COVID Sequencing-Still Early Days. Potential Is Great but Full Implementation Years Away.

Bloomberg Businessweek July 26, 2021 “Hunting Delta” “The U.S. system for tracking Covid variants is scattered and slow. Time to fix it.” By Cynthia Koons.



Image from GAO.GOV


Although the federal government has authorized a significant budget to facilitate rapid identification and publication of Covid variants the uptake is not well coordinated, is slow and remains an array of mostly underfunded efforts. The idea behind such a system of identifying Covid variants is that the information can guide public health solutions, can help understand the likelihood that variants will circumvent immune defenses induced by current vaccines, and even help “pharmaceutical companies to plan booster shots.” Experts agree that getting a “more robust National Bioinformatics Infrastructure is a multiyear project and [that we're] just getting started.”


“Kenny Beckmamn (University of Minnesota) believes that the CDC “should create a robust, user-friendly tracker that surveils virus mutation in something close to real time, much as the National Hurricane Center tracts storms. Further such a system should be extended to other threats like “other viruses to antibiotic resistant bugs to foodborne pathogens.” In terms of American Covid sequencing capability, although the technology is principally American, we probably are only sequencing 10% of all Covid cases and we rank “36th in terms of percentage of reported case sequenced and submitted to GISAID, the global mutation database.” Currently “the national goals are to find variants that evade vaccines, don’t respond to existing treatments, or are highly transmissible.”


Some argue that sequencing won’t become more widely adopted until health insurers pay for the testing. Currently, having sequencing data doesn’t alter treatment and therefore “It’s not approved as a medical health activity” says James Crawford (Northwell Health). It is hoped that sequence data will eventually define targeted therapies thereby making sequencing a reimbursable medical activity. Longer term the goal is to coordinate globally “to guard against new threats.”