Detection of SARS-CoV-2 variants requires urgent global coordination

Duarte, Carlos M.; Jamil, Tahira; Gojobori, Takashi; Alam, Intikhab

OBJECTIVES: We assessed the effort deployed by different nations and territories to sequence SARS-CoV-2 isolates, thus allowing the detection of variants, known and novel, of concern. DESIGN: We analyzed the sources of over one million full genome sequences of SARS-CoV-2 virus available in the COVID-19 virus Mutation Tracker (CovMT) to determine the number of variants in the RBD region of the genome determining infectivity detected in the various nations and territories. RESULTS: The number of variants detected increased as the square root of sequencing effort of sequencing effort by nations. Eight nations contributed 79% of all SARS-CoV-2 isolates sequenced, with 2/3’s of all unique variants, adding to 1118 RBD variants, reported by 5 nations. The median number of isolates sequenced required to detect, on average, one novel RBD variant is 24.05, a threshold only achieved by 70 nations. CONCLUSIONS: Many developing nations have not contributed any sequences due to lack of capacity, with a risk of dangerous virus variants in these undersampled regions spreading globally before being detected. A collaborative program to sequence SARS-CoV-2 isolates, and other pathogens of concern, is needed to monitor, track and control the pandemic.