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Diagnostics

Shortage of RNA extraction kits hampers efforts to ramp up COVID-19 coronavirus testing

Qiagen vows to ramp up production of kits as scientists turn to social media to plea for donations

by Megha Satyanarayana
March 19, 2020

 

20200319lnp1-kits.jpg
Credit: Michelle Monje
Neuroscientist Michelle Monje filled the back of a car with RNA preparation kits after a call came out for donations at Stanford University.

Qiagen, an international company that makes a critical part of diagnostic tests for the novel coronavirus, announced this week that it is ramping up production of their RNA extraction kits in the face of overwhelming global demand.

This shortage of supplies adds to the struggles of clinical labs in the US trying to test people for the virus, called SARS-CoV-2. As of March 18, there were 7,038 confirmed cases of COVID-19, the illness caused by the virus, but public health officials say the actual number of infected people is much larger. Earlier this month, testing hit a snag when the initial roll out of the test from the US Centers for Disease Control and Prevention contained faulty reagents. In response to the recent material shortages, labs have made pleas for donations of the critical kits, and the scientific community has responded.

The diagnostic tests for SARS-CoV-2 involve looking for the virus’s RNA in patient samples. To do that, the tests rely on a technique called reverse transcriptase polymerase chain reaction (RT-PCR), in which the viral RNA gets copied into DNA and then amplified many times for detection. But to isolate RNA from a patient sample, technicians must first use an RNA extraction kit, like the ones made by Qiagen.

RNA extraction is a delicate process—both cells and the environment around them are full of enzymes that degrade the nucleic acids. The kits used to do these extractions vary in exact specifications from company to company, but for the most part, they contain sterile buffers, solutions that break open, or lyse, cells, and a way of separating the RNA from the DNA, protein, and other macromolecules found in cells.

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The kits, in general, have a few steps, scientists tell C&EN. First, the patient sample is mixed with a solution that lyses the cells. The resulting cellular debris gets removed, and the remaining liquid is treated with buffered solutions and filtered to isolate RNA from other molecules. The extracted RNA can then go on to the RT-PCR step.

Qiagen, based in the Netherlands, is one of largest of the companies that makes RNA extraction kits. Company officials have acknowledged that their current production and allocation is stretched and say that by the end of June, they will produce enough of their kits to power 10 million coronavirus tests per month.

Many labs make their own RNA extraction reagents, but the commercial kits are highly quality controlled and standardized, says Joy Wu, an endocrinologist and bone biologist at Stanford University. That standardization helps with reproducibility in experiments, and test-to-test comparison, Wu says. It’s also critical for diagnostics, she says.

Wu is one of several scientists who put a call out on social media urging colleagues in academia and industry to skim their shelves for RNA extraction kits. She uses the kits to study what genes are active at different points in bone development.

“The response has been really tremendous,” Wu says. “Many Stanford labs had already donated kits. Many companies, locally, in pharma and biotech are donating kits.”

Michelle Monje, a neuroscientist at Stanford who uses the kits to study how cancer cells and nerves talk to each other, was one of several people who donated kits to the university’s diagnostic lab. She says that she and a fellow researcher, Kyle Loh, gathered enough of the bright red Qiagen boxes from colleagues to fill a small office. She estimates that the donations she drove over to the clinic contain about 1,000 reactions worth of material.

The calls for kit donations came as the US Food and Drug Administration rapidly approves coronavirus diagnostics based on RT-PCR to ease the US’s testing backlog. The backlog is being blamed on several factors. Despite the availability of coronavirus diagnostics used in China and Europe early on in the pandemic, the CDC opted to develop their own diagnostic to be used in the US. Stanford and other universities and health systems are deploying their own tests. Wu says Stanford scientists are gearing up to test 1,000 people per day. Companies like Roche also have approved tests that can be used.

When Stanford scientists learned there was a need for extraction kits, many were scrambling to close down their labs in the wake of the Bay Area’s March 16 shelter-in-place order. She says the donations underscore the scientific community’s desire to support efforts to quell the virus’s spread.

“Everybody has these in their labs,” she says. As scientists did what they had to do to pause their experiments, “everybody in the building stopped everything and got their Qiagen kits.”

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Comments
D (March 22, 2020 5:36 PM)
There are plenty of recipes for this buffer. Why does everybody have to purchase it?
Tim Bishop (March 24, 2020 2:34 PM)
What specifically are the reagents in short supply?
Kate (March 25, 2020 10:20 AM)
Because when you’re doing RT-qPCR— you need very specific quality control for the reagents and this is usually so difficult. It is safer to have the kits for diagnostic and treatment reasons. Also, the false negative rate for RT-PCR tests is often high when reagents are made in a regular lab and not in a dedicated facility. Any contamination with RNAse means all the kits are ruined! Qiagen and Roche have dedicated facilities and extensive research on the ideal amounts of reach reagent for each reagent in the kits.

Also getting the actual reagent reagents is also tight right now. Most chemicals originate in China and many reagents are backordered because they had a rough time with the SARS-CoV-2 pandemic.

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