The first stop in a La Jolla laboratory’s COVID-19 testing process is Bootes. Named for the star constellation and pronounced like the footwear, he’s an automated liquid handling platform developed by the company Hamilton.
Bootes is the first in a series of automated machines at Helix laboratory running COVID tests from county sites, and they can be thrown off by inconsistencies. On a recent weekday, Bootes repeatedly refused to intake a batch of test tubes because a barcode on one vial was tough to read.
Lead clinical lab scientist Jason Nguyen, Bootes’ human handler, said the problem was hand sanitizer frequently used by county staff collecting specimens can sometimes cause the barcode to rub off.
“We have some known issues with the alcohol,” said Nguyen, who entered the sample ID manually, which always has to be verified by another person.
Machines like Bootes depend on uniformity to process thousands of COVID tests in a day, but their services and daily supplies needed to keep them running are in high demand across the country. Materials are becoming scarce — a flashback to the pandemic's early weeks — and some supply gaps are easier to navigate than others.
The problem trickled down to San Diego County’s public health lab earlier this month when a supplier couldn’t provide its usual weekly shipment. Helix stepped in to help fill that gap and provide additional testing over the next few months. The genomics start-up that jumped into COVID testing as need grew in supplying the county with collection materials and processing for up to 2,000 daily tests.
David Becker, Helix vice president of quality and research and development, said uniformity is crucial when using machines like Bootes. That applies to something as seemingly insignificant as the size of the tube that carries swabs from testing sites to the lab.
“You don't get a tube that is half an inch in diameter one day and three quarters of an inch in diameter the next day; that your robotic systems and your processes don't handle those very well,” Becker said during an interview at the company’s La Jolla lab.
It takes time and people to reprogram the machines for these fluctuations, but that doesn’t mean they’re always manageable.
Marc Laurent, Helix vice president of partnerships and operations, said the current situation has them in regular contact with the various producers behind their equipment and materials to plan far ahead of any supply changes.
“We've been working directly with the manufacturer to listen to what options they have at that time for a given week to understand, ‘OK, so the normal supply is constrained. You have another two that's close enough that we could adjust to and work with,’” Laurent said. “These are the conversations we have weeks ahead so we’re not surprised.”
Swabs that collect samples and the liquid in the tube that keeps the specimen viable can also be difficult to obtain, but the greater constraint is among materials needed for the actual processing.
Laurent said because the testing technology is often proprietary, certain components are not interchangeable, such as the reagents, or chemicals that help identify if coronavirus is present, and plastic tips called pipettes. About a dozen are required for every specimen because they help mix in the multiple reagents but are tossed in the trash after adding each one.
Companies may also be limited to certain materials based on their test application submitted to federal regulators.
This means labs can’t always look to a different source when their suppliers are out.
The county’s public health lab faced a similar dilemma earlier this month when officials nearly cancelled appointments at its testing sites because a supplier, Hologic, had to short the county’s weekly shipment of collection supplies known as testing kits. Unlike Helix, Hologic’s testing process requires only one machine that is operated at the county’s lab but requires the company’s collection materials.
“We were facing a real tough situation of needing to close down some of our county testing sites,” county Health and Human Services Director Nick Macchione said during a July 13 news conference.
Hologic, which said it provides millions of COVID tests each month nationwide, told KPBS that manufacturing output varies by week and the reduction to the county was temporary. Michael Watts, the company’s vice president of investor relations and corporate communications, said shipments of testing kits have since rebounded and the company plans to provide the county’s health lab with 20,000 tests a month.
But at the time, Macchione said Helix provided a last-minute reprieve.
“Our ability to test will stabilize because of this new partnership, but we’re always looking to bolster our resources, in fact that’s how we found Helix,” he said.
Helix CEO Marc Stapley said the company developed its test to require a type of swab that’s more abundant, at least for now and it selected a transport media that can stay at room temperature instead of needing to be chilled.
“You need the refrigeration either in the packaging or the transportation itself in order to keep everything at a stable ... temperature and so we’ve obviated that issue in the supply chain by picking the transport media we did,” Stapely said.
Still, the company will have to further navigate the challenges as it plans to significantly expand its daily testing capacity to 10,000 by the fall. That later may even grow to 25,000 as Helix plans to use next-generation sequencing technology that can manage tens of thousands of tests a day.
That’ll require the use of their high-throughput machines called next-generation sequencers, which Helix staff have already nicknamed Vesuvius and Fuji. Bootes will still play his role in the process.
