NEW YORK – Agena Bioscience will sell and distribute a new mass spectrometry-based assay for detecting SARS-CoV-2 mutations that runs on its MassArray system, the company said this week.
Seq-It, a Kaiserslautern, Germany-based molecular services provider, developed the new test. The assay is being positioned as an alternative to next-generation sequencing-based approaches, which its creators view as ponderous and pricey.
The arrangement is unique for San Diego-based Agena, which usually develops assays on its own, as well as for Seq-It, which builds assays for clients for specific projects but does not commercialize them.
"Agena historically designs the MassArray panels in house," noted Keith Jackson, marketing director for the firm. "In this case, there existed an opportunity to accelerate the availability of this important tool by leveraging the work done by Seq-It," he said. "Their progress, combined with additional in-house development by Agena, enabled [the] rapid creation and deployment of this valuable tool."
The new assay tests for 20 mutations related to B.1.1.7, commonly called the UK variant; B.1.351, or the South African variant; B.1.248/P.1, known as the Brazilian variant; Cluster 5, the Danish variant; and D614G, a notable mutation in European variants of the virus. The assay retails at about $25 per sample and has a turnaround time of a few hours.
Agena believes the assay might win users among its existing customer base. Jackson said the company does not disclose how many systems it has installed but said there is an "extensive network of instruments" within clinical and public health laboratories globally, including in the US, Europe, Middle East, Africa, and Asia.
While Agena just launched the offering, Jackson said the firm is already seeing "strong global demand" for the panel.
The new assay is for research use, he stressed, and is being sold for surveillance. Agena will manage any future regulatory submissions. Assay panel sets are available in both 96- and 384-reaction formats, meaning that users can scale to thousands of samples per day, if needed.
Agena's MassArray System does have emergency use authorization from the US Food and Drug Administration for SARS-CoV-2 testing, which the company obtained in October.
Seq-It is a subsidiary of the diagnostics laboratory Institute of Immunology and Genetics in Kaiserslautern, located about 80 km west of Heidelberg. The company, which has about 15 employees, is a MassArray service provider but also has Illumina next-generation sequencing platforms in house, including MiSeq and NextSeq. In addition to its expertise in infectious diseases, Seq-It also works in oncology, pharmacogenetics, forensics, and plant and animal genetics.
"We are not a large sequencing center, we are more specialized on different topics and have a broad area where we work together with universities and other companies," said Seq-It Managing Director Alexander Thielen. "We also have specialists on staff working in these fields."
According to Thielen, the company decided to pursue an assay for SARS-CoV-2 mutations on the MassArray system, versus its Illumina instruments, because of the mass spec system's faster turnaround time and lower assay cost.
"If you are interested in full-genome sequencing, of course you can't use MassArray, but if you have a small SNP panel, you can be quite quick and cheap with MassArray," Thielen said. "In terms of coronavirus testing, we can detect 20 mutations in a few hours for less than $30 or so. Sequencing takes several days and is more expensive."
The company also had experience it drew upon to craft the assay. "We have a strong virological background," said Thielen, noting that Seq-It has been working on HIV drug resistance testing for more than 15 years. It is also connected to other German laboratories, including those at Charité Medical University Berlin, which began to make primers available for real-time PCR-based SARS-CoV-2 testing a year ago. Thielen said that Seq-It's work on COVID-19 dates back to early last spring.
The catalyst for the mutation test, however, came in the fall, when a mutation detected in mink farms in Denmark made a jump into the local population. When a strain of SARS-CoV-2 called B.1.1.7 was detected in the UK at the end of the year, Seq-It decided to assemble the most relevant variants into an assay.
Thielen noted that the resulting test, while having a fast turnaround time and low cost, does not replace the need for using next-generation sequencing to monitor the emergence of new variants. Rather, it can be used to monitor the prevalence of mutations at high throughput. At the moment, German authorities, together with partners like Charité, are continuously sequencing a proportion of positive cases to keep abreast of the emergence of any new strains in the local population.
"With sequencing you can find all new mutations," said Thielen. "If you want to check if the sample has the UK or South African variant, then Agena is fine," he said, "but if you are looking at new mutations, such as those appearing in California, then we cannot detect them at the moment and you have to rely on sequencing."
Thielen also noted that while the new mutation test on the MassArray platform is intended for research use only, labs can still validate it internally for clinical use.
Thomas Alef, head of development at Seq-It, said this is the first time that Seq-It has seen one of its assays commercialized by an external partner. "We have developed assays for a lot of national and international partners, but these are normally closed projects," Alef said. "This is the first time assay development has ended in this kind of partnership."
In addition to serving as a sequencing service provider for university partners, Seq-It counts pharmaceutical companies among its customer base. These firms, which Alef declined to name, also rely on its sequencing expertise, which remains its forte. "Obviously, we named the company Seq-It for a reason," he said.
The company will continue to develop its panel if needed, Alef said, and will within weeks submit a paper detailing its validation of the test. He underscored that according to German authorities, all SARS-CoV-2 positive samples should be typed for variants, and labs will have to decide whether to continue to rely on sequencing or move to mass spectrometry.
"The method to do this is not prescribed, so it is up to the respective laboratory," said Alef. "[Some] are doing it with sequencing at the moment, [while] we are already using the MassArray system to do so."