Panel shares outlook on future of pathogen surveillance, beyond pandemics into clinical and broader use - the full potential is yet to be realised

On Friday June 10th, more than 120 scientists and public health leaders attended a panel discussion in Washington D.C. on the future of pathogen surveillance, hosted by Oxford Nanopore Technologies. The panel described how genomic surveillance tools are transforming public health action by providing rapid insight into pathogens, their evolution and spread.

“I haven’t seen a time like this since real-time PCR was added as a diagnostic in the early 2000s – it’s really exciting and there’s so much we can do... It’s going to transform public health and clinical microbiology.” – Kimberlee Musser, Wadsworth Center, NYSDOH

There was agreement across the panel that the COVID-19 pandemic raised the global profile of the critical role that sequencing can play in pathogen surveillance. Scientists and public health leaders around the world have been deploying sequencing platforms to quickly detect emerging variants of concern and respond to outbreaks in real-time. But it has taken time to develop sequencing capacity.

“In early 2020, we were pushing for a national effort to do genomic surveillance for SARS-CoV-2. There was very little coordinated effort. It really took the alpha variant - the actual event that you should be surveilling for happening - for action to be taken. There is capacity there now, but it is a question of sustaining the will to continue to do the work.” – Kelly Wroblewski, APHL

In other parts of the world, including East Africa, significant infrastructure challenges have traditionally prevented widespread adoption of sequencing capacity. In these settings, portable and compact sequencing technologies are demonstrating their valuable role in the fight against emerging pathogens, however further barriers – most notably distribution and broader infrastructure – need to be further addressed.

“The SARS-CoV-2 outbreak exposed us as a scientific community for not doing things equitably... many people don’t have the internet, or they don’t have power.

The pandemic has also highlighted that there is one type of technology that has the capacity to equalise the game and it is the portable technology that [Oxford Nanopore Technologies] has. This has the capability to empower a lot of people quickly.” – Laura Boykin Okalebo, TED Senior Fellow and Senior Scientific Consultant at BioTeam

Following the dramatic acceleration of capacity and capability, public health laboratories and academic institutions are now considering wider applications and opportunities. These include applying genomic surveillance to a wider range of pathogens, moving to sequencing long DNA or RNA fragments in real-time, pathogen-agnostic sequencing, and potential clinical applications.

“We’re really using the information now to stop the transmission of antimicrobial resistance in healthcare facilities and nursing homes. For Legionella, we are able to use this rich genomic data to turn off cooling towers and get foods off the market. So the genomics are getting put to good use.” – Kimberlee Musser, Wadsworth Center, NYSDOH

The panellists described training, funding and innovative approaches to data sharing, storage and analysis as key to sustaining the use of this capacity going forward.

“In the US, a lot of money has been thrown at building genomic capacity but the challenge is sustaining funding rather than being reactionary. Key here will be the versatility and the flexibility of sequencing technology to answer all kinds of questions and to help solve all kinds of public health problems.” – Kelly Wroblewski, APHL

The panel discussed ideal methods for developing sustainable and equitable capacity and capabilities in LMICs, noting that an appropriate balance of international collaboration, sustainable local infrastructure, skills and funding would likely yield optimal outcomes.

“Instead of just collecting samples [in a country], process them there, so you are building capacity and expertise. Have them do the workflows, the sequencing and analysis, so we have a transfer of technology and transfer of information.” - Rebecca Colman, FIND

The panel commended ongoing coordination of efforts to develop a true network for early pathogen detection and recognised that there is still more work to be done. Oxford Nanopore Technologies believes that robust and widespread genomic surveillance is vital to respond to and be proactive in current and future pathogen threats.

Oxford Nanopore Technologies is committed to continued progress towards global health goals and working in partnership with public health, clinical and academic leaders to realise the true potential of genomic sequencing.