A further expansion to meet the Biden administration’s target would be “doable,” Gunsalus added. And Cooper noted that not every state needs to hit the benchmark, as long as the country as a whole had doubled down on sequencing.
Lack of federal leadership complicates work, states argue
But many states, including Kansas, argued they have been hampered because the CDC and federal authorities haven’t been able to coordinate a national push to ramp up the practice.
That has meant conflicting guidance on how to conduct sequencing and report it to federal authorities. Kansas has had to resort to a partnership with public health officials in Michigan, for instance, to determine the best way to publicly display its sequencing work.
“CDC, they were not a leader in guiding the states for sequencing or how to report it — there are still challenges with how to report it and how to display it,” Gunsalus said. “They’re just now getting into some sort of a rhythm.”
Prior to the start of the pandemic, the state’s lab had the capacity to conduct genetic sequencing but it was primarily targeted at foodborne illnesses.
Through piecing together funds, KDHE has been able to purchase more sophisticated machinery, including equipment that automates the more labor-intensive parts of the sequencing process.
More help is on the way — under federal relief legislation passed earlier this year, $1.75 billion is earmarked to help sequencing skyrocket nationally.
And more resources will help the state publish and share the genetic makeup of the variants they discover in databases, which are available to other researchers both domestically and abroad.
Since the start of 2020, the state says roughly 2,100 sequences have been uploaded to public repositories, a fraction of the 305,000 COVID-19 cases in Kansas. Sometimes it is redundant to upload samples but in other cases officials are unable to do so because of a lack of manpower.
“It does take effort,” Gunsalus said. “So that is a little bit of a barrier to getting more uploaded, and we have increased our uploads, but … that may be a place we can improve.”
Officials deploy other strategies as ‘early warning’ against variants
Sequencing is not a silver bullet — health officials say it should be part of a broader suite of tools used moving forward.
That includes the public health equivalent of dumpster diving: testing wastewater in particular communities as an early warning signal for the potential spread of the variants. COVID-19 can show up in the sewage a week or more before an outbreak is actually discovered, giving officials a heads up on what might be coming in the future.
Wastewater testing has continued in a handful of Johnson and Wyandotte County communities and the city of Lawrence has conducted its own program in partnership with the University of Kansas for much of the pandemic.
But KDHE is set to expand to conduct weekly samples of towns in western Kansas to get a better sense of any variant cases in that part of the state.
Having a better sense of where the variants might be cropping up can show where other state resources might need to be directed, according to Tom Stiles, director of KDHE’s Bureau of Water.
“It always started out as early warning, but we’re now at a point where we need to further define what the problem we’re trying to solve is and then directly see what role wastewater surveillance can play,” Stiles said.
Despite mask mandate, testing setbacks, state plans for future
The variants are hitting Kansas at a unique time in the pandemic.
Republican legislators, buoyed by decreasing case counts and new oversight of Gov. Laura Kelly’s emergency powers, repealed the statewide mask mandate last month and only a few municipalities across the state have opted to keep a local order in place.
Meanwhile, testing rates are down, both across the state and across the country. That is in large part due to residents getting vaccinated and perceiving that testing is no longer necessary.
But if individuals opt not to get tested, it is harder for health experts to get a sense of what is really going on.
“If you don’t test, you don’t sample,” said Cooper, the University of Pittsburgh microbiologist. “And if you don’t sample then you can’t sequence.”
While it isn’t yet known whether every vaccine provides protection against new forms of COVID-19, early indicators are promising. This has created a hope that the state can win a race against time to tamp down the impact variants will have going forward.
“I think we are all holding our breath in terms of the vaccine administration going up, up and up,” said Norman, the KDHE secretary.
But the need for genomic sequencing is still high, Norman and other experts note. That isn’t just to deal with COVID-19 but to build up an infrastructure needed to tackle future disease outbreaks.
Investing in building up a qualified workforce, as well as new technology, Cooper said, would pay dividends later on.
“They are going to be critical for prolonged understanding the future of this particular pandemic, which is not going to end this year. We’re stuck with this thing,” Cooper said. “But, more importantly, there will be more pathogens … and because of this, we’re going to understand and be prepared to handle the next pandemic.”
