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The coronavirus Delta variant is in the Philadelphia area, posing a threat to unvaccinated people

In Philadelphia — where COVID-19 cases have plummeted since the January peak, mostly because of vaccination — genetic sequencing suggests new infections are “all variants now,” Penn says.

Lab assistant Tammy Brown dons personal protective equipment as she prepares positive coronavirus tests for sequencing to look for variants at the University of Maryland School of Medicine.
Lab assistant Tammy Brown dons personal protective equipment as she prepares positive coronavirus tests for sequencing to look for variants at the University of Maryland School of Medicine.Read moreMichael Robinson Chavez

Because the coronavirus’ genetic code is constantly changing, U.S. health officials this spring came up with a way to classify emerging variants based on their threat.

So far, the world has no known “variants of high consequence” — those that could defy diagnostic tests, medicines, and vaccines, while spreading and killing more readily.

But the list of “variants of interest” and “variants of concern” keeps growing. These have one or more worrisome mutations that are suspected, or known, to increase transmission and disease severity. Some also reduce the effectiveness of antibody therapies and vaccines.

In the greater Philadelphia area — where vaccination has driven a steep decline in COVID-19 cases since the January peak — genetic sequencing suggests new infections are “all variants now,” University of Pennsylvania microbiologist Frederic Bushman said Tuesday.

The worrisome Delta variant, which is predicted to become dominant in the United States within a few months, has been identified only four times among the 1,651 respiratory samples that Bushman’s team has sequenced since January. The samples come from people who tested positive for COVID-19 in Pennsylvania and South Jersey, most of them patients of the University of Pennsylvania Health System.

“We’re just starting to see the Delta strain,” Bushman said. “So it’s definitely here. I have to assume it’s widely seeded.”

The Delta strain is more transmissible and ripped through India last year. But data show the Pfizer and Moderna vaccines provide good protection against the variant — after the second dose.

Bushman said his team has never sequenced a local case caused by infection with the original strain that launched the pandemic in Wuhan, China, in December 2019. But that means the virus is rapidly evolving.

“We’ve seen multiple waves of variants replacing older strains,” Bushman said. “Now, the United Kingdom strain is dominant in our area, and the New York variant is the second most abundant.”

The U.K. strain, also known as Alpha, is classified as “of concern,” while the New York variant, also known as Iota, is “of interest” because its harmfulness is still being assessed.

The use of the Greek alphabet to label variants is a recent change proposed by the World Health Organization. The WHO recognized that referring to variants by the place of origin can be stigmatizing, yet the public and the media were stumped by the arcane scientific labels, such as B.1.1.7 for the U.K. variant.

Although worldwide coronavirus surveillance efforts have been growing, there is no comprehensive system for detecting significant changes in the coronavirus’ genetic code. The microbe often makes errors in that code as it replicates inside cells.

Most mutations are inconsequential or bad for the virus, but with billions of people around the globe providing opportunities for genetic typos, the virus has almost incalculable chances of evolving in ways that give it an edge. And while international travel helps to spread dangerous variants, these can also emerge repeatedly, spontaneously, and independently around the globe — a phenomenon called “convergent evolution.”

Extensive data are needed to determine whether a variant has worse properties than its predecessors, and health authorities may disagree. For example, India’s health ministry says studies show that a new descendant of the Delta variant — the so-called Delta plus variant — spreads more easily and binds more readily to lung cells, but other experts say it’s too soon to tell.

In any case, experts see vaccination as the only hope for getting control of the pandemic, yet resistance to immunization is proving to be surprisingly strong, even in developing countries such as India where the shots are in short supply.

In the United States, where shots are readily available, the slowing of vaccine uptake is attributed to vaccine hesitancy and socioeconomic disparities.

As The Inquirer reported last week, more than half of Philadelphians, almost 853,000 people, have received at least one vaccine dose, including 66% of people age 18 and older, according to data from the Centers for Disease Control and Prevention.

But fewer and fewer people are rolling up their sleeves, and there is wide variation in vaccination and infection rates by zip code. For example, Center City West, where 61% of residents were fully vaccinated, had less than one COVID-19 case for every 10,000 residents in the first two weeks of June. North Philadelphia, where less than a third of residents were fully vaccinated, had five cases per 10,000 residents.

Bushman noted that the four seasonal coronaviruses, which cause mild respiratory infections, subside in hot weather, and surge in winter. The pandemic virus is more complicated and unpredictable. Possible seasonal effects, immunity from past infection or vaccination, variants, and vaccine hesitancy will shape future outbreaks.

“My guess is it will come back in the fall in vaccine ‘deserts,’” Bushman said.