Building a Collaborative and Equitable Viral Genomic Surveillance Program: A Playbook for Researchers, Clinicians, Administrators, and Allies

Genomic surveillance is the process of sequencing microbial genomes to determine which viruses, viral variants, or bacteria are present in a population or geographic area and to understand how these microbes evolve. Throughout the COVID-19 pandemic, genomic surveillance efforts have allowed researchers around the world to detect and monitor variants like Delta and Omicron and track their spread.

In the United States, however, those efforts have not been distributed equally. Medically underserved communities are underrepresented in the national data, leading to blind spots in local public health guidance and sometimes even healthcare. The problem stems from a lack of sample coordination and genome sequencing in these communities, in part due to absence of the trained professionals, equipment, or broader networks necessary to sequence samples.

As it stands, commercial laboratories sequence SARS-CoV-2 genomes from RNA left over from diagnostic PCR testing. By designating the source material as medical waste, commercial sequencing laboratories forgo the informed consent process. Moreover, CDC-contracted commercial sequencing laboratories only label sequences with the state in which the sample was collected. They do not report the county, city or town. Thus, even when samples from underserved communities are sequenced, sample donors don’t usually know that their sample is being used, and their community may never benefit because the results don’t make it back to local health officials or healthcare providers.

This model represents a different approach. It is predicated on the belief that sample donors and the clinicians who collect those samples are partners in this work and should be treated and recognized as such. That means ensuring that these stakeholders, as well as the researchers who work with them directly, have a sense of ownership over the program and the data it generates and feel confident that they will be recognized for their contributions.

Viral genome sequencing should be available to every community so that local health officials have the data necessary to make informed recommendations and these communities can contribute to global pandemic prevention efforts. Given the rapid advancements in sequencing technology over the last two decades, that vision is within reach.

This Playbook is intended for academic researchers who want to collaborate with local clinics to collect respiratory specimens from informed patients for sequencing and for anyone who wants to support that mission.