When he became associate dean of professional programs and graduate affairs at Northeastern University (NU), Dr. Jared Auclair never imagined he would be leading a campus-wide effort to test thousands of staff and students for a deadly virus, not to mention creating a new CLIA-certified lab from the ground up. But in spring 2020, that’s exactly what he did. A year on, NU’s Life Science Testing Center (LSTC) has become a gold standard for on-campus COVID-19 testing. As of April 21, 2021, the LSTC has completed more than 975,000 COVID-19 tests.
“We built everything from scratch,” says Auclair, a protein chemist and the director of the Biopharmaceutical Analysis Training Laboratory at NU. “We basically spun up the lab in six weeks […] but when I first said that we could do it, I was completely naive to what that meant.”
“It surprised me that there were so many different pieces we had to put together that I didn't think about as full-time jobs at the beginning—which they are,” he says.
The lab went up quickly. After going fully remote in March 2020, NU soon instituted a task force on COVID-19 testing, and by June, the initial setup of the LSTC began at NU’s Innovation Campus in Burlington, MA.
To get these types of testing programs off the ground, many institutions partner with their medical schools. This posed a challenge for NU, which did not have any CLIA-certified labs on campus at the time.
“Northeastern is a university that has no medical school—we have a nursing program and other things in the clinical area, but there’s nothing clinical that the University thinks about at a high level. Having to grapple with what it means to have a clinical lab inside of a regular university without a medical school has been an interesting experience,” says Auclair.
Without a clinical infrastructure they could lean on to build their clinical testing facility, NU hired consultants to help with SOPs and certifications. By July 2020, the facility was State and CLIA certified, and on August 17, the facility processed its first COVID-19 samples. An initial capacity of 1,500 tests/day quickly grew to 5,000 tests/day in September, and to 14,000 tests/day in October.
After expanding the facility in October 2020, the LSTC currently operates 24/7 and has approximately 50 full-time clinical testing staff and houses 16 biological safety cabinets, 13 liquid handlers, and 15 qPCR machines.
Deciding on a SARS-CoV-2 test
Another challenge was devising a testing strategy. As a protein chemist with experience studying drug resistance in HIV, Auclair had a clear vision of how he wanted to approach testing for a constantly mutating RNA virus from the initial planning stages of the project.
“My experience studying HIV was in the back of my mind. RNA viruses replicate and mutate—that’s what they do,” says Auclair. “So, I wanted to make sure that we started out with a test that would catch those potential mutations.”
LSTC’s SARS-CoV-2 assay uses Applied BiosystemsTM MagMAXTM Viral/Pathogen Nucleic Acid Isolation Kit and TaqPATHTM COVID-19 Combo Kit for RT-PCR, approved for Emergency Use Authorization by the FDA. The assay targets the S and N genes, which encode the virus’s spike and nucleocapsid proteins, respectively, as well as the ORF1ab gene, which encodes well-conserved non-functional viral proteins. “If one of the [RT-PCR] primers doesn’t anneal, the other targets will still amplify,” Auclair explains. “The likelihood that you would get a mutation in all those areas where it would prevent binding of all three primers is pretty low.”
Expanding to outside communities
The LSTC receives tests from all NU campuses, which are located in Boston, Burlington, MA, Portland, ME, and Charlotte, NC. Students are tested approximately every three days, while full-time faculty and staff are tested twice a week. The facility also provides pooled household sampling for employees’ families. But even with these frequent tests, the LSTC has only been using about half of its 14,000 tests/day capacity.
In April 2021, the facility joined a statewide effort to provide COVID-19 testing to public K–12 schools in Massachusetts. As part of this program, the lab currently processes about 1,200 pooled COVID-19 samples from these schools each week but hopes to increase testing to between 5,000 and 8,000 samples a week, according to a recent NU article.
Looking for the next innovation
Though the lab still uses the same RT-PCR test they started with last summer, part of Auclair’s program is to continuously look for and evaluate new PCR-based tests on the market that may be cheaper, better, or faster than the lab’s current test. So far, he hasn’t found anything better, even with the new SARS-CoV-2 variants.
The only change has been in tracking those variants. “We started a small-scale next-generation sequencing program to sequence all of the viruses on campus to understand which variants are present, if and when variants might arise,” he says. “We are prioritizing sequencing based on our assay. When we detect an S gene drop out, we can prioritize that sample for sequencing, which gives us insight into what might be mutated there.”
According to Auclair, the LSTC is still working through a backlog of sequencing samples, but has identified the B.1.1.7 (“UK”) variant at NU. “We haven’t definitively identified other variants of concern but are looking for those and new variants,” he says.
Apart from tracking SARS-CoV-2 variants, the lab is also involved in research to help NU faculty and outside companies test newly developed COVID-19 diagnostic assays in a real-world clinical setting.
So far, Auclair says LSTC has stayed away from serological tests for clinical testing because they do not have sufficient sensitivity and specificity. Even so, he is actively looking for and evaluating new serological assays when they become available because they may be useful in other ways. “We could link people's [serological] test results to whether they’ve been vaccinated or not,” he says. “If all of a sudden, we're seeing ten, fifteen, twenty people that have been vaccinated who are getting infected, clearly there's a strain evading the vaccines.”
The future of LSTC
Auclair believes NU’s LSTC is a prime example of how to quickly plan and build a COVID-19 testing lab in a short time. “We did a really thorough job building it, and the approach that we followed made a lot of sense—thinking broadly and keeping your options open at first, and then homing in on what the best strategy is for you as an institution,” he says.
Post-pandemic, Auclair says that if COVID-19 testing is no longer needed, the lab could be repurposed to test for other upper respiratory viruses, such as the flu. Other options, he adds, would be to use it to develop a new clinical lab training program or for clinical research, including validating different types of diagnostics or developing new biomarkers.
“There's a lot of opportunity,” he says. “The world is our oyster.”
Webinar: Tuesday, May 25, 2021 at 1:00 PM EDT
Join Clinical Lab Manager and Dr. Jared Auclair, who will discuss how Northeastern University's Life Science Testing Center was set up and licensed in approximately six weeks in order to offer on-campus COVID-19 testing.