by Nancy Maddox, MPH, writer
On January 21, the US Centers for Disease Control and Prevention (CDC) reported the first US case of a novel, SARS-like coronavirus that has infected thousands of people in China, killing hundreds.
The respiratory bug was first detected in the central Chinese city of Wuhan in late 2019, but quickly spread throughout Asia, from South Korea to Singapore. It took only a few weeks to reach the US mainland in Washington State and just a few days more to show up in Chicago and then California.
Yet, despite the alarm raised by the novel virus—US authorities are already screening passengers arriving from China at select US airports—some state public health laboratories will be challenged to test for it.
The Virginia Division of Consolidated Laboratory Services (DCLS), for example, has experienced a steady erosion of federal funding for non-influenza respiratory virus testing, which includes testing for coronaviruses. Denise Toney, PhD, who heads the laboratory, explained, “If [a pathogen] isn’t flu and we want to rule out all the other viruses, we now have to prioritize and limit the testing to be most efficient with our reduced resources.”
The Virginia facility—which has provided surge capacity testing for the National Capital Area—once routinely tested a portion of all non-influenza respiratory outbreak specimens for a slate of other respiratory viruses, “so we could at least identify a causative agent for an outbreak.” But with less federal funding that is no longer feasible.
For public health laboratories struggling to, as Toney puts it, “provide the support we know we can provide,” the fiscal year 2020 (FY2020) budget enacted this past December will be neither a disaster nor a game changer.
Said APHL Policy Director Peter Kyriacopoulos, the budget “does not represent the kind of increases we would get excited about. It also does not represent the kind of decreases that had been proposed. Congress, again, kept us going at a modest level.”
CDC got a $637 million boost over the agency’s FY2019 budget, almost a 9% increase, discounting inflation. Just over a third of this will go to building projects on the CDC campus.
Among the good news items for public health are funds for an urgently needed data initiative (see sidebar), $140 million for a new Ending HIV/AIDS Initiative, an additional $75 million for the Global Health Security Agenda (totaling $183 million for GHSA) and an extra $35 million for the Infectious Disease Rapid Response Reserve Fund, which was established in FY2019 with an initial $50 million in funding.
There were no new funds for influenza planning and response, vector-borne diseases, CDC’s Advanced Molecular Detection program, opioid overdose surveillance, laboratory training, laboratory safety and quality, public health workforce development or the Public Health Emergency Preparedness (PHEP) Cooperative Agreement, the main source of federal support for state and local public health emergency preparedness and response. (Kyriacopoulos guesstimates that about 10% of overall PHEP funding goes to public health laboratories.)
Other CDC programs, such as emerging infectious diseases, food safety and the Antibiotic Resistance Initiative, got a two or three million dollar bump each—a negligible gain after factoring in inflation.
At the same time, the FY2020 CDC budget includes no supplemental funding for Ebola, which had provided around $120 million/year on average for GHSA activities from FY2015 through FY2019.
Although the budget news could have been worse, it continues a worrying, long-term trend of public health underfunding. According to data published by the advocacy group Trust for America’s Health (TFAH), there is a $4.5 billion gap between current funding levels and what is needed to achieve “an adequate level of public health protection” nationwide.
TFAH reports that between FY2010 and FY2019, CDC’s budget actually fell by 10%, after adjusting for inflation.
One measure of the funding shortfall for public health laboratories is the CDC Epidemiology and Laboratory Capacity (ELC) cooperative agreement, which builds capacity for emerging infectious disease control in the 50 states, District of Columbia, eight US territories and six US cities. In 2019, CDC received over $400 million in qualified ELC funding requests, but had only $231 million to award.
“When our budget is reduced, we accept fewer samples”
Although the majority of public health laboratory revenue comes from fees or state or local government outlays, the federal contribution is critical.
Grace Kubin, PhD, head of the Texas Department of State Health Services (DSHS) laboratory and APHL president, said federal funding (mostly ELC and PHEP cooperative agreement funding) comprises about 9% of her overall budget. But, she said, it is “maybe 40%” of the laboratory’s routine emergency response budget and as much as 90% of its emergency response funding during a major event, such as the 2009 H1N1 influenza outbreak, a 2012 Dallas-area West Nile virus outbreak, the 2015-17 Zika virus outbreak in Texas and a few other states, and Hurricane Harvey in 2017.
“All of these were supported by federal funding, eventually,” said Kubin.
Typically, she said, federal crisis funding follows a predictable cycle: “First, the lab becomes overwhelmed with samples and we start using our normal funds that should really be earmarked for other things to try to get that [emergency] testing done. And it can be several months afterward when it does hit a crisis level that funds become available. Then federal funds may be available for at least a year, maybe two, and by the time you do a no-cost extension it might cover a little bit more than two years.”
“It’s a crutch,” she said. “It enables us to do what we need to do. On occasion, it might provide the flexibility to improve some of our processes, maybe purchase more automated equipment instead of having to do manual work; in that regard it kind of lives on. But if there’s not another crisis, you’re left trying to figure out how to continue these activities and prioritize the most important things that have to get done.”
Zika virus is an example of a once-novel disease that outlasted its federal crisis funding—just last year, two cases of the mosquito-borne illness were reported in Texas. Ongoing surveillance is necessary, Kubin said, to determine what mosquito vectors and mosquito-borne diseases are in the state and where. Are there Aedes aegypti, which carry the Zika virus and are controlled by backpack spraying close to homes, where they tend to congregate to be near their blood meals? Or are there Culex mosquitos, which carry West Nile virus and can be controlled by street spraying, since they prefer to throng around stagnant water?
Ironically, Hurricane Harvey, provided “a little bit of money” to support ongoing vector-borne disease testing through the Hurricane Recovery Crisis cooperative agreement. Altogether, CDC disbursed approximately $64.5 million to nine jurisdictions for response to hurricanes Harvey, Irma and Maria. However, the one-time cash infusion must be spent down by August 2021, when a no-cost extension is up.
“When that money goes away, if the samples are still coming to us, we’re going to have to figure something out,” said Kubin. “Or else we’ll just test fewer samples.”
The Texas laboratory requested ELC “contingency” funds last year to enable a rapid ramp-up of clinical and animal testing in the event of a new vector-borne disease outbreak, but was denied the full amount requested. (It was also denied funding to fully support routine Salmonella whole genome sequencing.)
In Virginia, Toney has faced similar fiscal struggles owing to categorical cuts in the commonwealth’s ELC funding. In addition to reducing capacity for reflex influenza testing (to identify non-flu respiratory pathogens), she said, “We lost funding to support a full FTE to do non-flu respiratory disease testing.”
Gone too are the laboratory’s programs for rotavirus testing, arbovirus testing and Bordetella speciation. Significant budget cuts also threatened DCLS’s culture-independent diagnostic testing and testing for carbapenem-resistant bacteria—a class of drug-resistant microbes that commonly cause infections in healthcare settings—but aggressive outreach resulted in state funds to replace lost ELC monies.
Last year, DCLS lost a critical laboratory liaison position responsible for tracking grant spending and pulling together testing statistics and outbreak status reports for state epidemiologists. Now, any requests for data fall back on the scientists and technicians doing the testing, “if it’s [provided] at all.”
Another hard-hit area is foodborne disease testing, funded partly through the Food Emergency Response Network (FERN), coordinated by the US Food and Drug Administration (FDA) and the US Department of Agriculture.
Any reduction in funding, said Toney, “impacts the amount of work we can do and the timeliness with which we can do it, because our capability and capacity for food testing is directly aligned with our funding. When our budget is reduced, we accept fewer samples [for testing].”
Just in the past few years, FERN support contributed to the resolution of several Virginia outbreaks, including clusters of illness linked to Listeria-tainted sprouts, Salmonella Javiana-tainted clam chowder and Salmonella Weltevreden-tainted kratom (an unregulated supplement reputed to have psychotropic effects). The last of these triggered FDA’s first mandatory product recall.
Toney’s food-testing staff also provided FERN surge capacity testing for a multistate outbreak of Salmonella Braenderup tied to shell eggs used at a national chain restaurant.
With decreased FERN support, Toney said, the state has had to cut back on FERN training and to prioritize implementation of new methods based on state needs rather than federal surveillance needs. On a national level, she said, “I think the amount of data we have is going to be less than we’ve had in the past and may negatively impact our understanding of the outbreaks we’re investigating. ...I definitely think it is going to slow our ability to identify contaminated food. And anytime we have a slow response, it means there is a source of contamination that is still out there causing disease.”
“This is really important work.”
The rapid dissemination of novel coronavirus from China is a stark reminder that disease control cannot be limited to the United States. Although the FY2020 CDC budget includes a $75 million boost for the GHSA—a multinational effort focused on building capacity for infectious disease control worldwide—this gain must be balanced against the loss of over $100 million/year from supplemental federal funding for Ebola control.
Frances Pouch Downes, DrPH, a public health professor at Michigan State University and former head of the Michigan Public Health Laboratory, said “We don’t think strategically when we make these development investments; when you whittle away the funding, you open up gaps or fail to fill gaps.”
She said, “When something scary happens we throw money at it. But when the emergency subsides the need [for global public health capacity] doesn’t subside. There will be a next infectious disease.”
Downes, who has been involved in the development of a national laboratory network in Indonesia, said every piece of the GHSA is “relevant, important work”—things like safety training to assure proper containment of biohazards, quality laboratory systems to assure the accuracy of test results and rapid data transfer to inform public health decision-making. Yet, on a visit to Capitol Hill last year, Downes said many of the Congressional staffers she met with either “had no idea” how GHSA funds are spent or were “only vaguely aware” of the program.
Her advice for effective disease control boils down to two words: sustained funding. “The kind of changes that are needed aren’t going to happen within a single funding cycle.”
Stephen Redd, MD, deputy director for public health service and implementation science at CDC, said CDC is moving to a new global health strategy precisely so the agency can “have a global presence that wouldn’t depend on disease-specific funding or supplemental funding for an emergency.”
While there is no immediate plan to close country offices, CDC will segue from “bilateral” staff to “regional” staff who will develop and maintain connections to multiple countries. Gains in efficiency, Redd said, “would make health security not dependent on funding sources that wax or wane.”
“This is really important work,” he said, “and I think Congress recognizes its importance.”
In the US, public health laboratories have employed their own strategies to cope with funding losses. Kubin, for example, has tapped an APHL bioinformatics fellow to help establish a newborn screening bioinformatics program, taken advantage of the APHL Emerging Leader Program for staff training and sent staff to meet with clinical partners to assure specimens are collected and shipped correctly.
Of course, sometimes, the only way to balance the budget is to reduce services.
Said Toney, “Anytime we are faced with infectious diseases or other public health situations that affect our communities and individual lives and we do not have the tools we need to respond, that’s problematic. ...Knowing what we are capable of doing, and what [capabilities] we have lost...well, we owe it to our citizens to provide a lot more.”