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

OBJECTIVES

To assess the efforts deployed by different nations and territories in sequencing SARS-CoV-2 isolates, thus enabling detection of variants, known and novel, of concern.

METHODS

The sources of over one million full genome sequences of SARS-CoV-2 virus available in the COVID-19 virus Mutation Tracker (CovMT) were analyzed 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 detected variants increased as the square root of sequencing effort by nations. Eight nations have contributed 79% of all SARS-CoV-2 isolates that have been sequenced, with two-thirds of all unique variants, adding to 1118 RBD variants, reported by five nations. The median number of sequenced isolates required to detect, on average, one novel RBD variant is 24.05, which is a threshold achieved by 70 nations.

CONCLUSIONS

Many developing nations have not contributed any sequences due to lack of capacity. This poses a risk of dangerous virus variants in these under-sampled 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.