Scientists trace the roundabout route that coronavirus took from bats and pangolins to people

Alan Boyle
A transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19, isolated from a patient in the U.S. Virus particles are emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles are key to their ability to infect human cells. (NIAID-RML Photo)

Two newly published studies shed light on the origins and spread of the coronavirus pandemic, starting with bats and pangolins in China and ending up with New York’s dramatically deadly outbreak.

One study, published today in the open-access journal Science Advances, analyzed 43 genome sequences from three strains of coronavirus similar to the one that causes COVID-19 in humans. These strains were identified in bats and in pangolins, anteater-like animals prized for their scales. The two pangolins that yielded samples of coronavirus were smuggled into China and seized by customs officials.

The type of coronavirus that has caused the human pandemic, SARS-CoV-2, is more similar to bat viruses than to pangolin viruses. But a key piece of genetic material, relating to the ability of the SARS-CoV-2 spike protein to bind itself to human cells, was identified in pangolin viruses but not in bat viruses.

None of the viruses that were studied is likely to be in the direct line leading to the virus that made the leap to humans, but their diversity suggests that SARS-CoV-2 went through cross-species evolution before making the leap to humans.

“Very much like the original SARS that jumped from bats to civets, or MERS that went from bats to dromedary camels, and then to humans, the progenitor of this pandemic coronavirus underwent evolutionary changes in its genetic material that enabled it to eventually infect humans,” senior study author Feng Gao, a professor of medicine at Duke University School of Medicine, said in a news release.

Scientists have long surmised that China’s “wet markets” serve as cross-species breeding grounds for new virus strains, and for months, they’ve pointed to bats and pangolins as potential culprits for coronavirus. The newly published study lays out one scenario for how SARS-CoV-2 picked up its deadliest trick. It also lays out a prescription for heading off future cross-species infections, known as zoonoses.

“While the direct reservoir of SARS-CoV-2 is still being sought, one thing is clear: reducing or eliminating direct human contact with wild animals is critical to preventing new coronavirus zoonosis in the future,” Gao and his colleagues write.

Another study, published today in the journal Science, looks at samples of all-too-human coronavirus from 84 patients who were treated at Mount Sinai Health System facilities in New York in March. Researchers analyzed the genetic sequences of the patients’ different viruses and matched them against more than 2,000 SARS-CoV-2 genomes from around the world.

They found limited evidence to suggest that the New York viruses were introduced directly from China. The evidence lent more support to the view that there were multiple introductions of the virus, mainly from Europe and other parts of the U.S. Two introductions were traced to the Seattle area’s main outbreak in February.

In addition to Gao, the authors of the Science Advances study, “Emergence of SARS-CoV-2 Through Recombination and Strong Purifying Selection,” include Xiaojun Li, Elena Giorgi, Manukumar Honnayakanahalli Marichannegowda, Brian Foley, Chuan Xiao, Xiang-Peng Kong, Yue Chen, S. Gnanakaran and Bette Korber.

The Science study, “Introductions and Early Spread of SARS-CoV-2 in the New York City Area,” has 35 authors, including senior authors Harm van Bakel, Viviana Simon and Emilia Mia Sordillo of Mount Sinai’s Icahn School of Medicine.

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