Coronavirus Test Kits Contaminated With Coronavirus

By | May 5, 2020

Inadequate testing for COVID-19 across the U.S. in the early stages of the pandemic has been blamed for allowing widespread transmission of the virus to occur, during a time when it potentially could have been contained without the need for extensive shutdowns.

In January 2020, German scientists developed the first diagnostic test for COVID-19. In early February 2020, the World Health Organization shipped about 250,000 tests to 159 laboratories around the world.1

Rather than use the WHO test, the U.S., under the direction of the CDC and FDA, decided to create its own, as it had done with tests during past outbreaks of Ebola and Zika. On February 4, when there were only about a dozen confirmed coronavirus cases in the U.S., the FDA approved the U.S. COVID-19 test, and the CDC shipped 90 of them to state public health labs days later.2

The tests, however, led to inconclusive results that caused further delays in getting accurate COVID-19 diagnoses. The CDC has been tight-lipped about what caused the testing glitches, but an investigation by The New York Times reported that the CDC’s tests were contaminated with coronavirus.3

‘Lack of Expertise,’ Protocol Violations Led to Tainted Tests

According to the Times, “sloppy laboratory practices” at the CDC rendered the first U.S. coronavirus tests ineffective, with two of the three CDC laboratories creating the test kits violating their manufacturing standards. When the FDA sent in an official to assess the issue, he noted an “astonishing lack of expertise in commercial manufacturing.”4 The Times reported:

“Problems ranged from researchers entering and exiting the coronavirus laboratories without changing their coats, to test ingredients being assembled in the same room where researchers were working on positive coronavirus samples, officials said.

Those practices made the tests sent to public health labs unusable because they were contaminated with the coronavirus, and produced some inconclusive results.”

In March, Axios also reported that Timothy Stenzel, the FDA’s director of the Office of In Vitro Diagnostics and Radiological Health, visited a CDC lab in Atlanta and raised concerns about inappropriate procedures and potential contaminants.5

The CDC had previously stated that a manufacturing problem with one of the reagents had caused the test failures, but FDA official Stephanie Caccomo stated, “CDC did not manufacture its test consistent with its own protocol.”6 When the problems initially surfaced and the CDC manufactured new tests, labs had to send samples to the CDC for testing, which led to delays of up to 48 hours.7

In March, The New York Times summed up U.S. testing failures as “the lost month” — a time between late January and early March 2020 during which widespread testing may have changed the course of the pandemic in the U.S.,8 and said of the latest investigation:

“The F.D.A. confirmed its conclusions … after several media outlets requested public disclosure of its inquiry, which assuredly is part of a larger federal investigation into the C.D.C. lab irregularities by the Department of Health and Human Services.

Forced to suspend the launch of a nationwide detection program for the coronavirus for a month, the C.D.C. lost credibility as the nation’s leading public health agency and the country lost ground in ways that continue to haunt grieving families, the sick and the worried well from one state to the next.

To this day, the C.D.C.’s singular failure symbolizes how unprepared the federal government was in the early days to combat a fast-spreading outbreak of a new virus and it also highlights the glaring inability at the onset to establish a systematic testing policy that would have revealed the still unknown rates of infection in many regions of the country.”

UK’s Imported Tests Were Also Contaminated

At the end of March 2020, Eurofins Scientific, a Luxembourg-based testing laboratory, informed U.K. government labs that “probes and primers” for COVID-19 tests would be delayed because they were found to be contaminated with traces of coronavirus.9 It’s unclear how the tests became contaminated, but Eurofins stated that other COVID-19 test suppliers had also encountered contaminated test supplies.

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In the CDC’s case, The Washington Post said they had separately confirmed that FDA officials believe the CDC violated its own laboratory practices and in so doing caused the test kits to become contaminated:10

“The cross contamination most likely occurred because chemical mixtures were assembled into the kits within a lab space that was also handling synthetic coronavirus material. The scientists also said the proximity deviated from accepted procedures and jeopardized testing for the virus.

… The troubled segment of the test was not critical to detecting the novel coronavirus, experts said. But after the difficulty emerged, CDC officials took more than a month to remove the unnecessary step from the kits, exacerbating nationwide delays in testing, according to an examination of federal documents and interviews with more than 30 present and former federal scientists and others familiar with the events.

… This account confirms for the first time the contamination’s role in undermining the test and the CDC’s failure to meets its lab standards.”

FDA Red Tape Caused Further Testing Delays

The CDC’s production of contaminated tests caused serious delays at a crucial point in the disease outbreak. “It was just tragic,” Scott Becker, executive director of the Association of Public Health Laboratories, told The Times. “All that time when we were sitting there waiting, I really felt like, here we were at one of the most critical junctures in public health history, and the biggest tool in our toolbox was missing.”11

Adding to the problem, the FDA also prevented commercial laboratories from producing their own tests in the early stages. While laboratory-developed tests typically do not require FDA preapproval, the declared public health emergency triggered rules that required labs to receive an Emergency Use Authorization (EUA) from the FDA in order to roll out tests for COVID-19.

As mentioned, this meant labs weren’t allowed to develop tests until late February. The Alliance for Natural Health USA reported:12

“According to former FDA officials, in previous outbreaks EUAs could be obtained in a matter of days; but during this outbreak, the application process reportedly became so complicated it took weeks to receive the authorization. Initially, labs were not allowed to begin testing until they got approval from the FDA, even if the lab had confirmed internally that the test worked.

The FDA later relaxed this requirement, allowing certain accredited labs to begin testing as they awaited approval for an EUA — but not before weeks had passed when hospitals and labs were not able to use accessible COVID-19 tests.”

Some labs even developed at-home tests for COVID-19, but the FDA said it had not approved any at-home tests, leading companies to pause distribution and even destroy samples that had already been collected. South Korea, which has been producing 400,000 COVID-19 tests per week, has also been shipping the tests to U.S. states and private labs, but gaining FDA approval on the tests remains a significant hurdle.

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Why Accurate COVID-19 Testing Is so Important

At the University of Oxford’s Our World in Data, researchers highlighted that in order to understand how COVID-19 is progressing, data on testing is essential. It’s the number of confirmed cases that informs the world about the development of the pandemic, but without testing data, you can’t have a clear number of confirmed cases. They report in a March 2020 publication:13

“It [Testing] is one of our most important tools in the fight to slow and reduce the spread and impact of the virus. Tests allow us to identify infected individuals, guiding the medical treatment that they receive. It enables the isolation of those infected and the tracing and quarantining of their contacts. And it can help allocate medical resources and staff more efficiently.

In addition, testing for COVID-19 also informs our understanding of the pandemic and the risks it poses in different populations. This knowledge is important if we are to properly assess the interventions that should be implemented, including very costly interventions such as social distancing and the shutdown of entire regions and industries.”

In other regions, like Hong Kong and Singapore, officials didn’t implement widespread shutdowns until recently, in large part due to early and aggressive testing.

Singapore, which had conducted about 12,800 tests per million population by April 13, 2020, and Hong Kong, which had performed 13,800 tests per million, had two of the highest testing rates worldwide at that time. They avoided widespread shutdowns initially, quarantining only those who tested positive along with their close contacts.14

When an uptick in cases occurred in Hong Kong in late March, enhanced restrictions were put in place, and as they begin to go down restrictions are likely to be loosened. This “suppress and lift” strategy15 may prove useful in the long run, but its effectiveness depends, again, on widespread testing. As it stands, however, many countries are not providing clear and complete data on testing.

There are two types of tests now available in the U.S. — one, known as the polymerase chain reaction (PCR) test, uses a nasopharyngeal swab; and the other, a serological test, uses blood samples to detect COVID-19 antibodies. Differences exist in rates of false positives and false negatives among the different tests, adding further confusion.

Checklist for Best Practices in COVID-19 Testing

According to Our World in Data, not only is widespread testing needed, but the data must be able to be accurately interpreted. The site names Iceland and Estonia as two countries that are going above and beyond to provide detailed and current COVID-19 testing data, but most countries are not.

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“For citizens to trust and understand the published data and for countries to learn from each other, it is crucial that every country provides the data on testing in a clearly documented way,” the site states. Toward that end, they recommend the following checklist as a form of guidance:16

Countries need to first keep track of COVID-19 testing data and then make it easily accessible — “Currently, the available data is often not easy to find, because some countries are releasing figures at unpredictable intervals in ad-hoc locations (including social media or press conferences).”

Clarify “performed tests” or “individuals tested” — Because an individual may be tested more than once, the number of performed tests is not the same as the number of individuals tested.

Clarify whether figures include negative test results and/or the number of tests that have pending results.

Clarify whether the figures include all tests conducted in the country — “Figures reported by countries may only be partial if not all laboratories are reporting to the central authority.”

Clarify if all regions and laboratories within a country are submitting data on the same basis — “In order to assess the reliability of aggregate testing data, it needs to be clear if heterogenous data [are] being summed together. The U.S. COVID Tracking Project, for instance makes it clear that their U.S. totals combine data for tests performed and individuals tested, depending on which is reported by individual states.”

Clarify what period the published figures refer to — “The key question that needs to be answered is whether the figures published at some date (attempt to) include all tests conducted up to that date.”

Address any issues that affect the comparability of data over time — “The Netherlands, for instance, makes it clear that not all labs were included in national estimates from the start. As new labs get included, their past cumulative total gets added to the day they begin reporting, creating spikes in the time series.”

Clarify typical testing practices in the country — “For instance, how many tests does a case investigation require? What are the eligibility criteria to be tested? Are health workers, or other specific groups, being routinely retested?”

Address any information that may be lost in translation — “Many countries report testing data in multiple languages — this helps disseminate the information to a broader audience, whilst helping prevent misinterpretations.”

In the U.S., meanwhile, multiple hurdles still stand in the way of COVID-19 testing, from lack of supplies, like swabs and machines needed to run the tests, to labs losing revenue as fewer elective tests are being performed, yet being expected to ramp up COVID-19 tests, which have low reimbursement rates.

COVID-19 tests may also not be sensitive enough and could lead to false negatives, while, as of April 10, 2020, the U.S. also lacked reliable tests to check people for COVID-19 immunity.17 Many experts agree, however, that widespread testing is needed in order for the U.S. to loosen shutdowns, reopen its economy and get back to a sense of normalcy.