Boston-based Northeastern University fully reopened in Fall 2021 thanks to a rigorous COVID testing program, universal vaccine requirements, and an in-house laboratory that was built from scratch. 

By Ann H. Carlson

In the spring of 2020, as the COVID-19 pandemic swept through the United States and schools shifted to virtual learning, the leadership at Boston’s Northeastern University contemplated how to reopen the campus safely to its community of 30,000 students and staff.

Months before vaccines became available, the obvious answer was testing—and lots of it—in order to identify COVID cases early, quarantine those who tested positive, and prevent a campus-wide outbreak. Initially, the university decided to require PCR testing every three days for students coming to campus.

Unlike neighboring universities, however, Northeastern University is not affiliated with a specific hospital, which means there was no existing clinical laboratory infrastructure in place to support regular testing at such a high volume. After weighing options such as partnering with nearby institutions, the private university ultimately decided to build its own testing laboratory from scratch. 

“Having our own testing lab gave us the most freedom and flexibility to adapt and adjust as the pandemic adapted and adjusted,” says Jared Auclair, PhD, technical supervisor for the university’s testing center, director of Northeastern’s Biopharmaceutical Analysis & Training Lab (BATL), and associate dean of professional programs and graduate affairs. “It also gave us some control over the turnaround time and the quality of the tests.” 

In just six weeks of intense work, Auclair and his team built, staffed, equipped, and launched Northeastern’s Life Sciences Testing Center, an in-house CLIA- and CAP-certified laboratory at the university’s Burlington, Mass., campus. Between August 2020 and November 2021, the laboratory processed approximately 1.25 million tests, and it currently averages more than 5,000 tests per day with a turnaround time of between 14 and 16 hours. The lab, which is open 24/7, also supports the pool testing program for K–12 schools in Massachusetts, Maine, and New Hampshire. 

Funding for the entire testing project and facility is provided by the university. For this academic year, all Northeastern students and faculty are required to test once per week, regardless of vaccination status. Auclair credits regular testing with keeping the positivity rate on campus very low, especially in relationship to the surrounding area and the state. Last academic year, the average positivity rate was 0.18%. As of the end of November 2021, prior to the emergence of the Omicron variant, the positivity rate for this academic year was only slightly higher at about 0.3%. 

The early success of the testing program was encouraging, especially as the Delta variant became dominant throughout the country.

“It provides peace of mind, clearly, to the faculty, staff, and students, that we’re in a safe environment,” Auclair says. “I think probably the largest success is the university really taking a science- and data-driven approach and really being committed to keeping our community safe and healthy.”

Staying Ahead of an Evolving Virus

Because Northeastern’s testing program was developed in response to an unfolding pandemic, adaptability has been key to its success. For example, the program began before vaccines were widely available to the majority of the university community, so, initially, on-campus attendees were required to test more frequently. With the advent of vaccines, that requirement has been reduced to once per week.

This academic year, COVID vaccinations are mandatory for all on-campus students and employees, and the university boasts a 99.6% vaccination rate for students and a 97.7% vaccination rate for faculty and staff. In light of the surge in cases due to the Omicron variant, all university students, faculty, and staff are required to have a booster shot.

Part of the impetus toward regular testing was to help protect the broader community, as the Northeastern campus is integrated into the city of Boston, which has a vaccination rate that’s lower than the university’s. Another consideration is that some students are from countries that offer different vaccines from those approved in the United States.

“The efficacy of many of the other vaccines that are approved around the world is not as good as the three that are in the United States,” Auclair says. “So, we wanted to make sure that the population remained safe as we mixed that population of vaccinated people with different vaccines.”

Regularly testing vaccinated students and staff also allows the lab to track breakthrough infections, which helps the university to react more quickly to any uptick in positive cases.

“It’s also interesting from a scientific perspective to see where we’re getting positive cases and what vaccine those individuals have had,” Auclair notes. “Thinking about what we can learn from that and how we can evolve that situation is really interesting.” 

To accommodate such a large university population for weekly testing, the sample collection procedure is designed to be simple and efficient. COVID testing for asymptomatic students, faculty, staff, and contractors on the Boston campus happens at the Cabot Physical Education Center, home of the Husky athletics program. 

The samples are pooled in sets of five, which reduces the cost by 50%, according to Auclair, and relieves supply chain issues for products such as plastics. If a pool is positive, it is deconvoluted in the laboratory to identify the positive patient. 

“It’s a really efficient process,” Auclair says.

Symptomatic patients are tested at the Huntington Testing Center, and these samples are additionally screened for influenza A and influenza B. Positive samples are often retested to confirm results.

“We anticipate the flu to be pretty robust this season,” Auclair says. “We want to be able to differentiate flu from COVID since clinically they present very similarly.”

Testing sites are open from 7 a.m. to 7 p.m. by appointment only. The tests are self-administered and observed by trained professionals to make sure that the samples are collected correctly. Because the process is so efficient, the Northeastern community quickly adapted to the new routine without much pushback.

“Before people started doing the testing process, I would say there was a lot of uncertainty and nervousness, but it’s been generally embraced,” Auclair says. “They can get in the line, check in, swab their nose, and be out the door within 3 to 5 minutes. It’s just part of the routine, and people don’t mind it at all.”

Another advantage to regularly testing the entire university population is the potential for early detection of new coronavirus variants. Auclair spoke to CLP in late November, just days after South African scientists announced the discovery of the Omicron variant of the coronavirus. Although the global impact of this discovery was still unclear, Auclair noted that his laboratory team has been preparing for the eventuality of coronavirus mutations since the earliest planning stages of Northeastern’s testing program.

“Our testing protocols were adapted and implemented just for these scenarios specifically,” says Auclair, who studied drug resistance for HIV-1 protease as a PhD student. “HIV is obviously an RNA virus. The first thing I thought when they asked me to think about the tests for the lab was, ‘This is an RNA virus, it’s going to mutate like crazy.’ We’re going to want to ensure that we’re not missing any of the virus circulating in the population, but also be able to get information on what the different variants might be that are circulating. So, that was part of my thought process pretty early on.”

The key to catching emerging variants early is using a PCR test that allows for the monitoring of multiple genes. Auclair specifically selected the Thermo Fisher TaqPath COVID-19 Combo Kit because of the ability to detect changes in the orf1AB, the S, and the N genes. 

“We’re monitoring the beginning, the middle, and the end of the viral genome,” Auclair says. “It’s sort of like a highway that has 10 exits. We’re monitoring exits 2, 5, and 9, as opposed to many of the PCR tests that are only measuring exit 9.”

Because different coronavirus variants affect different genes, monitoring these three genes allows the technicians to detect virus trends and emerging variants early.

“For example, Omicron, just like the Beta variant, causes an S gene dropout,” Auclair says. “Once we get an S gene dropout, we can use that as an opportunity to prioritize those samples for genetic sequencing and confirmation of the variant. So, that’s part of all of our program.”

Building a Campus Lab from Scratch

As the university’s testing program began to ramp up, Northeastern outsourced some of the workload to the laboratory at the Broad Institute. However, the plan was always to process the majority of the tests on site. 

As luck would have it, Northeastern had broken ground in 2018 on a $70-million, mixed-use research building on its Burlington campus that was set to open in June 2020. The university initially housed the COVID testing lab in the new building as part of the BATL biopharmaceutical research lab where Auclair serves as director. 

“Setting up any clinical lab, especially if you’re trying to do it quickly, is not for the faint of heart,” says Auclair, who credits the university for coming together with the supports needed to make the fast turnaround possible. 

Within an intense six weeks, the lab was staffed, equipped, and certified. The Life Sciences Testing Center officially opened on Aug. 17, 2020. 

“The game plan was always to start off with maybe 300 or 400 samples, and by the end of the week ramp up to 1,000,” says Eduardo Sanchez, one of the lab’s seven general supervisors and a Northeastern graduate student pursuing a master’s of science in biotechnology with a concentration in scientific information management. “But I remember that we started that first day with 1,300 samples.”

Kristen McIntire, MPH, also a general supervisor for the lab and a nursing student at Northeastern, remembers the nervous energy of that first day, too. “They got twice as many as they were supposed to get, and now if we get that amount of samples and that’s a slow day for us,” she says.

To handle the sheer volume of the workload, the COVID testing side of the laboratory quickly expanded to today’s footprint of 1,000 square feet. The lab originally opened with two liquid handlers and four PCRs, but it is now equipped with 13 liquid handlers and 16 PCRs. 

While dealing with active construction certainly had its challenges as the team was finding its footing, McIntire notes it also had its advantages, such as the ability to make the lab as customized and efficient as possible. 

“[One team] actually looked at things like how many steps is it from this bench to this hood, and how we could maximize the efficiency of the person walking from doing this step of the process to the next one,” she says. “So, the lab is now like a really well-oiled machine, just from all of that careful analysis. It’s felt like a clean slate where we can establish the kind of work environment that we want to have for our staff.”

In addition to CLIA-certified and trained laboratorians, the testing center required a business manager, a supply chain manager, quality control support, IT technicians, and administrative support staff. The lab quickly grew from a skeleton staff to 55 employees, including about a dozen Northeastern students. 

“Developing this kind of lab really just emphasizes the need for collaboration,” Sanchez says. “We all had great chemistry. It’s important to get the right team.”

One of the biggest challenges of getting the lab up and running was staff training. “When we first started, all of us were kind of training at the same time, which isn’t ideal,” McIntire says. “We had a couple of technicians help us think through an onboarding sequence of what makes sense, so everybody went through the same training.” To make sure everyone was on the same page regardless of experience level, this involved going back to the basics, such as how to properly pipette, how to avoid contamination, and even on how to mix the plates.  

With any high-volume testing process, mistakes will happen. Though these incidents are rare, sometimes there is an instrument issue or an incorrectly collected sample. The key, Sanchez says, is to identify mistakes immediately so they can be corrected and avoided in future.  

“The worst thing about a mistake is if you don’t say anything at all,” Sanchez says. 

Both McIntire and Sanchez emphasize the importance of being patient under pressure and advise staff to take their time, rather than rush through sample batches. Sanchez encourages staff to remember that each sample represents a person, who might be trying to catch a flight or to see their grandparents for the first time in a long while. 

“You don’t know who is on the other side of that sample,” he says. “It’s not about coming in here and being as fast as you can, because that’s when mistakes happen. So, we’d rather you really master what’s going on and really take your time. It’s being patient in a stressful situation, which is the hardest thing to do.”

Although some staff have experienced breakthrough infections, the laboratory has not had any major outbreaks of COVID to date, which McIntire credits to its daily testing policy. 

“The people who came up positive would find out literally the first day that they were positive for the disease, so we were able to send them home and not worry about it spreading to other staff,” she says. “We really believe that it’s important for us to continue doing it that way just for our own safety. Also, if we had an outbreak, we would have a lot less people being able to process the test, so it’s also to protect the community at large as well.” 

Focusing on Continuing Research

For the current academic year, Northeastern’s rigorous testing protocols are here to stay. But as the pandemic moves to an endemic phase, the Life Sciences Testing Center may be able to shift focus from daily testing to other research avenues. 

To prepare for this eventuality, the staff is split into teams that each focus on different research projects in addition to their general testing duties. For example, one team is responsible for running mutant panels specifically to identify the different known SARS-CoV-2 variants as well as isolate any unknowns for genetic sequencing.

“I think the next couple of months is really going to be data-driven,” Sanchez says. “We’re going to be collecting a lot of sequencing data, and sequencing is still a space for a lot of research to be done. In some parts of the world that don’t have the infrastructure that we have here in the United States, access to sequencing isn’t readily available. So, when you do decide to sequence, how do you use this precious resource?”

Another avenue is looking into different kinds of testing, such as the ability to take blood samples, which could tell researchers more about the effects of the virus. “We really want to look at what’s in everyone’s blood who’s had COVID, and I think there’s just a lot of potential for new research to come out of that,” McIntire says.

In the meantime, the focus will remain on testing and sequencing. “The virus is very humbling,” McIntire says. “You know, right when you get used to something, you get hit with a new variant.”

Despite the uncertainty of these pandemic days, McIntire is curious about what the future will hold and what technologies will emerge from the data gathered during the time. “With the amount of progress we’ve made in a single year, I can only imagine what’s going to happen 10 years from now,” she says.

No matter what the future holds, the Life Sciences Testing Center will always have a role to play at Northeastern. Auclair notes that in his entire professional life, he has never seen so many different parts of a university—from procurement to human resources to IT—come together to support one project so entirely. 

“I’m super proud of what we were able to accomplish,” Auclair says. “It truly was a university effort and really speaks to the commitment to health and a good learning environment that we try to emphasize.”

Featured Image: Northeastern University has developed a rigorous COVID-19 testing program, which included setting up its own in-house lab, which expedites collection and reporting, and keeps costs down. Photo: Matthew Modoono/Northeastern University

Ann H. Carlson is a regular contributor to CLP.