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Helix, San Diego County Partner on COVID-19 Molecular Testing

This article has been updated from a previous version to clarify that Helix has initiated COVID-19 testing while FDA Emergency Use Authorization is pending.

NEW YORK – Helix said on Monday afternoon that it is partnering with California's San Diego County to provide up to 2,000 COVID-19 molecular diagnostics tests per day out of its San Diego lab.

Under the terms of the agreement, the financial details of which were not disclosed, San Diego County will be using the Helix COVID-19 Test, a laboratory-developed RT-qPCR assay workflow intended for the qualitative detection of SARS-CoV-2 nucleic acid in upper respiratory nasopharyngeal, anterior nares, and oropharyngeal swab specimens from individuals suspected of COVID-19 by their healthcare provider.

Accessioning, sample prep, and testing will only be able to take place in Helix's high-complexity, CLIA-certified, CAP-accredited laboratory in San Diego, and the company said it can return results the next day following sample receipt. The assay will specifically use the Thermo Fisher Scientific TaqPath COVID-19 Combo Kit run on Thermo Fisher's QuantStudio 7 instrument, which already has FDA EUA. Helix said that its testing workflow has shown 100 percent sensitivity and specificity using a mix of clinical remnants and contrived clinical samples, and that it has a limit of detection of 1,000 viral copies/ml.

Helix has submitted the workflow for FDA EUA and said that it is actively working with the agency and that authorization is "pending." In the meantime, the company can perform testing under FDA regulations stipulating that a lab can initiate clinical testing as soon as it notifies the agency that it has completed validation testing of its COVID-19 assay and until formal EUA is granted. 

Like many companies in the genomics space, Helix's COVID-19 testing plans represent a significant shift from its primary business of next-generation sequencing-based population genomics.

"We were founded in 2015 right here in San Diego, and we've got five years of expertise operating a clinical lab and collecting and processing samples at massive scale," Mark Stapley, president and CEO of Helix, said during a webcast press conference on Monday. "So, we're well-prepared for this challenge."

"We intentionally built our lab from the ground up to be able to be highly automated and scalable, making it a unique fit for the ever-growing demand of COVID-19 testing," Stapley added. "We've shifted the majority of our resources to ... support this effort. While we continue to service our population genomics customers, we're incredibly focused on COVID-19 testing because it's needed by our community and around the entire nation."

Stapley noted that Helix can provide a fast turnaround time for its COVID-19 assay because it's the only test the lab will perform alongside its NGS assay for population genomics.

"We are of course subject to the same supply chain constraints as other labs for some of the components and raw materials used in our testing," he said. "But as we designed our test, we intentionally focused on addressing some of those areas where we could avoid the existing choke points in the supply chain."

For example, he said that anterior nasal swabs are more comfortable for patients and easier to procure. In addition, the alternative transport material Helix is using does not require cold chain, and can be shipped and stored at ambient temperature.

As previously reported, Helix is also developing a second COVID-19 test based on next-generation sequencing. This test will be based on Illumina's NovaSeq system. 


"In addition to being more scalable, we believe this will be … one of the most sensitive tests on the market [and] will have significantly fewer supply chain constraints because it has a different supply chain than the tests that are being run today," Stapley said during the press conference.

Helix, which launched with significant financial backing from Illumina, last year closed two offices and laid off a number of employees as it shifted its focus away from selling consumer-oriented apps based on customer genomic data and toward population genomics projects and partnerships.

In January of this year, Helix announced that it had teamed up with the Mayo Clinic Center for Individualized Medicine to launch a new clinical genomics study called Tapestry that aims to enroll 100,000 Mayo Clinic patients over the next five years.