Researchers find worrying new coronavirus variant in New York City

Two separate teams of researchers said this week they have found a worrying new coronavirus variant in New York City and elsewhere in the Northeast that carries mutations that help it evade the body’s natural immune response — as well as the effects of monoclonal antibody treatments.

Genomics researchers have named the variant B.1.526. It appears in people affected in diverse neighborhoods of New York City, they said, and is “scattered in the Northeast.”

One of the mutations in this variant is the same concerning change found in the variant first seen in South Africa and known as B.1.351. It appears to evade, somewhat, the body’s response to vaccines, as well. And it’s becoming more common.

“We observed a steady increase in the detection rate from late December to mid-February, with an alarming rise to 12.7% in the past two weeks,” one team, at Columbia University Medical Center, write in a report that has yet to be published, although it is scheduled to appear in pre-print version this week.

It’s the latest of a growing number of viral variants that have arisen in the US, which has had more coronavirus cases — 28 million — than any other country and where spread is still intense.

It’s “home grown, presumably in New York,” Dr. David Ho, Director of the Aaron Diamond AIDS Research Center at Columbia, who led the study team, said by email.

Viruses mutate all the time. The more people who are infected, and the longer they are infected, the more chance the viruses have to change. A patient’s body will be loaded with billions of copies of a virus, and may will be slightly changed, or mutated. Most will come and go.

But sometimes a mutation or pattern of mutations takes hold and gets passed along. If viruses with such patterns become more common, they’re called variants. Again, it’s not unusual for variants to arise but if they give the virus worrying properties, such as better transmissibility or the ability to evade treatments and vaccines, that’s when doctors start to worry.

The mutation in this variant that most concerns researchers is called E484K and it gives the virus the ability to slip past some of the body’s immune response, as well as the authorized monoclonal antibody treatments. This mutation is popping up independently in many different cases but appears in one particular variant, as well — the one called B.1.526.

“It is this novel variant that is surging, alarmingly, in our patient population over the past few weeks,” the Columbia team wrote in a copy of their report provided to CNN.

“We find the rate of detection of this new variant is going up over the past few weeks. A concern is that it might be beginning to overtake other strains, just like the UK and South African variants,” Ho told CNN.

“However, we don’t have enough data to firm up this point now.”

But the E484K mutation is seen in at least 59 different lineages of coronavirus, they said — which means it is evolving independently across the nation and across the world in a phenomenon known as convergent evolution. It may give the virus an advantage.

“Everything we know about this key mutation suggests that it appears to escape from antibody pressure,” Ho said.

Separately, a team at the California Institute of Technology said they developed a software tool that also spotted the rise of B.1.526 in New York. “It appears that the frequency of lineage B.1.526 has increased rapidly in New York,” they wrote in a pre-print — a report that has not been peer-reviewed but has been posted online.

On Tuesday, two teams reported on another variant that appears to be on the rise in California.

They fear that the variant might not only be more contagious, but may cause more severe disease, as well. As with the New York reports, their research is in its very early stages, has not been published or peer reviewed, and needs more work.

A team at the University of California, San Francisco, tested virus samples from recent outbreaks across California and found it was becoming far more common. It wasn’t seen in any samples from September but by the end of January it was found in half the samples.

This variant, which the team calls B.1.427/B.1.429, has a different pattern of mutations than the variants first seen in the UK, called B.1.1.7 or B.1.351. One mutation, called L452R, affects the spike protein of the virus, which is the bit that attaches to cells the virus infects.

“One specific mutation, the L452R mutation, in the receptor-binding domain of the spike protein may enable the virus to dock more efficiently to cells. Our data shows that this is likely the key mutation that makes this variant more infectious,” Dr. Charles Chiu, associate director of the clinical microbiology lab at UCSF, who led one of the studies, told CNN.

And they found some evidence it is more dangerous. “In this study, we observed increased severity of disease associated with B.1.427/B.1.429 infection, including increased risk of high oxygen requirement,” they wrote in their report, which is to post to a pre-print server later this week after public health officials in San Francisco review it.

Chiu said it should be designated a variant of concern and should be made a priority for study.

A second team at Unidos en Salud, a San Francisco-based nonprofit offering fast testing in San Francisco’s Mission District, tested 8,846 people over the month of January and sequenced the virus from 630 of the samples. They also found a rapid increase in the variant.

“The research findings indicate that the L452R variant represents 53% of the positive test samples collected between January 10th and the 27th. That is a significant increase from November when our sequencing indicated that this variant comprised only 16% of the positive tests,” Dr. Diane Havlir, an infectious diseases expert at UCSF who is helping lead the study, said in a statement.

Havlir’s team is also preparing findings for publication.