Project ACCESSIBLE GENOMICS II
Participating to challenge(s): OpenCovid19 - Grant Review Round 5
- Short Name: #ProjectACCESSIBLEGENOMICSII
- Status: Active/Ongoing
- Project maturity: Implementation of the solution in a public setting
- Looking for collaborators: ✅
- Grant information: Received €4,700.00€ from the OpenCOVID19 Grant Round 4/5 on 03/24/2021
Slack channel: #proj-accessible-genomics
Project site: accessiblegenomics.org
1 minute intro video:
Project presentation video:
- To better manage this pandemic (e.g. identify SARS-CoV-2 variants) 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.
- Project ACCESSIBLE GENOMICS has demonstrated a solution. In Part I of this project (funded by JOGL with EUR1,500 on October 30, 2020), we brought in training, equipment and reagents to a lab in Mindanao, Philippines. On March 9, 2021 that lab was the first ever to sequence SARS-CoV-2 through the enablement of an international volunteer team through an open science platform.
- With that knowhow acquired, we will deploy SARS-CoV-2 sequencing operations in other labs, targeting to produce at least 100 SARS-CoV-2 whole genomes within 30 days of signing up a lab.
Problem and Background
We are already in the second year of the pandemic and we still don't know what variants are circulating in most areas of the world. Only countries with a significant number of SARS-CoV-2 genomes sequenced could discover, analyze and track variants of interest (Figure 1).
Part I of this project demonstrated a solution. We see a solution for establishing a SARS-CoV-2 sequencing lab in less than a month and with more genomes produced:
- Use the ONT 96 Barcode set: up to 192 genomes on the first run instead of 48 (2 flow cells).
- Have equipment and reagents in-country: setup in 7 days instead of 90 days.
- Have a team ready to do the wet lab work alongside the people being trained: immediate sequencing instead of waiting for training to be completed.
- Centralize the bioinformatics pipeline: for locations with slow internet, airmail FAST5 or FASTQ files in hard drives.
- Numbers game: approach public hospital labs, private hospital labs, university labs, local government labs and COVID-19 testing facilities and work with the fastest organizations across the country.
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.
Part I of this project demonstrated that a volunteer team across the world could enable a LMIC lab to sequence SARS-CoV-2. Based on that experience, we propose a solution that will help other labs go from 0 to 100 SARS-CoV-2 genomes in 30 days.
Solution summary in technical terms
The goal is to get a lab to start producing SARS-CoV-2 whole genomes as quickly as possible. Based on our experience with Part I of this project, we believe that we could help a lab go from 0 to 100 genomes within 30 days with the following:
- If we have the equipment and reagents stocked in-country, they could be deployed to various cities and towns within 7 days instead of 90 days.
- If we visit the new labs with the molecular biologists trained through Project Accessible Genomics Part I, the training for the new lab could immediately produce the first set of genomes.
- If we use the 96 Barcodes instead of the 1-12 and 13-24 Native Barcodes of ONT, two flow cells could produce a maximum of 192 genomes instead of 48. The 96 Barcode set costs higher but reduces the per sample cost.
- We worked with public hospitals under the Department of Health in Project Accessible Genomics. They have very bureaucratic processes and large organizations. If we work with private hospital labs, university labs, local governments and COVID-19 testing labs, and if we approach many of them, we could work with the most agile organizations among them.
State of advancement of the project (as of 13Mar2020): Part I complete!
- May 2020 - project initiation via JOGL.io
- June - Sep 2020 - team building, grant applications
- October 2020 - EUR1,500 microgrant given by JOGL.io
- November 2020 - Philippine Genome Center Mindanao joined the project. Trainings started (see links to recordings here: http://accessiblegenomics.org/training)
- December 2020 - all equipment and reagents on their way to the lab
- January 2021 - trainings completed
- February 16, 2021 - all equipment and reagents needed for sequencing in the lab
- March 9, 2021
- First ever SARS-CoV-2 sequencing enabled by and an international volunteer team on an open science platform
- First ever sequencing of any organism in Mindanao, Philippines
- March 2021: Fundraising for Part II (one lab for every USD 12,000)
- Other grants
- April 2021: Outreach to other labs in Mindanao: apply to receive training, a sequencer and reagents for SARS-CoV-2 sequencing in your locality.
- May 2021: Select partner lab/s (number depending how much we can raise). First come first serve in terms of ethics approval. Training. Sequencing.
Visit the project website: www.accessiblegenomics.org