An assay using mass spectrometry could go to clinical trial within two years
Dark Daily has regularly observed that humans generate a variety of volatile substances—particularly in breath—which can be used for diagnostic purposes. But what if people, like certain trained animals, could smell the presence of disease before the onset of symptoms? What types of clinical laboratory testing biomarkers could be developed based on human-generated volatile organic compounds?
Researchers at the University of Manchester (UM) in the United Kingdom (UK) say their “breakthrough” test to diagnose Parkinson’s disease “can diagnose disease from skin swabs in three minutes,” according to a university press release.
Perdita Barran, PhD (right), head of the University of Manchester research team that developed the mass spectrometry Parkinson’s test, is shown above with Joy Milne (left), the retired nurse from Scotland who inspired Barran’s team to develop a new Parkinson’s biomarker and method for identifying it. “We are tremendously excited by these results which take us closer to making a diagnostic test for Parkinson’s Disease that could be used in clinic,” she said in a press release. A viable clinical laboratory test for Parkinson’s disease is greatly needed, as more than 10 million people worldwide currently live with the neurodegenerative disorder. (Photo copyright: University of Manchester.)
Using Mass Spectrometry to Analyze Sebum
The UM scientists hypothesized that the smell could be due to sebum, a light oily substance on skin that was going through a chemical change due to the Parkinson’s disease, Hull Daily Mail explained.
Increased sebum, which is produced by the sebaceous glands, is a hallmark of Parkinson’s, the researchers noted.
Their new method involves analysis of sebum using mass spectrometry, according to the JACS AU paper. The method, the researchers claim, makes it possible to diagnose Parkinson’s disease from skin swabs in three minutes.
“There are no cures for Parkinson’s, but a confirmatory diagnosis would allow [Parkinson’s patients] to get the right treatment and get the drugs that will help to alleviate their symptoms,” Perdita Barran, PhD, told the Hull Daily Mail. Barran is Chair of Mass Spectrometry in the Department of Chemistry and Director of the Michael Barber Centre for Collaborative Mass Spectrometry at UM’s Manchester Institute of Biotechnology. “What we are now doing is seeing if (hospital laboratories) can do what we’ve done in a research lab in a hospital lab,” she added.
Sebum Analyzed with Mass Spectrometry
Parkinson’s disease—the world’s fastest growing neurodegenerative disorder—needs “robust biomarkers” that could advance detection and head off onset of motor symptoms such as tremor, rigidity, and postural instability, the researchers note in their paper.
Their recent study builds on earlier 2019 findings they published in ACS Central Science about volatile compounds in sebum possibly being used as Parkinson’s biomarkers.
“Sebum is an underexplored biofluid, which is readily obtained from non-invasive skin swabs, which primarily consists of a mixture of triglycerides, cholesterol, free fatty acids, waxy esters, and squalene,” the researchers explained in their JACS AU paper.
The scientists sought, “to develop a method to analyze sebum in its native state to facilitate rapid assessment of the Parkinson’s disease status. Paper spray ionization mass spectrometry, which allows the direct analysis of compounds from paper, has previously been demonstrated to detect small molecules from unprocessed biofluids, such as blood and urine, but not to date with sebum,” they wrote.
The UM researchers used mass spectrometry to analyze sebum collected on cotton swabs from the backs of 79 people with Parkinson’s and 71 healthy individuals, BBC Scotland News reported.
Depanjan Sarkar, PhD, Research Associate, University of Manchester, further explained the technique in the UM news release:
Sebum is taken from the swab to filter paper cut in a triangle.
Using a solvent and voltage, sebum compounds transfer into the mass spectrometer.
“When we did this, we found more than 4,000 unique compounds of which 500 are different between people with Parkinson’s compared to the control participants,” Sarkar said.
Fatty Acids Make Assay Possible
Could fatty acids pave the way to an assay? The UM researchers believe so.
“We have identified two classes of lipids, namely [triglycerides] and diglycerides, as components of human sebum that are significantly differentially expressed in PD,” the researchers wrote in JACS AU. “Non-invasive sampling followed by PS-IM-MS [paper spray-ion mobility–mass spectrometry] analysis targeting these compounds could provide an inexpensive assay to support clinical phenotyping for the confirmatory diagnosis of Parkinson’s disease.”
A clinical trial for their test, which costs about $20, may be done within two years in Manchester area, the Daily Mail reported.
When Dark Daily reported in 2020 on Joy Milne’s unique ability to smell her husband’s Parkinson’s disease before it was formally diagnosed, we predicted a diagnostic test for Parkinson’s may be years away. And here it is, albeit with regulatory clearance needed following clinical trials.
It may in fact be possible to leverage sebum analysis to detect other diseases, the UM researchers noted.
For diagnostics developers, this story of Joy Milne and her husband Les Milne is a useful example of how, in tracking the life of a specific patient with a specific disease and close family members, researchers were able to identify a new class of biomarkers that could be used in a diagnostic assay.
It will be interesting to follow the University of Manchester researchers in their quest for a diagnostic mass spectrometry clinical laboratory test for Parkinson’s disease. According to Parkinson’s Foundation statistics, about 10 million people worldwide live with the neurodegenerative disorder. Such a new diagnostic test could be vitally important to medical laboratory care, and to patients and their families.
South Asian nation aims to do what US, UK, and Europe failed to do during start of COVID-19 pandemic and slow spread of disease while case counts are low
With monkeypox quickly spreading around the world, India may be taking a lesson from western nations’ delayed response to COVID-19—including a sometimes slow availability of clinical lab testing for monkeypox—and preemptively increasing its national surveillance of the deadly social disease.
On Aug. 29, the Hindustan Times reported that in an attempt to slow the spread of monkeypox, India’s central government “has designated 15 viral research and diagnostic laboratories (VRDLs) spread across 13 states to monitor the incidence of monkeypox in the country.”
In the United States, the disease has spread with alarming speed, reaching all 50 states, as well as Washington, DC, and Puerto Rico. At 23,893 confirmed cases as of Sept. 14, the US now has the most cases in the world, according to the federal Centers for Disease Control and Prevention (CDC).
Reuters reported on Aug. 4 that the US Department of Health and Human Services (HHS) had declared a public health emergency. It was in May when monkeypox was detected in the United Kingdom (UK). Both the UK and several countries in Europe have struggled to control spread of the disease.
India hopes its decision to designate 15 VRDLs across 13 states to monitor the disease’s spread will enable it to do a better job than other countries at containing or eradicating monkeypox in the nation of 1.4 billion people, the Hindustan Times reported.
“The probability of containment is diminishing daily,” American infectious disease epidemiologist Anne Rimoin, PhD, a monkeypox expert at the UCLA Fielding School of Public Health, told STAT. “It’s really unfortunate because we do have the tools. This is not an unknown virus … We have vaccines that are already available, even vaccines with indications for monkeypox. Therapeutics. And we know what’s needed to be done.’’ Clinical laboratory testing for monkeypox will certainly increase over the coming months. (Photo copyright: KTLA.)
Keeping Up Their Guard
“Fortunately, India has not seen a surge in cases and the situation here is well under control. However, we cannot drop the guard just as yet. Therefore, a network of VRDLs has been established for surveillance purposes,” a top government expert told the Hindustan Times, seeking anonymity. “It will help pick signs early in case more cases get reported.”
As of Sept. 19, 2022, India reported just 12 cases of monkeypox resulting in one death, while, as noted above, the US had 23,892 confirmed cases and one death, according to CDC statistics. In the UK, confirmed cases totaled 3,552 with no deaths. And, as of that date, the European Union reported 19,379 confirmed cases.
Until recently, monkeypox was endemic only in West and Central Africa. India reported its first case of monkeypox on July 14. So far, most, but not all, of its cases have been related to international travel.
“The isolated cases of monkeypox reported in Delhi with no prior travel history emphasize the importance of tracing the source of the infection, perhaps transmission through rodent population,” Diwakar Kulkarni, PhD, former Director and Principal Scientist at the Indian Council of Agricultural Research, National Institute of High Security Animal Diseases, told Think Global Health.
Homosexuality a Vector in India
While India’s scientists are focused on containing the monkeypox outbreak, the country’s government may encounter societal roadblocks because of the disease’s connection with homosexuality. Gay sex is believed to be fueling the spread of the disease, ABC News reported. Until a Supreme Court of India ruling in 2018, gay sex was punishable by up to 10 years in prison in India.
Virologist and noted HIV expert Ishwar Gilada, MD, who opened India’s first AIDS clinic in 1986, told Bloomberg “anti-gay stigma” in India is causing male patients to avoid getting tested and treated for the disease. He said even before the first monkeypox cases were reported in India, two of his patients—a gay man and a man who identified as bisexual—refused to get tested because they feared being the first monkeypox case in the country.
“They are going underground,” Gilada told Bloomberg.
Did the US Wait Too Long to Begin Testing for Monkeypox?
The rapid growth in cases worldwide and the geographic spread of the disease has left global health experts pessimistic monkeypox can be contained.
NPR reported in June that some experts believe public health agencies ran too few tests in the early months of the outbreak because state health officials used a narrow definition of monkeypox when determining who qualified for testing, and that the US had “dropped the ball” on monkeypox testing.
As of Sept. 19, 2022, there were 62,406 confirmed cases worldwide, according to the CDC.
As clinical laboratories attempt to recover from the workload created by the COVID-19 pandemic, monkeypox appears to be the next endemic to test the mettle of lab professionals. Only time will tell if America and other western nations failed to act as expeditiously as India in curbing spread of this latest deadly disease.
Clinical labs should proactively investigate how a vendor will respond to a data security incident and how quickly, says expert
Clinical laboratory managers in New York and surrounding areas should be aware that almost one million protected health information (PHI) records from as many as 28 healthcare providers appear to have been stolen from a medical records company that services these providers.
Practice Resources LLC (PRL), a company that provides billing services for dozens of hospitals and medical providers in Central New York, announced in August they were the target of a ransomware attack that occurred on April 12 of this year. The Syracuse-based organization stated that hackers may have captured personally identifiable information (PII) such as names, home addresses, treatment dates, health plan numbers, and internal account numbers of 934,138 patients.
The data breach affected the patient records of dozens of medical providers and the clinical laboratories that service them, as well as physical therapists, pediatricians, gynecologists, orthopedic surgeons, and more.
“When a lab’s vendor has some type of breach, the lab entity that provided the compromised information could have some liability related to the breach,” explained Jim Giszczak, JD (above), McDonald Hopkins, in an interview with The Dark Report over a similar data breach in 2019. “That’s why every lab should be proactive and do a review to understand each vendor’s policies, procedures, training, and response in the event of a breach. Because your lab needs to know how a vendor will respond to a data security incident, and importantly, how quickly it will respond, it’s critical for lab officials to review the contracts they have with vendors that acquire, or have access to, PHI.” (Photo copyright: McDonald Hopkins.)
Not a Scam
“Unfortunately, it’s not a scam,” stated David Barletta, President and CEO of PRL, in an interview with local Syracuse news WSYR. “This really did happen in April—there was a ransomware attack on our system. We brought in forensic accountants and forensic information teams to come and look at what happened.”
PRL sent out more than 940,000 letters to potential victims of the cyberattack in August, noting that some patients may receive more than one letter.
The complete list of “healthcare entities on whose behalf Practice Resources LLC is providing notice of data incident,” according to PRL, includes:
Although their investigation did not uncover any evidence that personal data was misused, PRL has arranged credit monitoring services free of charge for one year from the date of enrollment. The company is also offering proactive fraud assistance to help people with any questions or in case they become a victim of fraud.
“There were no patient social security numbers that were taken. No medical record information was taken,” Barletta told WSYR. “We really, just out of an abundance of caution, felt that it was necessary that we provide them with credit monitoring for a year—just in case.”
Hundreds of Thousands of Patients Affected by Breach
When PRL discovered the data breach, the company took immediate steps to secure its systems and scrutinize the nature and extent of the incident. They then hired a forensic team to investigate what patient data may have been accessed by the hackers, a process that took several months.
“It does take a long time because each client has hundreds of thousands of patients maybe,” Barletta explained. “We have several large clients that really bore the brunt of this.”
According to Barletta, PRL bills about $450 million annually for its clients, which include some major institutions in Central New York. The New York state Attorney General’s office is investigating the hacking incident and delving into whether PRL’s data security was adequate.
As a result of the breach, FamilyCare Medical Group, which serves more than 80 physicians and thousands of patients, lost all of its laboratory data, according to the group’s CEO, Mitchell Brodey, MD. They had to close their lab for several months while their computer system was rebuilt. During this time, all their lab work was sent to another laboratory for analysis, MSN reported.
The PRL ransomware attack was what is commonly known as a third-party data breach. This type of breach occurs when sensitive data is stolen from a third-party vendor, or when their systems are used to access and steal sensitive information stored on other systems.
In the United States, the Federal Trade Commission (FTC) is responsible for enforcing federal privacy and data protection regulations. If a breach affects 500 or more individuals, the company must issue a press release and notify the FTC and all affected consumers within 60 days of the discovery of the breach.
Clinical Labs Should Proactively Review Member Agreements
In 2019, our sister publication The Dark Report covered a major data breach affecting more than 20 million patients. That breach occurred when hackers gained access to the data systems of a third-party bill collector and impacted four of the nation’s largest clinical laboratories:
At that time, The Dark Report asked James Giszczak, JD, Chair of the Litigation Department and Co-Chair of the Data Privacy and Cybersecurity Practice Group at McDonald Hopkins, to provide insight on what steps clinical laboratory leaders should take to avoid and handle data breaches.
“One important lesson from this data breach is how critical it is for clinical labs and pathology groups to be proactive in making sure they review their vendor agreements,” Giszczak stated. “In that review, labs need to know the specific measures each vendor is taking to protect the information the lab is providing to their vendors.”
Giszczak suggested that clinical laboratory leaders make sure they understand each vendor’s policies, procedures, training, and response in the event of a data breach. He reiterated that labs could have some liability related to the breach.
Will health monitoring with finger rings become more popular than wrist worn devices? One company hopes the answer is yes!
Personal health monitoring devices continue to grow smaller. Now there is a company selling a smart ring that fits on an individual’s finger. Clinical laboratory managers and pathologists may find this an interesting development, particularly because it shows progress in miniaturizing diagnostic capabilities and putting them into ever-smaller devices.
At the same time, health monitoring devices are becoming increasingly popular with consumers who want to track their overall health and certain medical conditions. However, devices currently on the market generally attach at the wrist like the Apple Watch and Fitbit.
Introduced by Movano, Inc. of Pleasanton, Calif., at the 2022 CES (Consumer Electronic Show) in Las Vegas, the Movano Ring tracks “sleep, heart rate variability, body temperature, and more,” according to the company’s website. Whether clinical laboratories will be involved with this data remains to be seen.
Primarily targeted at women, the Movano Ring offers “superior health-tracking technology and the convenient form,” according to Digital Trends.
The new smart ring device is expected to be released in beta form later this year. It is similar to the Oura Ring, which was launched in 2017 by OURA, located in Oulu, Finland (US office in San Francisco).
The Movano Ring (above) will come in four styles and be available later this year. The monitoring device “measures a user’s heart rate, temperature, SpO2, calories consumed, and steps taken, among other parameters generally tracked by smart wear. However, Movano’s app is the killer feature, as it can give actionable insights to users into their health so that they can make short-term, as well as long-term, changes,” Digital Trends reported. Clinical laboratories may one day be processing data streamed from these devices if the FDA grants class II medical device designation. (Photo copyright: Movano.)
Movano Seeks FDA Clearance
In an interview with MedTech Intelligence, Movano’s CEO John Mastrototaro, PhD, said the company saw a gap in the wearables market. “There was a real lack of solutions designed specifically for women and some of the unique health challenges women face as they age.”
Cuffless blood pressure testing and blood glucose monitoring are “holy grails for wearable tech,” and Movano plans to add them over time and testing of its radio frequency, The Verge reported.
“We’re taking the regulatory side of things very seriously,” Mastrototaro told The Verge.
In a news release, Movano announced completion of a study it conducted with University of California San Francisco “to assess the accuracy of the Movano Ring’s blood oxygen saturation (SpO2) and heart rate data.
“With results that exceeded the requirements of the industry standard used by FDA for evaluating SpO2 devices, this successful study is a promising step toward the company’s goal to provide medically-validated data to consumers and healthcare professionals,” the news release stated.
Seven participants wearing Movano Ring prototypes participated in the study to test the device’s accuracy during mild, moderate, and severe hypoxia, as well as heart rate changes while they were deprived of oxygen.
Comparing data to other reference devices, the researchers found the Movano Ring resulted in a 2% margin of error, which was well below the FDA’s 4% margin of error requirement for blood oxygen saturation, the news release stated.
Ring Works with Sensors, App
Sensors embedded in the Movano Ring collect data which is available to wearers through a smartphone application.
“Data from sensors that are embedded within the ring revolve around heart rate, heart rate variability, sleep respiration rate, temperature, blood oxygen, steps, calories, and other women-centric features. We want to have the app experience where all that sensor data is going to the app,” Mastrototaro explained in an interview with Medical Device and Diagnostic Industry.
“One of our goals is to translate those measures into what it means about your overall health. We don’t want to bombard people with data … we want to distill it all down to insights for people that help them understand how activities of daily living and their lifestyle affect their overall health,” he said.
Another Smart Ring
Meanwhile, wearable health device developer OURA recently released a third-generation ring model of its Oura Ring, which Engadget called a “technical marvel.”
“Taking the sensors from a smartwatch or fitness tracker and shrinking them into a ring is worthy of enormous praise … There’s much more tech crammed in this time around … including continuous heart rate tracking, temperature monitoring, blood oxygenation, and (menstrual) period prediction,” Engadget said.
OURA developed a new SpO2 feature to help ring wearers uncover problems in breathing while sleeping. In a blog post, scientists explained: “Typically, SpO2 is measured by placing a pulse oximeter on the tip of the finger … the Oura Ring measures light reflected back from the tissue. Fingertips provide good optical characteristics for this noninvasive measurement as blood vessels have thinner walls and are more diffused.”
The Oura Ring Generation 3 costs $299 and comes in silver, black, stealth, and gold finishes. There is a $5.99 monthly membership fee, and the app is compatible with Android and Apple iOS operating systems.
Wearable Health Monitoring Device Trend on the Rise
Over the years, Dark Daily and our sister publication The Dark Report have regularly covered the growing trend of consumers using wearable technologies to monitor their own health and the health of loved ones.
It should be clear to clinical laboratory leaders that popularity of wearable monitoring devices and digital healthcare is expanding among consumers. The data collected may soon find its way into new treatments for chronic illnesses and early warnings for diagnosticians.
Federal judge must rule on her bid for a new trial, after former Theranos lab director Adam Rosendorff’s statement that he regrets his testimony during her criminal fraud trial
It is a rare event for a board-certified clinical pathologist to be named in national news headlines, but that is what is happening now to Adam Rosendorff, MD, who served as the CLIA laboratory director at Theranos for several years.
Rosendorff is once more the subject of news headlines because of his recent statements expressing “regret” about his testimony for the prosecution during the trial of Elizabeth Holmes, founder and ex-CEO of now defunct Theranos. This development caused attorneys for Holmes to file a motion for a new trial.
In August, Rosendorff showed up at the residence of Elizabeth Holmes and made statements to her attorneys that are the basis for the motion to conduct a new trial.
In a recent court filing requesting the new trial, Holmes’ attorneys described Rosendorff as a “star witness” for the prosecution and pointed out, “The government mentioned him more than any other government witness in both opening and closing statements, and Dr. Rosendorff testified longer than any other government witness.”
During four days of testimony last October, Rosendorff emerged as a central prosecution witness. On the stand, he supported prosecutors’ contention that Holmes knew about the accuracy issues with Theranos’ Edison blood-testing device and intentionally mislead investors and patients.
In court testimony, Adam Rosendorff, MD (above) said, “I had frequent conversations with Elizabeth about concerns that I had in the laboratory,” and [that] she was often copied on emails discussing issues, the Wall Street Journal reported at the time. As clinical laboratory leaders who closely followed his testimony know, Rosendorff was Theranos’ laboratory director from April 2013 to November 2014. (Photo copyright: LinkedIn.)
Rosendorff Attempts to Meet with Holmes
The “Dr. Rosendorff’s Encounter at Ms. Holmes’ Home” section of the 17-page filing states Rosendorff appeared at the home of Holmes and her partner William Evans on August 8 after leaving a voicemail earlier in the evening asking for a meeting with Holmes. Rosendorff allegedly had two short conversations with Evans, who told him Holmes could not speak to anyone and asked Rosendorff to leave. Rosendorff was described by Evans as speaking in a “trembling” voice and appearing to be “in distress.”
The filing goes on to state Rosendorff told Evans “that he wanted to speak to Ms. Holmes because it would be ‘healing for both himself and Elizabeth to talk.’ He stated that ‘when he was called as a witness, he tried to answer the questions honestly but that the prosecutors tried to make everyone look bad’ and that ‘the government made things sound worse than they were when he was up on the stand during his testimony.’”
The filing continues: “Dr. Rosendorff stated that ‘Theranos was early in his and [Ms. Holmes’] career,’ that ‘everyone was just doing the best they could,’ and ‘everyone was working so hard to do something good and meaningful.’”
The section concludes, “He stated that ‘he fe[lt] guilty’ and that he ‘felt like he had done something wrong,’ apparently in connection with his testimony in Ms. Holmes’ case. He stated that these issues were ‘weighing on him’ and that “he was having trouble sleeping.’”
Rosendorff’s Regrets Unlikely to Trigger New Trial
In the filing, Holmes’ attorneys wrote, “under any interpretation of his statements, the statements warrant a new trial under Rule 33. But, at a minimum … the Court should order an evidentiary hearing and permit Ms. Holmes to subpoena Dr. Rosendorff to testify about his concerns.”
Bloomberg, however, quoted criminal defense attorney Michael Weinstein, JD, Chair of Cole Schotz P.C.’s White-Collar Litigations and Government Investigations Practice, as saying Rosendorff’s misgivings about his testimony are unlikely to warrant a new trial.
“A witness having second thoughts and how they were generally perceived is not new in criminal trials but often don’t lead to new trials or much of anything,” Weinstein told Bloomberg. “The burden for that is simply too high.” Weinstein was not involved in the Holmes case.
CBS News reached out to Rosendorff via LinkedIn, who responded he had no comment, adding, “Do not contact me.”
Nevertheless, Holmes’ lawyers have proposed an October 3 hearing to discuss why they believe a new trial is merited. Their request for a new trial came less than a week after U.S. District Judge Edward Davila rejected the defense team’s bid to have Holmes’ January convictions thrown out, the Mercury News reported.
“The evidence does support the jury’s findings,” Davila said at a September 1 hearing in San Jose, California, in which he issued a preliminary ruling denying her bid to have the verdict thrown out.
Theranos Saga Continues
At the hearing, Holmes’ lawyer Amy Mason Saharia, JD, told Davila the defense team would make another attempt to overturn the jury’s findings based on “new evidence,” the Mercury News stated. That new evidence appears to be Rosendorff’s admission that he has regrets about his testimony in the case.
Holmes, 38, is currently free on bail, but faces up to 20 years in prison and a fine of $250,000, plus restitution on each of four counts. She will be sentenced on October 17. The court originally set her sentencing date for September 26, but agreed to delay her sentencing without giving a reason for the delay, CBS News reported.
Will former Theranos laboratory director Adam Rosendorff, MD’s, regrets alter the court’s previous decisions? Who knows? Many clinical laboratory directors and medical laboratory scientists followed Elizabeth Holmes’ nearly four-month long fraud trial with rapt interest. They will now have to wait a few more weeks to find out if the disgraced Theranos executive will get a new trial or a prison sentence.
Researchers surprised that process designed to detect SARS-CoV-2 also identifies monkeypox in wastewater
Early information about an outbreak in a geographical region can inform local clinical laboratories as to which infectious agents and variants they are likely to see when testing patients who have symptoms. To that end, wastewater testing has become a rich source of early clues as to where COVID-19 outbreaks are spreading and how new variants of the coronavirus are emerging.
Ongoing advances in genetic sequencing and digital technologies are making it feasible to test wastewater for infectious agents in ways that were once too time-consuming, too expensive, or simply impossible.
“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation, or the capacity to do sufficient testing and sequencing,” said Knight in a UCSD press release. “We’ve shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community.” (Photo copyright: UC San Diego News.)
Same Process, Different Virus
Following August’s declaration of a state of emergency by California, San Diego County, and the federal government, UCSD researchers added monkeypox surveillance to UCSD’s existing wastewater surveillance program.
“It’s the same process as SARS-CoV-2 qPCR monitoring, except that we have been testing for a different virus. Monkeypox is a DNA virus, so it is a bit of a surprise that our process optimized for SARS-CoV-2, which is an RNA virus, works so well,” said Rob Knight, PhD, Professor of Pediatrics and Computer Science and Engineering at UCSD and one of the lead authors of the study in the press release.
According to the press release, RNA sequencing from wastewater has two specific benefits:
It avoids the potential of clinical testing biases, and
It can track changes in the prevalence of SARS-CoV-2 variants over time.
In 2020, at the height of the COVID-19 pandemic, scientists from the University of California San Diego and Scripps Research looked into genetic sequencing of wastewater. They wanted to see if it would provide insights into levels and variants of the SARS-CoV-2 within a specific community.
Individuals who have COVID-19 shed the virus in their stool.
The UCSD/Scripps researchers deployed commercial auto-sampling robots to collect wastewater samples at the main UCSD campus. They analyzed the samples for levels of SARS-CoV-2 RNA at the Expedited COVID-19 Identification Environment (EXCITE) lab at UCSD. After the success of the program on the campus, they extended their research to include other facilities and communities in the San Diego area.
“The coronavirus will continue to spread and evolve, which makes it imperative for public health that we detect new variants early enough to mitigate consequences,” said Knight in a July press release announcing the publication of their study in the journal Nature, titled, “Wastewater Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission.”
Detecting Pathogens Weeks Earlier than Traditional Clinical Laboratory Testing
In July, the scientists successfully determined the genetic mixture of SARS-CoV-2 variants present in wastewater samples by examining just two teaspoons of raw sewage. They found they could accurately identify new variants 14 days before traditional clinical laboratory testing. They detected the presence of the Omicron variant 11 days before it was first reported clinically in the community.
During the study, the team collected and analyzed 21,383 sewage samples, with most of those samples (19,944) being taken from the UCSD campus. They performed genomic sequencing on 600 of the samples and compared them to genomes obtained from clinical swabs. They also compared 31,149 genomes from clinical genomic surveillance to 837 wastewater samples taken from the community.
The scientists distinguished specific viral lineages present in the samples by sequencing the viruses’ complete set of genetic instructions. Mutational differences between the various SARS-CoV-2 variants can be minute and subtle, but also have notable biological deviations.
“Nothing like this had been done before. Sampling and detection efforts began modestly but grew steadily with increased research capacity and experience. Currently, we’re monitoring almost 350 buildings on campus,” said UCSD’s Chancellor Pradeep Khosla, PhD, in the July press release.
“The wastewater program was an essential element of UC San Diego Health’s response to the COVID pandemic,” said Robert Schooley, MD, Infectious Disease Specialist at UC San Diego Health, in the press release. Schooley is also a professor at UCSD School of Medicine, and one of the authors of the study.
“It provided us with real-time intelligence about locations on campus where virus activity was ongoing,” he added. “Wastewater sampling essentially allowed us to ‘swab the noses’ of every person upstream from the collector every day and to use that information to concentrate viral detection efforts at the individual level.”
Monkeypox Added to UCSD Wastewater Surveillance
In August, UCSD officially added the surveillance of the monkeypox virus to their ongoing wastewater surveillance program. A month earlier, the researchers had discerned 10,565.54 viral copies per liter of wastewater. They observed the levels fluctuating and increasing.
On August 2, the scientists detected 189,309.81 viral copies per liter of wastewater. However, it is not yet clear if the monitoring of monkeypox viral loads in wastewater will enable the researchers to accurately predict future infections or case rates.
“We don’t yet know if the data will anticipate case surges like with COVID,” Knight said in the August UCSD press release announcing the addition of monkeypox to the surveillance program. “It depends on when the virus is shed from the body relative to how bad the symptoms are that cause people to seek care. This is, in principle, different for each virus, although in practice wastewater seems to be predictive for multiple viruses.”
Utilization of genetic sequencing of wastewater sampling will continue to develop and improve. “It’s fairly easy to add new pathogens to the process,” said Smruthi Karthikeyan, PhD, an environmental engineer and postdoctoral researcher in Knight’s lab who has overseen wastewater monitoring at UC San Diego. “It’s doable on short notice. We can get more information in the same turnaround time.”
Thus, clinical laboratories engaged in testing programs for COVID-19 may soon see the addition of monkeypox to those processes.
