NEW YORK (GenomeWeb) – Pathogen sequencing company Pathogenica has moved to Lausanne, Switzerland and rebranded itself as BioInnovation Solutions, Clinical Sequencing News has learned.
Additionally, in a collaboration with the US Army Medical Research Institute of Infectious Diseases, it is developing a next-generation sequencing panel for filoviruses — which include the Ebola virus and Marburg virus — that it described in a recent PLOS One paper.
Pathogenica was spun out from Harvard Medical School in 2009 by cofounders George Church and Yemi Adesokan. The firm's proprietary capture technology, DxSeq, was used to develop its BioDetection HAI kit, a CE-marked hospital-acquired infection assay.
BioInnovation Solutions CEO Pat Bayer, who joined the company a few months ago, told CSN that BioInnovation is using the same DxSeq technology that was developed by Pathogenica. In addition, Yemi Adesokan, who had previously been CEO of Pathogenica, is now at BioInnovation Solutions.
The company is still focusing on pathogen detection and is still selling the CE-marked BioDetection HAI kit. In addition, it continues to collaborate with the Netherlands' University Medical Center Groningen and Amphia Hospital.
However, Thermo Fisher and Illumina, with whom Pathogenica had inked co-marketing agreements for the kit, are no longer marketing the BioDetection HAI kit, spokespersons from the respective companies told CSN.
BioInnovation Solutions is "essentially Pathogenica reborn in Europe," Bayer said. The company is a stand-alone firm that was created from the work that Pathogenica developed, he added. And, because it markets a CE-marked kit, it made sense to be in Europe, he said.
BioInnovation has also developed a research-use-only kit for hospital-acquired infections, dubbed HAI BioInnova Kit, which can be used with any next-generation sequencing platform. According to its website, when run on the Ion Torrent PGM with the 316 chip, total turnaround time is between 12 and 12.5 hours, including 2.5 hours for library prep, a nine-hour sequencing run, and 30 minutes to 60 minutes for automated analysis.
The kit screens for 12 pathogens and 18 antibiotic resistance genes and can work on human-derived samples — sputum, stool, and urine.
In BioInnovation's PLOS One paper, the researchers describe a panel that includes probes for the five ebolaviruses — Sudan, Ebola, Reston, Taï Forest, and Bundibugyo — as well as three Marburg virus variants — Musoke, Ci67, and Angola.
"The goal is to sample populations in endemic hotspots and put in place the right measures before there's an outbreak or before further spread," Bayer said.
The work was done under a cooperative research and development agreement with USAMRIID. According to Tim Minogue, chief of systems development at USAMRIID and an author of the PLOS One study, USAMRIID began collaborating with Pathogenica several years ago when USAMRIID was looking at better methods for biosurveillance.
Minogue said that BioInnovation's targeted sequencing panel would likely be an "interim solution" until the field moves toward whole-genome sequencing. "We're segueing toward sequencing-based diagnostics, which is the future," he said, because it allows one to "agnostically assess a sample."
Bayer said that the collaboration with USAMRIID is ongoing and BioInnovation Solutions is "working with them to take the test from publication to clinical use." In addition, the company is interested in partnering with governments in other countries that want to use the test and "localize it to their geographies."
In the study, the researchers used the DxSeq capture technology, which involves the use of linear oligonucleotide probes. Sequencing was done on either the Illumina MiSeq or GAIIx.
The probes contain complementary sequences that hybridize to the target sequence. A polymerase then fills in the target sequence, and a ligation reaction captures the sequence within a circularized single-stranded probe. Exonucleases remove the non-circularized probes and the off-target DNA that is not captured. Finally, PCR is done to amplify the captured sequence.
For the filovirus panel, the researchers identified conserved regions for probe hybridization that also contained viral sequence to differentiate the filovirus isolates. A probe design algorithm was used to design probes that do not interact and that can discriminate between closely related viruses. The group designed panels of 15 probes for each filovirus that were then pooled and tested on different samples.
The group tested the panel on RNA from virus-infected cells. The percentage of total reads that mapped to the target filovirus genome ranged from 5 percent to 91 percent. The panel did not work on cells infected with the Reston virus — with no reads mapping to the Reston viral genome — despite the fact that the individual probes were able to detect the Reston virus.
Adesokan told CSN that this is one area that the group is working to optimize.
Next, they tested the panel on archived clinical samples and compared it to real-time PCR. In six Ebola virus samples, the panel was able to identify the virus in three of the samples with the highest viral load. Looking at samples from humans with a potential exposure to the Bundibugyo virus, who all eventually showed signs of infection, the panel identified three out of the five samples that were called with RT-PCR as positive. One sample that was called negative with RT-PCR was positive with BioInnovation's panel, and two samples — one negative and one positive by RT-PCR — gave mixed results.
Since publishing, Adesokan said the company has improved the assay's sensitivity and specificity, although he didn't disclose the current specifications.
Minogue added that one area that still needs further optimization is the turnaround time, which he said is currently between 12 and 14 hours. "For clinical diagnosis, 12 to 14 hours, especially for filoviruses, may be too long," he said.
He said that for surveillance, the time frame is sufficient, but before it could be moved into clinical use, it would have to be improved upon.