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Viral Transmission Study Sees Signs of Extensive Human-to-Animal Spread

NEW YORK – A viral genomic analysis focused on the evolutionary drivers behind viral host jumps suggests that human-to-animal "spillover" events are more common than previously suspected.

Beyond the so-called zoonotic host changes documented when viruses cross over from animal hosts to humans, the work highlighted the extent to which host jumps can occur in both directions between humans and other animals. Host swaps appeared to be particularly common for viruses with relatively high rates of viral evolution or host ranges that are already broad.

The study, published by investigators at the University College London and the Francis Crick Institute, appeared in Nature Ecology and Evolution on Monday.

"[W]e often overlook the fact that viruses jump from humans to animals and between animals, too," first and corresponding author Cedric Tan, a Ph.D. student affiliated with UCL Genetics Institute and the Francis Crick Institute, said in an email. "We therefore set out to investigate the patterns and drivers of viral host jumps across all vertebrates, including wild and domestic animal species."

To do so, the researchers analyzed viral genome sequences and metadata for some 11.6 million viruses in the NCBI Virus portal housed at the US National Center for Biotechnology Information. Some 68 percent of the sequences in the database were SARS-CoV-2 genomes generated during the COVID-19 pandemic, but even after SARS-CoV-2 sequences were removed from the analysis, single-stranded RNA viruses and viruses associated with vertebrate host species made up the vast majority of the sequences present.

In an effort to understand the nature and frequency of viral host jumps, the team focused on a subset of 58,657 quality-controlled viral genomes and used a species-agnostic analytical approach to track genetic diversity- and network-informed taxonomic units dubbed "viral cliques" within that sample.

Within the set of viruses considered, which spanned 32 viral families and was linked to animal hosts from 62 vertebrate orders, the investigators identified more than 5,100 viral cliques and found that some 62 percent of those viral cliques were made up of viruses associated with nonhuman animals.

When the team turned to genome sequence alignment and phylogenetic analyses to trace these host jumps, meanwhile, it saw 2,904 apparent vertebrate host jumps involving nearly 12,700 viral lineages from 174 viral cliques. In the host swaps that involved humans, human-to-animal viral spread occurred roughly 64 percent of the time, while the remaining 36 percent of host jumps involved animal-to-human spread.

"We've known that viruses can sometimes jump from humans to animals. For example, we passed SARS-CoV-2 to farmed minks, cats, and wild white-tailed deer soon after it started circulating in humans," Tan explained, noting that the new findings suggest that such human-to-animal transmission events "are even more frequent than we thought."

The investigators' analyses also suggested that viruses already capable of infecting a broad range of host animal species are more apt to jump to additional hosts than more specialized viruses with a narrow host range, likely because broadly infective viruses require fewer new adaptations to make such a move.

"[P]ast studies have shown that viruses with broad host ranges are more at risk of jumping into humans," Tan explained. "However, we extend these findings by showing that this pattern is not limited to animal-to-human (zoonotic) jumps but is a more general pattern across the animal kingdom."

The team is continuing to dig into the host jumps uncovered in the current study to better understand whether there are key animal species that tend to contribute to viral flow and is considering models for following viral flow between humans and animals, Tan said.

Moreover, he suggested that an automated version of the analytical methods used in the current study may eventually help in developing a real-time surveillance strategy for flagging emerging viral conditions, regardless of whether they originate in humans or other animals.

More broadly, the study points to "our massive impact as a single species on the environment and the animals around us," Tan said, adding that "[w]e hope that our new findings will encourage more research on assessing the risk and impacts of human-borne viruses on wildlife."