Metagenomic sequencing is an approach that characterizes all of the genetic material (DNA and RNA) that is present in a sample. Recent developments in metagenomics, namely the advent of next-generation sequencing (NGS) technologies, have enabled billions of base pair reads in a single run — allowing for a relatively fast and inexpensive analysis of all the genetic content of a sample. Metagenomic next-generation sequencing (mNGS) is different from most other approaches in that it can be untargeted as opposed to involving the targeting of specific pathogens.

As additional context, the following is a relevant description about mNGS by the American Society for Microbiology:

Metagenomic NGS (mNGS) is simply running all nucleic acids in a sample, which may contain mixed populations of microorganisms, and assigning these to their reference genomes to understand which microbes are present and in what proportions. The ability to sequence and identify nucleic acids from multiple different taxa for metagenomic analysis makes this a powerful new platform that can simultaneously identify genetic material from entirely different kingdoms of organisms.

The purpose of this question is to understand whether untargeted metagenomic next-generation sequencing will be utilized on a large scale in the US for pathogen identification.

Will the U.S. CDC sponsor or support a nationwide metagenomic sequencing program before 2025?

This question will resolve as Yes if the US CDC is either sponsoring or supporting a nationwide metagenomic sequencing program that has at least 50 total sites in at least 10 different counties at any time before December 31, 2024, according to credible media reports. At least one of the goals of such a program should be identification of novel pathogens. The program must be active on or before December 31, 2024, meaning that at least 50 sites across at least 10 counties are actively doing metagenomic sequencing on envrionmental samples or random clinical samples.

As an example of what form such a nationwide metagenomic sequencing program might take, consider the CDC's ongoing COVID wastewater surveillance program. This COVID-specific program involves state, tribal, local, and territorial health departments submitting testing data to CDC, and CDC then standardizing and interpreting the data. As of June 5, 2022, there are 748 sites with "current data," and hundreds of US counties are represented.