Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States

The evolution of SARS-CoV2 virus has led to the emergence of variants of concern (VOC). Children, particularly <12 years old not yet eligible for vaccines, continue to be important reservoirs of SARS-CoV-2 yet VOC prevalence data in this population is lacking. We report data from a genomic surveillance program that includes 9 U.S. children’s hospitals. Analysis of SARS-CoV-2 genomes from 2119 patients <19 years old between 03/20 to 04/21 identified 252 VOCs and 560 VOC signature mutations, most from 10/20 onwards. 75.00% of the VOC signature mutations detected were in children <12 years old, including 32 cases of B.1.1.7 and 346 of B.1.419/B.1417. From 02/21 to 04/21, B.1.1.7 prevalence increased from 1.28% to 72.22% corresponding with the decline of B.1419/B.1417 from 52.57% to 5.56% at one institution. There continues to be a need for ongoing genomic surveillance, particularly among young children who will be the last groups to be vaccinated.