Our paper Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance, was recently published in Health Security. 

TL;DR

Metagenomic sequencing is a really good thing, and lots of people are working on making the technologies work. But getting the tech to work is only half of the problem - we also need it to be implementable and useful for policy, and legally acceptable. There are a bunch of important questions which need to be addressed to make sure this isn’t a problem, and the paper intends to start a discussion of how to solve those problems - so that a decade from now, we don’t look back and say that the technology works, but it’s not going to be used for pandemic prevention because of these other issues, which are far harder or impossible to fix post-hoc. This paper serves to put these problems on the agenda now so they can be addressed by the relevant academic, policy, advocacy and professional communities.

Abstract

The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for “widespread metagenomic monitoring” to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.

The paper is broken down into 3 sections:

• Present State of Biosurveillance (Where we are)
• Potential Metagenomic Monitoring Futures (Qualities of an ideal metagenomic future)
• Way Points and Obstacles in a Transition (How to get from here to there)

Present State of Biosurveillance

Global biosurveillance efforts together only provide partial coverage. Existing genomic data collection and analysis is often siloed and very difficult to integrate for a comprehensive disease landscape. Biosurveillance efforts that have tended to maintain funding are foodborne pathogens and rare reportable diseases. 

Potential Metagenomic Monitoring Futures 

To transition to Widespread Metagenomic Monitoring (WMGM) responsibly and with maximized biosecurity benefits, there needs to be a common understanding of qualities we expect to see in a high-investment and ambitious scenario. See this section for specifics.
 

Way Points and Obstacles in a Transition

We mention some antecedents of a WMGM along with a table of Critical Technological Advances. For example, Shean and Greninger¹ propose a near-term future resting on widespread deployment of clinical sampling. Another near-term possibility is the Nucleic Acid Observatory,² which proposed ongoing wastewater and watershed sampling across the United States to find sequences that recently emerged or are increasing in frequency, indicating a potential new pathogen or other notable events. We identify the following as systemic obstacles on the path to WMGM which need to be addressed by the relevant professional communities and institutions:

• Suboptimal use and high prices
• Privacy and data abuse
• Peacetime usefulness
• Enabling crisis response

Thank you to the Center for Effective Altruism Long Term Futures Fund for financial support for Chelsea’s work.

Citations:

1. Shean RC, Greninger AL. One future of clinical metagenomic sequencing for infectious diseases. Expert Rev Mol Diagn. 2019;19(10):849-851.
2. Nucleic Acid Observatory Consortium. A global nucleic acid observatory for biodefense and planetary health. Preprint. arXiv:2108.02678 [q-bio.GN]. Submitted August 5, 2021. Accessed September 5, 2021. http://arxiv.org/abs/2108.02678