Project ACCESSIBLE GENOMICS

Project ACCESSIBLE GENOMICS

#accessiblegenomics

We are creating an open playbook for deploying low-cost genomic pathogen surveillance in the global south. See more: accessiblegenomics.org

Created on: May 17, 2020
Last update: October 15, 2020

by Kahlil Corazo

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Slack channel: #proj-accessible-genomics

Project site: accessiblegenomics.org


1 minute intro video:


Project presentation video:


Key points

  • To better manage this pandemic and prevent future ones, genomic pathogen surveillance is needed on top of diagnostics.
  • Currently, only rich countries have access to genomic pathogen surveillance. Yet future outbreaks will most likely originate from the developing world. The lack of genomics in the global south is a global problem.
  • Doing this wouldn’t have been possible a few years ago, with the high capital cost of sequencing machines. This has recently become possible due to advancements in low-cost and portable genomics.
  • The technology is here, and many scientists have shown its viability in austere environments. What is missing is a deployment manual.
  • Project ACCESSIBLE GENOMICS will create an open manual for deploying genomic pathogen surveillance in developing countries.
  • Our team is composed of experts in portable genomics and project professionals with years of experience operating in the developing world.
  • We will use the microgrant to purchase an Oxford Nanopore MinION Starter Kit (USD 1,000). The remainder will be used to run a crowdfunding campaign to reach our minimum target amount (USD 2k - 7k, depending on the equipment and consumables that our partner institutions have). Whatever is left or raised will go to equipment and reagents. We also hope to benefit from the volunteer campaigning experience and the network of JOGL to make this crowdfunding successful. The crowdfunding itself will be a way to get more people to know and support JOGL.



Problem and Background

Project Accessible Genomics will create an open manual for deploying genomic pathogen surveillance by deploying in a city in the Philippines and sharing the resulting project collateral and lessons learned to other developing countries.


Genomic pathogen surveillance is needed on top of diagnostics to better manage the current pandemic and future ones. RT-PCR and antibody tests are fast and require minimal training to administer. However, they cannot identify the lineage of specific cases.


Currently, genomic pathogen surveillance is only available in high-income countries. We made a count of SARS-CoV-2 genomes uploaded in GISAID (a global database of viral genomes) from the top 50 countries in terms of GDP and population. Almost half of the genomes were produced by the UK. The USA produced a third of the rest.


At the bottom are 17 countries with each less than 10 SARS-CoV-2 genomes. Their combined population total to 1 billion people and they are represented by only 17 genomes in GISAID.

 


Future epidemics will most likely originate from the developing world, which has the fastest rates of urbanization. Urbanization increases human-to-wildlife interfaces and emergence of novel pathogens. The lack of genomic pathogen surveillance in the global south is a global concern.


Solution summary in simple terms

Deploying a genomic pathogen surveillance in developing countries has become recently possible because of the Oxford Nanopore MinION. Previously, sequencers cost more than a car. The MinION costs less than an iPhone.


Multiple scientists have demonstrated that the MinION can operate in rural environments in the developing world. Scientists have also created detailed procedures on how to prepare samples for the sequencing and for processing the resulting data.


To scale the deployment of this solution, there needs to be a manual to help guide organizations deploy in their own localities (eg, Care.org’s Emergency Toolkit). The goal of this project is to produce this manual. We will create this manual by deploying a genomic pathogen surveillance lab in Davao City, Philippines, then documenting our lessons and project collateral. We will then share this manual to other developing countries.


Solution summary in technical terms

A deployment manual is a common tool for scaling new technology. Examples are the following:


We will create a deployment manual for genomic pathogen surveillance lab using recent low-cost genetic sequencing technology. We will use the well-established framework of the Project Management Body of Knowledge (PMBOK) for the structure of this manual.


In terms of project execution, this is our high-level work breakdown structure:

  • Getting funding
  • Logistics of bringing in equipment and reagents
  • Training in library preparation and bioinformatics
  • Getting SARS-CoV-2 samples
  • Adding a genomics layer to a partner lab or equipping a lab from scratch
  • Ensure biosafety
  • Doing the actual sequencing and genome assembly
  • Creating the manual and the training to use the manual
  • Outreach to other developing countries
  • Helping other localities in their deployment


State of advancement of the project (as of 14Oct2020)

  • Built a team with the right scientific backgrounds and project management capabilities
  • Created a detailed bill of materials 
  • Established a Grant Pursuit Team, headed by a PhD
  • Agreements made
  • Flyingtigersexpress.com - logistics at cost
  • Bugseq.com - bioinformatics services
  • Initiated the application for mentorship in the Philippine Genome Center Mindanao (access their laboratory, network, and genomics and local grant application expertise)
  • Grant application to Merck submitted
  • Launched the website accessiblegenomics.org
  • Presented Project Accessible Genomics as a poster with video in the Wellcome Genome Informatics Conference


Project Timeline

Phase 0 is crowdfunding. Once we start the procurement of equipment and reagents, Phase I could be accomplished in 3 months:

  • Logistics of bringing in equipment and reagents
  • Recruiting a partner laboratory and adding a genomics layer to their current setup
  • Training local laboratory technologists in library preparation and local bioinformaticians on our pipeline
  • Getting SARS-CoV-2 samples
  • Ensure biosafety
  • Doing the actual sequencing and genome assembly


Another 1-2 months is needed for Phase II, creating the manual.


Phase III is a 18- to 24-month sub-project, where we will do systematic promotion and outreach to organizations across the developing world, provide training, consult in their own deployment, and incorporate lessons from deployments in varied environments to the manual.

Depending on the outcome, the next step could be to transition to a permanent organization. The laboratories built and personnel trained through this project will have the capability and capacity to identify pathogens of emerging epidemics in the future. The same organizations could also identify other animal and plant pathogens. Agricultural pathogen genomics is an emerging tool to protect our food supply. With additional training, the same organization could also help in protecting wildlife biodiversity through DNA barcoding, and in molecular species identification of agricultural products, which could be used against fraud and mislabeling.


Visit the project website: www.accessiblegenomics.org

Read the full JOLG microgrant application

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Project application - project 285 - 14-10-2020.pdf

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