Molecular probes designed to spot minute amounts of pathogens in biological samples may aid clinical laboratories’ speed-to-answer
Driven to find a better way to isolate minute samples of pathogens from among high-volumes of other biological organisms, researchers at Canada’s McMaster University in Hamilton, Ontario, have unveiled a bioinformatics algorithm which they claim shortens time-to-answer and speeds diagnosis of deadly diseases.
Two disease pathogens the researchers specifically targeted in their study are responsible for sepsis and SARS-CoV-2, the coronavirus causing COVID-19. Clinical laboratories would welcome a technology which both shortens time-to-answer and improves diagnostic accuracy, particularly for pathogens such as sepsis and SARS-CoV-2.
Their design of molecular probes that target the genomic sequences of specific pathogens can enable diagnosticians and clinical laboratories to spot extremely small amounts of viral and bacterial pathogens in patients’ biological samples, as well as in the environment and wildlife.
“There are thousands of bacterial pathogens and being able to determine which one is present in a patient’s blood sample could lead to the correct treatment faster when time is very important,” Zachery Dickson, a lead author of the study, told Brighter World. Dickson is a bioinformatics PhD candidate in the Department of Biology at McMaster University. “The probe makes identification much faster, meaning we could potentially save people who might otherwise die,” he added.
Sepsis is a life-threatening response to infection that leads to organ failure, tissue damage, and death in hospitals worldwide. According to Sepsis Alliance, about 30% of people diagnosed with severe sepsis will die without quick and proper treatment. Thus, a “shortcut” to identifying sepsis in its early stages may well save many lives, the McMaster researchers noted.
And COVID-19 has killed millions. Such a tool that identifies sepsis and SARS-CoV-2 in minute biological samples would be a boon to hospital medical laboratories worldwide.
“We currently need faster, cheaper, and more succinct ways to detect pathogens in human and environmental samples that democratize the hunt, and this pipeline does exactly that,” Hendrik Poinar, PhD (above), McMaster Professor of Anthropology and a lead author of the study, told Brighter World. Poinar is Director of the McMaster University Ancient DNA Center. Hospital medical laboratories could help save many lives if sepsis and COVID-19 could be detected earlier. (Graphic copyright: McMaster University.)
Is Bioinformatics ‘Shortcut’ Faster than PCR Testing?
The researchers say their probes enable a shortcut to detection—even in an infection’s early stages—by “targeting, isolating, and identifying the DNA sequences specifically and simultaneously.”
The probes’ design makes possible simultaneous targeted capture of diverse metagenomics targets, Biocompare explained.
But is it faster than PCR (polymerase chain reaction) testing?
The McMaster scientists were motivated by the “challenges of low signal, high background, and uncertain targets that plague many metagenomic sequencing efforts,” they noted in their paper.
They pointed to challenges posed by PCR testing, a popular technique used for detection of sepsis pathogens as well as, more recently, for SARS-CoV-2, the coronavirus causing COVID-19.
“The (PCR) technique relies on primers that bind to nucleic acid sequences specific to an organism or group of organisms. Although capable of sensitive, rapid detection and quantification of a particular target, PCR is limited when multiple loci are targeted by primers,” the researchers wrote in Cell Reports Methods.
According to LabMedica, “A wide array of metagenomic study efforts are hampered by the same challenge: low concentrations of targets of interest combined with overwhelming amounts of background signal. Although PCR or naive DNA capture can be used when there are a small number of organisms of interest, design challenges become untenable for large numbers of targets.”
Detecting Pathogens Faster, Cheaper, and More Accurately
As part of their study, researchers tested two probe sets:
one to target bacterial pathogens linked to sepsis, and
another to detect coronaviruses including SARS-CoV-2.
They were successful in using the probes to capture a variety of pathogens linked to sepsis and SARS-CoV-2.
“We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 [Human coronavirus NL 63] in a human RNA background and seven bacterial strains in human blood. HUBDesign has broad applicability wherever there are multiple organisms of interest,” the researchers wrote in Cell Reports Methods.
The findings also have implications to the environment and wildlife, the researchers noted.
Of course, more research is needed to validate the tool’s usefulness in medical diagnostics. The McMaster University researchers intend to improve HUBDesign’s efficiency but note that probes cannot be designed for unknown targets.
Nevertheless, the advanced application of novel technologies to diagnose of sepsis, which causes 250,000 deaths in the US each year, according to the federal Centers for Disease Control and Prevention, is a positive development worth watching.
The McMaster scientists’ discoveries—confirmed by future research and clinical studies—could go a long way toward ending the dire effects of sepsis as well as COVID-19. That would be a welcome development, particularly for hospital-based laboratories.
Federal regulators continue to recognize value of clinical laboratory testing in near-patient settings
To help in the diagnosis and management of two sexually-transmitted diseases, another point-of-care diagnostic test will soon be available for use in physician’s offices, urgent care clinics, and other healthcare settings. The federal Food and Drug Administration (FDA) announced it granted a CLIA waiver for the binx health io CT/NG assay, a molecular platform used to detect sexually transmitted diseases—chlamydia and gonorrhea—at the point of care (POC).
This will be welcome news to many medical professionals, as it indicates federal regulators recognize the value of diagnostic testing in near-patient settings.
Allows Non-Laboratorian Processing at Point of Care
In 2019, binx health received FDA 510k clearance to market its binx io rapid point-of-care (POC) platform for women’s health. “The binx io platform is a rapid, qualitative, fully-automated test, designed to be easy to use, and intended for use in POC or clinical laboratory settings … In the company’s recently completed 1,523-person, multi-center clinical study, 96% of patient samples were processed on the binx io by non-laboratorians in a POC setting,” a binx press release noted.
According to the Boston-based biotech company’s website, the binx io platform (above) combines ultra-rapid, polymerase chain reaction (PCR) amplification with binx health’s proprietary and highly sensitive electrochemical detection technology. The io instrument processes a single-use, CT/NG cartridge that contains all reagents for testing self- or clinician-collected vaginal swabs and male urine samples. No sample preparation is required. Test results are available in less than 30 minutes. (Photo copyright: binx health.)
“With ever-increasing sexually transmitted infection rates, point-of-care and CLIA-waived platforms like the binx io are essential additions to our sexually-transmitted-infection-control toolbox, which will increase accessibility and decrease the burden on traditional healthcare settings,” Barbara Van Der Pol, PhD, Professor of Medicine and Public Health at University of Alabama at Birmingham, said in a binx press release.
According to binx, the Centers for Disease Control and Prevention (CDC) estimates that one in five people in the US has a sexually-transmitted disease (STD), with an estimated 108 million Americans potentially in need of routine STD testing. Additionally, chlamydia and gonorrhea are the two most treated STDs globally.
Study Finds Binx Health POC Assay Comparable to Traditional Clinical Laboratory NAATs
Van Der Pol led a team of researchers who compared the binx io chlamydia/gonorrhea POC assay to three commercially-available nucleic acid amplification tests (NAATs). The binx-funded study, published in JAMA Network Open, analyzed swab samples from 1,523 women (53.6% with symptoms) and urine samples from 922 men (33.4% symptomatic) who presented to 11 clinics in nine cities across the US.
The molecular point-of-care assay proved on par with laboratory-based molecular diagnostics for vaginal swab samples, while male urine samples were associated with “good performance.”
For chlamydia:
Sensitivity of the new POC assay was 96.1% (95% CI, 91.2%-98.3%) for women and 92.5% (95% CI, 86.4%-96.0%) for men.
Specificity of the new POC assay was 99.1% (95% CI, 98.4%-99.5%) for women and 99.3% (95% CI, 98.4%-99.7%) for men.
For gonorrhea:
Sensitivity estimates were 100.0% (95% CI, 92.1%-100.0%) for women and 97.3% (95% CI, 90.7%-99.3%) for men.
Specificity estimates were 99.9% (95% CI, 99.5%-100%) for women and 100% (95% CI, 95.5%-100%) for men.
Van Der Pol told Reuters News, “The bottom line is that chlamydia and gonorrhea are still the most frequently reported notifiable diseases in the US, and it costs us in the $5 billion to $6 billion range to manage the consequences of untreated infections. Unfortunately, about 70% of women who are infected don’t have any symptoms, so they don’t know they need to be tested.”
“The ability to diagnose at a point-of-care setting will help with more quickly and appropriately treating sexually-transmitted infections, which is a major milestone in helping patients,” said Tim Stenzel, MD, PhD (above), Director of the Office of In Vitro Diagnostics and Radiological Health at the FDA’s Center for Devices and Radiological Health, in the FDA announcement. “More convenient testing with quicker results can help patients get access to the most appropriate treatment. According to the CDC, one in five Americans are diagnosed with sexually-transmitted infections every year, which is why access to faster diagnostic results and faster, more appropriate treatments will make significant strides in combatting these infections,” he added. As point-of-care testing for specific diseases increases, clinical laboratories that process these tests may see a decrease in specimen processing orders. (Photo copyright: Duke University.)
The CLIA waiver allows binx to distribute the chlamydia/gonorrhea test to 220,000 CLIA-waived locations across the US through the company’s national commercial distribution partnership with McKesson. Obstetrician/gynecologist and primary care offices, urgent care facilities, community health clinics, STD clinics, and retail settings are all potential testing sites.
Binx says its testing platform can improve health outcomes by:
Increasing treatment compliance,
Limiting onward transmission,
Minimizing the risk of untreated conditions, and
Ensuring the right treatment is provided.
In the binx health press release, binx CEO Jeffrey Luber, JD, said, “The io instrument’s demonstrated clinical effectiveness, ease of operation, and patient convenience make it a much-needed tool with transformative implications for public health, especially now during the COVID-19 pandemic, where STI [sexually-transmitted infection] prevention services nationwide have been dramatically reduced or cut altogether as resources have been allocated to focus on the COVID response.”
Should Clinical Laboratories Be Concerned about POCT?
It happens often: after consulting with his or her doctor, a patient visits a clinical laboratory and leaves a specimen. The test results arrive at the doctor’s office in a few days, but the patient never returns for treatment. That is why point-of-care tests (POCTs) came to be developed in the first place. With the patient in the clinic, a positive test result means treatment can begin immediately.
As the US healthcare system continues toward more integration of care and reimbursement based on value, rather than fee-for-service, point-of-care testing enables physicians and other healthcare providers to diagnose, test, and prescribe treatment all in one visit.
Thus, it is a positive step for healthcare providers. However, clinical laboratories may view the FDA’s increasing endorsement of waived point-of-care testing as a trend that is unfavorable because it diverts specimens away from central laboratories.
There also are critics within the medical laboratory profession who point out that waived tests—often performed by individuals with little or no training in laboratory medicine—have much greater potential for an inaccurate or unreliable result, when compared to the same assay run in a complex, CLIA-certified clinical laboratory.
Dozens of Chicago-area schools were reopened with the help of an $11 COVID-19 saliva test, but the qualifications of the clinical laboratory, and whether it complied with federal regulations, were called into question
It was only a matter of time when newly-formed clinical laboratories—taking advantage of the federal government’s loosening of regulations to promote COVID-19 testing—drew the attention of state regulators and the national news media. This is what happened at New Trier High School in Winnetka, Ill.
In March, the New York Times published an article, titled, “Why Virus Tests at One Elite School Ran Afoul of Regulators.” The article highlighted the coronavirus screening program implemented at New Trier High School and suggested that “New Trier may have inadvertently violated federal regulations on testing,” adding that “the Illinois Department of Public Health (IDPH) opened an investigation into the lab.”
SafeGuard Surveillance of Brookfield, Ill., was contracted to perform the routine saliva-based testing. SafeGuard analyzed saliva samples from students, teachers, and school staff to detect the presence of the SARS-CoV-2 coronavirus. New Trier was just one of several school districts that contracted with SafeGuard for the testing, which costs $11 per test. The samples were typically processed the same day.
“This has been a really valuable safety mitigation for our district to make our staff, students, and community feel safer,” Chris McClain, Assistant Superintendent for Finance and Operations at Glenbard High School District 87, told the Chicago Tribune. “We’ve been very pleased with the program.” Glenbard also contracted with SafeGuard for the COVID-19 surveillance screening.
COVID-19 Surveillance or Screening?
Though the surveillance screening testing was working as intended for multiple Chicago areas school systems, the New York Times article called into question whether SafeGuard—which at the time lacked CLIA (Clinical Laboratory Improvement Amendments) certification—was qualified to conduct COVID-19 screening testing.
The article also alleged that SafeGuard was led by a scientist who was not qualified under the federal guidelines to run a diagnostic laboratory, and that the saliva test being used was not authorized for COVID-19 testing by the federal Food and Drug Administration (FDA).
It came down to whether SafeGuard was conducting “surveillance” testing, which does not require CLIA-certification, or “screening” which does.
SafeGuard was founded by Edward Campbell, PhD, Assistant Professor in the Department of Microbiology and Immunology at Loyola University in Chicago. Campbell, a virologist with decades of experience developing tests for HIV, “adapted a saliva-based coronavirus test last summer and first established a [COVID-19] lab for the suburban school district where he serves on the board,” Patch News reported.
Microbiologist Edward M. Campbell, PhD (above), founded SafeGuard Surveillance toward the end of 2020 after demand for COVID-19 screening he had been conducting for various local school systems increased dramatically. In January, the startup clinical laboratory was running about 25,000 tests per week, the Riverside/Brookfield Landmark reported. (Photo copyright: Loyola University.)
SafeGuard Claims It Complied with Federal Regulations
SafeGuard’s COVID-19 screening tool utilizes RT-LAMP (reverse transcription loop-mediated isothermal amplification) to look for the SARS-CoV-2 coronavirus in saliva samples. This test is less sensitive than the more commonly used polymerase chain reaction (PCR) test that uses a nasal swab to detect the virus. However, the RT-LAMP test is considered reliable, particularly in individuals with a high viral load. The RT-LAMP test also is less expensive than the PCR test, which makes it appealing for public school systems.
To use the RT-LAMP test, faculty, staff, and students spit into test tubes at home and then take the sample to their school or other drop-off location. Campbell’s lab then processes the samples.
After the New York Times article came out, both New Trier and SafeGuard denied they had done anything wrong, and that their screening program complied with government regulations for COVID-19 testing. Campbell maintained that he did not need the CLIA certification to operate his lab for testing and that SafeGuard complied with all federal regulations. Nevertheless, in March, SafeGuard applied for and received CLIA-certification to “conduct ‘screening’ testing, instead of just ‘surveillance’ testing,” Patch News reported.
“We’re doing everything we can to operate in good faith under the guidance that clearly exists,” Campbell told The Chicago Tribune.
In a statement, New Trier district officials said, “New Trier has also met with local and state health authorities to review our use of the program and they have not directed us to change our use of it. From the time the program began, New Trier has been clear that the saliva program is non-diagnostic and must be confirmed by a lab test. To suggest otherwise is false,” Patch News reported.
Surveillance Testing versus Screening
In August, the federal Centers for Medicare and Medicaid Services (CMS), which oversees CLIA labs, released guidelines that stated COVID-19 testing could be performed in clinical laboratories that were not CLIA-certified so long as patient-specific results are not reported.
This “surveillance testing” is intended to identify the disease within a population group and not diagnose individuals. If a person tests positive for COVID-19 via SafeGuard’s saliva test, the individual is directed to get an FDA-approved test to confirm the diagnosis.
“We do definitely see the value of surveillance testing and how that can be used to help schools make informed decisions about remote, in-person, or hybrid learning,” Melaney Arnold, State Public Information Officer for the Illinois Department of Public Health (IDPH) told the Chicago Tribune. She added that the IDPH wants to provide schools with the tools they need to navigate the pandemic.
Following the New York Times article about New Trier High School and SafeGuard’s COVID-19 screening program, the Illinois Department of Public Health opened an investigation into the company. However, the investigation has ended, and the state agency is not taking any further action against SafeGuard, Patch News reported.
It’s worth noting that it was the FDA’s relaxing of federal regulations that encouraged the development of startup clinical laboratories like SafeGuard in the first place. There is, apparently, a fine line between surveillance and screening, and clinical laboratories engaged in one or the other should confirm they have the required certifications.
Because air travel volumes are low, experts believe it is timely to develop COVID-19 testing systems and gain insight on which protocols are most effective
As the COVID-19 pandemic surges on, several international airlines now require customers to complete at-home COVID-19 testing before they can travel. This is triggering unusual business practices. For example, one airline allows its passengers to use frequent flier miles to purchase mail-in COVID-19 test kits.
Frequent Flyer Miles for COVID-19 Testing
Across the United States, Hawaii has one of the lowest rates of infection, partly thanks to the state’s strict quarantine regulations. In a state, however, that depends on tourism for its economic health, the pandemic has caused serious financial difficulties. In an effort to prevent spread of the coronavirus while also encouraging tourism, Hawaiian Airlines now offers “Pre-travel COVID-19 Test Options” on its website.
To be allowed to skip the state’s mandatory 14-day self-quarantine before arriving on the islands, flyers can take a pre-travel coronavirus test with the following conditions:
The test must be from a state-approved testing provider.
The test must be administered no more than 72 hours prior to the scheduled departure time of the final leg to Hawaii.
For trans-pacific travel, test results must be received prior to flight departure.
Additionally, the airline accepts frequent flyer miles to pay for mail-in COVID-19 tests. In exchange for 14,000 HawaiianMiles, a passenger receives a test kit in the mail. The kit features a video call during which a healthcare professional guides the consumer on taking a saliva sample. The user then ships the sample to a qualified clinical laboratory. Results are returned electronically within 24 hours of the lab receiving the sample.
Hawaii’s COVID-19 portal states, “The state of Hawaii will ONLY accept Nucleic Acid Amplification Test (NAAT) from a certified Clinical Laboratory Improvement Amendment (CLIA) lab test results from Trusted Testing and Travel Partners” that are participating in the state’s pre-travel testing program. Honolulu and Maui are the only two arrival airports allowed. A negative result must have come from a test performed within 72 hours prior to the final leg of the passenger’s trip to Hawaii, according to the portal.
“A negative pre-travel test is an alternative to two weeks in self-isolation for arrivals to the archipelago,” the UK’s Independent reported.
JetBlue and Vault Health Partner to Offer COVID Testing to Airline Passengers
In another instance of an airline getting involved in at-home testing, JetBlue (NASDAQ:JBLU) is partnering with Vault Health to offer at-home testing. The process is similar to the Hawaiian Airlines program. However, rather than purchasing the test with frequent flyer miles, JetBlue offers polymerase chain reaction (PCR) tests at a discount.
Business Travel News reported that passengers must provide a confirmation code while ordering the $119 test from Vault Health’s webpage. “Vault provides a kit for an at-home saliva test, and users administrate it while on a video chat supervised by Vault to ensure the test is done properly. The user sends it overnight to a clinical laboratory and the results are provided within 72 hours,” Business Travel News stated.
“We continue to hear from health officials that [COVID-19] testing is incredibly important in the fight against the coronavirus, and we want to make sure our customers have options for testing, especially prior to travel,” said Joanna Geraghty, President and Chief Operating Officer, JetBlue, in a press release. “As more and more regions reopen, many are requiring test results to enter. Now with easier testing options, those safety requirements may not be a deterrent for travel, but rather provide greater public health and peace of mind with little inconvenience.” (Photo copyright: Spectrum News NY1.)
In addition to airlines such as Hawaii Airlines and JetBlue instituting programs for coronavirus testing, some airports are as well. Tampa International Airport, for example, test-piloted a voluntary testing program for all arriving and departing passengers from October 1st to October 31st. The airport partnered with BayCare, a 15-hospital Tampa area healthcare network, to provide both rapid antigen and PCR tests.
“Testing services will be offered on a walk-in basis … seven days a week from 8 a.m. until 2 p.m. The pilot will be open to all ticketed passengers who are flying or have flown within three days and can show proof of travel. The PCR COVID-19 test costs $125 and the antigen test costs $57,” a press release stated.
Tampa Airport CEO Joe Lopano told the Washington Post, “This could be—especially if adopted by other airports—another way to instill confidence.”
COVID-19 Testing by Retailers Expanding as Well
Travelers aren’t the only people who need testing. Some employers also are requiring negative tests before employees can return to work.
As with all at-home kits, the consumer collects their own specimen and sends it off to a qualified clinical laboratory for processing. AZOVA, a telehealth company, supplies the kits to Costco for resale and provides a smartphone app where customers can check and display the test results.
P23 Labs’ TaqPath SARS-CoV-2 assay is the test being used, which, according to P23, “has a 98% sensitivity and 99% specificity,” Business Insider reported.
The researchers found that “All seven SARS-CoV-2 genomes were genetically identical, with the exception of a single mutation in one case, and all genomes had five signature mutations seen in only six other genomes from the >155,000 genomes sequenced globally. Four of these six related genome sequences were from Switzerland, the country of origin of the suspected index case.”
They added, “By combining information on disease progression, travel dynamics, and genomic analysis, we conclude that at least four in-flight transmission events of SARS-CoV-2 likely took place.”
At-home test kits for COVID-19 are here to stay. That large businesses in multiple industries are now partnering with COVID-19 test developers and clinical laboratory companies to accomplish testing of customers and employees means independent labs that process coronavirus testing can look forward to increasing COVID-19 testing business.
“We need to be using the time now, when [travel] volumes are relatively low, to test the systems and gain insight on which protocols are most effective,” Mara Aspinall, biomedical diagnostics professor at Arizona State University, President and CEO of the Health Catalysts Group, an investment and advisory firm, and former President/CEO of Ventana Medical Systems (now Roche Tissue Diagnostics), a billion-dollar division of Swiss pharmaceutical and diagnostics manufacturer Roche, told the Washington Post.
Even more impressive is that the automated testing lab can reportedly process (with results in four hours) up to 3,000 patient samples daily for SARS-CoV-2, the coronavirus that causes the COVID-19 illness.
“All of our laboratories do PCR every day. But for this test we need to go above and beyond to ensure accurate detection,” said Jennifer Doudna, PhD, IGI Executive Director and UC Berkeley Professor of Molecular and Cell Biology, in an IGA news release.
“We put in place a robotic pipeline for doing thousands of tests per day,” she continued, “with a pipeline for managing the data and getting it back to clinicians. Imagine setting that up in a couple of weeks. It’s really extraordinary and something I’ve never seen in my career.”
Robert Sanders, UC Berkeley’s Manager Science Communications, told Dark Daily the COVID-19 lab performs about 180 tests per day and has tested 1,000 people so far—80% of the samples came from the campus community. About 1.5% to 4% of the tests were found to be positive for the SARS-CoV-2 coronavirus among the groups tested.
“We hope other academic institutions will set up testing labs too,” he said.
How Did Berkeley Set Up a COVID-19 Diagnostic Lab So Fast?
To get up and running quickly, university officials drew from the campus and surrounding business community to equip and operate the laboratory, as well as, train researchers to do clinical analysis of patient samples.
Though the methodology to test for the coronavirus—isolating RNA from a biological sample and amplifying it with PCR—is standard fare in most research labs worldwide, including at UC Berkeley, the campus’ research labs were shuttered due to the spread of the coronavirus.
IGI reached out to the idle labs for their high-throughput PCR systems to start-up the lab. Through its partnership with University Health Services and local and national companies, IGI created an automated sample intake and processing workflow.
Additionally, several research scientists who were under government-mandated stay-at-home orders made themselves available. “My own research is shut down—and there’s not very much I can do other than stay in my home … finally I’m useful,” said PhD candidate Holly Gildea in a Berkeleyside article which noted that about 30 people—mostly doctoral students and postdoctoral researchers—are being trained to oversee the process and monitor the automated equipment.
Postdoctoral fellows Jenny Hamilton (left) and Enrique Shao (right) with an automated liquid-handling robot (Hamilton Microlab STAR), which will be used to analyze swabs from patients to diagnose COVID-19. Hamilton and Shao volunteered to train to become CLIA certified so as to process patient samples. When analyzing real samples from patients, they would be wearing full personal protective equipment (PPE), including mask, face shield, gown and gloves. (Photo and caption copyright: Max and Jules Photography/UC Berkeley.)
Federal and State Authorities Remove Hurdles
In her article, “Blueprint for a Pop-up SARS-CoV-2 Testing Lab,” published on the medRxiv servers, Doudna summarized “three regulatory developments [that] allowed the IGI to rapidly transition its research laboratory space into a clinical testing facility.
“The second was California Governor Newsom’s Executive Order N-25-20, which modified the requirements for clinical laboratory personnel running diagnostic tests for SARS-CoV-2 in a certified laboratory.
“The third was increased flexibility and expediency at the state and federal levels for certification and licensure requirements for clinical laboratory facilities under the Clinical Laboratory Improvement Amendments (CLIA) program. Under these emergency conditions, the California Department of Public Health (CDPH) was willing to temporarily extend—once the appropriate regulatory requirements have been fulfilled—an existing CLIA certificate for high-complexity testing to a non-contiguous building on our university campus.”
“These developments,” wrote Doudna, “enabled us to develop and validate a laboratory-developed test (LDT) for SARS-CoV-2, extend the UC Berkeley Student Health Center’s clinical laboratory license to our laboratory space, and begin testing patient samples.”
Lessons Learned Implementing a Pop-Up COVID-19 Testing Laboratory
“Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to others in setting up similar testing centers,” she wrote.
Learned strategies Doudna says could aid other academic research labs transform to a “SARS-CoV-2 Diagnostic Testing Laboratory include:
Leveraging licenses from existing CLIA-certified labs;
Following FDA authorized testing procedures;
Using online HIPAA training;
Managing supply chain “bottlenecks” by using donated equipment;
Adopting in-house sample barcoding;
Adapting materials, such as sampling tubes, to work with donated equipment;
Cost of equipment and supplies (not including staff) was $550,000, with a per test cost of $24, Doudna noted.
“As the COVID-19 pandemic continues, our intention is to provide both PCR-based diagnostic testing and to advance research on asymptomatic transmission, analyze virus sequence evolution, and provide benchmarking for new diagnostic technologies,” she added.
Medical laboratory leaders understand that the divide between clinical and research laboratories is not easy to surmount. Nevertheless, UC Berkley’s IGI pulled it off. The lab marshaled resources as it took on the novel coronavirus, quickly developed and validated a test workflow, and assembled and trained staff to analyze tests with fast TAT to providers, students, and area residents. There’s much that can be learned from UC Berkeley IGI’s accomplishments.
