The coronavirus circulating across the globe may have close relatives that have not yet been discovered, a hint that the current pandemic will not be the last one to threaten humans.
New research published Tuesday in the journal Nature Microbiology finds the current strain, known in the scientific literature as SARS-CoV-2, diverged genetically from other known viruses that circulate in bats between 40 and 70 years ago.
Because coronaviruses recombine and evolve into new species frequently, it is all but certain that other strains have evolved within bat populations in China during those intervening years. That means other viruses more closely related to SARS-CoV-2 than its current closest known relative may pose the potential for future outbreaks.
“From this ancestor in the 1960s and 1970s, there are probably other descendants, there are probably other lineages that have existed and circulated quietly in bats for the past 40 or 50 or 60 years,” said Maciej Boni, a biologist at the Center for Infectious Disease Dynamics at Penn State and a co-author of the study. “This does mean that there probably will be another coronavirus pandemic. Whether it happens in 2025 or 2075, nobody knows.”
The research found that while the SARS-CoV-2 virus can also infect pangolins, mammals native to China, Southeast Asia and Subsaharan Africa, the virus was most likely passed to humans directly from a bat.
“There is no evidence that pangolins are facilitating adaptation to humans,” the researchers wrote.
The SARS-CoV-2 virus is a sarbecovirus, a subgenus of the coronavirus family that also includes SARS, another virus that caused severe respiratory disease in humans. The virus that is most closely related to SARS-CoV-2, known as RaTG13, was identified in horseshoe bats in China’s Yunnan Province in 2013.
Research shows that the two viruses are about 96 percent similar. Evolutionarily speaking, that 4 percent gap is a genetic chasm; there is less difference between humans and orangutans than between the two viruses.
What makes the SARS-CoV-2 virus — and any of its yet-to-be-discovered relatives — dangerous to humans is that its spike protein combines to ACE-2 receptors, which exist in cells in the lower respiratory tract. Those cells become infected, spreading the virus and causing the COVID-19 disease that has so far killed more than 140,000 people in the United States.
It is unlikely that researchers will ever conclusively identify an index case, the very first person infected with the SARS-CoV-2 virus by a bat, probably some time in November 2019. But more research into bat populations around the world is likely to uncover some of the close relatives of the current virus, Boni said.
“We’re never going to find the very first case, but it’s likely with better sampling we’ll find bat lineages that maybe in 2010 or 2015 were circulating in bats but were very similar to the current SARS-2 virus,” he said. “The more sampling we do, the more likely it is that we’ll find a more recent bat virus.”
The researchers called for an international surveillance network, both of bat populations around the globe and in humans who might contract new viruses. Past research has been limited to a few scientists studying a few bat populations, surveillance Boni said is insufficient to fully capture the true number of potentially harmful pathogens that might spill over to humans.
“Of course it’s a monumental task to begin sampling tens of thousands of bats and characterizing all of their viruses,” Boni said. “When you’re trying to catch something that’s emerging from an animal population to a human population, you need surveillance on both sides.”
“It has to be internationally coordinated. It can’t be a piecemeal effort,” he said.