NEW YORK (GenomeWeb) – Aldatu Biosciences, a start-up that is pioneering a diagnostic technology to tackle rapidly-evolving organisms, has received new funding to develop a test detecting all lineages of Lassa virus.
The funding is a Phase I Small Business Innovation Research grant from the National Institute of Allergy and Infectious Diseases totaling $300,000. It marks an expansion of the firm's technology beyond its original application of HIV resistance testing.
Viruses like Lassa and HIV are known to mutate frequently, making detecting them with nucleic acid-based methods an ongoing challenge.
Sometimes, they can mutate in ways that confer drug resistance, and knowing whether a patient has a strain that is resistant to a particular treatment can obviate giving an inappropriate, expensive, medicine that may have serious side effects. But they can also mutate in ways that affect strain typing as well.
Aldatu's core technology is called pan-degenerate amplification and adaptation, or PANDAA. It is a method of using proprietary primers to mitigate the presence of target-proximal polymorphisms in the probe binding site, according to David Raiser, co-founder of Aldatu.
"We have primer design that has a region of the primers that overlaps with the probe region, which is pretty different from traditional qPCR design," Raiser said. In essence, the primers have a pan-degenerate region and a 3' adapter region to remove the polymorphisms present in the probe binding site during the early rounds of PCR, he explained.
This enables the firm to use consensus probes to distinguish different targets. "We've done this more than 20 times now for positions in the HIV genome that are relevant to drug resistance or drug susceptibility," Raiser said.
In particular, the firm has developed HIV products that can be used in settings where HIV genotyping is not the standard of care, as "a potentially scalable option for genotyping that can help guide and manage drug failure in a cost-effective way," he said.
Outside of HIV, the target doesn't have to be a drug-resistance conferring SNP, however, but rather it can be a region where there is variability across different species or strains that could affect assay performance.
In Lassa fever, the variability of the virus across circulating lineages is so high that no single currently available molecular test is able to reliably detect all circulating strains, Raiser noted.
Indeed, the current testing algorithm requires two real-time PCR assays to be run in sequence. "If a negative comes up on the first assay, you need to run a second assay to ensure that it is not a false-negative due to poor coverage of that lineage," said Raiser, noting that the PANDAA approach can be used to overcome this sequence variability.
The jump from HIV to Lassa was in part due to the fact that both are viruses that can have a lot of variability. In addition, Raiser said that its HIV products have brought the company into the realm of a number of global health-focused organizations, and discussions about diagnostic gaps and strong fits for the PANDAA technology with these connections also influenced the decision.
"Lassa just kept coming up as an unsolved diagnostic technology-based challenge," Raiser said.
The company has also garnered some enthusiasm from these potential collaborators, and it got a letter of support for its SBIR application from the Foundation for Innovative Diagnostics. In the letter FIND noted that, pending review of available data and acceptable analytical performance, the organization would support future clinical trials to validate the technology as well as provide technical guidance.
This could be extremely valuable, because for rare diseases like Lassa, samples can be hard to come by.
FIND also noted that a recent Lassa outbreak in Nigeria infected more than 400 people, with a 25 percent case fatality rate.
Aldatu is not currently testing samples from the current ongoing Lassa outbreak in Nigeria — "We are admittedly new kids on the block when it comes to hemorrhagic fevers," Raiser said — but the firm has established relationships that it believes will help it secure samples future.
Another key element of Aldatu's technology is that the firm can mitigate variability while still making very specific assays, Raiser said. And, the way the reagents work is agnostic to the position or identity of the polymorphisms, he added, including de novo polymorphisms in the probe binding site.
"That has been a challenge in some real-time PCR-based diagnostics for viruses — the evolution of the virus is so fast that the assay needs to be redesigned every few years," he said. Thus, PANDAA may extend the time for which an assay has good coverage and sensitivity.
Aldatu is supporting research and development at the company through grant funding. However, for the test to have maximal impact in an outbreak situation, it might need to be paired with a system that can integrate sample preparation and perhaps also detection, Raiser said.
Specifically, the Lassa test in development will ultimately be manufactured by Aldatu in a kit format, but Raiser said the company is also in discussions with industry players to potentially port the Lassa test onto their instruments.
He was not at liberty to discuss ongoing negotiations, but there are a handful of systems with a presence in the appropriate markets that would be an obvious fit. These include the Cepheid GeneXpert, particularly the new Flex cartridge program, and the Abbott m2000, which has a presence in centralized labs in Africa and the ability to run lab-developed tests.
The field tests and distribution plans for the Lassa test will likely follow the same strategy as the firm's HIV products, Raiser said, which involves key users and customers aligned with ministries of health in Africa. This is for the sake of adoption, but also to be eligible for funds from global donors and to support procurement.
The company is also engaged with an organization called Innovation in Laboratory Engineered Accelerated Diagnostics, or iLEAD, an initiative funded in part by the Bill and Melinda Gates Foundation that intends to harmonize regulatory requirements across countries in Africa and may be able to help facilitate regulatory approval for innovative new diagnostics. Aldatu has had conversations with an iLEAD site in Senegal, Raiser said, which could also be a potential for sample sourcing and future field testing.