Coordinating SARS-CoV-2 genomic surveillance in the United States (opens in a new tab)

The United States has rapidly responded to the emergence of new severe acute respiratory syndrome coronavirus 2 variants of concern by scaling up genomic surveillance. Tens of thousands of viral genomes are now sequenced in American labs each week to track the spread of variants originating in the United States (Annavajhala et al. 2021; Deng et al. 2021) or imported from other countries (Washington et al. 2021) to keep diagnostics, therapeutics, and vaccines up to date (Walensky, Walke, and Fauci 2021). An influx of Federal funding provides an unprecedented opportunity to build a new US genomic surveillance system from the ground up, informed by in-country expertise (National Academies of Sciences 2020; Black et al. 2020) as well as existing models of successful genomic surveillance systems established in other countries (COVID-19 Genomics UK (COG-UK) 2020; Seemann et al. 2020; Msomi, Mlisana, and Tulio 2020). Fully leveraging genetic data require a centrally coordinated national sampling strategy and consortiums for sharing valuable metadata, which are needed to study how new variants evade host immunity, cause severe disease, or transmit differently in human populations. However, US public and private labs have a history of autonomy and strong protections for patient privacy, presenting ongoing barriers to central coordination and data sharing.