Aegis Sciences Corporation was a tiny, well-established facility with a specific niche prior to SARS-CoV-2. The Nashville-based company, founded in 1990, specialized in anti-doping testing and medication compliance. They later began partnering with small and medium-sized pharmaceutical businesses to do genetic testing for cancer clinical trials. Aegis had no infectious disease business until 2020.
COVID-19 altered that. When the pandemic struck, Aegis responded quickly. In 18 months, the company grew from six full-time lab employees to 550. Its COVID diagnostic testing capability increased from 3000 PCR tests per day at the start of the pandemic to 130,000 PCR tests per day during the Delta wave. Aegis was excellently placed to assist the Centers for Disease Control and Prevention (CDC) in monitoring changes in SARS-CoV-2 with this capability. Aegis sequenced 2000 to 18,000 samples every week using the Illumina COVIDSeq Test. The business was once responsible for roughly 15% of all North American sequences deposited in the Global Initiative to Share All Influenza Data (GISAID).
“We were hiring and onboarding 50 people per week for eight weeks,” says Matthew Hardison, PhD, Aegis’ senior vice president of Lab Operations. “We completed four construction projects to expand capacity without shutting down for one minute.”
Aegis had one Illumina MiSeq before the epidemic. When their surveillance efforts increased, they purchased two NovaSeq 6000 Systems and borrowed a third from Illumina to keep up. It was the start of a wonderful friendship.
“We’ve had a great, collaborative relationship with Illumina,” Senior Scientist Cyndi Clark, PhD explains. “They aided us in scaling quickly, and their support has been outstanding.” They were there that day or the next if we required an engineer or a field application scientist.”
In addition to SARS-CoV-2 pathogen surveillance, As the COVID crisis subsided, Aegis was forced to repurpose its hard-won infectious disease expertise. The corporation recognized the importance of ongoing monitoring and introduced a more thorough testing menu.
They rapidly switched from COVIDSeq to the Illumina Respiratory Pathogen Infectious Disease/Antimicrobial Resistance Panel (RPIP), which contains information on over 280 microorganisms. Bacteria, viruses, fungi, antibiotic resistance genes, and even novel pathogens can be identified and characterized by the panel. Illumina’s Explify RPIP data analysis tools on BaseSpace Sequence Hub (BSSH) really impressed the Aegis team. The RPIP program, a recent addition to the Illumina Connected Software portfolio, converts raw FASTQ information into scalable, actionable insights. It detects, profiles, and quantifies DNA and RNA respiratory pathogens using the Amazon Web Services (AWS) platform.
Aegis’ capability and quality put it on the CDC’s radar for tracking SARS-CoV-2 variants. The National Institutes of Health later hired the lab to perform SARS-CoV-2 genotyping. The Bill & Melinda Gates Foundation funded the lab because of these connections and its overall capabilities.
During the outbreak, clinicians, scientists, and public health officials concentrated solely on SARS-CoV-2—but were other infections present? Aegis was uniquely placed to provide an answer to that issue. The team chose 4400 biobank nasal swab samples from all 50 states, plus the District of Columbia, Puerto Rico, and the US Virgin Islands, which had previously only been tested for SARS-CoV-2. The lab also had deidentified symptom, risk factor, and demographic information that may be linked to the sequencing results.
The Bill & Melinda Gates Foundation awarded Aegis a $2.8 million grant to study those samples and detect probable co-infections. RPIP provided the lab with the required resources to conduct this retrospective study.
“The underlying goal was to create an approach we could take to a developing country as a guidebook on doing multi-pathogen surveillance at scale and not just looking at one pathogen at a time,” Hardison said. “We created capacity models and cost models to show how to run this workflow to boost turnaround times, increase cost efficiencies, and get it up and running in the lab.”
These are just a handful of the research that Aegis and its collaborators could conduct. The ability to respond quickly, coordinate, and scale the broad examination of pathogens and host genomes opens up a universe of potential interrogations.
“We are heavily focused on how we can align the newest, best molecular approaches in conjunction with more old school (but still effective) methodologies to determine antibiotic resistance,” adds Hardison. “Certainly, antibiotic stewardship is going to become more important in coming years.”