Cornell researchers have identified a shift that occurs in canine coronavirus that points to a possible pattern of change found in other coronaviruses and which may provide clues to how they transmit to humans from animals.

A new canine coronavirus was first identified in two Malaysian human patients who developed pneumonia in 2017-18. A group of other scientists isolated the canine coronavirus, sequenced it and published their findings in 2021.

Now, a team led by Cornell and Temple University researchers has identified a pattern that occurs in a terminus of the canine coronavirus spike protein – the area of the virus that facilitates entry into a host cell: The virus shifts from infecting both the intestines and respiratory system of the animal host to infecting only the respiratory system in a human host.

The researchers identified a change in the terminus – known as the N terminus – a region of the molecule with alterations also detected in another coronavirus, which jumped from bats to humans, where it causes a common cold.

The paper, “Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein,” was published April 21 in the journal Viruses.

“This study identifies some of the molecular mechanisms underlying a host shift from dog coronavirus to a new human host, that may also be important in the circulation of a new human coronavirus that we previously didn’t know about,” said Michael Stanhope, professor of public and ecosystem health in the College of Veterinary Medicine. First author Jordan Zehr is a doctoral student in the lab of co-author Sergei Kosakovsky Pond, professor of biology in the Institute for Genomics and Evolutionary Medicine at Temple University.

In the study, the researchers used state-of-the-art molecular evolution tools developed in Pond’s lab to assess how pressures from natural selection may have influenced the canine coronavirus’ evolution.

In humans, the main receptor that the Alphacoronavirus (the genus to which canine coronavirus is classified) spike protein binds with in order to enter a human cell is called APN, but there are also co-receptors. One of these co-receptors is sialic acid, which is found in gastrointestinal cells in a variety of mammals. The researchers identified a region of the spike protein in the N-terminus called the O-domain, which is known for binding with sialic acid. In the analysis of the canine coronavirus found in the Malaysian patients, parts of the O-domain were changing in unique ways.

The canine coronavirus found in the Malaysian patients appeared to be in the process of losing its O-domain – but not completely. “But it has a molecular evolution history that suggests that the sialic acid binding region is no longer doing the same job,” Stanhope said. The researchers found evidence of “relaxed evolution,” where the pressures of natural selection become reduced, which facilitated the shift.

The researchers compared this shift and loss of the O-domain to other related coronaviruses. One, called transmissible gastroenteritis virus (TGEV), infects pigs and causes respiratory and intestinal disease. A variant of this pig virus, called porcine respiratory coronavirus, is almost identical to TGEV, but it has lost its O-domain and is entirely a respiratory pathogen. Similarly, a coronavirus known to cause common human colds originated in bats as a gastrointestinal virus, lost its O-domain, and jumped to a human host as a respiratory virus.

“So this is a pattern that seems to be repeating itself in coronavirus evolution and in particular in coronavirus evolution associated with these tropism shifts, where we go from a gastrointestinal infection originally and then jumping to an alternate host, where it’s now respiratory,” Stanhope said.

The same variant of canine coronavirus found in Malaysia was also reported in 2021 in a few people in Haiti, who also had respiratory illness. More study is needed to understand if the viral shifts and jumps to humans occurred spontaneously in different parts of the world or if this coronavirus, which would represent the eighth known human coronavirus, has been circulating for perhaps many decades in the human population without detection, Stanhope said.

The N-terminus domain of SARS-CoV2, which causes COVID-19, is receiving increasing attention from researchers, and this study provides additional rationale to focus on this specific area of the molecule.

Co-authors include Laura Goodman, assistant research professor in the Department of Public and Ecosystem Health and the Baker Institute for Animal Health; Gary Whittaker, professor of virology in the Department of Microbiology and Immunology; and Kristina Ceres, a doctoral student working closely with Stanhope and Goodman. Goodman and Whittaker are both part of the Cornell Margaret and Richard Riney Canine Health Center.

The study is funded by the U.S. Food and Drug Administration’s Veterinary Laboratory Investigation and Response Network and the National Institutes of Health.