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Inside the NY lab churning out 15,000 COVID-19 saliva tests per day to keep colleges open

David Robinson
New York State Team

SYRACUSE - An upstate New York laboratory hummed like a scientific assembly line recently as it churned out results of a COVID-19 saliva test poised to improve how the U.S. combats the deadly respiratory disease.

Scientists in white coats and blue facemasks scurried around carrying clear plastic containers and bags stuffed with test swabs that resemble oversized Q-tips, each one sealed tightly in a vial with liquid.

The meticulously orchestrated infectious-disease hunt began by scanning a bar code on each vial, setting the pace for a high-stakes race to screen 15,000 samples per day inside the lab at SUNY Upstate Medical University in Syracuse.

Once in the system, each sample passed through a series of stations where workers pooled, purified and tested saliva gathered from college students across New York for SARS-CoV-2, the virus that causes COVID-19.

Each stop along the line inched closer to identifying and isolating infected students early enough to keep colleges open amid the pandemic.

Brian Haarer, an assistant professor of biochemistry and microbiology, works in a lab at the State University of New York Upstate Medical University that conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

After surveying the well-oiled workflow, lead scientist Frank Middleton said: “This is all about keeping the most people safe and disease free as possible.”

And now the COVID saliva test, which initially had limited state Health Department approval for use in higher education, is set to begin protecting all aspects of society after gaining federal Food and Drug Administration approval last week.

SUNY Chancellor Jim Malatras touted the development as a game changer, saying the innovative test “will now help communities across the country better pinpoint and contain COVID-19.”

How COVID testing helps New York get through the fall

A lab at the State University of New York Upstate Medical University conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

The push to expand use of the saliva test developed by Upstate Medical and its private-sector partner Quadrant Biosciences comes amid mounting concerns about a COVID-19 resurgence this fall.

Despite robust testing and a statewide infection rate hovering around 1%, outbreaks have already forced SUNY Oneonta to close its campus and halted in-person classes at SUNY Oswego.

Infections at dozens of K-12 schools statewide have prompted student quarantines and closed classrooms. Growing clusters in parts of New York City and its suburbs have authorities warning some community reopening plans there may be paused.

Meanwhile, a wide variety of COVID-19 saliva tests are being used nationally and each one, including the Upstate Medical model, is another key addition to the outbreak containment toolbox, experts said.

Jimmy Boyer works in a lab on Sept. 22 at the State University of New York Upstate Medical University that now conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state.

“The more that we can diversify and create options, especially in terms of supply chain, is going to be really important to get us through the fall,” said Dr. Christi Wojewoda, vice chair of the College of American Pathologists Microbiology Committee.

Further, Middleton asserted the expansion of Upstate Medical’s saliva test has “the potential to help provide millions of tests to people who might not otherwise have access to testing” by allowing other labs to use the technique.

More:SUNY enrollment dips amid COVID

How Upstate’s COVID saliva test works

Frank Middleton, a top neuroscience researcher at State University of New York Upstate Medical University, shifted gears during the pandemic. He is now leading the Upstate Medical lab conducting COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state.

SUNY Oswego’s emergency COVID-19 response offered a case study in outbreak detection and containment.

The pandemic safety net included a system that monitors wastewater to identify the presence of COVID-19 on campus early, which helped guide public health decisions at SUNY Oswego earlier this month.

As the number of infected students ticked upwards, SUNY Oswego officials on Sept. 13 suspended many on-campus activities, including athletics, Greek life and residence hall visitation to slow the virus’ spread.

Meanwhile, saliva testing at Upstate Medical quickly defined the outbreak scope.

A lab at the State University of New York Upstate Medical University conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

Rather than having medical workers use test swabs inserted into a person’s nose for individual diagnostic tests, thousands of students used self-administered mouth swabs to collect saliva samples that were shipped to Upstate Medical’s lab.

Much of the early testing used a pooled technique, in which saliva from 10 to 25 people is pooled into a single sample. If it comes back negative, the whole group is presumed to be COVID-free at the time.

For the positive pooled samples, each individual saliva sample was quickly re-tested to pinpoint exact positive cases, which is what makes Upstate Medical’s system unique.

Many other saliva tests require collecting another sample to test individuals, delaying the emergency response.

On Sept. 18, SUNY Oswego had uncovered 82 COVID-19 cases during a two-week span and announced it would halt in-person classes for a 14-day period to curb the outbreak.

The list of colleges making saliva sample deliveries to a lab at the State University of New York Upstate Medical University that conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

“I believe that with diligence and perseverance the SUNY Oswego community will rise to this pivotal moment to finish the job and flatten the curve so that they can continue to flourish on campus,” Malatras said at the time.

“In doing so they will help establish a proven model for controlling virus surges on college campuses everywhere,” he added.

The campus was scheduled to resume in-person classes Oct. 5.

So far this semester, it had 276 total confirmed cases, of which 230 had recovered, according to data posted on its website Tuesday.

More: SUNY's new COVID protocols: What could get you kicked out of college

More:COVID-19 clusters growing in Mid-Hudson, Southern Tier and Brooklyn: What you need to know

Why COVID testing alone is not enough

People wearing masks walk by the State University of New York Upstate Medical University campus on Tuesday, Sept. 22, 2020.

In many ways, the combination of wastewater monitoring, surveillance testing and diagnostic testing is the best strategy available for trying to contain outbreaks, experts said.

The State University of New York’s plan included spending $100,000 this month on five COVID-19 testing machines, increasing weekly saliva testing capacity to more than 120,000 across SUNY’s 64 colleges and universities. One of the machines also expanded wastewater testing for COVID-19.

But the risk of COVID-19 evading even the most robust safety nets will loom large until a vaccine is widely distributed, experts said, noting social-distancing, handwashing and other public health measures remain crucial.

“As a pathologist, testing is my world, but I really would like people to focus on prevention methods,” Wojewoda said, addressing concerns of a false sense of security through testing.

A COVID-19 testing machine at the State University of New York Upstate Medical University lab conducting pooled and individual saliva testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

“Sometimes it gives a feeling of 'we’re testing we’re going to find it,' rather than 'let’s not find it because we’re doing the right thing and we’re staying apart and wearing masks,'” she added.

More: 'SWAT team' targeted New York's latest COVID-19 hot spots: What to know about rapid tests

Pooled testing, for instance, only works in limited scenarios. It is best used to screen patients who show no symptoms, and it is mainly reserved for communities where fewer people are infected and rates of positive tests are low, experts said.

Kelly Wroblewski, the Association of Public Health Laboratories' director of infectious disease, said group testing works best when disease prevalence does not exceed 5% to 7% of a community. When that rate reaches double digits, labs will get too many positive tests.

"That’s where it stops being a resource save and it becomes a resource drain," Wroblewski said. "It takes more time. It takes more manpower and it takes more supplies."

SUNY's rate of infection has hovered below 1% of those tested.

A lab at the State University of New York Upstate Medical University conducts COVID-19 pooled surveillance testing for all SUNY schools and a variety of other colleges across the state. Tuesday, Sept. 22, 2020.

SUNY officials on Friday announced new severe punishments for students violating COVID-19 safety rules, alluding to the role parties and gatherings played in fueling outbreaks.

For those violating COVID rules, students now face immediate academic and housing suspension, as well as possible dismissal, and student organizations could face a permanent campus ban.

“While a vast majority of our students are complying with the rules, we cannot let a few people ruin it for everyone,” Malatras said in a statement.

More: SUNY Oneonta: In-person classes canceled for fall semester, students to be sent home

More: SUNY Oswego halting in-person classes due to rising COVID-19 cases. What to know

Ken Alltucker of USA TODAY contributed to this report.

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David Robinson is the state health care reporter for the USA TODAY Network New York. He can be reached atdrobinson@gannett.com and followed on Twitter:@DrobinsonLoHud