Researchers used CRISPR-based assays to develop new clinical laboratory point-of-care blood test which boasts accuracy, affordability, and accessibility
According to UPI, the test can “distinguish between influenza A and influenza B—the two main types of seasonal flu—as well as identifying more virulent strains like H1N1 and H3N2.”
Many research teams are working to develop paper-based diagnostic screening tests because of their lower cost to produce and usefulness in remote locations. Should this near-patient point-of-care test become clinically viable, it could mean shorter times to answer, enabling speedier diagnoses and earlier start of treatment.
It also means patient specimens do not have to be transported to a clinical laboratory for testing. And reduced cost per test makes it possible to test more people. This serves the public health aspect of monitoring outbreaks of influenza and other diseases and gives hope for improved treatment outcomes.
“Being able to tease apart what strain or subtype of influenza is infecting a patient has repercussions both for treating them and public health interventions, said Jon Arizti Sanz, PhD, co-lead study author and postdoctoral researcher at the Broad Institute of Harvard and MIT, in a Broad Institute news release.
“Ultimately, we hope these tests will be as simple as rapid antigen tests, and they’ll still have the specificity and performance of a nucleic acid test that would normally be done in a laboratory setting,” Cameron A. Myhrvold, PhD (above), Assistant Professor of Molecular Biology at Princeton University in New Jersey, told CIDRAP. Influenza tests that can be performed at the point of care and in remote locations may reduce the number of screening tests performed by clinical laboratories. (Photo copyright: Michael James Butts/Hertz Foundation.)
Her team developed their tests using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), “a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform,” the researchers wrote in their Journal of Molecular Diagnostics paper.
“SHINE has a runtime of 90 minutes, can be used at room temperature and only requires an inexpensive heat block to heat the reaction. The SHINE technology has previously been used to identify SARS-CoV-2 and later to distinguish between the Delta and Omicron variants,” Bioanalysis Zone reported.
“The test uses genetically engineered enzymes to identify specific sequences of viral RNA in samples,” the researchers told UPI. Originally designed to detect COVID-19, the team adapted the technology to detect influenza in 2022 “with the aim of creating a screening tool that could be used in the field or in clinics rather than hospitals or high-tech diagnostic labs,” they said.
Influenza A and B as well as H1N1 and H3N2 subtypes were the targets of the four SHINE assays. “When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously,” the researchers wrote in their paper.
The team used “20 nasal swabs from people with flu-like symptoms during the 2020-2021 flu season, nasal fluid from healthy people as the control, and 2016-2021 influenza sequences downloaded from the National Center for Biotechnology Information Influenza (NICB) database. They compared the results with those from quantitative reverse transcription-polymerase chain reaction (RT-PCR) tests,” CIDRAP reported.
The original 2020 test (shown above) takes 90 minutes to develop at room temperature. The test developers aim to drop this down to 15 minutes. In comparison, typical polymerase chain reaction (PCR) testing requires medical laboratories to have specialized equipment, trained staff, and prolonged processing times, the Broad Institute news release notes. (Photo copyright: Broad Institute.)
Implications of the New Tests
The ease of the new tests is an important development since approximately only 1% of individuals who come down with the flu see doctors for testing, according to the news release. And researchers had this in mind, looking at speed, accuracy, and affordability as a means to “improve outbreak response and infection care around the world,” UPI reported.
There are great benefits to strain differentiation that be achieved with the new test. Doctors are hopeful the test will help dial in the best treatment plans for patients since some strains are resistant to the antiviral medication oseltamivir (Tamiflu), UPI noted. This is significant since Tamiflu “is a common antiviral,” said Sanz in the Broad Institute news release.
“These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance,” the Journal of Molecular Diagnostics paper noted. This allows for more strategic treatment planning.
“Using a paper strip readout instead of expensive fluorescence machinery is a big advancement, not only in terms of clinical care but also for epidemiological surveillance purposes,” said Ben Zhang, an MD candidate in the Health Sciences and Technology at Harvard and co-first author of the study, in the Broad Institute news release.
Future Plans for Tests
“With further development, the test strip could be reprogrammed to distinguish between SARS-CoV-2 and flu and recognize swine flu and avian flu, including the H5N1 subtype currently causing an outbreak in US dairy cattle,” the study authors told CIDRAP.
The team is also looking at ways to help prevent H5N1 from crossing into human contamination, Sanz told UPI.
The new Princeton/MIT/Harvard tests echo the trend to bring in affordability and ease-of-use with accurate results as an end goal. Faster results mean the best treatments for each person can start sooner and may render the transport of specimens to a clinical laboratory as a second step unnecessary.
As research teams work to develop paper-based viral tests for their plethora of benefits, clinical laboratories will want to pay close attention to this development as it can have a big implication on assisting with future outbreaks.
Additional research is needed before these tests are going to be commonplace in homes worldwide, but this first step brings inspiration and hope of what’s to come.
In addition to viruses, wastewater analysis can also be used to detect the presence of chemical substances such as opioids
Wastewater surveillance and analysis continues to be a useful tool for detecting the prevalence of viruses such as SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) in a community. Perhaps more importantly, wastewater surveillance can fill in gaps where clinical laboratory testing data may be days or weeks behind the true spread of viral infections.
One sign of the value of testing wastewater for infectious diseases is the fact that government officials are financing a continuing program of wastewater testing. In September, the federal Centers for Disease Control and Prevention (CDC) awarded a contract to conduct wastewater surveillance/analysis worth millions of dollars to Verily Life Sciences, a Google company, rather than renewing its contract with Biobot Analytics, which had been doing the work since 2020. One interesting twist in the award of this contract is how an ensuing dispute pulled the plug on a significant portion of the wastewater analysis in this country.
In their September Morbidity and Mortality Weekly Report (MMWR), the CDC highlighted a CDC study during which wastewater samples were taken from 40 wastewater treatment plants located in Wisconsin’s three largest cities. The samples were collected weekly and tested for influenza and RSV. The findings were then compared with data regarding emergency department (ED) visits for those diseases.
The CDC found that higher detections of flu and RSV were associated with higher rates of ED visits for both illnesses. The study also suggests that wastewater might detect the spread of these viruses earlier than ED visit data alone.
“During the COVID-19 pandemic, wastewater surveillance for SARS-CoV-2 provided valuable insight into community incidence of COVID-19,” said Peter DeJonge, PhD (above), a CDC Career Epidemiology Field Officer, in an interview with Infectious Disease Special Edition. “[The CDC’s] report supports the idea that wastewater surveillance also has the potential to serve as a useful method with which to track community spread of influenza and RSV.” Local clinical laboratories are also involved in the CDC’s wastewater surveillance programs. (Photo copyright: CDC.)
Keeping Communities Informed about Spread of Viral Infections
The CDC’s study was conducted from August 2022 to March 2023. The wastewater samples from all three cities tested positive for the viruses in advance of increases in ED visits. After the ED visits for those viruses had subsided, the viral material remained in sewersheds for up to three months.
“Both influenza and RSV can cause substantial amounts of illness, hospitalization, and even death during annual epidemics, which often occur during winter months in the US,” Peter DeJonge, PhD, a CDC Career Epidemiology Field Officer assigned to the Chicago Department of Public Health, told Infectious Disease Special Edition (IDSE). “Clinical providers and public health officials benefit from surveillance data to understand when and where these diseases are spreading in a community each year. This type of data can help prepare clinics [and clinical laboratories] for anticipated cases, tailor public health messaging, and encourage timely vaccination.”
“The collective burden from these respiratory viruses is staggering. With these viruses circulating simultaneously and potentially shifting in seasonality and severity, communities must be able to understand the full impact of each of these illnesses to inform awareness and public health responses that can prevent infections, hospitalizations, and even deaths,” said Mariana Matus, PhD, CEO and cofounder of Biobot Analytics, in an August press release announcing the launch of a “Respiratory Illnesses Panel” that will monitor wastewater for Influenzas A and B (seasonal flu), Respiratory Syncytial Virus (RSV), and SARS-CoV-2 (COVID-19).
“Traditional testing methods for these illnesses do not provide a comprehensive picture of the number of people infected due to inaccurate reporting, as well as asymptomatic or misdiagnosed cases,” Matus continued. “By monitoring wastewater concurrently for influenza, RSV, and SARS-CoV-2, we can fill in these gaps and provide important information to communities.”
CDC Moves to Change Wastewater Surveillance Contractor Mid-stream
As new variants of SARS-CoV-2 emerge, a recent contract dispute may be the cause of a time delay in efforts to perform wastewater surveillance for the disease, as well as for other viral infections, according to Politico.
The CDC’s move to replace Biobot Analytics with Verily Life Sciences to do wastewater surveillance has led to Biobot filing a protest with the Government Accountability Office (GAO).
According to World Socialist Web Site (WSWS), “The scope of the [Biobot] contract [to provide extended data for the public health agency’s National Wastewater Surveillance System (NWSS)] included data from more than 400 locations from over 250 counties across the entire United States, covering 60 million people. On top of this, Biobot also conducted genomic sequencing to identify the latest variants in circulation.”
About one quarter of the wastewater testing sites in the country have been shut down due to Biobot’s contract being suspended in September. The remaining 1,200 sites that are not covered under the original contract will continue wastewater testing, Politico reported.
The GAO hopes to have a decision on the contract dispute in January. Verily says it is ready to proceed with testing in all locations and already has its infrastructure in place.
“We are committed to working with the CDC to advance the goals of the … testing program, initiate testing on the samples already delivered when allowed to resume work, and make wastewater data available as quickly as possible,” Bradley White, PhD, Principal Scientist/Director at Verily, told Politico.
Under the terms of Verily’s contract, the company will collect samples from wastewater treatment centers cross the county and analyze the samples for COVID-19 and the mpox (monkey pox) virus.
This contract marks the first agreement between the CDC and Verily.
The CDC has not disclosed why it decided to change contractors, but it is probable that cost may have been played a role in the decision. Verily’s contract is for $38 million over the course of five years and Biobot’s most recent contract was for around $31 million for a period of less than 18 months, Politico reported.
In a LinkedIn post, Matus reported that Biobot had already laid off 35% of its staff due to the contract decision by the CDC.
Competition in Wastewater Surveillance Market
When seeking viruses in wastewater, scientists use gene-based detection methods to locate and amplify genetic signs of pathogens. But public health officials are just beginning to tap into the potential opportunities that may exist in the analysis of data present in wastewater.
Wastewater surveillance is also being looked at as a way to combat America’s opioid epidemic.
“Wastewater surveillance is becoming more mature and more mainstream month after month, year over year,” Matus told Time.
Thus, regardless of which companies end up working with the CDC, it appears that wastewater surveillance and analysis, which requires a great deal of clinical laboratory testing, will continue to help fight the spread of deadly viral infections, as well as possibly the nation’s drug epidemic.
By analyzing strains of the bacterium from a hospital ICU, the scientists learned that most infections were triggered within patients, not from cross-transmission
Tracking the source of Hospital-acquired infections (HAI) has long been centered around the assumption that most HAIs originate from cross-transmission within the hospital or healthcare setting. And prevention measures are costly for hospitals and medical laboratories. However, new research puts a surprising new angle on a different source for some proportion of these infections.
The study suggests that most infections caused by Clostridioides difficile (C. Diff), the bacterium most responsible for HAIs, arise not from cross-transmission in the hospital, but within patients who already carry the bacterium.
A researcher performed whole genome sequencing on 425 strains of the bacterium isolated from the samples and found “very little evidence that the strains of C. diff from one patient to the next were the same, which would imply in-hospital acquisition,” according to a UM news story.
“In fact, there were only six genomically supported transmissions over the study period. Instead, people who were already colonized were at greater risk of transitioning to infection,” UM stated.
Arianna Miles-Jay, PhD, a postdoctoral fellow in The Snitkin Lab at the University of Michigan and Manager of the Genomic Analysis Unit at the Michigan Department of Health and Human Services, performed the genomic sequencing. “By systematically culturing every patient, we thought we could understand how transmission was happening. The surprise was that, based on the genomics, there was very little transmission,” she said in the UM news story.
“Something happened to these patients that we still don’t understand to trigger the transition from C. diff hanging out in the gut to the organism causing diarrhea and the other complications resulting from infection,” said Evan Snitkin, PhD (above), Associate Professor of Microbiology and Immunology, and Associate Professor of Internal Medicine, Division of Infectious Diseases at University of Michigan, in a UM news story. Medical laboratories involved in hospital-acquired infection prevention understand the importance of this research and its effect on patient safety. (Photo copyright: University of Michigan.)
Only a Fraction of HAIs Are Through Cross-Transmission
In the study abstract, the researchers wrote that “despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States.”
Citing data from the US Centers for Disease Control and Prevention (CDC), HealthDay reported that “nearly half a million C. diff infections occur in the United States each year. Between 13,000 and 16,000 people die from the bacterium, which causes watery diarrhea and inflammation of the colon. Many of these infections and deaths have been blamed on transmission between hospitalized patients.”
The new study, however, notes that 9.3% of the patients admitted to the ICU carried toxigenic (produces toxins) C. diff, but only 1% acquired it via cross-transmission. The carriers, the study authors wrote, “posed minimal risk to others,” but were 24 times more likely to develop a C. diff infection than non-carriers.
“Our findings suggest that measures in place in the ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms —were effective in preventing C. diff transmission,” Snitkin told HealthDay. “This indicates that to make further progress in protecting patients from developing C. diff infections will require improving our understanding of the triggers that lead patients asymptomatically carrying C. diff to transition to having infections.”
Recognizing Risk Factors
Despite the finding that infections were largely triggered within the patients, the researchers still emphasized the importance of taking measures to prevent hospital-acquired infections.
“In fact, the measures in place in the Rush ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms—were likely responsible for the low transmission rate,” the UM news story noted.
One expert not involved with the study suggested that hospitals’ use of antibiotics may be a factor in causing C. diff carriers to develop infections.
“These findings suggest that while we should continue our current infection prevention strategies, attention should also be given to identifying the individuals who are asymptomatic carriers and finding ways to reduce their risk of developing an infection, like carefully optimizing antibiotic usage and recognizing other risk factors,” Hannah Newman, Senior Director of Infection Prevention at Lenox Hill Hospital in New York City, told HealthDay.
Snitkin, however, told HealthDay that other factors are likely at play. “There is support for antibiotic disruption of the microbiota being one type of trigger event, but there is certainly more to it than that, as not every patient who carries C. diff and receives antibiotics will develop an infection.”
Another expert not involved with the study told HealthDay that “many patients are already colonized,” especially older ones or those who have been previously hospitalized.
“A lot of their normal flora in their GI tract can be altered either through surgery or antibiotics or some other mechanism, and then symptoms occur, and that’s when they are treated with antibiotics,” said Donna Armellino, RN, Senior VP of Infection Prevention at Northwell Health in Manhasset, New York.
This research also demonstrates the value of faster, cheaper, more accurate gene sequencing for researching life-threatening conditions. Microbiologists, Clinical laboratory scientists, and pathologists will want monitor further developments involving these findings as researchers from University of Michigan and Rush University Medical Center continue to learn more about the source of C. diff infections.
Free at home clinical-laboratory testing for COVID-19 has been provided in the past, but this time the federal government wants to manufacture as many tests as possible in the US
Pathologists and clinical laboratory managers may be interested to learn that the US market is about to be flooded with millions of at-home COVID-19 rapid tests. The federal government has contracted with 12 US-based test manufacturers to produce 200 million at-home self-tests aimed at detecting “currently circulating COVID-19 variants” through the end of this year, according to a US Department of Health and Human Services (HHS) news release.
Federal officials want to head off “supply chain issues” that developed in the past with reliance on tests made overseas, and to address a possible COVID-19 surge during the fall and winter, the Associated Press (AP) reported.
In fact, 500 million tests have already been distributed through US government channels to long-term care facilities, schools, and low-income senior housing.
“Manufacturing COVID-19 tests in the United States strengthens our preparedness for the upcoming fall and winter seasons, reduces our reliance on other countries, and provides good jobs to hardworking Americans,” said Assistant Secretary for Preparedness and Response Dawn O’Connell, JD (above), in an HHS news release. “ASPR’s investments in these domestic manufacturers will increase availability of tests in the future.” With the federal government preparing for what it expects to be a surge in demand for COVID-19 testing, clinical laboratories may want to track the CDC’s weekly reports on the number of positive COVID-19 cases as this year’s influenza season progresses. (Photo copyright: Administration for Strategic Preparedness and Response.)
In Vitro Diagnostics Test Makers Get Government Gigs
This is not the first time federal officials sent out free COVID-19 tests to consumers. According to the AP, more than 755 million tests went out to US households in previous efforts to fight the spread of infections. But unlike those tests, these tests will be manufactured entirely within the US.
The government’s latest wave of free tests is meant to “complement ASPR’s ongoing distribution of free COVID-19 tests to long-term care facilities, low-income senior housing, uninsured individuals, and underserved communities, with 500 million tests provided to date through these channels,” the HHS news release noted.
Both large and lesser-known in vitro diagnostics (IVD) manufacturers were selected by the federal government to receive funding. They include:
HHS advises people to take the test at the first sign of symptoms (fever, sore throat, runny nose, others), after coming into contact someone who has COVID-19, or prior to gathering with a group, as a preventative to spread of the coronavirus.
Reporting laboratories say existing antibodies work against the BA.2.86 variant.
The variant does not appear to be linked in the US with increasing infections or hospitalizations.
It is “unclear how easily BA.2.86 spreads” relative to other variants.
BA.2.86 has been detected in nine states: Colorado, Delaware, Michigan, Ohio, Pennsylvania, Virginia, Washington, and in wastewater in New York and Ohio, as well as in other countries.
For week ending Sept. 23, the CDC reported the following statistics compared to the prior week:
19,079 COVID-19 hospitalizations, down 3.1%.
Total hospitalizations: 6.3 million.
2.7% of total deaths were due to COVID-19, up 8%.
COVID-19 test positivity rate was 11.6%, down 1.1%.
1.8% of emergency department visits were diagnosed with COVID-19, down 11.7%.
According to Verywell Health, BA.2.86 carries more than 30 mutations.
“Even with a lot of mutations, there are a lot of spots in the virus that can be recognized by our immune system, and there are many shared mutations as well. There will be some protection from new vaccine booster as well as prior infections,” Rajendram Rajnarayanan, PhD, Assistant Dean of Research and Associate Professor, Basic Sciences, Arkansas State University, told Verywell Health.
It’s worth noting that the common cold, influenza, SARS, and SARS-CoV-2 are all in the coronavirus family, and thus closely related with similar symptoms. It would not be a surprise that SARS-CoV-2 joins those other viruses as an endemic virus with a similar yearly cycle of infection rates.
If that happens, and no surge in infections appears that would motivate orders for the new COVID-19 at-home tests, the government may find itself with a lot of unused tests at the end of the year. The US Food and Drug Administration (FDA) is aware of this possibility and provides a website where people can check to see if their test has an extended expiration date.
Plus, folks who are tired of the pandemic may not respond at all to the government’s insistence to prepare for possible surges in infection rates.
“Whether or not people are done with it, we know the virus is there, we know that it’s circulating. We know, if past is prologue, it’ll circulate to a higher degree and spread, and cases will go up in the fall and winter seasons,” said Assistant Secretary for Preparedness and Response Dawn O’Connell, JD, in the HHS new release. “Anticipating that that would be true again, or something similar, we want to make sure the American people have these tools.”
Clinical laboratories may want to prepare as well. Many people are not comfortable with at-home self-testing and prefer to have their local medical labs perform the tests.
Clinical laboratories could play a key role in helping users collect their samples correctly, interpret results, and transfer flu test data to their health records
Clinical laboratories may have another opportunity to provide service to their clients and the physicians who treat them. With the success of at-home COVID-19 testing, consumer demand for self-tests is changing and advances in diagnostic technology now make it feasible to make more influenza (flu) tests available for consumers to buy and use at home.
At-home tests for SARS-CoV-2 can be found at pharmacies all across America. But that’s not the case with tests for influenza.
Should self-test flu kits eventually become available and common, clinical laboratories could offer the service of helping consumers understand:
that the test was conducted correctly (specimen collection and analysis),
“Home flu testing would ensure that those who do need and receive antiviral medication for influenza are the ones who need it the most,” and that “we are making our treatment decisions based on data,” infectious disease specialist Christina Yen, MD (above), University of Texas Southwestern Medical Center, told STAT News. At-home flu self-tests could also bring opportunities for clinical laboratories to provide service to healthcare consumers and the physicians who treat them. (Photo copyright: UT Southwestern Medical Center.)
Pros and Cons of Consumers Doing At-home Influenza Testing
According to the federal Centers for Disease Control and Prevention (CDC), COVID-19 and influenza are both upper respiratory illnesses with similar symptoms. So, why don’t we have more at-home flu tests available? Partly because at-home testing is a relatively new phenomenon in modern healthcare.
“It’s really rare, and it’s really new that people are allowed to know about what’s happening inside their body without a physician in the middle,” Harvard epidemiologist Michael Mina, MD, PhD, told STAT News. The article uses the example of at-home pregnancy tests. Despite a prototype for an at-home pregnancy test being created in 1967, it took another decade before an over-the-counter pregnancy test became available to the public.
“The general thinking was, ‘How could a woman possibly know what to do if she found out she was pregnant on her own without a doctor in the room?’ That is a ridiculous concern because women have been doing that for millions of years,” Mina added.
So, why be cautious when it comes to giving patients the option of at-home flu testing?
There are some cons to at-home influenza tests. Average citizens are not clinical laboratory professionals. They might obtain too little sample for an accurate reading or read the results incorrectly. Then, there is the possibility for false-negatives or false-positives.
An at-home test user is not likely to consider the possibility of a false result, however clinicians look at the situation with more nuance. If the patient was still symptomatic or in a high-risk community, the provider could administer a more sensitive medical laboratory test to confirm the previous test results.
“In a Facebook post from mid-November with hundreds of responses, concertgoers compared symptoms and positive test results, many of those from tests taken at home. But those data weren’t added to state public health tallies of COVID’s spread,” STAT News noted.
The larger concern is that samples obtained by at-home self-test users are not submitted for genomic sequencing. This could lead to incomplete data and delay identifying new variants of the coronavirus in communities.
Another barrier to at-home flu testing is that rapid influenza diagnostic testing can be unreliable. In 2009, the rapid influenza tests could only detect the H1N1 influenza virus in a mere 11% of samples, STAT News reported. Because of this, the FDA now requires manufacturers to test their rapid tests against eight different strains that change every year depending upon which strains are prevalent. This could present a problem if individuals use leftover tests from the previous flu season.
Do Pros of At-home Testing Outweigh the Cons?
At-home testing is convenient and makes testing more accessible to patients who may not be able to get to a clinic. Being able to test at home also encourages individuals to take precautions necessary to stop the spread of whichever illness they may have. Given the similarities in symptoms between influenza and COVID-19, people could benefit from having tools at home that correctly identify their illness.
At-home COVID-19 tests are here to stay, and at-home influenza tests may be on the way soon. Clinical laboratories could play an important role in educating the public on the correct handling of these tests.
