We hope this preprint serves as a catalyst for more untargeted wastewater metagenomics efforts, growing the systems and infrastructure needed to prevent emerging threats to human health.
Link to preprint: doi.org/10.64898/202...
This sequencing explains the seasonality of these viruses, the strains that are circulating, and the unique composition of wastewater samples by location. We demonstrate the viability of deep, untargeted wastewater metagenomics for tracking existing and novel human pathogens.
We found that this sequencing closely tracks wastewater PCR and clinical data for SARS-CoV-2, influenza A, and RSV, while simultaneously capturing emerging infections like avian influenza, West Nile, and measles.
“Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States” represents half of all wastewater sequencing publicly available, and demonstrates the untapped potential of this technology.
CASPER is a national wastewater surveillance program that collected and analyzed 1,206 samples covering more than 13 million people. For this preprint, a total of 1.2 trillion read pairs were generated, which represents the largest wastewater sequencing effort ever undertaken.
Our work isn't changing. We're continuing to defend against pathogens designed to evade detection: evaluating biosurveillance approaches, developing lab and computational methods, and piloting early warning systems.
SecureBio now has two major areas of work: Detection and AI. Both teams collaborate closely, and operating under one name makes it easier to understand what we do and how the pieces fit together.
The Nucleic Acid Observatory is now SecureBio Detection. We're the same team, at the same organization, doing the same work, but the new name makes it clearer how we fit into SecureBio as a whole.
Read a longer summary on our blog (naobservatory.org/blog/airplan...) and the full preprint at www.medrxiv.org/content/10.6...
Work done in collaboration with Ginkgo Biosecurity and the CDC.
This mechanism suggests novel viruses will be easier to detect in composite airplane wastewater than expected from previous municipal wastewater studies.
Higher abundance of human-associated viruses and bacteria along with lower abundance of sewer-associated bacteria suggests a mechanism where airplane wastewater has a higher ratio of human- to sewer-derived input, boosting human viruses across the board.
Preprint: We applied untargeted viral metagenomics to composite airplane wastewater and found that human viruses had much higher relative abundance (median 13-fold) compared to municipal treatment-plant wastewater. This could substantially cut costs of using metagenomics to detect emerging viruses.
2025 was another eventful and impactful year for SecureBio's AI team – we've written up the highlights of what we accomplished and hope to build on this year.
open.substack.com/pub/securebi...
Read our full announcement over on Substack:
open.substack.com/pub/securebi...
We’ve been chosen by the European Commission to build out their AI bio-eval program. 🇪🇺
We'll be carrying out this work over the next three years as part of a consortium of AI safety organizations led by @far.ai
We expanded both leadership and technical capacity, adding expertise across laboratory science, partnerships, and detection response:
Kelly Chafin, Biosecurity Response
Chris Doering, Genomic Biosecurity
Siham Elhamoumi, Partnerships
Michael Gomez, Lab Technician
James Kremer, Laboratory Science
We modeled how such a system could integrate metagenomic sequencing to detect both known and novel pathogens: naobservatory.org/blog/biothreat_radar
Metagenomic sequencing has been gaining traction, with The President’s FY 2026 Budget proposing a $52M allocation to CDC for Biothreat Radar, a new pathogen detection system.
Further, a thorough analysis of 18 months of CASPER sequencing data from Columbia, MO has been published on medRxiv: www.medrxiv.org/content/10.1...
Our paper on the sensitivity of wastewater metagenomic sequencing for early detection of viruses has now been published in The Lancet Microbe: www.thelancet.com/journals/lan...
By now, our detection system frequently flags suspicious reads. But it doesn't recover the surrounding genome.
Earlier this year, we showed how our outward assembly pipeline can recover these genomes, testing the algorithm on a flagged SARS-CoV-2/plasmid construct where it did extremely well.
We’ve enhanced our data analysis systems, scaling metadata management, improving automated detection pipelines, and beginning integration of frontier LLMs for automated viral flag analysis.
Zephyr, our Boston-based swab sampling program, has also expanded.
With four dedicated field samplers working most weekdays, we collect 300-800 nasal swabs weekly.
Viral reads are available via our dashboard: data.securebio.org/sampling-met...
Since July, CASPER—our wastewater surveillance coalition—has grown substantially, now sequencing ~60B read pairs weekly from 30+ sites.
CASPER data identified measles in and West Nile Virus in two US communities:
health.hawaii.gov/news/newsroo...
content.govdelivery.com/accounts/MOD...
Nucleic Acid Observatory updates:
- Major wastewater surveillance scaling: expanded to 31 sampling sites across 19 cities.
- Zephyr swab program scaling, now 400-800 swabs per week.
- New team members that lead response, wet-lab, and partnerships work.
At the Nucleic Acid Observatory, we usually rely on Illumina technology for wastewater viral sequencing.
Recently we benchmarked different Oxford Nanopore sequencing workflows.
In a new post, we examine these workflows in detail and explain why one emerges as our top choice.
Overall, we find that outward assembly did really well: it recovered 959bp of the plasmid at 99.4% identity.
However, usability for time-sensitive investigations could be improved, which we’re planning to do this quarter.
Read more: naobservatory.org/blog/outward...
The suspicious sequence was a SARS-CoV-2 protein stuck to a synthetic construct.
We identified the construct as a manufactured plasmid with a known genome.
Since we knew the genome we were supposed to recover, we had a rare chance to evaluate outward assembly in the real world.
