As researchers now report the existence of several new variants that have appeared in the US, the agency’s best hope to level its order effort is now based on a $ 1.9 billion relief package that is now slowly turning through Congress. The House version contains $ 1.75 billion aimed at securing the country 15 percent of all positive Covid-19 samples.
“The challenge we have had with the order in the public health space with regard to SARS-CoV-2 is that it has not really been prioritized, or that the need for it has not been articulated at a national level until recently,” he said. Kelly Wroblewski, director of infectious programs at the Association of Public Health Laboratories, said.
While countries such as the United Kingdom and Denmark have been running extensive Covid-19 sequencing programs for months, the US has long relied on contributions from a patchwork of academic, state and commercial laboratories. The federal government only launched a large-scale, coordinated order effort in early 2021, when President Donald Trump’s government announced that it had signed contracts with several commercial laboratories to strengthen the country’s order efforts.
The delay “is inexcusable,” according to Luciana Borio, a former director of medical and bioprotective preparedness at the National Security Council, who served on President Joe Biden’s advisory board and Covid-19 health transition team. She told a subcommittee of the House this month that the United States still largely “blindly flies in detecting the introduction or emergence of new varieties or monitoring their geographical distribution.”
Yet there are signs of improvement. Quest Diagnostics – one of the labs called in by the Trump administration – now tracks 2,000 samples a week. And more than 40 public health labs in 33 states have also joined, Wroblewski said.
According to Greg Armstrong, who manages the CDC’s advanced molecular detection program, the total number of Covid-19 samples followed each week by the federal program and independent academic and government efforts each week has more than doubled.
Information obtained from sequencing is crucial for policymakers to find out if coronavirus precautions need to be relaxed, such as restrictions on indoor eateries and gyms or school closures. The limited order of the United States limited the first months of the pandemic when diagnostic tests were restricted, making it difficult for health officials to detect where the virus was spreading and take the necessary steps. With more contagious variants, the same officials need the sequence of data to understand how they can change their pandemic playbook.
“A lot of people get a little whiplash in and out of social distance, we see people getting tired of it,” said Phil Febbo, chief medical officer of Illumina, one of the companies contributing to the federal sequencing program. ‘The more public health officials, governors, mayors have the best information on the variants and the impact on their communities, the less likely they will have to turn somehow. And they can set appropriate expectations if we try to end the pandemic. â
The new proposals that the CDC is reviewing from commercial contract laboratories and large academic laboratories will further build the federal order for networking. The agency is still evaluating what it would do with the $ 1.75 billion in successive money that Congress weighs.
“It’s going to be a combination of things,” Armstrong said. ‘We are going to expand the order in which we do this [commercial] laboratories in the short term to quickly scale up how much data we get nationally. We are going to support state and local health departments that are in progress with order. â
Another priority of the agency is the acquisition of computer analysis tools that can link sequence data with other epidemiological data to inform decision making.
“Between now and when the next pandemic strikes, we want to make sure we build the infrastructure,” Armstrong said. “Unfortunately, that is $ 1.75 billion in one-time funding. But we plan to use it to invest in areas that are going to have a long-term return. â
Developing a system that meets the task is likely to require resources from other agencies with expertise in computer biology, including the National Institutes of Health and the Department of Energy, said Caitlin Rivers, an epidemiologist at Johns Hopkins University. .
“We have a lot of sequencing capability and a lot of scientific capability to do the characterization,” Rivers, co-author of a new report from the Johns Hopkins Center for Health Security, asked the U.S. to develop a world-leading sequencing program. such as that of the United Kingdom “It’s really just about the system that will allow us to really utilize that capacity and make good use of it.”
One immediate challenge facing the federal sequencing effort is the limited amount of critical materials needed to analyze samples. This material contains specialized pipette tips that are used to prepare samples for laboratory-based diagnostic tests for Covid-19, as well as for the sequence of virus samples.
Labs use 20 to 30 tips to analyze a single virus sample, Armstrong said.
While large commercial laboratories say they have enough pipette tips in stock, smaller laboratories run into problems. Kelly Oakeson, who leads the sequence of efforts at the Utah Public Health Laboratory, said his factory has been trying to acquire pipette tips that are a ‘new order’ until the end of this month, end of next month – just because their production on capacity is. ‘
Meanwhile, the CDC insists on increasing the number of virus samples that its network analyzes maintain each week, with the goal of reaching “far above” 10,000, according to Armstrong.
“We do not stop there,” he said. “We are still trying to expand the network of laboratories.”