Global variation in sequencing impedes SARS-CoV-2 surveillance

Surveillance is essential to successful, rapid response of infectious disease outbreaks. While public health surveillance has historically focused on monitoring clinical cases and consequences of infection (e.g., case reports and hospitalizations) [1], technological advances in genomic sequencing rooted in the Human Genome Project and other large-scale investments in human genetics and genomic research and technologies now allow the unprecedented opportunity for pathogen surveillance down to base pair patterns of variation. Despite the availability and ubiquity of sequencing in several countries, the adoption of genomics as a strategy for pathogen surveillance has been slow, difficult, and inconsistent. An extreme example of the slow adoption is that, as of early April 2021, the United States ranked 33th in the world in Severe Acute Respiratory Syndrome Coronavirus 2 (SARSAU : PleasenotethatSARS CoV 2hasbeendefinedasSevereAcuteRespiratorySyndromeCoronavirus2atitsfirstmentioninthesentenceAnextremeexampleoftheslowadoptionisthat; as:::Pleasecorrectifnecessary: -CoV-2) sequencing for variant surveillance, up from 36th a few weeks earlier [2–4]. For a country that led the sequencing of the human genome more than 2 decades ago, the lack of accrual of sequencing data in the midst of this pandemic is unbelievable and problematic. Capacity and expertise exist across several key academic centers and industry partners, yet these resources remained relatively dormant until recently with fewer than 7,000 new sequences the week of March 6 from more than 415,000 new cases in the same period [5–7]. At that point in time, several commentaries and interviews [2,3,8] provided factors associated with this genomic bottleneck, e.g., lack of funding, lack of robust sample tracking and data pipelines, and strict regulations governing biospecimen and data sharing. These variables, which are not unique to the US, have been successfully addressed by other countries such as Denmark and the United Kingdom (UK) [9]. Given the role of the US in developing and utilizing sequencing technologies in the study of human diseases, initial failure to extend this into the study of SARS-CoV-2 to track viral mutations and improve public health represents a troubling, self-inflicted barrier to battling Coronavirus Disease 2019 (COVIDAU : PleasenotethatCOVID 19hasbeendefinedasCoronavirusDisease2019atitsfirstmentioninthesentenceGiventheroleoftheUSindevelopingandutilizing:::Pleasecorrectifnecessary: -19), especially in light of the high prevalence of SARS-Cov-2 infection in the US over the past year. Historically, genomic studies in the US have been financially and scientifically well supported by several agencies including the US Department of Energy, National Institutes of Health (NIH), and private industry. Today’s mega-biobanks with electronic health records (EHRs) and other health-related data linked to DNA samples collected for genome-wide genotyping and whole genome sequencing are efforts supported by the Veterans Administration [10], medical centers, NIH, and private industry. Nearly absent from the US genomic-centric efforts is explicit collaboration with and investment by the primary public health agency, the Centers for Disease Control and Prevention (CDC). Maintaining zip code is more relevant to health than genetic code [11], the CDC did not initially prioritize genomic research with