The COVID virus has mutated so much since 2019 that some experts say it should be renamed SARS-CoV-3

As the COVID public health emergency ends, experts say there's a real chance for a new variant to surge

By Troy Farah

Science & Health Editor

Published April 13, 2023 5:30AM (EDT)

Man taking off his surgical mask (Getty Images/Andres Barrionuevo Lopez)
Man taking off his surgical mask (Getty Images/Andres Barrionuevo Lopez)

On Monday, April 10, President Joe Biden signed a bill that immediately terminated the COVID-19 national emergency, first enacted in 2020 as the SARS-CoV-2 virus gripped the country. So does this mean the pandemic is finally, officially over?

Though COVID still makes occasional headlines, some (but not all) Americans have been living life as though the virus has ceased to exist. Wearing a mask in public is no longer the norm save for certain professional settings; relatively few people got the most recent bivalent vaccine; and contracting SARS-CoV-2, the virus that causes COVID, is now typically seen as more of an inconvenience than a life-threatening illness.

"This virus remains unstable — it has not settled into a predictable pattern, which means surveillance systems need to be sensitive to pick up the early signs of another surge."

For others, especially people with weakened immune systems or long COVID, the pandemic is still an omnipresent threat. Even though vaccines, therapeutics and immunity from previous infections are protecting the public from hospitalization and death, not everyone walks away from a COVID infection these days unscathed.

Yet while cases and hospitalizations are trending down, roughly 1700 Americans died from COVID the week ending April 5. Those death rates are only slightly lower than they were in July 2021. Given this, how much progress have we actually made?

Furthermore, every summer for the last three years the United States witnessed a surge in COVID cases — with 2022 bringing a long, sustained plateau of infections and deaths that wasn't historically high, but definitely not low either.

Cases aren't the only thing dropping either — so is surveillance of the virus. We're doing less testing and less sequencing of SARS-CoV-2 genetics.

Given all this, the question begs to be asked: Are we letting our guard down while waving the Mission Accomplished flag?

When asked if there is adequate surveillance for new variants happening, Dr. Margaret Harris, a spokesperson for the World Health Organization (WHO), flatly said no.

"Current trends in reported COVID-19 cases are underestimates of the true number of global infections and reinfections as shown by prevalence surveys," Harris told Salon in an email. "This is partly due to the reduction in testing and delays in reporting in many countries. Reduction in testing means a reduction in genetic sequencing, as you need to find the virus first in order to sequence it."

"We continually call on member states to maintain strong testing and sequencing in order to identify new variants but also to understand the level of SARS-CoV-2 transmission going on in their populations," Harris continued. "This virus remains unstable — it has not settled into a predictable pattern, which means surveillance systems need to be sensitive to pick up the early signs of another surge."

XBB.1.5, nicknamed by some as "Kraken," is thus far the dominant variant for most of 2023, with estimated cases of Kraken exceeding 70 percent since the week of Feb 11. It has far eclipsed the BQ.1 and BQ.1.1 variants. Meanwhile BA.2 and BA.5, the two variants that dominated case counts for most of 2022, have all but disappeared.

Want more health and science stories in your inbox? Subscribe to Salon's weekly newsletter The Vulgar Scientist.

According to the latest CDC variant tracking data, the only other variants really circulating in the U.S. are XBB.1.5's offspring: XBB.1.9 and XBB.1.5.1. Meanwhile, XBB.1.16 is spreading rapidly in India and could eventually make its way to North America. Notably, XBB was first detected in Singapore before its offspring made the jump across the Pacific, though XBB.1.5 was first detected in the U.S. and likely originated in the Northeast.

All these names may sound like gobbledygook to most non-experts — and there is a reason it's so confusing. When variants of the virus mutated and evolved into new strains with significant advantages over old lineages, the WHO began giving these "variants of concern" names from the Greek alphabet. Hence, variants like delta and gamma made headlines when they emerged and began to spread — but the WHO has yet to assign any variants a new Greek name since omicron surged in late 2021. Instead, we have this alphabet soup of named variants, all of which are technically different sub-strains of omicron.

Even a minor variation in a virus' genetics can equate to a huge difference in how well immunity from vaccines and previous infections can stop them. If the virus evolves some kind of advantage — as viruses are prone to do and just as SARS-CoV-2 has done many times throughout the pandemic — another surge is not out of the question.

In mid-March, the WHO updated their definition of what makes COVID variants threatening and currently classifies XBB.1.5 as a "variant of interest," which means it is seen as less threatening than previous variants of concern.

Nonetheless, some virologists have argued that XBB and its close relatives are so genetically different from the very first strain of SARS-CoV-2 that it should technically be renamed a new virus, SARS-CoV-3.

"XBB.1.5 does show a growth advantage and a higher immune escape capacity, but evidence from multiple countries does not suggest that XBB and XBB.1.5 are associated with increased severity or mortality," Harris said. "In countries where the variant has driven an increase in cases, the waves are significantly smaller in scale compared to previous waves."

That's good news, but as the virus bounces between hemispheres, it may gain new mutations that allow it to infect more effectively or evade immunity. Some of our treatments, but not all, have stopped working against XBB strains. Monoclonal antibodies don't stop it, but antiviral drugs like Paxlovid and bivalent booster vaccines are still very effective.

But the combined lack of public interest in the pandemic, exemplified in victory marches from political leadership, has led to a shrinking pool of data on COVID as there is less funding afforded to tracking and research. As we've seen in previous surges, the situation can change without warning. The situation is made worse by wild animals that harbor COVID, a viral reservoir that could spill back to humanity if given the opportunity.

"Very few of us have had the bivalent booster, so in terms of protection, we are kind of vulnerable," Rajnarayanan told Salon.

"The level of genomic surveillance has been dropping off, and there are also indications that funding for wastewater monitoring will be ending in some places," Dr. T. Ryan Gregory, an evolutionary and genome biologist at the University of Guelph in Canada, told Salon in an email. "We have far less information than we used to, which hampers the ability to detect and track new variants. It's also worth noting that India and China include about one-third of the world's population, and we have very little information on variants there."

While overall trends are down, many people would be especially vulnerable to a COVID infection right now, according to Dr. Rajendram Rajnarayanan, an assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Arkansas.

"Very few of us have had the bivalent booster, so in terms of protection, we are kind of vulnerable," Rajnarayanan told Salon. He noted that COVID is still a serious, life-threatening disease for immunocompromised people and those over 70. Most people who got bivalent booster shots — if they did so at all — received the jab in the fall. By now, that immunity has likely waned and there hasn't been much communication about when or if a new booster will come out later this year. According to NPR, the Food and Drug Administration has said it will allow some people over the age of 65 to get a second bivalent booster, but it hasn't been officially announced yet.

So while infections are trending downward, immunity is as well. In the past, major gaps in immunity have been followed by major surges, such as with delta and omicron.

"When there is a big pause, and some new variant comes, we are not really protected. But when there are repeated waves, the previous wave usually protects the next wave." Rajnarayanan said. "Every time the variant goes down, something goes up later on. Just the gap between the two peaks has changed."

Despite the unpredictability of SARS-CoV-2, the strategy for fighting it hasn't changed. Masking in public, improving indoor ventilation, testing when appropriate, staying home when sick and keeping up with vaccines when possible are good strategies for keeping the virus at bay. But overall, it's not enough to say the emergency is over. We need to be strategic and keep a close eye on the evolution of COVID as well.

"People have changed, our approaches have changed, and we don't need any modern approaches to defeat this virus," Rajnarayanan said. "We know how to do this . . .  we have to do it collectively. That's all there is to it."

By Troy Farah

Troy Farah is a science and public health journalist whose reporting has appeared in Scientific American, STAT News, Undark, VICE, and others. He co-hosts the drug policy and science podcast Narcotica. His website is and can be found on Twitter at @filth_filler

MORE FROM Troy Farah

Related Topics ------------------------------------------

Covid Epidemiology Health Pandemic Public Health Sars-cov-2 Science Variants Virus Evolution