SecureBio, Inc.
@securebio.org
More details here: naobservatory.org/blog/updates...
NAO Updates, November 2025
Since July, we’ve made major strides in scaling CASPER, expanding Zephyr, and automating our analysis systems. As always, if you have questions ...
naobservatory.org
November 12, 2025 at 6:30 PM
More details here: naobservatory.org/blog/updates...
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
Kelly Chafin, Biosecurity Response
Chris Doering, Genomic Biosecurity
Siham Elhamoumi, Partnerships
Michael Gomez, Lab Technician
James Kremer, Laboratory Science
November 12, 2025 at 6:30 PM
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
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
November 12, 2025 at 6:30 PM
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.
November 12, 2025 at 6:30 PM
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...
November 12, 2025 at 6:30 PM
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...
November 12, 2025 at 6:30 PM
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.
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.
November 12, 2025 at 6:30 PM
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.
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.
November 12, 2025 at 6:30 PM
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...
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...
November 12, 2025 at 6:30 PM
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...
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...
CASPER data identified measles in and West Nile Virus in two US communities:
health.hawaii.gov/news/newsroo...
content.govdelivery.com/accounts/MOD...
November 12, 2025 at 6:30 PM
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...
CASPER data identified measles in and West Nile Virus in two US communities:
health.hawaii.gov/news/newsroo...
content.govdelivery.com/accounts/MOD...
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...
However, usability for time-sensitive investigations could be improved, which we’re planning to do this quarter.
Read more: naobservatory.org/blog/outward...
Evaluating Outward Assembly on a Surprising Junction
Investigating a lab-contamination chimera that joins SARS-CoV-2 with a synthetic plasmid, this post shows how outward assembly quickly rebuilt ≈...
naobservatory.org
July 25, 2025 at 4:32 PM
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...
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.
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.
July 25, 2025 at 4:32 PM
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.
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.
Find the full updates with a lot more information here: naobservatory.org/blog/updates...
NAO Updates, July 2025
We have a lot to share since our April update! As always, if you have questions or see opportunities to collaborate, please let us know; we’re e...
naobservatory.org
July 10, 2025 at 9:31 PM
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...
We will refine these estimates as we generate more sequencing data.
naobservatory.org/blog/swab-ba...
July 10, 2025 at 9:31 PM
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...
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.
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.
July 10, 2025 at 9:31 PM
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.
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/
Find the dashboard here: dholab.github.io/public_viz/
July 10, 2025 at 9:31 PM
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/
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”.
With the new data, our genetic engineering detection system has now analyzed 892B read pairs, flagging 413 chimeras, with 43 “benign positives”.
July 10, 2025 at 9:31 PM
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”.
With the new data, our genetic engineering detection system has now analyzed 892B read pairs, flagging 413 chimeras, with 43 “benign positives”.
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
Estimating the sensitivity of wastewater metagenomic sequencing using nasal swabs
We thank Vanessa Smilansky for processing and sequencing swab samples, Jeff Kaufman for reviewing drafts of this post, and Evan Fields for code ...
naobservatory.org
June 26, 2025 at 1:50 PM
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
Linking this prevalence data with wastewater data, we estimated how easily different pathogens are detected in sequenced sewage.
SARS-CoV-2 was again confirmed to be readily detectable, but cold viruses showed relatively low detectability.
SARS-CoV-2 was again confirmed to be readily detectable, but cold viruses showed relatively low detectability.
June 26, 2025 at 1:50 PM
Linking this prevalence data with wastewater data, we estimated how easily different pathogens are detected in sequenced sewage.
SARS-CoV-2 was again confirmed to be readily detectable, but cold viruses showed relatively low detectability.
SARS-CoV-2 was again confirmed to be readily detectable, but cold viruses showed relatively low detectability.
Using this we were able to estimate prevalence.
We found that cold viruses are highly prevalent in winter: Many have a prevalence of 1% or higher!
We found that cold viruses are highly prevalent in winter: Many have a prevalence of 1% or higher!
June 26, 2025 at 1:50 PM
Using this we were able to estimate prevalence.
We found that cold viruses are highly prevalent in winter: Many have a prevalence of 1% or higher!
We found that cold viruses are highly prevalent in winter: Many have a prevalence of 1% or higher!
We created these estimates by analyzing nasal swabs, a recently added NAO sample stream.
Collecting, pooling, and sequencing nasal swabs, we got a lot of information about the presence of cold viruses in the population, which we then linked with paired wastewater data.
Collecting, pooling, and sequencing nasal swabs, we got a lot of information about the presence of cold viruses in the population, which we then linked with paired wastewater data.
June 26, 2025 at 1:50 PM
We created these estimates by analyzing nasal swabs, a recently added NAO sample stream.
Collecting, pooling, and sequencing nasal swabs, we got a lot of information about the presence of cold viruses in the population, which we then linked with paired wastewater data.
Collecting, pooling, and sequencing nasal swabs, we got a lot of information about the presence of cold viruses in the population, which we then linked with paired wastewater data.