VANCOUVER, BC — Tessarae, a Potomac Falls, Va.-based firm that develops arrays for pathogen identification, this month added two new tests to its menu of resequencing microarray assays.
Agnieszka Lichanska, a senior scientist at the firm, said that Tessarae is now selling the TessArray RPM-HFV Kit, a whole-genome resequencing array for hemorrhagic fever viruses; and the TessArray RPM-TEI Kit, designed to identify tropical and emerging infections.
The chips complement Tessarae’s flagship RPM-Flu 3.1 array, launched last year, which can detect known and unknown viral and respiratory pathogens (see BAN 4/24/2007). Tessarae plans to submit the RPM-Flu 3.1 for US Food and Drug Administration 510 (k) clearance, while the firm has not yet decided whether to seek clearance for the HFV or TEI arrays.
“RPM-TEI detects and identifies human and animal viral and bacterial pathogens, as well as some toxin genes, so it is similar to RPM-Flu in that it contains two or three loci per organism,” Lichanska said of the new array. However, it “focuse[s] on highly pathogenic agents that are also considered biological threats including hemorrhagic fever viruses” like Ebola or the flavivirus that causes Dengue fever.
“So if you want to work on Dengue Type 1 or on Ebola or [the] Marburg [virus], you can just basically grab your samples from wherever you are — most of these would be in Africa, though some are in South America — and you can look at the sequence of the entire genome and see what the differences are, and look at the phylogenetic relationship between the new isolate and the known strains tiled on the arrays,“ said Lichanska, who spoke with BioArray News during the Fourth Annual World Microarray Congress, held here this week.
She added that the two new chips can be used together. “If you detect these [pathogenic] agents on the RPM-TEI, then you can say, ‘Oh, I am really interested in looking at the whole genome of [the pathogen],’ so then you can take that and use one of the RPM-HFV whole genome-sequencing arrays,“ she explained.
How They Work
Tessarae’s chips are manufactured by Affymetrix and its RPM assays employ a similar workflow to Affy’s. Matthew Lorence, Tessarae’s vice president of sales and marketing, told BioArray News in an e-mail this week that the assays typically call for the user to obtain a clinical sample, either via throat swab or nasal wash. The total nucleic acids, both DNA and RNA, are then isolated, and the RNA genomes are reverse-transcribed into cDNA.
Tessarae then instructs the user to amplify the cDNA and DNA genomes in four multiplexes, representing a total of 186 different loci. “The amplified sample is pooled, hybridized, and that’s it. And it’s the same as for other Affymetrix arrays in terms of washing and staining,“ Lorence said.
“Ultimately, it is a tool to qualify those sequences that should be compared to the database for sequence identity versus those that should not.”
According to Lorence, Tessarae uses Affy’s GSEQ software to translate the image of the array into sequence data as a Fasta file. The file is then uploaded by the user via the Internet to a secure Tessarae website where the quality of the sequence data is evaluated using a parameter called C3.
“Basically, it is the percentage of the detected sequence that appears in clusters of three or more called bases, so the longer the contiguous sequence you have, the higher your C3 score will be,” he said. “So if you have a very high load of pathogen in your sample, the C3 score could be quite high, approaching 100 percent. Ultimately, it is a tool to qualify those sequences that should be compared to the database for sequence identity versus those that should not.”
After the sequence is identified, results are e-mailed back to the user, “typically in less than 15 minutes as a high-level report of the bacterial genera and/or viral types present in the sample,” Lorence said.
Lorence said that users can use real-time PCR to confirm the pathogens that its arrays have identified. He said that RPM-Flu, for example, is “ideally suited to detect and identify any of the pathogens that one could expect to find in a respiratory specimen with sensitivity greater than or equal to PCR, but is a qualitative assay.
“Real-time PCR is ideally suited to quantitate the amount of a pathogen present in a specimen, but will only detect those pathogens that one specifically tests for,” Lorence said. “So, once the pathogens present in the specimen are identified with RPM-Flu, PCR is the ideal complement to quantify the amount of pathogen.”
The company charges $300 for a kit that includes arrays designed for use in the assays, plus reagents, Lorence said. Additional supplies can be purchased from other vendors.
Studies and Submissions
During her presentation in Vancouver, Lichanska showed data from a recent study performed at the Naval Health Research Center in San Diego that used the RPM-Flu kit for pathogen detection.
“Basically the aim was to look at respiratory infections among basic military trainees, because once you crowd people into dormitories, you often get adenovirus outbreaks as well as other infectious diseases,” she said.
NHRC collected specimens from eight different training venues, and initially tested them for influenza A and adenovirus using culture and PCR. Those same samples were then tested with the RPM-Flu kit and confirmed with culture and PCR.
“That is a nice validation for us,” said Lichanska.
The validation study also provided data that the company will use as it prepares to submit the RPM-Flu for FDA clearance. “The FDA submission for the RPM-Flu is already being prepared,” she said.
Lorence said that Tessarae is currently in different stages of discussions with “several potential collaborators, primarily in hospital settings, either academic or commercial, both in the US and abroad” to validate the RPM-HFV and RPM-TEI chips.
“We plan to announce these collaborations as the work is completed and published,” he said.