With researchers now reporting on the existence of several new variants that appear to have appeared in the U.S., the agency’s best hope of bringing its sequencing effort into line now resides with a $ 1.9 trillion aid package that is now slowly reaching Congress. The Chamber version contains $ 1.75 billion to ensure that the country sequences 15% of all positive Covid-19 samples.
“The challenge we had with sequencing in the public health space in relation to SARS-CoV-2 is that it was not really prioritized, or the need for it was not articulated at the national level until recently,” said Kelly Wroblewski, director of health programs. infectious diseases of the Association of Public Health Laboratories.
Although countries like the United Kingdom and Denmark have run extensive Covid-19 sequencing programs for months, the United States has long relied on contributions from a patchwork of academic, state and commercial laboratories. The federal government did not launch a large-scale coordinated sequencing effort until early 2021, when President Donald Trump’s government announced that it had signed contracts with several commercial laboratories to support the country’s sequencing efforts.
This delay “is inexcusable,” according to Luciana Borio, former director of medical preparation and bio-defense for the National Security Council who served on President Joe Biden’s Covid-19 advisory board and the health transition team. She told a House subcommittee this month that the United States is still “flying blind when it comes to detecting the introduction or emergence of new variants or monitoring its geographic distribution”.
Even so, there are signs of improvement. Quest Diagnostics – one of the labs that the Trump administration recruited – is now sequencing 2,000 samples a week. And more than 40 public health laboratories in 33 states have also joined, said Wroblewski.
The total number of Covid-19 samples sequenced each week by the federal program and independent academic and state efforts has more than doubled since December, to about 7,400 per week in late January, according to Greg Armstrong, who directs the program. advanced molecular detection of CDC.
The information collected from the sequencing is crucial for policymakers who are trying to find out if they relax coronavirus precautions, such as limits on indoor meals and gyms or closing schools. The United States’ limited sequencing capacity goes back to the early months of the pandemic, when diagnostic tests were limited, making it difficult for health officials to track where the virus was spreading and take appropriate action. With the spread of more contagious variants, these same employees need sequencing data to understand how to modify their pandemic manual.
“A lot of people are having a little whip going in and out of social distance, we see that people are getting tired of it,” said Phil Febbo, medical director at Illumina, one of the companies that contribute to the federal sequencing program. “The more public health officials, governors, mayors, the better information about the variants and the impact on their communities, they are less likely to have to over-rotate in one way or another. And they can set the right expectations as we try to end the pandemic. “
The new proposals that the CDC is analyzing from contracted commercial laboratories and large academic laboratories would further increase the federal sequencing network. The agency is still evaluating what it would do with the $ 1.75 billion in sequential cash that Congress is weighing.
“It will be a combination of things,” said Armstrong. “We are going to expand the sequence we are doing with these [commercial] laboratories in the short term to rapidly increase the amount of data we are obtaining at the national level. We will support state and local health departments that are starting to work with sequencing. “
Another priority for the agency is to obtain computational analysis tools that can link sequencing data to other epidemiological data to inform decision making.
“We want to make sure that we build this infrastructure between now and when the next pandemic comes,” said Armstrong. “Unfortunately, that $ 1.75 billion is just one-off funds. But we intend to use it to invest in areas that will have a long-term return. “
Developing a system up to the task would likely require resources from other agencies with experience in computational 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 capacity and a lot of scientific capacity to do the characterization,” said Rivers, co-author of a new report from the Johns Hopkins Center for Health Safety that asks the US to develop a world-leading sequencing program like the UK ” In fact, it’s just about discovering the system that will allow us to really take advantage of that ability and make good use of it. ”
An immediate challenge faced by the federal sequencing effort is the limited supply of essential materials needed to analyze the samples. These materials include specialized pipette tips that are used to prepare samples for laboratory diagnostic tests for Covid-19, as well as sequencing virus samples.
Labs use 20 to 30 tips to analyze a single virus sample, said Armstrong.
While major commercial labs claim to have enough pipette tips in stock, smaller labs are facing problems. Kelly Oakeson, who leads the sequencing efforts at the Utah Public Health Laboratory, said that her facility tried to buy pipette tips that are on hold “by the end of this month, end of next month – just because their production is over the limit” .
Meanwhile, the CDC is pushing to continue increasing the number of virus samples that its network analyzes each week, with the goal of reaching “well above” 10,000, according to Armstrong.
“We are not going to stop there,” he said. “At the moment, we are still trying to expand this network of laboratories.”