Scientists Find a New Coronavirus in Bats That Is Resistant to Current Vaccines

It’s the news that public health experts expect but dread: virus-hunting researchers have discovered a new coronavirus in bats that could spell trouble for the human population. The virus can infect human cells and is already able to skirt the immune protection from COVID-19 vaccines.

Reporting in the journal PLoS Pathogens, scientists led by Michael Letko, assistant professor in the Paul G. Allen School for Global Health at Washington State University, found a group of coronaviruses similar to SARS-CoV-2 that were initially discovered living in bats in Russia in 2020. At the time, scientists did not think the virus, called Khosta-2, posed a threat to people.

But when Letko’s team did a more careful analysis, they found that the virus could infect human cells in the lab, the first warning sign that it could become a possible public health threat. A related virus also found in the Russian bats, Khosta-1, could not enter human cells readily, but Khosta-2 could. Khosta-2 attaches to the same protein, ACE2, that SARS-CoV-2 uses to penetrate human cells. “Receptors on human cells are the way that viruses get into cells,” says Letko. “If a virus can’t get in the door, then it can’t get into the cell, and it’s difficult to establish any type of infection.”

Khosta-2 doesn’t appear to have that problem, since it seems to infect human cells readily. Even more troubling, when Letko combined serum from people who have been vaccinated against COVID-19 with Khosta-2, the antibodies in the serum did not neutralize the virus. The same thing happened when they combined the Khosta-2 virus with serum from people who had recovered from Omicron infections.

“We don’t want to scare anybody and say this is a completely vaccine-resistant virus,” Letko says. “But it is concerning that there are viruses circulating in nature that have these properties—they can bind to human receptors and are not so neutralized by current vaccine responses.”

The good news is that Letko’s studies show that, like the Omicron variant of SARS-CoV-2, Khosta-2 does not seem to have genes that would suggest it could cause serious disease in people. But that could change if Khosta-2 starts circulating more widely and mixing with genes from SARS-CoV-2. “One of the things we’re worried about is that when related coronaviruses get into the same animal, and into the same cells, then they can recombine and out comes a new virus,” says Letko. “The worry is that SARS-CoV-2 could spill back over to animals infected with something like Khosta-2 and recombine and then infect human cells. They could be resistant to vaccine-immunity and also have some more virulent factors. What the chances of that are, who knows. But it could in theory happen during a recombination event.”

It’s a sobering reminder that pathogens are ready and waiting to jump from any number of animal species into humans. And in many cases, as with SARS-CoV-2, these microbes will be new to people and therefore encounter little resistance in the form of immunity against them. “These viruses are really widespread everywhere, and are going to continue to be an issue for humans in general,” says Letko.

The findings come as the World Health Organization’s (WHO) ACT—Accelerator’s Council Tracking and Accelerating Progress—working group report that continued response to the COVID-19 pandemic, in the form of testing, vaccinations, and treatments, is stalling. With lower global immunity to the current SARS-CoV-2 virus, combating any new pathogens, including new coronaviruses like Khosta-2, would become more difficult. According to the latest data collected by the WHO, a quarter of people around the world still have not received a primary series of COVID-19 vaccination.

Ultimately, having deeper dossiers on the microbial world, especially information on how well certain viruses can infect human cells, for example, will be important to making the response to public health threats more efficient and more powerful. Letko is working on building a database that includes information on which human receptors viruses use to infect cells, and whether or not those viruses can evade existing vaccines. That way, he says, when new microbes are discovered that are similar to those in the database, researchers could have a head start on understanding how to control them. “At some point in the future, as these outbreaks continue, we won’t have to scramble whenever a new virus spills over into people,” he says. “We could plug the virus into the database, and understand that it probably uses these receptors to get into human cells, and might be resistant to these types of vaccines or treatments. It’s a 10- to 20-year goal, but it’s possible. It’s not just a pipe dream.”