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New COVID variant BA.2.86 in at least four states— what to know about the highly mutated strain

BY ALEXANDER TIN
UPDATED ON: AUGUST 30, 2023 / 12:18 PM / CBS NEWS
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Health authorities and scientists say they are now racing to study BA.2.86, a new strain of the virus that causes COVID-19, after the highly mutated variant was spotted spreading in multiple countries around the world and at least four different U.S. states.

For now, officials say they remain well-equipped to deal with the strain if it continues to spread. Early assessments suggest current treatments and tests, as well as upcoming vaccines to be rolled out in September, will not be rendered useless by BA.2.86.

But a number of questions remain about the variant, nicknamed "Pirola" on social media, whose mutations could amount to an evolutionary jump on par with the emergence of the Omicron variant in 2021.

Here's the latest on what we know about the strain.

Is there a new COVID variant?
The Centers for Disease Control and Prevention and World Health Organization say they have been closely tracking the emergence of a new, highly mutated COVID-19 variant that scientists have labeled BA.2.86.

The new variant first raised concerns earlier this month after variant trackers noticed a handful of new sequences showing up in global virus databases with a large number of genetic changes different from other circulating strains.

When compared to the XBB.1.5 variant, which drove a wave earlier this year and was picked out to be targeted by the upcoming fall booster shots, BA.2.86 has 36 mutations. Sequences of early Omicron variants in 2021 also had a similar number of mutations, when compared to the original strain of the virus.

BA.2.86's mutations include changes at key parts of the virus that could help the variant dodge the body's immune defenses from prior infections or vaccinations.

Authorities still consider BA.2.86 technically a part of the Omicron variant family, though the WHO told reporters that this could change if the strain spreads more widely.

"We will use a Greek letter when we have a variant of concern and we won't hesitate to use those Greek letters should they be needed," Maria Van Kerkhove, the WHO's COVID-19 technical lead, said Aug. 25.

More could be known soon about the impacts of the strain, from experiments done by scientists testing the strain's mutations against antibodies for the virus.

Among them is Peking University Professor Yunglong Cao, whose rapid assessments of variant abilities to dodge antibodies have played a key role in helping global authorities judge the threats posed by past strains. Cao told CBS News on Aug. 24 he expected to have some data on BA.2.86 by "early next week."

Where has the new COVID variant BA.2.86 been detected?

At least 24 confirmed infections have been reported to the global virus database GISAID or announced by health authorities. As of Aug. 30, 10 are in Denmark, four are in Sweden, three are in the U.S., two are in South Africa, two are in Portugal, one is in Israel, one is in the United Kingdom and another is in Canada.

A number of countries have also reported signs of the variant's spread using wastewater testing in areas that have yet to spot human cases, including in the U.S.

No deaths have been reported, according to an Aug. 24 WHO report.

None of the early cases had a known "epidemiological link" with each other, an official for the U.N. agency said Aug. 25, or had compromised immune systems. Experts have speculated that previous highly mutated variants arose in immunocompromised patients battling lingering infections.

The first reported U.S. case was reported from a sample collected on Aug. 3, according to metadata reported to GISAID by a lab at the University of Michigan. A spokesperson for Michigan's health department said that sample was collected from an adult who lived in the state's Washtenaw County.

A second U.S. case of BA.2.86 was reported to GISAID from a sample collected on Aug. 10 at Dulles International Airport in Virginia. Contractors for CDC's airport testing program had detected the case, in a woman who had traveled from Japan to the Washington, D.C. area airport.

The third U.S. case of BA.2.86 has been confirmed in Ohio, a spokesperson for the state's health department told CBS News. Records reported to GISAID show the sequence was from a sample collected by the Cleveland Clinic on July 29, from a 26-year-old patient in Ohio's Cuyahoga County.

New York became the fourth to report the variant, after spotting BA.2.86's distinctive mutations in New York City's wastewater. Ohio had previously confirmed it was also investigating with the CDC a "preliminary detection" of BA.2.86's distinctive mutations in its sewers. No other states have reported BA.2.86 in their wastewater so far, a CDC spokesperson said Aug. 30.

Scientists in several other countries have also announced spotting at least preliminary signs of the strain in their sewers, according to Sorin Sion of the EU Sewage Sentinel System for SARS-CoV-2, including Denmark, Germany, Spain, Switzerland and Thailand.

Marc Johnson, a professor of microbiology and immunology at the University of Missouri, said on social media the Ohio detection was based on results published from the CDC's sewer testing program. Those were first released on Aug. 17, from a sample collected in late July from the Ohio city of Elyria.

Do COVID tests pick up the new COVID variant BA.2.86?
Current COVID-19 tests are expected to still work for BA.2.86, early analyses suggest.

"Based upon available information at this time, the FDA believes that most existing tests used to detect COVID-19 appear to be effective with this variant," FDA spokesperson James McKinney said in an Aug. 28 email.

McKinney said the FDA is continuing to study the performance of current COVID-19 tests, including through an ongoing relationship with a National Institutes of Health program that manually rechecks tests against new samples of the virus. Health authorities also do detailed computer modeling that can predict when variants might evade current tests.

Tests found to have reduced performance for BA.2.86 will be listed on the FDA's website, McKinney said.

"The agency will update this page when significant new information becomes available, including when the FDA's analyses identify tests for which performance may be impacted for known SARS-CoV-2 variants," McKinney said.

In 2021, the NIH's effort had flagged early signs that the real-world performance of tests was slipping for new Omicron variants. The FDA ultimately began to urge Americans to do repeat testing with at-home COVID-19 rapid antigen tests, after NIH-backed scientists confirmed an increase in false negative results.

Do the symptoms of the new COVID variant BA.2.86 differ from previous strains?
There are some promising early anecdotes, but for now it is too early to know for sure whether BA.2.86 will cause new or worse symptoms.

Michigan's health department said their case was in "an older adult with mild symptoms and has not been hospitalized." The traveler in Virginia was asymptomatic, according to the metadata submitted by the CDC's contractors.

Ohio's health department declined to comment on whether their case was hospitalized. A Cleveland Clinic spokesperson said they forward to the state "a random subset of our COVID-positives which includes both inpatients and outpatients" for sequencing.

In Denmark, the country's Statens Serum Institut said their first three cases did not have symptoms "other than those normally seen in the course of COVID-19." Canadian health authorities made a similar statement about their case, who was not hospitalized.

"What we would need to make sure we understand is the full spectrum of disease that is caused by BA.2.86. My reservation in giving a lot of detail around this is I don't want to draw any conclusions coming from eight or nine patients," the WHO's Van Kerkhove said.

The strain's emergence comes as COVID-19 hospitalizations had already been rising around the country driven by less-mutated variants. So far, those trends do not appear to be worsening more around early sightings of the strain.

"At this time, locations where this variant have been detected have not experienced increases in transmission indicators (e.g., cases, emergency department visits) or hospitalizations out of proportion to those seen in neighboring locations," the CDC said the CDC said in a risk assessment published Aug. 23.

Will vaccines work for the new COVID variant BA.2.86?
Upcoming vaccines are expected to help for BA.2.86, though more needs to be known.

The variant's emergence comes as health authorities are preparing for the rollout of new COVID-19 vaccines next month, which are expected to be available soon after a meeting of the CDC's outside vaccine advisers on Sept. 12.

Those shots were designed to target the XBB.1.5 variant, which at the time of the Food and Drug Administration's pick in June was seen as the option best suited to further broaden immunity for the virus.

If BA.2.86 becomes dominant, Jesse Bloom, an evolutionary biologist at the Fred Hutch Cancer Center, told CBS News that the strain's mutations could be enough to make those shots a poor match to fend off infections from the virus.

However, Bloom says the body's other immune defenses could still work to blunt the strain's danger. The CDC says it currently assesses that the updated vaccine "will be effective at reducing severe disease and hospitalization."

"I would note that while strain specific neutralizing antibodies (which can be escaped by new variants) provide the best protection against infection, there are also broader mechanisms of immunity elicited by vaccination and infection that provide some protection against severe disease," Bloom said in an Aug. 17 email to CBS News.

I assume it's this new strain.... we've had several people at my work out due to covid... seems to spread fairly easily...

Something to watch.

It's going to be like the flu. New strains become prevalent each season and hopefully we get the right vaccine to mitigate the health risk. Unlike the flu, it is a new virus and us humans haven't been exposed long enough to build up some natural immunity. Hopefully the previous vaccines, while they don't prevent contracting this variant, will help mitigate the heath impact if we do catch it.

I had to pick up some Meds at CVS the other day and they had the flu vaccine, they weren't busy so I got that shot a few days ago. I have taken that shot for many years now. When the new Covid vaccine comes out this fall, I will get that. I think they will be available in October.

New boosters come out in mid-September.

I guess they were able to predict these new strains, as the new booster is said to protect against the XBB.1.5, BA.2.86 and EG.5 strains.

It seems like everyone has Covid-19. Here’s why this wave is probably worse than official data suggests

CNN
DEIDRE MCPHILLIPS, CNN
September 1, 2023 at 9:56 AM
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Covid-19 certainly didn’t take a vacation this summer. Virus levels in the US have been on the rise for weeks, but it’s hard to know exactly how widely it’s spreading.

Federal data suggests that the current increases have stayed far below earlier peaks and notable surges. But judging by word of mouth among family, friends and coworkers, it can seem like everyone knows someone who’s sick with Covid-19 right now.

“We have several folks down with Covid, unfortunately,” one health-focused nonprofit told CNN when seeking comment for this story.

Rates of severe disease may be staying at relatively low levels, but experts agree that there are probably more infections than the current surveillance systems can capture.

“There is more transmission out there than what the surveillance data indicates,” said Janet Hamilton, executive director of the Council of State and Territorial Epidemiologists. “And we should be paying attention to it, because we are starting to see an increase.”

From 2020 to 2022, the University of Washington’s Institute for Health Metrics and Evaluation produced regular estimates of Covid-19 case rates and projections for trends. But the research institute paused that modeling in December.

All of the measures that factored into the model had stopped being reported or had changed in some way, said Ali Mokdad, professor of health metrics sciences and chief strategy officer of population health at the University of Washington.

“The surveillance system was not adequate anymore to capture changes in Covid-19,” he said. “We felt that the margin of error became really too big for us to make a prediction that we could stand by and defend.”

Mokdad declined to quantify an estimate for current case counts, but he said he’s been getting lots of calls and questions about Covid-19 recently — similar to what he experienced around the end of last year. In mid-December, the US Centers for Disease Control and Prevention was reporting about 500,000 cases a week. And IHME estimates from that time suggest that the US was in one of the worst waves of the pandemic, second only to the Omicron surge.

Two imperfect measures of transmission
Tracking Covid-19 trends has always had its challenges. But the rise of rapid home tests — and general waning of public interest in testing at all — has all but erased the ability to grasp current case counts nationwide. The CDC officially stopped reporting aggregate Covid-19 case counts months ago, noting that data had become less representative of actual infections or transmission levels over time.

As case counts started to become less reliable, some experts first pointed to hospitalization metrics as a reasonable substitute to gauge transmission. Hospitals were regularly testing all patients, whether they were coming in for Covid-related symptoms or for something else entirely, and they are required to report positive cases. The idea was that case rates in a hospital could serve as a proxy for case rates in the broader community.

There were about 15,000 new hospital admissions for Covid-19 in the week ending August 19, according to CDC data — less than half of what the numbers were at this time last year and lower than they were for about 80% of the pandemic.

But hospitals have shifted their testing practices, balancing changing federal requirements and recommendations with local risk assessments, which makes it difficult to compare data from different points in time.

“When testing supplies first were readily available, we moved to testing everyone, including health care workers routinely, including anybody who was coming in the door for any reason,” said Nancy Foster, vice president of quality and patient safety for the American Hospital Association. “Anybody and everybody got tested.”

Although hospitals are still required to report any positive cases, they’ve eased back on testing to be more in line with guidance around other infectious diseases. The focus is on those who are symptomatic, have been exposed or might be around other high-risk patients.

“Hospital admissions is much more of an indication of severity at this point in time, than I think it is of generalized transmission,” Hamilton said.

Many measures of Covid-19 and other public health surveillance rely on people to seek out clinical testing or medical treatment, and those behaviors have changed over the past few years. Wastewater surveillance offers a more consistent approach by monitoring the amount of virus shed in sewage systems.

But interpreting that data can be complicated — and with Covid, wastewater levels can’t be directly translated to case counts.

The amount of virus that an infected person sheds depends on a many factors, including the presence of antibodies from a vaccine or previous infection and the severity of the current infection.

Data from Biobot Analytics, a biotechnology firm that has partnered with the CDC, shows that wastewater concentrations of the coronavirus are similar to what they were at the start of the first winter surge in 2020.

But now that the vast majority of people in the US have some immunity to Covid-19 through vaccination, infection or both, those same viral concentrations could translate to a larger number of infected individuals with milder — but still contagious — infections.

The upward trend is clear
Even if the exact number of new infections isn’t clear, experts say, the rising trends in the data that is available are enough to raise alarm.

“Surveillance data is across a continuum. We want to have multiple different types of data that tell us different kinds of things. When they’re all pointing in the same direction, that’s maybe a time to get even more concerned,” Hamilton said.

And right now, many key measures are indicating an increase.

Weekly hospital admissions have nearly doubled over the past month, including a 19% bump in the most recent week, CDC data shows. And a sample of laboratories participating in a federal surveillance program show that test positivity rates have tripled in the past two months.

There are some hopeful signs: Biobot data shows that wastewater levels may be starting to flatten, and relatively low hospitalization rates suggest that there may be a lower risk of severe disease for many.

But despite the clear signs of a summer surge, the US has been living in a “fantasy world” where people pretend Covid-19 is “not relevant,” Dr. Deborah Birx, the White House Coronavirus Response Task Force coordinator during the Trump administration, told ABC’s “Start Here” podcast.

“We wanted to make it like flu because that was easier, but it’s never going to be like flu,” Birx said, explaining that Covid-19 comes in more frequent waves, makes people sicker, kills more people and can have longer-term complications such as long Covid. “So let’s just all agree it’s not flu. It will never be flu. Following it and surveying for it like we do for flu will never be adequate in this country.”

Precautions like masking and staying up-to-date on vaccinations are especially important as this rise in Covid-19 carries into the broader respiratory virus season, experts say.

“With every respiratory disease season — whether it’s Covid, whether it’s influenza, whether it’s RSV — those increases can impact different individuals in different ways, and there are always severe outcomes associated with respiratory disease season,” Hamilton said.

“Now is the time for us to be practicing good respiratory etiquette. Now is the time for us to remind ourselves to think about our own individual health status and those individuals that we may be around.”

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