Worrisome COVID-19 variants are taking hold in Pa. and N.J., threatening the success of vaccines

While data are limited and sketchy, it is clear that worrisome coronavirus variants are becoming more common in Pennsylvania and New Jersey, even as the pace of vaccination accelerates.

A particularly ominous sign for the Philadelphia area: More than a third of samples taken over the last month from 80 COVID-19 patients had mutations known to make the virus more transmissible or resistant to current vaccines, or both, according to a University of Pennsylvania analysis.

“The proportion of worrisome viral variants is rising,” Penn microbiologist Frederic Bushman said Monday. Since January, his team has genetically sequenced the virus in about 350 respiratory samples.

Penn’s finding reflects national and state trends. Although there is no comprehensive, systematic surveillance, the U.S. Centers for Disease Control and Prevention on Monday reported that 26% of recently sequenced U.S. samples had the variant first identified in the United Kingdom in December. That strain, now dominant in far-flung parts of the world, is 50% more contagious than the pandemic coronavirus that emerged in China 15 months ago.

CDC Director Rochelle Walensky said Monday during a COVID-19 White House briefing that she has a “recurring feeling of impending doom” as she watches U.S. trends mirror the resurgence of cases in Europe a few weeks ago.

Why are more transmissible variants gaining a foothold even though large swaths of the U.S. population are now vaccinated? The answer, experts say, is that too many people are letting their guard down, falsely reassured by the vaccination numbers and the fact that cases have plummeted from the January peak.

“If you look at the state of Pennsylvania, cases in the Southeast are up sharply in the last few weeks. And we’re up nationally,” said Bushman at Penn. “So it’s a battle that’s right on the edge. The more infections, the more spread, the more opportunity for the virus to mutate. It is critical for everyone to keep up precautions such as mask-wearing, and to get vaccinated when your turn comes up.”

In New Jersey, the state is sequencing only about 2% of COVID-19 cases to check for variants, although Health Department officials say they intend to ramp that up. So far, more than 500 variant-driven cases have been identified, most linked to the U.K. strain and another first found in New York City.

”We’re assuming [variants] are in the state all over the place,” Gov. Phil Murphy said Monday. New Jersey’s rate of new COVID-19 cases per capita now ranks first in the nation; Pennsylvania is sixth.

Viruses are constantly introducing mistakes, or mutations, in their genetic code as they replicate within the human cells they have infected. Occasionally, a mistake or a combination of mistakes gives the virus a survival advantage, so that version outcompetes others to become dominant.

Travelers help these more insidious strains to hopscotch the globe. But recent genomic sequencing suggests that harmful coronavirus mutations also have been arising spontaneously, rapidly, independently — and largely undetected — around the world. Scientists call this phenomenon “convergent evolution.”

The Penn team found that of the 80 respiratory samples, 14 had a variant first identified in New York, and two had variants identified in California. Eight samples had the U.K. variant, scientifically called B.1.1.7.

Four other samples had a variant, called R1, that is not listed on outbreak.info, a Scripps Research tracker of worrisome variants. However, R1 has a mutation that makes it able to resist or even escape the protective antibodies generated by vaccines; the same mutation is present in the U.K. strain and one first identified in Brazil.

Systematic surveillance of these emerging threats is not easy, and the U.S. effort is behind that of many other countries.

“Genetic sequencing is quite expensive and labor intensive,” said John Zurlo, chief of infectious disease and chair of the COVID-19 clinical task force at Jefferson University Hospital.

Jefferson’s 14-hospital health system recently began sequencing a random sampling of cases. Of 50 samples, about a quarter had the U.K. variant, Zurlo said.

Jefferson has also launched a study to see whether the small fraction of employees who get COVID-19 despite being vaccinated have a variant of concern.

But that, too, is challenging because the 5% to 10% of vaccinated people who still get infected generally have a low level of virus in their respiratory samples — sometimes too low for analysis, said Bushman at Penn.

Moderna and other vaccine makers are planning to develop “booster” vaccines, in case a variant arises that completely evades the current inoculations. But if boosters are needed, it will further complicate the herculean worldwide vaccination effort.

“I do think it’s a race against time,” said Zurlo at Jefferson. “We just have to get more people vaccinated” to suppress the pandemic.

Staff writer Allison Steele contributed to this article.