Behind the paper: A collaborative approach to improving representation in viral genomic surveillance

In this post, we speak to the authors of a recent PLOS Global Public Health article, A collaborative approach to improving representation in viral genomic surveillance, about the story behind the research. The paper was written by Paul Y. Kim, Audrey Y. Kim, Jamie J. Newman, Eleonora Cella, Thomas C. Bishop, Peter J. Huwe, Olga N. Uchakina, Robert J. McKallip, Vance L. Mack, Marnie P. Hill, Ifedayo Victor Ogungbe, Olawale Adeyinka, Samuel Jones, Gregory Ware, Jennifer Carroll, Jarrod F. Sawyer, Kenneth H. Densmore, Michael Foster, Lescia Valmond, John Thomas, Taj Azarian, Krista Queen, and Jeremy P. Kamil.

What led you to decide on this research question?

Social inequities of all sorts felt magnified during the pandemic. This came across in who would have the luxury of being able to work from home, as well as in access to tests, vaccines, treatments, and yes, even in how resources to do viral genomic surveillance were being distributed. Many talented colleagues, even ones who were part of Covid PCR testing centers with good access to samples, were struggling to find support to get sequencing up and running. Most rural, less affluent areas were completely in the dark about these viral variants that were starting to emerge. So, when we were invited to apply to become part of The Rockefeller Foundation’s network of US Regional Accelerators for Genomic Surveillance, we were excited to throw our hat in the ring. The focus of our project was less on the technical aspects of sequencing and more about the social dynamics of “how do you build trust to establish sustainable genomic surveillance efforts across disadvantaged communities?” We believed that by offering folks information about what genomic surveillance was and how it would benefit them and their larger community, and by conducting our work through trusted local clinics and universities with roots in the area, that people would feel more connected to the results and be more willing to participate.

Could you talk us through how you designed your study? What was important for your team as you created the study team?

We wanted to be as representative, inclusive, transparent, and fair as possible, and to ensure that our data would represent and benefit all Americans. So, we focused on engaging with and collecting samples from underserved populations in a region with low sequencing capacity. We built up a diverse group of collaborators including researchers at HBCUs, and rural and minority clinicians. Finding health care workers who were willing to educate their patients about viral genomic surveillance was important to building trust. We also felt it was key to attribute authorship of the resulting viral genomic sequences to everyone at the clinics and universities who contributed to obtaining and sequencing the specimens. Undergraduate students were essential to our study team because they’re trusted members of these communities and they also represent the next generation of health workers, educators, and scientists. We hoped that by involving these students in community engagement and providing them hands-on experience with cutting-edge research tools that this would empower them to make a meaningful difference, a lasting impact.

What challenges did you encounter during your study?

At first, it was a bit chaotic trying to establish partnerships with five universities across the Southern US – it was just a lot of paperwork before we could collect and share patient specimens and the resulting data from sequencing. Then there were various logistical aspects of doing this work at multiple sites that required changes along the way like how to best handle multiple streams of metadata, or how to deal with supply chain issues, and how to secure informed consent from patients without overburdening our clinician partners who were already spread thin in their day-to-day work. We needed to listen and respond to them to make this process as easy as possible. Overall, there was learning for us to do.

What did you find most striking about your results? How will this research be used?

The most striking outcome was seeing how well our humble surveillance network could rapidly detect emerging variants. Our partner site, Mercer Medicine detected some of the first BQ.1.1 and BA.2.75 variants recorded from Georgia (GA), the home base of the US CDC, which was striking. In another example, one of our partner clinics picked up the first confirmed case of Omicron in Northeast Louisiana. Many in the community had a misconception at the time that Omicron was just a “big city problem.” After the clinicians alerted the local media, this made the headlines the next day, providing an important warning that this highly infectious variant was indeed already circulating. It was also gratifying to see how undergraduate students with no prior experience in public health or virology were able make substantial contributions in the midst of this historic pandemic. As far as how this research will be used, we were lucky to have support from The Rockefeller Foundation to write a Playbook that distills our key learnings into modules that academic teams can use to develop their own pathogen genomic surveillance networks. We hope funding agencies will find ways to sustain support for these types of partnerships between universities and local health clinics. We think it’s a fantastic model to enable faster detection and tracking of outbreaks, while also serving as training grounds for a diverse and representative global health workforce of tomorrow.

What further research questions need to be addressed in this area?

One intriguing question is whether making pathogen genomic surveillance programs more local and more participatory would have a “halo effect” on how everyday people perceive science and public health, and if so, how can we measure the impact of that? Most of the time it’s anonymous “outsiders” who sequence virus genomes from remnants of PCR tests without informed consent. The CDC even had to issue a statement refuting a harmful rumor that labs were sequencing human genomes from COVID tests! We think that when the health workers and scientists involved in viral genomic surveillance are members of the community they are collecting samples from, that could help alleviate some of this mistrust.

Why did you choose PLOS Global Public Health as a venue for your article?

The mission and scope of PLOS Global Public Health was a natural fit for our project. The editors are such well respected leaders in the field, we felt confident that by choosing this journal we would get a great opportunity to improve our work through peer review and ultimately to reach the right audience. Plus, we’ve had positive experiences publishing in other PLOS journals, like PLOS Biology, PLOS Pathogens, and PLOS ONE. We’re happy that PLOS has established this venue for researchers from all over the world to publish their work in this hugely relevant field.

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.