One such story is about how a team in the Clinical Sequencing Division came together to successfully launch a new NGS panel, the Ion AmpliSeq SARS-CoV-2 Research Panel, in record time. The assay is designed to support epidemiological studies of SARS-CoV-2, with the ultimate goal of enabling accurate data to inform potential intervention strategies that may help limit the devastating impact of the crisis.
We met with Dr. Anjali Shah, Senior Director of Product Management in the Clinical Sequencing Division, who led the team and development program that resulted with the launch of the Ion AmpliSeq SARS-CoV-2 Research Panel.
Interviewer: Dr. Shah, what was the motivation behind the Ion AmpliSeq SARS-CoV-2 program, and can you describe your experience of working with the team?
Dr. Shah: Certainly—in these challenging times, it is so important to rapidly enable discoveries of biological insights for the world to assist in solving this unprecedented public health situation, and I am extremely proud to say that this is one of the most defining moments in my 14 years at the company.
Different people from a variety of cross-functional teams came together and collaborated with leading researchers in the forefront of the SARS-CoV-2 crisis to deliver one of the most impactful solutions for epidemiological studies to understand this virus, study its mode of transmission, detect it’s sequence evolution as it traverses in different geographies and populations, and so we can better understand the epidemiological impact of the virus and the potential link to disease severity, as well as assist in vaccine development research.
From concept to launch, this research solution was delivered to market in only 6 weeks with the coordinated efforts of over 80 employees from research & development, product management, marketing, sales, field support, operations, legal, and regulatory teams. We were also lucky enough to work with over 20 global collaborators, who are experts in their fields, to really understand this virus and provide more information about its epidemiology.
You may have already seen or heard some of the press releases and social media posts that captured these customer stories and the impact of the data that our solutions are beginning to generate to really change the way we think about solving this public health issue.
Interviewer: That is very inspiring work. Could you tell us more about the need that you saw for what became the product that you have developed?
Dr. Shah: Yes of course. The solution we put together is the Ion AmpliSeq SARS CoV-2 Research Panel for the Ion GeneStudio S5 system and it encompasses our flagship Ion AmpliSeq technology.
As to what need we saw—well, first of all, we wanted to enable the largest install base of our customers to quickly gain biological insight about the SARS-COV-2 virus. Second, the modularity of the Ion GeneStudio S5 system really allowed us to optimize conditions to address the wide variety of the sample types that are being used in research across the globe—everything from sputum, nasopharyngeal swab, blood and even stool. All of these sample sources contain a wide range of viral load, so we really needed the solution to work across all of these potential sources and to optimize our solution so that for every sample being analyzed, we would be able to deliver the complete genomic sequence and key variants that could be used to study severity of infection and assist in vaccine development research.
Interviewer: Yes, it is obviously critically important to ensure that the solution works reliably in many different situations. Can you tell us more about the SARS CoV-2 research panel that you and your team developed? You also mentioned the genomic sequence and the key variants that are identified; can you tell us more about the data that is generated?
Dr. Shah: Well, the workflow is what we call a ‘sample-to-answer’ solution starting from as little as 1ng of input. And what I really want to highlight here is that we did some incredible work with our bioinformatics team in China, who were central to developing a new research plugin package to allow us to not only annotate those important key variants, but also to build consensus sequences of the virus for every single sample that was analyzed.
To provide you with some more details specifically about the panel – it is one assay that surveys the complete SARS-COV-2 genome and is intended for epidemiological investigation. It’s a two-pool solution that contains 247 amplicons—237 of those are specific to the virus, and there are 5 human expression controls in each pool. And those [human expression controls] really serve as an internal control for sample and library preparation so that we can get valuable sequences out of all of the samples processed. The panel covers over 99% of the SARS CoV-2 genome and we believe that this panel will be able to address all potential serotypes, which are basically the viral sub-species that are characterized by cellular antigens on the surface of the virus.
Interviewer: What about your next plans are for this panel, and do you have any final words as you look to the future?
Dr. Shah: Certainly. Our work does not stop here. Just a couple of weeks ago, we introduced the Ion AmpliSeq SARS-CoV-2 for our latest system, the Ion Torrent Genexus system, more of you will hear about why the rapid turnaround time and the incredible automation that this system delivers is going to be critical for studying the containment strategies that are essential for preventing or reducing the chance of SARS-CoV-2 resurgence.
I would just like to finish by saying a big “thank you!” to all those who have been involved in the initial project. It really exemplifies the passion and dedication of everyone who has contributed to this effort, and many more in the company are continuing to work tirelessly today to rapidly bring our NGS solutions to the world to serve the continuum of infectious disease research.
For Research Use Only. Not for use in diagnostic procedures.