An interesting piece. I would like to share a perspective as a scientist working in a resource-constrained setting. Pathogen-agnostic approaches are indeed critical for pandemic preparedness. But how can these strategies be realistically implemented in regions that lack centralized wastewater systems? Another pressing challenge is the cost of sequencing technologies: metagenomic studies remain largely inaccessible in low-resource contexts because sequencing platforms are still prohibitively expensive. What we urgently need are affordable, scalable systems that make pathogen-agnostic surveillance feasible beyond high-income settings.
After attending the Biosecurity Fundamentals course by BlueDot, two key themes stood out to me: the central role of pathogen detection and the importance of vaccines as preventive measures. However, translating these insights into practice has not been straightforward. Building collaborations and partnerships remains a challenge, particularly in regions like Nigeria where little is being done on pathogen-agnostic approaches.
After the course, I sought funding to conduct metagenomic studies in military settings in Nigeria, recognizing that most barracks have centralized wastewater systems. Soldiers, given their mobility and exposure to diverse environments, could serve as important sentinels for pathogen surveillance. I also proposed to study rivers, since much of the population disposes waste into them; however, concentrating pathogens from such diffuse sources poses significant technical challenges. Despite several efforts, I was unable to secure funding for these projects.
In my laboratory, we have access to a nanopore sequencer, which I believe is an excellent tool for real-time pathogen detection. Unfortunately, the high cost of consumables continues to limit its use, underscoring once again the urgent need for affordable solutions and locally adaptable innovations tailored to resource-constrained environments.
Given these realities, I would greatly value candid advice on how to frame biosecurity work in resource-limited settings in a way that not only addresses local needs but also makes it attractive to potential collaborators and partners.
I think it may still be too expensive to make sense, but in poorer areas I think nasal swabs + Nanopore does much better than wastewater for pathogen-agnostic detection:
The costs of collecting the swabs (both the people collecting and compensation to participants) are lower.
Nanopore sequencing is cheaper if you don’t need massive sequencing depth, and for swabs you probably don’t.
Thanks, Jeff. Interestingly, I already have access to both a qPCR system and a Nanopore sequencer. I’d be very interested in exploring this idea further. I can also envision expanding the work to include sampling from poultry farmers, abattoir workers, and even members of the general public for broader epidemiological insights
If you’re trying to flag something engineered, I think the general public makes more sense than people who work with animals. What we do at the NAO (we really need to write up a page on this!) is visit busy public places, put out a sign, and ask if people are interested in swabbing their nose for science. People swab their own noses, drop them in a shared container, and we pay a small amount per swab. It’s under IRB, and if you were looking to do something similar we could share our IRB documentation?
Thanks for this perspective. I’m very interested in collaborating. Please send the IRB documentation and any sample protocol or consent forms to eennadi@plasu.edu.ng.
I’ll review them and adapt what’s needed for local ethics submission here, and I can share practical notes on community engagement and sampling logistics for busy public venues in Jos. I also have prior field experience, I participated in house-to-house nasal sampling during the SARS-CoV-2 outbreak, so I’m familiar with operational realities.
If that sounds good, I’d welcome a short (20–30 minute) call to align on aims, data-sharing, and next steps. I’m keen to explore a pilot we could co-design and co-author.
An interesting piece. I would like to share a perspective as a scientist working in a resource-constrained setting. Pathogen-agnostic approaches are indeed critical for pandemic preparedness. But how can these strategies be realistically implemented in regions that lack centralized wastewater systems? Another pressing challenge is the cost of sequencing technologies: metagenomic studies remain largely inaccessible in low-resource contexts because sequencing platforms are still prohibitively expensive. What we urgently need are affordable, scalable systems that make pathogen-agnostic surveillance feasible beyond high-income settings.
After attending the Biosecurity Fundamentals course by BlueDot, two key themes stood out to me: the central role of pathogen detection and the importance of vaccines as preventive measures. However, translating these insights into practice has not been straightforward. Building collaborations and partnerships remains a challenge, particularly in regions like Nigeria where little is being done on pathogen-agnostic approaches.
After the course, I sought funding to conduct metagenomic studies in military settings in Nigeria, recognizing that most barracks have centralized wastewater systems. Soldiers, given their mobility and exposure to diverse environments, could serve as important sentinels for pathogen surveillance. I also proposed to study rivers, since much of the population disposes waste into them; however, concentrating pathogens from such diffuse sources poses significant technical challenges. Despite several efforts, I was unable to secure funding for these projects.
In my laboratory, we have access to a nanopore sequencer, which I believe is an excellent tool for real-time pathogen detection. Unfortunately, the high cost of consumables continues to limit its use, underscoring once again the urgent need for affordable solutions and locally adaptable innovations tailored to resource-constrained environments.
Given these realities, I would greatly value candid advice on how to frame biosecurity work in resource-limited settings in a way that not only addresses local needs but also makes it attractive to potential collaborators and partners.
I think it may still be too expensive to make sense, but in poorer areas I think nasal swabs + Nanopore does much better than wastewater for pathogen-agnostic detection:
The costs of collecting the swabs (both the people collecting and compensation to participants) are lower.
Nanopore sequencing is cheaper if you don’t need massive sequencing depth, and for swabs you probably don’t.
Thanks, Jeff. Interestingly, I already have access to both a qPCR system and a Nanopore sequencer. I’d be very interested in exploring this idea further. I can also envision expanding the work to include sampling from poultry farmers, abattoir workers, and even members of the general public for broader epidemiological insights
If you’re trying to flag something engineered, I think the general public makes more sense than people who work with animals. What we do at the NAO (we really need to write up a page on this!) is visit busy public places, put out a sign, and ask if people are interested in swabbing their nose for science. People swab their own noses, drop them in a shared container, and we pay a small amount per swab. It’s under IRB, and if you were looking to do something similar we could share our IRB documentation?
Hi Jeff,
Thanks for this perspective. I’m very interested in collaborating. Please send the IRB documentation and any sample protocol or consent forms to eennadi@plasu.edu.ng.
I’ll review them and adapt what’s needed for local ethics submission here, and I can share practical notes on community engagement and sampling logistics for busy public venues in Jos. I also have prior field experience, I participated in house-to-house nasal sampling during the SARS-CoV-2 outbreak, so I’m familiar with operational realities.
If that sounds good, I’d welcome a short (20–30 minute) call to align on aims, data-sharing, and next steps. I’m keen to explore a pilot we could co-design and co-author.
Best regards,
Nnaemeka
Thanks! I’ll pass this along to Simon who leads our swab sampling work.