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SecureBio, Inc.

@securebio.org

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SecureBio, Inc. @securebio.org · 23d

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.

Benchmarking three ONT-based workflows for untargeted sequencing of RNA viruses in wastewater

At the NAO, we use short-read Illumina technology as the gold standard for untargeted sequencing of RNA viruses in wastewater because it provide...

naobservatory.org

SecureBio, Inc. @securebio.org · Jul 25

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...

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

SecureBio, Inc. @securebio.org · Jul 25

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, Inc. @securebio.org · Jul 25

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!

SecureBio, Inc. @securebio.org · Jul 10

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

SecureBio, Inc. @securebio.org · Jul 10

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...

SecureBio, Inc. @securebio.org · Jul 10

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.

SecureBio, Inc. @securebio.org · Jul 10

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/

SecureBio, Inc. @securebio.org · Jul 10

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”.

SecureBio, Inc. @securebio.org · Jul 10

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.

SecureBio, Inc. @securebio.org · Jun 26

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

SecureBio, Inc. @securebio.org · Jun 26

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.

SecureBio, Inc. @securebio.org · Jun 26

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!

SecureBio, Inc. @securebio.org · Jun 26

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.

SecureBio, Inc. @securebio.org · Jun 26

At the NAO, we’ve created new estimates on how well wastewater sequencing detects different pathogens.

SARS-CoV-2 is again highly detectable, but common cold viruses are harder to detect.

We will use this research to compare wastewater sequencing to other detection strategies.

SecureBio, Inc. @securebio.org · Jun 19

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!

Chart of coronavirus and rhinovirus prevalence in the population

SecureBio, Inc. @securebio.org · Jun 19

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.

Chart of 1) relative abundance of various viruses in wastewater and 2) positive swab pools of those same viruses

SecureBio, Inc. @securebio.org · Jun 18

Food, drinks, and conversation provided. We would love to see you there! lu.ma/igclw31d

Accelerating Biosecurity Networking Event · Luma

Join us for an exciting evening with Ginkgo Biosecurity and SecureBio as we explore how we can accelerate biosecurity efforts in the next 1-3 years. With…

SecureBio, Inc. @securebio.org · Jun 18

We’ll have two short talks, one by Dr. Mitchell Wolfe, former CDC Chief Medical Officer and now Ginkgo VP, and our own Jeff Kaufman, co-lead at the Nucleic Acid Observatory (NAO). Afterward, we’ll have ample time for 1-1 conversations.

SecureBio, Inc. @securebio.org · Jun 18

There’s been a lot of action related to biosecurity recently (HHS potentially spending $52 million on a new “Biothreat Radar”, and both Ginkgo and the NAO scaling their surveillance efforts). If you want to discuss these developments, you can sign up here: lu.ma/igclw31d

Accelerating Biosecurity Networking Event · Luma

Join us for an exciting evening with Ginkgo Biosecurity and SecureBio as we explore how we can accelerate biosecurity efforts in the next 1-3 years. With…

SecureBio, Inc. @securebio.org · Jun 18

SecureBio, partnering with Ginkgo Biosecurity will host an evening event on how to accelerate biosecurity on Thursday, July 31st, from 6:00-8:30 pm, in Boston (sign-up link in the next post).

SecureBio, Inc. @securebio.org · May 23

New Substack post from the Executive Director – an overview of some recent major accomplishments by our AI and biosurveillance teams, and some organizational updates.

substack.com/home/post/p-...

Letter from the Executive Director

Some recent organizational updates

SecureBio, Inc. @securebio.org · May 20

SecureBio recently launched a Substack! You can subscribe here: securebio.substack.com

Our Substack lets you get blog posts from the Nucleic Acid Observatory and AIxBio team directly to your inbox.

SecureBio | Substack

Click to read SecureBio, a Substack publication. Launched a month ago.

securebio.substack.com

SecureBio, Inc. @securebio.org · May 16

The medical system collects millions of samples for medical diagnoses. After testing, leftover samples could be repurposed for early pathogen detection.

@jefftk.com and @lennijusten.bsky.social explore sequencing pooled lab discards: naobservatory.org/blog/lab-dis...

Pooled Lab Discards for Pathogen Detection

We’re excited about sampling strategies that can cheaply access many individual samples, approaching the coverage of municipal wastewater while ...

naobservatory.org

SecureBio, Inc. @securebio.org · Apr 25

Using outward assembly, we can recover meaningful genomic context from tens of billions of read pairs in under an hour. 4/4

Our latest blog post has the details: naobservatory.org/blog/outward...

Outward Assembly

The world is demonstrably vulnerable to biological threats. COVID-19 was a disaster, but future pandemics could be far worse. To protect society from future catastrophe, we need reliable early warning...

naobservatory.org