As the Omicron-fueled wave in COVID-19 cases ebbs and vaccination rates increase, the country is beginning to shift gears in how COVID-19 is measured.

The Centers for Disease Control and Prevention recently updated its guidelines for how it determines the risk level of COVID-19 in communities. Instead of relying primarily on the percent of positive tests, the method now emphasizes hospital admissions and occupied beds along with COVID-19 case counts. Meanwhile, demand for COVID-19 PCR tests is falling as more people are using at-home rapid tests, the results of which often aren’t reported to public health agencies.

In the US, all of this has prompted some jurisdictions to scale back COVID-19 testing capacity and contact tracing efforts. “W​e’re at a place where we can focus a little more on severe illness because we have such high immunity in our population, both through vaccination and through recent infection, particularly with Omicron,” says Crystal Watson, a senior scholar at the Johns Hopkins Center for Health Security. 

[Related: The CDC is relaxing indoor mask guidelines and shaking up how it measures COVID risk]

However, this could lead to gaps in our understanding of how widely COVID-19 continues to circulate. “Hospitalizations are a lagging indicator, so it’s really important to maintain surveillance where we can in order to have early warning that a surge is coming and to do surveillance for new variants that might be consequential,” Watson says.

Fortunately, there are several ways that we can continue to keep tabs on the novel coronavirus. What’s more, COVID-19 has galvanized government agencies to invest in new surveillance systems that could be adapted for other diseases down the road, experts say.

Strategic testing

Rather than testing large proportions of the population for COVID-19, public health officials could maintain “sentinel” surveillance sites that are carefully chosen to be representative of the population, Watson says. 

Meanwhile, if and when case counts begin to climb again, it will be easier for communities to increase the availability of PCR testing as needed, says Jeffrey Shaman, a professor of environmental health sciences at the Columbia University Mailman School of Public Health. The widespread use of both PCR and at-home tests is a major improvement compared to the early months of the pandemic. “What we’re seeing now, at least what I hope, is a little more of a fluid capacity to ramp up production again,” Shaman says. 

Another key component of monitoring COVID-19 is to determine the genetic code of the virus present in PCR test samples, a process known as genomic sequencing. This reveals whether a person was infected with Omicron, Delta, or some other version of the novel coronavirus. Right now, only a small fraction of tests are sequenced, Watson says. But researchers would have a better shot at spotting emerging variants if we increased the proportion of samples that undergo sequencing, as other countries such as Denmark have done

“We’re kind of switching from trying to track overall prevalence of COVID in a community to more watching for outbreaks, and especially watching for outbreaks from new variants,” says Aaron Packman, director of Northwestern University’s Center for Water Research. 

Surveying sewage

One relatively cheap, anonymous way to do this is testing municipal sewage for the presence of SARS-CoV-2. Remnants of the virus can be found in poop and other human waste. Wastewater surveillance takes advantage of existing sewer systems, captures asymptomatic or pre-symptomatic infections, and has been especially valuable in places where COVID-19 tests aren’t readily available, Packman notes. 

“When cases are low, that can help you understand that something is brewing,” Watson says. “It can be helpful in detecting a new surge [of infections] and helpful in that early detection of new variants.”

[Related: Poop could be the key to tracking COVID-19 outbreaks]

Wastewater surveillance does have limitations, Shaman says. Researchers are still working out how the amount of virus shed along with feces differs from person to person. As it flows through the sewers, the virus may break down before it can be sampled. Human sewage can also be diluted or contaminated with stormwater runoff or waste from animals infected with COVID-19 (or freeze during cold snaps).

“We’re still getting a handle on what we can and can’t do with that kind of information,” Shaman says. 

Packman and his collaborators are working on refining wastewater sampling techniques to pick up lower levels of the novel coronavirus. Similar monitoring efforts are in place around the country, and the CDC launched a National Wastewater Surveillance System in late 2020. 

Wastewater surveillance was already used to track public health issues such as polio before the pandemic. However, Packman says, “It’s only because of the pandemic really that there was this huge information need and this huge push to put wastewater surveillance into place all over the country.” Packman also sees the potential benefits of applying this fecal infrastructure to other concerns like influenza or opioid abuse in the future.

At-home test results matter

At-home COVID-19 tests can also be a valuable source of data, Watson says. “I don’t think most people are aware that they can report [their results],” she says, adding that it will be important to give people ways to privately and easily log positive tests with public health agencies going forward.

Right now, the steps involved in reporting at-home tests to official agencies varies from region to region. It’s a good idea to check your local health department website for instructions on how to share positive test results and notify your healthcare provider if your at-home COVID test turns positive.

[Related: Which at-home COVID-19 test should you buy?]

At-home tests could be useful for tracking other kinds of infectious diseases down the road as well, Watson says. 

“It’s worth putting in the work and the thought as to how we could harness that at-home awareness for the purpose of public health,” she says. Additionally, Watson says, “The more that we can maintain the amazing capacity that we’ve built for testing and surveillance during COVID-19, I think the better off we will be when we face the next infectious disease threat.”