserved community facilities” like homeless shelters. The two divisions are also investing $ 815 million to expedite test supplies production.

The CDC’s $ 200 million sequencing investment is dwarfed by a program proposed by some lawmakers as part of an economic bailout package that Democratic Congress leaders want to pass before mid-March. Senator Tammy Baldwin, Democrat of Wisconsin, passed legislation to improve his sequencing efforts. House lawmakers have allocated $ 1.75 billion to the effort.

In an interview, Ms. Baldwin suggested that the government sequence 15 percent of positive virus samples, a goal that goes well beyond what researchers believe is possible in the short term.

“This is to create the basis for a permanent infrastructure that enables us not only to monitor Covid-19 in order to discover new variants, but also to have this ability for other diseases.” she said of her proposal. “There are significant gaps in knowledge.”

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


Apr. 20, 2021, 9:30 a.m. ET

“Here we can take a look: What resources are currently available to us? What can we find to act quickly? ” She said. “But you know that going forward we need bigger investments and a systematic way to get this job done.”

Since 2014, the CDC Office of Advanced Molecular Detection has been using genome sequencing to track diseases such as influenza, HIV, and food-borne diseases. When the coronavirus pandemic hit the United States, the CDC was slow to adapt these tools to track the coronavirus. For weeks it just struggled to create a test for the virus.

In contrast, the UK launched a highly acclaimed sequencing program last March that leveraged the nationalized health system with a central genomics laboratory. It now sequences up to 10 percent of all positive coronavirus tests and provides a thorough, quick analysis of the results.

The CDC began increased surveillance efforts later in 2020, helping academic laboratories, commercial sequencing companies, and public health departments to collaborate and share knowledge. In November, the company invested in its own program called NS3 to analyze coronavirus genomes. Every two weeks, the agency asks state health departments to send at least 10 samples to their laboratory for sequencing.

In December it became clear that these efforts would not be enough. Researchers in the UK found a new variant called B.1.1.7 that was up to 50 percent more transmissible than other variants. Scientists now suspect that it’s probably more deadly too. In South Africa, another variant called B.1.351 was found not only to be more contagious, but also to be less susceptible to multiple vaccines.

CDC officials began to fear that B.1.1.7 had already spread widely in the United States, according to a senior federal health official. They started new efforts, including contracts with laboratory testing companies to run coronavirus testing.

Dr. Gregory Armstrong, the director of the Advanced Molecular Detection Program, said in an interview that his team concluded in January that sequencing from 5,000 to 10,000 samples per week was a good short-term goal.

“It’s the starting point,” said Dr. Armstrong. “The more we sequence about it, the faster we can identify these variants.”

At a press conference at the White House earlier this month, Jeffrey D. Zients, the White House’s Covid-19 response coordinator, recognized how difficult it would be to achieve that goal.

“We are 43rd worldwide in genome sequencing – totally unacceptable,” he quoted December data from the GISAID database. In a subsequent interview, he corrected himself and said that the US stands behind 31 other nations.

In the early days of administration, Dr. Walensky set an initial goal for the CDC to sequence 7,000 genomes per month. Since then, laboratories have not come close to that number.

The agency’s National Genomic Surveillance Dashboard showed that only 96 genomes were logged for the week of February 6th. The following week the number rose to 1,382 genomes. Dr. Walensky’s new goal of 25,000 genomes per week calls for a significant increase.

Caitlin Rivers, an epidemiologist at the Johns Hopkins Bloomberg School of Public Health, said it was a welcome development to invest $ 200 million quickly in surveillance variants before hoping for longer-term improvements. “Time is of the essence,” she said. “An initial investment in expanding genome monitoring while the complementary funding package comes together is a smart move.”

However, she warned that the plan could not be implemented immediately. It can take a month for the basic improvements to be achieved. By then, B.1.1.7 could already dominate US cases and jeopardize the current decline.

The larger program in the stimulus package will be critical to managing the pandemic in the long term, said Dr. Rivers.

“We may not be able to get very far on B.1.1.7, but what’s the next, in three months or six months or next winter?” She asked. “It’s not always just what’s in front of you. It’s what’s coming around the corner. “