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Above: A researcher works in a lab that is developing testing for the COVID-19 coronavirus at Hackensack Meridian Health Center for Discovery and Innovation on February 28, 2020 in Nutley, New Jersey. (Photo by Kena Betancur/Getty Images)

There's a massive shortage of COVID-19 (Coronavirus) test kits in the U.S., as cases continue to skyrocket in places like Seattle and New York City. This is largely due to the failure of the Centers for Disease Control and Prevention (CDC) to distribute the tests in a timely fashion.

But it didn't have to be this way. Back in January and Februarywhen cases of the deadly disease began aggressively circulating outside of Chinadiagnostics already existed in places like Wuhan, where the pandemic began. Those tests followed World Health Organization (WHO) test guidelines, which the U.S. decided to eschew.

Instead, the CDC created its own in-depth diagnostics that could identify not only COVID-19, but a host of SARS-like coronaviruses. Then, disaster struck: When the CDC sent tests to labs during the first week of February, those labs discovered that while the kits did detect COVID-19, they also produced false positives when checking for other viruses. As the CDC went back to the drawing board to develop yet more tests, precious time ticked away.

"I think that we should have had testing more widely available about a month earlier," Dr. Carl Fichtenbaum, professor of clinical medicine at the University of Cincinnati's School of Medicine, tells Popular Mechanics. "That would have been more appropriate so that we could have identified people earlier on and used some of the mitigating strategies that were using now."

As the spread of Coronavirus continues to escalate in the U.S., private institutions like academic research hospitals are scrambling in a mad dash to come up with more test kits. And there is hope: The Cleveland Clinic says it has developed a diagnostic test that can deliver results in just hours, as opposed to the time it takes the existing CDC tests, which can take days.

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Testing for COVID-19 comes in two primary forms: You'll either have your throat swabbed if you're in the U.S., or perhaps have your blood drawn if you're in another country, like China. The different approaches ultimately come down to how scientists have developed the lab tests.

In the U.S., the CDC's diagnostic tool relies on polymerase chain reaction testing (PCR), which detects genetic material found in the virus's DNA. Unlike in other methods, the virus doesn't have to be alive for its presence to be detected.

"We take parts of the virus and we [test] whats called the conserved parts of the virus, parts that dont change a lot," Dr. Fichtenbaum explains. "There are always mutations. Were looking at the genetic code and we take a sequence of what we call primers, or things that will match up with that genetic code, and we put them through a series of steps where the primers will match the genetic code if [the virus] is present."

PCR testing is generally too advanced to be done at a hospital, and is more in the wheelhouse of clinical laboratory settings. There, researchers extract the sample's nucleic acidone of the four bases found in DNA sequencesto study the virus genome. They can amplify portions of that genome through a special process called reverse transcription polymerase chain reaction. That way, scientists can compare the sample to SARS-CoV-2, the virus that causes the novel coronavirus.

SARS-CoV-2 has almost 30,000 nucleotides in total, which make up its DNA. The University of Washington School of Medicine's PCR test hones in on about 100 of those that are known to be unique to the virus.

The researchers are looking for two genes in particular, and if they find both, the test is considered positive. If they only find one, the test is inconclusive. However, the CDC notes, "it is possible the virus will not be detected" in the early stages of the viral infection.

In some cases, Dr. Fichtenbaum says, it's possible to quantify the number of copies of the viral gene present. It could be one, 10, or 10 million, he says, and the higher that amount is, the more contagious you may be, or the further along you may be in the illness.

U.S. Centers for Disease Control and Prevention

As of press time, the CDC has directly examined some 3,791 specimens in Atlanta, according to data produced on Thursday afternoon, while public health laboratories across the country have tested another 7,288. Notably, some data after March 6 is still pending.

Regardless, with about 1,000 confirmed cases in the U.S., those figures suggest roughly one in 11 people tested have actually contracted the novel Coronavirus. Surely, if more tests were available, those numbers would be higher, Dr. Fichtenbaum says. Because of the CDC snafu and an initial muted reaction to the outbreak from President Trump's administration, we're about a month behind on the diagnostics front, he adds.

Piling onto other reasons, Dr. Karen C. Carrolldirector of the Division of Medical Microbiology at Johns Hopkins University School of Medicinebelieves that the test shortage is "complicated" by the fact that no one expected COVID-19 to spread so quickly in the U.S.

Not to mention, manufacturers are now low on supplies that academic labs, like hers, require to develop and distribute test kits, she tells Popular Mechanics.

During a Congressional hearing on Wednesday, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said the public health care system is failing to make tests available to people who may have contracted COVID-19.

"The idea of anybody getting [the test] easily the way people in other countries are doing it, we're not set up for that. Do I think we should be? Yes, but we're not," he said.

The silver lining: The CDC is now working in tandem with private labs to make more tests available. The concern then becomes how many tests these labs can actually perform each day. Experts estimate that most labs will have the capacity to complete about 100 tests per day, which just isn't good enough to contain COVID-19 at this point.

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Just because your doctor may have ordered you a COVID-19 test, that doesn't mean you'll actually receive one.

According to CDC guidelines, there are three general classes of patients who seek the diagnostic test, and it's up to the discretion of the health care systems to administer them. With limited supply, those are tough decisions. The classes are:

Testing can be quite restrictive, and people who aren't in a high risk category, or who have traveled to a country where there are cases of COVID-19but had no known exposure to the virusare turned away.

"Once we relax the standards for testing so that we can test on anyone we think appropriate, and its not as complicated, we'll be able to reduce the spread," Dr. Fichtenbaum says.

Right now in Ohio, where Dr. Fichtenbaum is based, doctors must fill out a four-page form and conduct in-depth tracing of a patient's movements before they can administer a test, he says. Not only is it time-consuming, but it may result in the patient not receiving a test at alland could have contracted the virus.

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To expedite the availability of diagnostics, the U.S. Food and Drug Administration (FDA) announced in late February that academic hospital systems had the green light to develop their own test kits.

The move allows these institutions to rely on their own internal validation upfront, rather than wait on the time-consuming FDA approvals process before using the tests. While FDA approval is still ultimately required under this policy, once the hospitals themselves have determined the tests are accurate and safe, they can begin using them.

Dr. Carroll of Johns Hopkins says that her lab went live with their own test yesterday. "Now, we have 15 days to send [the FDA] our validation package," she says. Her lab can now use the test to check for COVID-19 in patients that come to the medical center, but a few more things must also happen in tandem to satisfy the FDA's requirements.

Once a private lab sends in their validation package, which includes data collected during the test development, the FDA may call back with questions about the kit or ask for clarification. If the labs get radio silence for a while, that's normal, according to Dr. Carroll, but eventually, they must be granted what is known as an Emergency Use Authorization.

Under section 564 of the Federal Food, Drug, and Cosmetic Act, the FDA Commissioner may allow unapproved medical productslike privately developed COVID-19 teststo be used in an emergency for diagnosis, treatment or prevention when there are no better alternatives.

"I dont know how quickly they will get back to laboratories, they havent told us that," Dr. Carroll says.

Labs must also have close communication with their state health department laboratory, which is essentially the top lab in the state, she added. The FDA is requiring private institutions to send their first five negative and first five positive testing results to their state lab to ensure uniformity and effectiveness.

"A public health laboratory monitors certain communicable diseases," Dr. Carroll explains. "Some even offer testing for the community, like STDs such as Gonorrhea."

Other hospitals across the U.S. are making strides in test development, too. In Washington, where the CDC's faulty tests stymied the progress of testing, potentially aiding the community spread seen there, the University of Washington Medical Center has developed a COVID-19 test based on WHO recommendations, unlike the CDC. The hospital system has the capacity to conduct about 1,000 tests per day, and is working to ramp that up to 4,000 or 5,000 daily tests.

The Cleveland Clinic's test, meanwhile, should only take about eight hours to turn around a positive or negative result and should be ready by the end of March.

In a statement provided Thursday to Popular Mechanics, the Cleveland Clinic says it will soon have the capabilities to conduct on-site testing. "We are in the process of validating our testing capabilities and will soon send out more information."

Moving forward, Dr. Fichtenbaum expects the FDA to soon approve what's known as multiplex testing, which will allow labs to run 96 tests at once, rather than work with one specimen at a time.

"They need to approve that at each lab and theyre slow," says Dr. Fichtenbaum. But he anticipates the FDA will give the all-clear in the next few days. Then, it's just a matter of manufacturing the tests, which should happen rapidly.

In the meantime, community spread continues, despite self-quarantine measures, countless canceled events, and sweeping work-from-home policies. The number of positive cases is probably significantly higher than the data shows, says Dr. Fichtenbaum, which only worsens the contagion.

"I think that COVID-19 is probably more prevalent in our communities than we think," he says.

And the clinical microbiologists working tirelessly at the front lines in hospitals fully expect to meet demand. Dr. Heba Mostafa, assistant professor of pathology at Johns Hopkins University, tells Popular Mechanics that she expects to see testing ramp up and really meet demand over the course of the next four to eight weeks.

And Dr. Carroll says that the spirit of collaboration between academic medical centers has been refreshing. The University of Texas and the University of Washington have each helped out the Johns Hopkins effort, she says. They helped supply the genetic material necessary to complete their test's validation. Still, it's grueling.

"Our hospital is very happy that we went live yesterday, but of course now theyre interested in how many tests we can do," Carroll said with a laugh. "I sometimes feel that clinical microbiologists are the unsung heroes."

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Why There Aren't Enough Coronavirus Tests in the U.S. - Popular Mechanics

This entry was posted on March 13, 2020 at 9:46 am and is filed under Genetic medicine. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed. |