The U.S. effort to track the emergence of new SARS-CoV-2 variants by sequencing the genetic codes of viruses from lab-confirmed cases struggled to get off the ground in 2020 but made significant gains in 2021. And last week, the Centers for Disease Control and Prevention’s (CDC’s) Office of Advanced Molecular Detection (OAMD), which oversees U.S. surveillance, announced a $185 million, 5-year initiative funding new Pathogen Genomics Centers of Excellence—pairings of state or local public health departments with academic centers to keep making U.S. surveillance efforts more nimble and effective.
Science Insider talked this week with Duncan MacCannell, OAMD’s chief science officer, about new challenges arising as SARS-CoV-2 cases have plunged to their lowest levels since July 2021, testing has fallen off dramatically, and CDC’s surveillance effort enters a new phase. This interview has been edited for brevity and clarity.
Q: How is U.S. surveillance going now?
A: Pretty well. One of the biggest things that has happened over the past 1, 1.5 years has been the increased number of state and local public health departments that have come online and been able to use sequencing as part of their ongoing surveillance strategy. Currently, we have 72 state and local public health labs that are routinely sequencing SARS-CoV-2 samples. In March of 2020, there were only six.
And there are other types of surveillance that we have brought online. The National Wastewater Surveillance System, for example, is working to harmonize wastewater surveillance from across the United States.
We are also working with academic partnerships that we are continuing to build. We are really excited about the Pathogen Genomics Centers of Excellence. I think it’s going to establish a new foundation for genomic epidemiology in the country.
Q: Early in 2021, the United States was sequencing fewer than 1% of lab-confirmed COVID-19 cases. By the summer, you had boosted that to 8.6%. Where are you now?
A: I want to steer you away from using percentages. The more important thing is where are you getting the data that you need? And are you able to make meaningful decisions as a result of the data you collect? Some of the changes we have enacted over the past couple of years have really sought to make sure that we are capturing data and sequences from a broad geography across the United States. It’s a really daunting problem when you are operating at that kind of scale.
Q: U.S. laboratory testing for COVID-19 has fallen sharply, down to about 622,000 daily tests, less than one-quarter of the average in mid-January. How important is continued testing to accurate and timely identification of new variants?
A: It’s definitely a consideration. If you have multiple municipalities that are starting to decrease the frequency with which they are testing, if they are focusing their testing on specific groups, that changes the sampling and perspective across the country. It doesn’t really matter as much when case rates are low because there aren’t that many circulating viruses to monitor. Where it becomes a challenge is if things turn around, if there is a surge.
But I think there are reasons for optimism. First, many state and local public health departments are able to do testing and sequencing in house. They are very closely engaged with their local communities, and they are able to access a lot of samples and understand what is circulating in the state and in the community.
[Through] large commercial labs and through state and local public health departments, there is ongoing baseline collection of samples from a broad geography.
Testing will continue to happen in most acute care settings. And we have a number of different unbiased systems like wastewater surveillance that aren’t going to be impacted by changes in testing.
Q: Do you have your eye on any particular variant in addition to the more infectious Omicron subvariant, BA.2, that CDC said Tuesday now accounts for more than half of new U.S. cases?
A: BA.2 is definitely the variant we are paying closest attention to right now. But we are monitoring a lot of different variants and a lot of different patterns of mutations to see whether any are concerning.
One of the things we are watching for closely right now is the potential emergence of recombinant viruses, especially with these large waves of different variants that rush through and crash into each other. More and more we are starting to see evidence of recombinant viruses from throughout the world. They have the potential to effect a sudden change in the behavior or properties of the virus. But so far, the numbers continue to be pretty low, and only a few appear to be circulating widely.
Q: What keeps you awake at night?
A: Mostly conference calls these days. Today was a 2 a.m. start.
Uncertainty. Right now, case rates are low. I worry that it’s easy to become complacent. Maintaining adequate surveillance [and] maintaining appropriate public health action are things I want to make sure we continue to do.