Sabrina Xie / Sun File Graphic

After over a year of having students on-campus with COVID-19, the University saw its largest outbreak to date — in part because of the spread of the Omicron variant.

December 17, 2021

How the Omicron Variant and the End of the Semester Created a ‘Perfect Storm’ for Cornell’s COVID Outbreak

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On Thanksgiving morning, Prof. Gary Whittaker, microbiology and immunology, like many Americans, woke up to news that would put a damper on the day’s festivities. Scrolling through his Twitter feed, he was hearing early news of an emerging variant of the pandemic coronavirus that was quickly spreading through South Africa. 

“Sorry, it’s Thanksgiving morning, but this is something to watch,” he told his lab, which has been studying mutations in the SARS-CoV-2 virus. Even then, however, he didn’t predict that this very variant would tear through his local community just two and a half weeks later. 

The variant, known as Omicron, was identified in the U.S. the following week, and then, as Cornell students returned from Thanksgiving travel to wrap up their semester in Ithaca, it became home to one of the country’s “first superspreader” events, according to Dr. Eric Topol, the director and founder of Scripps research translational institute. 

“It’s a perfect storm, you have people that are doing a lot of networking and gathering and at the same time, have a highly infectious variant,” he said. Without arrival testing, students may have unknowingly spread the virus at end of semester celebrations, holiday outings and other “social gatherings” that may have also increased the spread

While the University is still testing the samples of students that tested positive to confirm how many cases are the Omicron variant, Topol said that the steep rise in cases within the Cornell community — which is 97 percent vaccinated — is telling that the Omicron variant is at play. 

Preliminary evidence from the Tompkins County Health Department does show “a high rate of Omicron transmission amongst the 18-24 Cornell University student population and additional prevalence amongst the wider community,” according to a release from Frank Kruppa, the public health director.

“The initial batch of positive results from the 18-24 population, prioritized for sequencing due to the rapid spread observed and indication of Omicron, resulted in all 115 samples being confirmed cases of the variant,” Kruppa wrote. “These results indicate that the primary spread amongst this population is due to the more transmissible Omicron variant.”

Topol and others said the outbreak at Cornell is a dire precursor of what’s to come in the rest of the United States. If the variant could take hold in such a highly vaccinated community of younger people — with 97 percent of the on-campus population vaccinated — who are less likely to become severely ill, and spread so quickly despite weekly surveillance testing, cases elsewhere in the country could also skyrocket.


“The picture is we’ve got a very transmissible virus, that cases are really spiking everywhere and we’re in for a pretty hard winter,” Whittaker said. 

To some extent, a spike in cases following Thanksgiving was expected by the local health department, according to Kruppa. Last year, despite most students not returning to Ithaca after Thanksgiving, the campus saw an uptick in cases. 

In the past, the University has seen large numbers of cases as students return to campus at the start of semesters and the surveillance testing system identifies students who may have been asymptomatic or infected during travel. At the beginning of the fall semester, Cornell saw its largest spike up until that point — with 304 cases within the first seven days of classes. After Thanksgiving, students were not tested upon arrival to campus from Thanksgiving break travel and could have unknowingly spread the virus as they went to end of semester social gatherings.  

However, cases “accelerated in the student population in a manner that we haven’t seen before,” Kruppa said — including at the beginning of the semester when students arrived in Ithaca and gathered for O-week parties and celebrated a return to a fully in-person semester. 

This large influx of cases could be explained by a large number of them being the new variant. While data is still emerging globally, it is becoming increasingly clear that Omicron spreads faster and may fend off the protection offered by vaccines better than Delta — the variant that currently makes up the majority of cases in the country, according to Prof. John Moore, microbiology and immunology. The biggest unknown, however, is whether Omicron causes severe illness at the same rate as Delta. 

“The critically important unknown is verifying what everyone seems to think — that it causes much milder disease. Now, the balance of evidence says that that’s true,” Moore said. “So we have to hope that this continues to be the case, because something that’s capable of blowing past vaccine protection and causing severe disease, that’s very serious.”

Even if it is causing milder disease than previous variants, Omicron’s ability to spread through a population quickly can create problems for the healthcare system. As cases on Cornell’s campus skyrocketed, Cornell’s COVID dashboard and Cayuga Medical Center’s portal for viewing test results intermittently crashed. 

TCHD has also been strained, trying to keep up with contact tracing everyone who tests positive. “If you can imagine we’re struggling with case investigations and the contact tracing becomes that much more difficult,” Kruppa, the public health director, said. Previously, the health department aimed to reach out to those who tested positive within 24 hours, but in the past several days that has stretched to two to three days, if not more, he said. 

Part of what allowed the spike to grow so quickly was also the gradual loosening of public health precautions in recent months. 

“You kind of have to loosen up for things to get back to normal. Now we’ve loosened up and we’ve got a problem,” Whittaker said. “That fear had gone away. But what the virus did to us was trick us, big time.”

While this is may be one of the largest superspreader events tied to the variant in the U.S., it is likely spreading elsewhere. But Tompkins County is able to trace this spike to the variant because of how much testing and genomic sequencing Cornell is doing.

“We are a high testing community and so we will detect the presence of the infection. Where other communities that are not testing may have the variant, because they are not testing, it is not apparent that it is already circulating,” said Prof. Avery August, microbiology and immunology. 

The introduction of the new variant will likely not change how August, Moore or Whittaker go about their day-to-day lives. They all emphasized that they still keep their distance from others, wear a mask in public and get tested when appropriate. But Whittaker and Topol said that Omicron’s heightened ability to evade the body’s immune system is strengthening the case that COVID vaccines should be a three-shot series. 

“I think that it’s become pretty clear that a double vaccine is not enough. I think a triple vaccine is a whole lot better,” Whittaker said. “This is a virus that needs a three-dose vaccine, which is not unexpected.”

Cornell is not currently requiring students or employees to receive a booster at this time, but they “encourage [people] to consider receiving a booster.” Other universities, including Harvard, Columbia and Stanford have already said they will require the booster for students to return in the spring. 

As of Friday, the University had reported over 1,300 cases over the course of a week. No students have had severe illness or needed to be hospitalized, but Topol said he is still worried about the potential impacts of long COVID on students — and what Cornell’s outbreak can say about the rest of the country.

“It will have a big impact in the U.S., unfortunately,” he said. “We can’t be in a denial state. Look what happened in the ideal scenario, with 97 percent [vaccinated] young people who are not vulnerable or immunocompromised.”