What if all labs had access to genetic sequencing?
and making that happen isn’t so herculean afterall…
The word “surveillance” usually evokes extreme emotions in people, thanks to certain governments and movies like Snowden or Tom Cruise-starrer Minority Report. But the right kind of surveillance is actually capable of averting large-scale collapse, especially that of the public health sector. Pathogens are constantly evolving with changing circumstances, SARS-CoV-2 being one such prime example. 2021 has been the year of variants of SARS-CoV-2 with some of these being variants of varying degrees of concern. Genetic alterations accumulate over time leading to the emergence of new characteristics in pathogens. Some recent advancements in genomic sequencing and diagnostic technologies have ushered in an era of genomic surveillance. This kind of surveillance allows scientists to monitor the changing characteristics of pathogens and their impact on public health over time, by reading (read, sequencing) a pathogen’s genetic code. Although the cost of such sequencing has massively reduced over the past decades, the technology still remains extremely inaccessible especially in areas that have been historically identified as hotspots for emerging pathogens.
We at Just One Giant Lab (JOGL) came together and speculated this past month: what if all labs had access to genetic sequencing? The discussion was inspired by a stirring conversation I had with Kahlil Corazo from Accessible Genomics. Born and brought up in the Philippines, Kahlil, an entrepreneur, hails from a background in digital marketing and project management. With the world locking down in 2020, he began following the evolution and emergence of SARS-CoV-2 via global sequencing databases such as GISAID. Doing so he identified that currently, only rich countries have access to genomic pathogen surveillance yet future outbreaks will most likely originate from the developing world. The lack of genomic surveillance in the global south is a global problem. With most of the high-end functional sequencing devices only hosted in Manila (capital of the Philippines); Kahlil’s Accessible Genomics set out to bring together an international team of volunteers to develop and deploy low-cost SARS-CoV-2 sequencing operations in remote labs that originally lacked access to the technology.
No one else believed us — only JOGL was open enough to fund a bunch of strangers on the internet [with an aspirational idea]!
While Kahlil was simultaneously applying for other grants, he came across Just One Giant Lab. “No one else believed us — only JOGL was open enough to fund a bunch of strangers on the internet [with an aspirational idea]!”, says Corazo. JOGL Microgrants are distributed by a system pioneered during the COVID-19 pandemic in which projects are evaluated through community peer-review mechanisms. All of those that are situated above a certain threshold receive a microgrant. The microgrant helped Accessible Genomics circumvent the usual bureaucracy involved with funding agencies and set a model for remote labs around the world to set up their sequencing facility with open science. Powered by the microgrant and a group of volunteers and experts in logistics, biostatistics and genomic sequencing, Accessible Genomics worked with Philippine Genome Center (PGC) at Mindanao to train volunteers in lab techniques, shipped necessary reagents and equipment to undertake the first-ever sequencing of any organism in Mindanao, Philippines. The work with PGC has also resulted in a research publication: a gold-standard feat for those sceptical of Open Science and grassroots approaches. Upon being asked about some of the challenges faced while building Accessible Genomics from scratch, Corazo reflected that more often than not, lab technicians and staff lack energy, time and incentives to apply for grants and establish the setup necessary for genomic sequencing in their local labs. In the absence of a local manufacturing setup, navigating complicated local regulations to import required reagents was yet another hurdle.
That there is a pressing need to actively undertake genomic surveillance in inaccessible southeast Asian and African regions was echoed in the discussions during our What If Event. Attendees from Africa touched upon the significance of extensive genomic sequencing in analysing outbreaks in a time-efficient manner and removing bias in existing databases. Reliably detecting modes of transmission and avoiding gross overestimations are other advantages of genomic surveillance. The ‘What if’ question for this session even inspired some to ponder how colonialism in science and inaccessibility has prevented the budding of local innovators. Moreover, what would it take to build an open-source nucleotide sequencer and why we haven’t heard of one yet, despite the prevalent culture of open hardware and innovation?
Unlike traditional grant agencies, JOGL supports and funds ideas based on potential, irrespective of affiliation of ideators.
The secret to robust global genomic surveillance lies in two words: sequence and share. Undoubtedly it is crucial for such a network that is feeding in a constant stream of molecular real-time data to be representative of all regions- be truly global. While Accessible Genomics now looks forward to supporting its growing team in Africa, the success of Accessible Genomics is the aptest answer to What if all labs had access to genetic sequencing. Corazo pointed out that disruptive ideas usually bear the brunt of their ideators not being affiliated to reputed institutions. “Unlike traditional grant agencies, JOGL supports and funds ideas based on potential, irrespective of affiliation of ideators.”, says Corazo. With its community-driven, open and transparent funding process, JOGL strives to mobilise communities for change to create a safer and fairer world.
If you are interested in contributing to the project, or to learn more, don’t miss our next JOGL event at https://www.meetup.com/JustOneGiantLab/
