In the Lab

Behind Humboldt's efforts to expand COVID-19 testing capacity



Before the COVID-19 pandemic began, the Humboldt County Public Health Laboratory kept a pretty low profile. Tucked inside a nondescript building on Eureka's I Street, the small, cramped lab housed those doing the relatively unexciting work of typing influenza strains, monitoring for outbreaks of communicable diseases like chicken pox, measles and mumps. It tested shellfish for toxins and tested drinking water. Sometimes it processed rabies tests.

The lab received some brief notoriety — in public health circles, anyway — in July of 2019, when someone sent envelopes of white powder to Pelican Bay State Prison, forcing the quarantine of 116 people. A local hazmat team was sent in to retrieve the substance and it was sent to the lab on I Street for testing. There, Lab Manager Jeremy Corrigan and staff worked through the night, ultimately confirming the substance to be ricin powder, a toxic biological agent. The following day, an FBI agent arrived on a C-130 military transport aircraft to pick up the samples, according to an article on the Association of Public Health Laboratories' blog. As wild as the story is, the prospect of the lab being called into action for such a thing is a big part of what's kept it afloat in recent decades, buoyed by counterterrorism grants and funds in the wake of 9/11 as a regional resource in this remote, rural stretch of Northern California.

But few outside public health circles likely imagined a day when the small laboratory would prove a linchpin in a massive, countywide effort to curb the spread of the deadly COVID-19 pandemic. But under Corrigan's direction, the lab has ramped up its testing capacity more than 10-fold in a matter of months, providing the quick test results that enable effective contact investigations that identify and isolate positive COVID-19 cases, limiting spread of the disease.

"We have been evolving over the past six months," Corrigan says over the phone one recent afternoon, explaining the next step in that evolution will be the opening of a new laboratory through a first-of-its-kind partnership with United Indian Health Services, county of Del Norte, Humboldt State University and the state of California that is projected to more than double local testing capacity.

The new facility is slated to open just as cases are surging on the North Coast, as they are throughout the state and country. Humboldt County confirmed 328 new COVID-19 cases in November, accounting for 37 percent of its total cases to date. And local health officials expect the surge to continue, fearful that gatherings and travel over the Thanksgiving holiday will cause a further spike in case numbers over the coming weeks, making the ability to deliver fast, accurate test results all the more important.

It's not that the Humboldt County Public Health Laboratory didn't do genetic testing before COVID-19, it just didn't do much of it and was never designed to do it on a large scale. Polymerase chain reaction (PCR) testing is a complex process that amplifies small segments of DNA, the molecules that carry the genetic instructions for all living things, by copying them, making it easier for analysts to identify various attributes, including viruses like the SARS-CoV-2 coronavirus.

"[Prior to COVID-19], we'd do one or two PCRs in a day," Corrigan said. "I'd do maybe 120 PCRs throughout the entire calendar year."

The lab can now do up to 300 in a single day, the result of months of work to increase automation and capacity at each step in the testing process.

COVID-19 samples come into the laboratory in the form of swabs that have been wiped deep inside someone's nose to collect secretions. The first step of the testing process, Corrigan said, is to extract and purify the DNA from those swabs, getting rid of all the cellular debris and other contaminants.

"It's labor intensive," Corrigan said. "That was our choke point early on."

Corrigan said the lab was initially able to get an extractor to process 13 samples in an hour of runtime. He then procured another, effectively doubling the lab's output.

Once the DNA is extracted and purified, it goes through the PCR process, which Corrigan described as "finding a needle in a haystack."

"You have these millions and millions of pieces of straw — bacteria, viruses, cells — and you use primers and probes to find that single piece of hay you're looking for, then amplify it," he said.

Initially, the lab did this by loading samples into a tray with 96 separate wells that it loaded into a machine that would copy the DNA, looking for a single target — in this case, COVID-19. But the process was labor intensive and inefficient — again, the lab was never intended to conduct large-scale testing — and could only process about 20 samples a day, with a max capacity of about 75, Corrigan said, if staff worked around the clock.

There are a number of other COVID-19 tests available. For example, there's a Genexpert test that allows a technician to put a nasal swab directly into a cartridge, press go and retrieve results in about 45 minutes. But the cartridges cost $50 to $60 apiece, Corrigan said, and the test isn't as accurate as the PCR method. The test is widely used for point-of-care tests in hospitals and other settings, where speed takes priority, but Corrigan said isn't as good a fit for large-scale testing as PCR.

"We are working with one of the most sensitive tests that's out there and available, and one of the most specific tests that's out there and available, and I think that's a huge benefit," Corrigan said.

Over the months, Corrigan said his staff has worked to upgrade equipment and secure supply chains that have allowed it to steadily increase capacity. At one point, he said, the lab was maxing out at processing about 100 samples a day, with extractor capacity once again a choke point. But the lab was able to obtain a large King Fisher Flex extractor that can prepare 94 samples in 23 minutes of runtime, with about an hour of hands-on staff time. That and another PCR machine brought capacity up to about 200 samples a day, where it currently stands.

"That got us to where we needed to be," Corrigan said, adding the lab can expand to processing 300 samples a day in a surge capacity but that's not sustainable.

Corrigan said his lab has also nearly doubled its staff over the past nine months, having brought in disaster service workers, extra help staff from other departments and some new hires from Humboldt State University. The added help, he said, has helped ensure staff doesn't burn out.

"That long-term sustainability is important," Corrigan said. "It's been a long event."

While the county lab expanded capacity well beyond what was initially thought possible, it's pretty much maxed out at this point and the ability to process 200 samples a day falls well below what the pandemic response demands, especially as cases continue to surge.

For months, the state has contracted with OptumServe to operate a testing site at Redwood Acres Fairgrounds in Eureka. It's been a mixed bag. On the positive side, it initially gave the county the capacity to test hundreds of people for COVID-19 five days a week, before it was expanded to seven days on Nov. 30. But the site has also been plagued by some scheduling problems and has been dependent on corporate labs to process samples, and those labs have been overwhelmed by demand, leading to sometimes lengthy delays between a person being tested and receiving results, making contact investigations and efforts to contain the virus more difficult.

But part of that equation is slated to change under a $1.4 billion deal the state of California reached with PerkerElmer, a major medical diagnostics company. Under the contract, the company built a new state laboratory in Valencia that is coming online and promised to supply the state with all the testing reagents and supplies it needs. In a recent media availability, Humboldt County Health Officer Teresa Frankovich, whose last full day on the job was Dec. 1, said samples taken at Eureka's OptumServe site will now be sent to the new lab.

"There is an expectation that turnaround times will be better," she said.

The state has since expanded the Eureka testing site's operations to seven days a week, with the hope of adding some mobile services.

But the most promising development regarding local testing capacity is the regional partnership and new lab at United Indian Health Services announced in September that is expected to process some 400 samples a day. Under the agreement, UIHS is providing the laboratory space and a lab information system, HSU is providing some equipment and launching an internship program to help with staffing and the state is providing equipment and all the supplies needed through its contract with PerkerElmer. Once fully up and running, Corrigan said the lab should return test results in 24 to 72 hours, just like the Public Health Lab, allowing for effective contact investigations.

"There's a lot of people working really hard behind the scenes to kind of put control in our hands locally," said Corrigan, adding the partnership is also working on creating sample collection teams.

Some challenges, however, still remain.

At the recent media availability, Frankovich said the lab, initially hoped to be up and running in October, still does not have a target date to come online. She said the partners are still working on the information technology side of things to create interfaces that allow people to register for testing, track samples and receive results securely online.

"We want to make sure we can run it seamlessly," she said.

Amy Sprowles, chair of HSU's Department of Biological Sciences, said the university has provided the new facility with a biosafety cabinet that will provide clinical scientists a "safe and sterile" environment for processing patient samples and is standing by to create an internship program.

"Once the lab is fully operational, we will collaborate with the UIHS laboratory professionals and Humboldt County Public Health to design a program that allows students to efficiently acquire the skills they need," she said. "I imagine student interest will be quite high. When I've mentioned the possibility to current students, they are very excited about the opportunity to support our community."

Humboldt County Public Health Laboratory Manager Jeremy Corrigan in the lab. - COURTESY OF HUMBOLDT COUNTY PUBLIC HEALTH
  • Courtesy of Humboldt County Public Health
  • Humboldt County Public Health Laboratory Manager Jeremy Corrigan in the lab.
The push to get the new lab online and expand the OptumServe site comes as Humboldt County — and the rest of the state and country — enters a critical juncture in its COVID-19 response. Cases are soaring, with both the daily average of new cases and the percentage of COVID-19 cases that come back positive rising sharply in recent weeks. Throw in the onset of flu season, the arrival of cold, wet weather and the holidays, and it's what officials fear is a perfect storm that could send infection rates skyrocketing.

And the more the local caseload rises, the more demand there will be for testing that returns accurate and timely results, as more infections mean more contacts who will need to be tested. There's no question Humboldt County's early pandemic response benefitted greatly from the work of its local public health lab — one of just 29 left in the state. It's allowed local health officials to triage tests, making sure those most at risk of critical outcomes or spreading the virus widely are identified quickly. But without a coordinated national effort to increase testing capacity, Humboldt's approach has also been a patchwork one and questions remain as to whether it will be enough. A variety of leading national infectious disease specialists have said that to really contain virus spread on a national level, the United States would need to reach the capacity to test between 2 and 8 percent of its population daily, which would allow for robust surveillance testing — or the testing of swaths of the population who are asymptomatic to proactively identify case clusters before they spread and to protect vulnerable workforces, like healthcare workers and skilled nursing staff. In Humboldt County, that would mean testing between 2,700 and 10,800 people daily, which most concede is entirely unrealistic, at least presently.

Even an effort to conduct regular surveillance testing of healthcare workers in Humboldt County seems a daunting challenge, as there are approximately 1,500 nurses working locally, not taking into account the bevy of other technicians, assistants, specialists and doctors who work in the local medical field.

But Corrigan, Frankovich and other local health officials have said they are confident that once the UIHS site and the new state testing facility are fully online, there will be sufficient testing capacity locally. Once fully humming, Corrigan said there will be the capacity to process approximately 800 tests daily between Public Health and UIHS, with the potential for the state lab to process another 400 or so from the OptumServe site. That would be approximately 1,200 samples a day — or roughly 0.9 percent of the population — which is some 60 times the county's capacity just eight months ago.

"To be frank, I feel really good about our testing capacity," Corrigan said. "I feel like we've built that capacity up to where we need it to be."

Thadeus Greenson (he/him) is the Journal's news editor. Reach him at 442-1400, extension 321, or Follow him on Twitter @thadeusgreenson.


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