How the U.S. IS Watching for the Next COVID Variant

How Is the U.S. Watching for the Next COVID Variant? While sequencing efforts are better than before, experts say there's a long way to go Sophie Putka medpagetoday

The only certain thing about the future of SARS-CoV-2 variants is that nothing is certain -- but researchers in the U.S. are doing their best to keep an eye out for the next troublesome variant, even in the face of numerous challenges.

While the systems in place to identify and track new variants have come a long way, Stephen Morse, PhD, an epidemiologist at Columbia University's Mailman School of Public Health told MedPage Today that, "For the first time we have a really fairly detailed, not complete, but fairly detailed picture of how this is unfolding."

A key variant tracker is GISAID, which started as a way to track influenza but grew during the pandemic into a global database where almost anyone can upload COVID-19 sequencing data. It's been behind the discovery of new strains, and it's by far the largest repository of genetic data on the virus.

"People ... found some of these new sequences simply by looking at how people had uploaded [to GISAID], so that's kind of a reactive approach," said Morse, noting that more institutions are now actively sampling, and the CDC "is now testing and sequencing, or collecting sequences."

The CDC is collecting sequences through a program launched in November 2020 called the National SARS-CoV-2 Strain Surveillance (NS3) program. Initially, the project only asked for 10 samples from each state every 2 weeks, but is now sequencing many more than its initial goal of 750 samples per week.

Unlike GISAID, NS3 is meant to be nationally representative. The CDC asks states to send samples that represent a variety of demographics, locations, and clinical characteristics to reflect the makeup of the country as a whole -- but some states send more or less than their proportional share of the samples. ...