Omicron is spreading, and likely is why COVID-19 breakthrough cases are growing in Philly

Almost a third of Philadelphia’s reported COVID-19 cases in December have been among fully vaccinated people, the highest monthly rate since vaccines became available. At the same time, hospitals continue to report the vast majority of their COVID-19 patients are unvaccinated.

The December case information, made public by the Philadelphia Department of Public Health Tuesday, shows a surge in cases this month that’s likely to be among the worst of the year. The city tallied 11,201 COVID-19 cases as of Tuesday, the most in a single month since April, with still more than a week remaining in 2021. Of those, 3,300 were among fully vaccinated people. The data offer a first glimpse of case rates while the omicron variant is present in the city, but leave unanswered a slew of important questions.

Among the unknowns: How many of the vaccinated people who tested positive had the omicron variant, how many had booster shots, and how sick did the virus make them?

Despite the burgeoning case rate, hospitals report that the overwhelming majority of COVID-19 patients they see are unvaccinated. So far, one U.S. death has been attributed to the omicron variant in an unvaccinated Houston man. But most hospitalizations and deaths now likely are still connected to the delta variant.

“Thirty percent of all cases are breakthroughs — what do you mean by case?” said Thersa Sweet, associate professor in Drexel University’s department of epidemiology and biostatistics. “That’s the information I want to see, disease severity in those breakthrough cases.”

The focus on previous vaccinations has intensified as the region and the country prepare for a surge in new cases. Schools around Philadelphia moved to virtual learning Wednesday, and Temple University announced it would begin the second semester with two weeks of remote instruction. And the morning after pacing the sidelines in a win at Lincoln Financial Field, Eagles coach Nick Sirianni announced that he had tested positive.

Temple University Hospital reported Wednesday about 90% of its COVID-19 patients requiring hospitalization are unvaccinated. Tower Health Systems, which includes hospitals in Pottstown, Phoenixville, and Chestnut Hill, reported similar numbers, with vaccinated patients accounting for 13% of people hospitalized for COVID-19 and 7% of patients in intensive care. None of the health system’s 24 COVID-19 cases on ventilators are vaccinated. Penn Medicine and Cooper University Hospital, in Camden, reported about 80% of their hospitalized COVID-19 patients are unvaccinated, while Jefferson University Hospitals said most of their COVID-19 patients are unvaccinated. Of the people vaccinated and still needing hospitalization, a spokesperson there said, “many of them are older and several months from their second vaccination.”

The Centers for Disease Control and Prevention reported breakthrough cases should be expected as omicron spreads, because the vaccines — though still conferring strong protection against serious illness and death — are less effective at preventing infection with omicron.

“Given the CDCs recent announcement, we have to believe that a great and growing percentage of our positives are omicron,” said James Garrow, a Philadelphia Health Department spokesperson.

Also up for debate, how much society should be concerned about vaccinated people getting sick from COVID-19 if they’e not getting really sick.

“Completely stopping all infection, that’s not going to happen with the vaccines,” Sweet said, “and then the question is, do we care? What’s the goal? Is it to protect against infection or protect against severe disease?”

Health officials and experts said omicron hasn’t changed, though, the fundamentals of protection against COVID-19.

“Omicron’s just a variant. It’s not like a new monster,” said Susan Weiss, a microbiologist and codirector of the University of Pennsylvania Perelman School of Medicine’s Center for Research on Coronaviruses and Other Emerging Pathogens. “The bottom line is to urge people to get vaccinated and to get boosted.”

Zeroing in on the meaning behind growing case counts can be challenging. To some extent, a larger number of vaccinated people testing positive is simple mathematics — as a larger share of the overall population is vaccinated, more cases will emerge in vaccinated patients.

“The fact that 70% of cases are in the unvaccinated, shows how good the protection is,” Garrow said.

Colder weather driving people indoors, where transmission is more likely, and the fact that immune protection — whether from vaccines or an earlier infection — wanes over time also likely play roles in breakthrough cases.

Even home antigen tests could skew data, as people who test positive at home and experience mild symptoms may never report their infection.

“Are vaccinated people more likely to seek out testing because they’ve been following the guidance to a T, or less likely because their symptoms are less?” Garrow said. “Are unvaccinated people more likely to get tested because they simply aren’t sure, or less likely because [they may assume] what’s the difference anyways? Either one of those could be true, but we don’t have any information on which is more likely.”

Omicron accounted for 73% of new infections nationally last week, the CDC reported Monday.

Even as omicron becomes the dominant strain of COVID-19 in the United States, city health officials don’t yet know how prevalent the variant is locally, and how much it is responsible for breakthrough cases. Positive cases among vaccinated people first increased in November, before omicron was identified in the Philadelphia region.

Only a small percentage of positive COVID-19 test samples are subjected to genetic sequencing, needed to identify the specific variant, but there’s plenty of evidence that omicron is growing here. At the beginning of December, the Penn Center for Research on Coronavirus and Other Emerging Pathogens, one of the Philadelphia labs that does sequencing, had not found the omicron variant in the area. Less than three weeks later, omicron accounted for more than a quarter of all COVID-19 samples sequenced.

» READ MORE: Omicron variant is likely to come to Philly region. This Penn lab may be the first place that spots it.

The most recent data from state health officials show 31% of positive COVID-19 cases were among vaccinated people in the four weeks prior to Dec. 6, but omicron’s rapid spread means that rate could have changed significantly.

Both Pfizer and Moderna have said booster shots produce strong protection against omicron, but the city could not say how many breakthrough cases occurred in people with boosters. Less than 20% of fully vaccinated Philadelphians have received boosters, which are available six months after the second Pfizer or Moderna shot.

“It’d be really interesting to know if those people are boosted or not,” Weiss said.

Hospitalization rates in South Africa, where omicron was first identified, suggest the variant may be less severe than others. But people there may have avoided hospitals because high levels of immunity due to vaccines or prior infections — or just because patients are younger — which could have meant milder illness, the New York Times has reported.

“The other thing I think is important that we don’t know, we really want to know how virulent this virus is,” Weiss said. “I think that’s really important, because if it’s more mild that’s huge.”