Faulty probes are to blame for CDC coronavirus testing woes

Early batches of a kit developed by the US government to diagnose the novel coronavirus infection have been plagued by problems that initially limited their use and cast doubt on their accuracy. The problems were first reported by the Washington Post, and C&EN learned soon after that the kits contained faulty reagents that led to inconclusive readouts. The Centers for Disease Control and Prevention (CDC) has started an investigation into what exactly went wrong with the tests.

The CDC designed and manufactured the test kit, which detects the RNA genome of the virus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The US Food and Drug Administration has approved its use in public health departments nationwide.

As of March 5, SARS-CoV-2 has killed 10 people in the US and infected nearly 100. Several hundred people have been tested, but the CDC has now stopped reporting testing numbers in favor of what it says are more accurate state and local public health reports. CDC officials have said that positive SARS-CoV-2 tests at the state or local level must be confirmed by the CDC.

The CDC kit is based on a common technique for detecting genetic sequences called reverse transcriptase polymerase chain reaction, or RT-PCR. Used to detect RNA in a sample, the technique involves first creating a complementary DNA strand to the RNA present in the sample and then amplifying that DNA. If the target nucleic acids, such as coronavirus RNA, are present in the sample, the amplified nucleic acids produce a fluorescent signal.

Kelly Wroblewski, a microbiologist who leads infectious disease programs at the Association of Public Health Laboratories, says the reagents that didn’t work properly are nucleic acid probes designed to detect RNA sequences of all coronaviruses that infect humans, including milder strains that are endemic to the US population. These probes serve as a beacon, she says, that a coronavirus is present and that the sample should be tested further to determine whether that coronavirus is SARS-CoV-2 or another. It’s not clear at what step the probes failed or if they failed, for example, because of reaction conditions. Wroblewski also told Science that there were problems with signals appearing in a negative control experiment in the kit.

The kit contains two other sets of probes that are specific to SARS-CoV-2 and are used to determine whether a patient is infected with the novel coronavirus. CDC officials have said that with a revised protocol, the older kits can be used with just those two sets of probes. New kits, which presumably contain a working third set of probes, are being made. CDC officials did not respond to requests to clarify the problems with the older kits.

“It’s not necessary. It’s a nice to have, not a need to have,” Wroblewski says of the ability of the kits to detect other coronaviruses. “It doesn’t really impact the actual sensitivity of the assay when you are looking for novel coronavirus.”

Other companies are developing SARS-CoV-2 diagnostics for use in the US. CDC officials say that those tests will be available to hospitals and other health-care facilities. It’s not clear when the FDA will approve other tests.