Read a longer summary on our blog (naobservatory.org/blog/airplan...) and the full preprint at www.medrxiv.org/content/10.6...
24.02.2026 17:36
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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.
SecureBio’s NAO detection system flags suspicious reads, but doesn't recover the surrounding genome.
We can recover these genomes with our outward assembly pipeline.
We recently tested outward assembly on a flagged SARS-CoV-2/plasmid construct – it did extremely well!
Find the full updates with a lot more information here: naobservatory.org/blog/updates...
SARS-CoV-2 is highly detectable, but cold viruses are harder to detect.
We will refine these estimates as we generate more sequencing data.
naobservatory.org/blog/swab-ba...
After our sampling sprint earlier this year, we’ve been scaling our Boston-based swab sampling program, hiring several field samplers.
This has allowed us to collect 100-200 swabs per day. Over the coming quarter we will scale to additional weekdays and further optimize sampling.
Our partners @solidevidence and Dave O'Connor have created new dashboards that present which pathogens we see in wastewater.
Find the dashboard here: dholab.github.io/public_viz/
We’ve generated another 487B read pairs, through both our own sequencing, and through Marc Johnson’s lab (@solidevidence).
With the new data, our genetic engineering detection system has now analyzed 892B read pairs, flagging 413 chimeras, with 43 “benign positives”.
Nucleic Acid Observatory updates:
- We’ve further increased our sequencing capacity, producing 487B read pairs.
- Our partners created dashboards that summarize which pathogens we routinely see in wastewater.
- We’ve been scaling up our Boston-based swab sampling program.
As we scale our systems (naobservatory.org/blog/scaling-our-early-warning-system), we'll use evidence like this to compare investments in wastewater vs other sample types. Full blog post here: naobservatory.org/blog/swab-based-p2ra