by Melanie Padgett Powers, writer
Jocelyn R. Hauser, PhD, D(ABMM), laboratory director at the District of Columbia Public Health Laboratory, was checking email on her phone in her Cleveland hotel room before heading out for the final day of the APHL 2022 Annual Conference. An email caught her attention: an alert from the US Centers for Disease Control and Prevention (CDC) about monkeypox, later renamed mpox. It was May 20, 2022.
That CDC Health Alert Network advisory reported a confirmed case of mpox in Massachusetts and asked clinicians to be vigilant to the mpox rash.
“Immediately when they sent that out, I was emailing back and forth with my team: Where are we? Do we have all the reagents in case we get something? Do we have the trained people? Just trying to gear up just in case,” Hauser says.
A week later, Hauser was on a Zoom call with CDC’s Laboratory Response Network (LRN) when her state epidemiologist emailed her that DC had a suspected mpox case. Another one came in later that night, a few days before Memorial Day.
“It was essentially the holiday weekend that jump-started our response,” Hauser says. “From there, it became like a snowball of getting requests and having positive samples within the next two weeks. And then it kept snowballing with more samples.”
When mpox hit the United States last year, CDC activated the LRN, allowing for a coordinated response, standardized testing and information-sharing among laboratories. The mpox experience across the US highlighted the power of the LRN, but it also showcased its weaknesses—offering lessons in ways the network must modernize.
“The LRN is an underutilized resource that needs to be reimagined in terms of the world of today—and the world of today is that we’re going to have more frequent introductions to infectious diseases,” says Jill Taylor, PhD, APHL senior advisor for scientific affairs.
The Creation and Benefits of the LRN
The LRN was established in 1999 by APHL, CDC and the Federal Bureau of Investigation as a network of laboratories that could prepare for and respond to bioterrorism. Today’s LRN has two components: the LRN for Chemical Threats Preparedness (LRN-C) and the LRN for Biological Threats Preparedness (LRN-B). The LRN-B uses a tiered structure of thousands of clinical laboratories that serve as sentinels, ruling out and referring threats to reference laboratories. There are approximately 120 reference laboratory members, representing all 50 state public health laboratories plus some local public health, military, veterinary, agriculture, food, water and international laboratories. These reference laboratories detect and characterize biological threats such as anthrax and mpox. Another tier of the LRN-B is comprised of national laboratories such as those at CDC and Department of Defense. These laboratories perform additional characterization as well as assay development.
The LRN was also created in a world before the 9/11 terrorist attacks, a world without social media and a world with a blossoming internet that ordinary people were still discovering. In 1999, information did not travel so fast—and so widely—as it does in 2023. There have been massive advancements in technology over the past 20 years, along with new epidemics and emerging diseases that stress laboratories’ capabilities. The LRN finds itself stretched at times and is ripe for modernization, experts say. But CDC will need to push for and lead that modernization, and it will likely need more money to do so.
The LRN partnership “is paramount to the current response and to future responses,” says Scott Hughes, PhD, assistant commissioner and laboratory director of the New York City Department of Health and Mental Hygiene Public Health Laboratory. But funding is always an issue, he says.
“Funding spikes with an outbreak and then it goes away,” Hughes says. “That’s always something that is foremost in our minds—preparing for the next outbreak when there isn’t an outbreak. It’s very hard to justify that from a funding point of view, but it needs to be done. You need to have a response-ready team.”
During the 2022 mpox outbreak, being a part of the LRN meant laboratories could access assays and reagents from CDC and be a part of a constant communication network about how to respond to the outbreak. While mpox is not designated as a Select Agent, it is on the LRN list of tests, mostly to differentiate it from its cousin, the more dangerous and (almost) eradicated smallpox.
“We had the assay already available, and the LRN supplied us with our reagents to do the testing,” says Nicole M. Green, PhD, D(ABMM), director of public health laboratories at the Los Angeles County Department of Public Health. “Then we had a lot of communication with both CDC and APHL almost on a weekly basis in the very beginning, where the network would host these calls and people could call in to ask questions.”
Those LRN meetings with the CDC and other laboratory directors facilitated discussion on how to make testing more efficient, increase capacity and speed up turnaround times. When the outbreak happened, mpox already had an approved test ready for use. However, the test was manual, which slowed down testing especially as suspected cases increased.
“With input from public health laboratories, APHL worked with CDC to look at additional extraction platforms, specifically automated extraction platforms,” says Chris Mangal, MPH, APHL’s director of Public Health Preparedness and Response. “We saw an acceleration in how CDC evaluated automated extraction platforms, submitted performance data to the US Food and Drug Administration (FDA) and secured approval for laboratories to use automated extraction. The addition of automated extraction platforms was an important aspect of the mpox response to help laboratories handle testing surge.”
CDC also engaged commercial laboratories that had higher throughput testing, thereby increasing testing capacity.
How the LRN Should Modernize
The connectivity of the LRN helped bring about changes to the mpox outbreak as public health laboratories continued to learn what worked best and shared that information with each other, with CDC and APHL input. But it also illuminated cracks in the system that experts say need to be addressed for future outbreaks.
Mpox was a known pathogen and already had an approved test in place, albeit a manual one. While initially it had to be tested in a biosafety level-3 (BSL-3) suite—based on how contagious and deadly smallpox is—that was later changed to BSL-2, which opened up testing and personnel capacity. But how will the LRN respond to a larger outbreak, a more contagious and deadlier pathogen or an unknown pathogen? Or now, a very familiar one: SARS-CoV-2 the coronavirus that causes COVID-19, which has killed more than 6 million people globally.
One of the first tests of the LRN was the 2001 anthrax attacks, where laboratories not only had to respond initially but had to surge up as they were inundated with samples of all types of white powder that people feared were anthrax. In 2003, the LRN responded to a small outbreak of mpox, then SARS. Later there were ricin and tularemia scares, followed by H1N1 flu in 2009. The LRN was activated in all these outbreaks. Yet the LRN was never activated during the COVID-19 pandemic.
Mangal says it’s difficult to tease out why CDC never activated the LRN during COVID-19, but she points to the bioterrorism aspect of LRN’s conception.
“One of the things that we have to keep in mind is with mpox CDC had tests for a broad range of viruses to quickly rule out smallpox viruses so the network was prepared to respond. There are other instances where the LRN has been utilized to respond to emerging infectious diseases that don’t fit the profile for biological warfare. We’d like to say that the LRN is utilized for emerging infectious diseases outside of the bioterrorism space, but in reality, it hasn’t fully caught up to that expectation.”
Taylor adds, “The question becomes, ‘What is the LRN’s mission?’ The LRN was not used during the COVID-19 pandemic in any way. At the individual public health laboratories, LRN staff were used to add surge capability, but they didn’t use an LRN test. It wasn’t done in LRN laboratories, as such.
“SARS-CoV-2 as a new emerging pathogen was certainly not on the list of tests to develop,” Taylor continues, “but given the capability of the LRN laboratory at CDC to develop tests, one would have thought that they would do it.”
The LRN tests also need to be updated, experts agree. Tests need to be automated and available for a variety of high-throughput machines, not from only one or two vendors. Tests should also be multi-targeted. Taylor points out how helpful it would have been to have had one test last fall that could differentiate between SARS-CoV-2, influenza and respiratory syncytial virus.
“But ultimately, we need to be pathogen agnostic, meaning that we have to have a test that will detect an unknown,” Taylor says. “And the way to do that at the moment is metagenomic sequencing. Metagenomic sequencing is beyond a research test, but you need quite a bit of capability and informatics capability in laboratories to be able to do it. That needs to become a gold standard test rather than something that’s done in a very high capability laboratory.”
Last year, as the mpox cases and number of samples increased, CDC brought in commercial laboratories, which had BSL-2 capability. “The mpox outbreak that we just had spread incredibly quickly. The first identification was in Massachusetts, and then all of a sudden it was all over the country, and so high-throughput was needed,” Taylor says.
“If public health laboratories had had a test that did have more high-throughput capability, then the public health laboratory could have controlled the level of testing required,” Taylor continues. “So the LRN system worked, but it didn’t work as effectively as it ought to in this day and age.”
One challenge with using the commercial laboratories rather than improving capacity in the public health laboratories was that once the commercial laboratories took on much of the testing, it was difficult to collect public health information.
“There needs to be clarity on how the data coming out of the commercial laboratory is shared back to the public health world—and how those specimens are shared with the public health world,” Hughes says. The commercial laboratories may not be keeping specimens and are not necessarily giving the samples to the public health laboratories or CDC to learn more about the disease outbreak through sample culturing or sequencing.
“There is a risk to relying solely on commercial labs for public health-related testing,” Hughes says.
Another LRN bottleneck during the mpox outbreak was the CDC’s LRN Results Messenger (RM) system, which required laboratory staff to manually type in a lot of patient demographic data and a case history in order to report a mpox test result.
“It’s fine when you have one sample, but when you’ve got hundreds of samples … It was taking our team, for 10 to 20 samples, between an hour and an hour and a half to just put in the results and the data for each sample,” Hauser says.
Her team worked with CDC, which eventually allowed the laboratory to bulk-upload a spreadsheet of all the results, she says. Later, the CDC data team helped the laboratory switch over to electronic messaging and skip the RM portion.
“But for a really long time we were doing both,” Hauser says. “So, I think it’s worth spending the time and the resources to be able to get electronic reporting for these and be able to collect all the information that they would get from RM.”
The reason CDC asks for so much information is valid, Taylor says, allowing the agency to develop case reports, learn more about the disease and put out recommendations. “But in reality,” she says, “it’s more efficient to get the patient tested, and then when you get a positive result, the epidemiologists follow up with that individual and get the information for a case report.”
Also, she points out, when testing was switched to the commercial laboratories, those facilities were not required to provide as much data with the results.
Use of Whole Genome Sequencing
Los Angeles County began whole genome sequencing (WGS) in July 2022 to learn more about the mpox clade, but when the commercial entities took over, it also had trouble getting samples, Green says.
“The same thing happened with COVID-19—we were the only place in town to get the COVID-19 test and then it went off to the commercial laboratories,” Green says. “And now, because our role has changed … we don’t have anything to sequence. So now, we have to get the samples back from these laboratories.”
She compares it to a merry-go-round: “It seems kind of inefficient, that’s all.”
As Los Angeles County considered doing WGS on the mpox virus, Green’s staff heard about a laboratory at the Yale University School of Public Health that had developed a sequencing assay but had no samples to test it on. So, Los Angeles County reached out, and the two teams formed a partnership: Yale provided the laboratory with the test—and reagent initially—to evaluate their method with the county’s samples. It worked.
Sequencing in-house meant the laboratory could provide data about the virus to their epidemiologists faster, Green says. The laboratory learned several things from WGS. The team continued to confirm that the strain in the outbreak was the West African clade, not the deadlier Congo Basin clade. Furthermore, the laboratory detected genome deletions that could affect the accuracy of diagnostic tests.
“What we realized was that the parts of the genome that were missing potentially were areas that certain diagnostic tests were using as targets, meaning that if you had a patient that had a strain that had this deletion, it may not be detected,” she says.
Through WGS, the laboratory also identified mutations in samples that could make those patients resistant to tecovirimat, or TPOXX, which is approved to treat smallpox and is being used to treat mpox under an investigational new drug protocol. Green’s laboratory shared their data with CDC, the National Center for Biotechnology Information and with databases such as GISAID.
The Future of the LRN
While experts agree the LRN needs to be updated, modernization will likely require a different perspective—perhaps a reframing. Mangal believes the LRN needs elevation at the CDC, that more divisions need to consider it as the go-to laboratory response arm.
Taylor agrees: “It’s a preexisting network with highly trained people, with funding that goes up and down (which is a problem), and instead it needs to be the frontline of the response.
“I still consider the LRN a jewel in CDC’s crown,” Taylor continues, “but it’s an old jewel, and it has not adapted to the world we live in now. It simply needs to be reset for today and the future.”