Genomic pathogen surveillance in epidemic management
The SARS-CoV-2 pandemic has demonstrated how important pathogen data are for our lives and economies. Developed countries make use of genomics to better understand the threat of both known and novel pathogens. With the new generation of low-cost sequencing devices, it is now possible for developing countries to sequence pathogens on-site. This ability has implications not only for local management of the SARS-CoV-2 pandemic, but also for security against other current and future threats.
Why each developing country should have a genomic surveillance lab
Once different countries lift their quarantines, and we see new cases, how do we know if they are from the population or from outside? Should the government focus on border control or internal quarantine? Sequencing could answer this question. Once we have a vaccine, how should the authorities prioritize their administration? Genomics does not have all the answers, but it can help. If we see vaccine failures, how do we confirm if the cause is a new strain too genetically-divergent from the vaccine, or due to reversion to virulence of the vaccine itself?
RT-PCR tests is the appropriate tool for mass testing. However, to answer the questions above, we would need a sequencing laboratory. Sequencing requires more technical training and each sequencing run takes longer than a standard RT-PCR test (24 hours or more vs as little as minutes). However, on top providing data to guide epidemic management, a sequencing lab could be used to identify pathogens, both known and novel, not only viral, but also bacterial and fungal. When the next outbreak happens, we do not need to wait for tests to be manufactured if we have a local sequencing kit. In terms of price per test, they are roughly the same at volume.
In the past, a sequencing lab would cost at least hundreds of thousands of Euros. Today, using the latest generation of sequencing technologies, a mobile “lab-in-suitcase” could be assembled for only €8,000 (Figure 1). The key innovation is the Oxford Nanopore MinION. Previously, sequencers cost at least $20,000 and need to be stored in a laboratory. The Oxford Nanopore MinION could be purchased for $1,000 and is small and sturdy enough to be carried on-site.
OpenPM is a metaproject to my current project: bringing genomic pathogen surveillance to my city, Cebu, Philippines. The lessons and project management collateral from this project would be useful for others who want to bring genomic surveillance to their own locality. I was a project manager during my corporate tech days, so I'll be using the framework of the PMBOK to document and share the output and lessons from this project.
This is the high-level work breakdown structure of this project:
Project Management - The planning and execution of all these will be done using tools from the Project Management Body of Knowledge. 💡I was a project manager in my corporate tech days. I'll teach PM to the participants.
Training - Masters of Pipettes \m/ and bioinformaticians need to be trained. The training could be from the manufacturers or the academics that create the library preparation and sequencing protocols, and bioinformaticians that design the bioinformatics pipelines. 💡In doing this, we will learn how to prepare and execute capability building, as well as familiarize ourselves with the tech and processes in Nanopore sequencing. If you are experienced, you can help the rest of us learn
Acquisition of equipment and reagents - The work involves creating a bill of materials based on lab-in-suitcase papers and then selecting the best choice of best equipment and get it for the lowest price. Then getting everything in the Philippines. 💡Hands-on procurement, negotiation and global logistics. If you are experienced in procurement, you can teach the rest of us.
Planning and running sequencing runs - Creating and executing an operational system based on lab-in-suitcase papers, documenting lessons learned and iterating. 💡How to turn academic work into live system. If you are experienced in procurement, you can teach the rest of us.
Documentation and publishing of the resulting process and lessons learned - share the project management collateral (and how to use it), playbooks, etc. 💡Science communication. If you are experienced in procurement, you can teach the rest of us.
Get funding - I'm focusing on sending proposals to the Department of Science and Technology of my country to fund this project for my city. Others could help look for funding for other localities. 💡This is a hands-on way to learn the world of raising funds for science. If you're experienced, you will help future scientist navigate this maze.
Subject matter experts
Requirement: you are a professional in the one of these fields:
Work: tell us if we are doing something stupid, consult as needed