Newly discovered virus family infects human oral amoeba
In 2019, researchers reported a new family of DNA viruses, Redondoviridae, which is frequently found in human buccal swabs and is particularly abundant in cases of periodontitis and other diseases. Until now, however, it was unknown whether Redondoviridae infects human cells themselves or any of the resident eukaryotic microbes in the mouth; the genomic sequences of the viruses suggested bacteria were unlikely to be the hosts.
A new study published today (1 December) in Cell host and microbe points to the protist Entamoeba gingivalis as a host of these viruses, based on phylogeny, co-occurrence of the two organisms in human samples, and culture analyzes of the amoeba. These results reinforce a computer prediction made independently by another group and published on September 16 in Evolution of viruses– while the new study was being reviewed – which suggested this eukaryote was the most likely host.
“We wanted to know what cell they were growing on,” because redondoviruses are so abundant in disease-associated human samples, says University of Pennsylvania microbiologist Frederic Bushman, who led the teams that proposed redondoviruses as a new family and conducted the new study on their putative host. These viruses “grow particularly well in [cases of] periodontitis,” he adds, so “we started looking at the cells that are in the gingival crevice” of humans, where the teeth meet the gums.
A first series of analyzes led them to E. gingival– commonly found in this crevice and associated with periodontitis – as a potential candidate. A first clue was that one of the closest relatives of redondoviruses, the Naryaviridae family, infected another’s cells Entamoeba species. Then, as the researchers searched for possible co-occurrences of E. gingival and redondoviruses in human samples, using their own previously published data and data from other research groups, they found a strong positive association.
Verifying this association in the laboratory was more difficult, says Bushman. So far, it is not possible to grow this amoeba alone in culture. Instead, the team got a E. gingival culture of American type culture collection which also contained feeder bacteria. In it, the researchers detected redondovirus DNA and RNA. Because the culture had “spread for a while,” everything in it “presumably had to replicate in it,” in the absence of human cells, Bushman says.
Finally, his team used a method called Hi-C to cross-link nearby DNA sequences in culture. If a DNA virus grows inside a cell, fragments of its DNA should bind to those of the host when this method is used, Bushman says. He and his colleagues found chimeric sequences of E. gingival and redondoviruses with a higher frequency than expected by chance alone, adding further evidence that the amoeba is most likely the previously incognito host.
Identifying a virus in culture is, historically, the “gold standard” in virology for confirming a host, says Cormac Kinsellacomputational biologist at UMC Amsterdam and co-author of the Evolution of viruses paper. This, combined with DNA cross-linking analysis and the rest of the data from the new study, provides a “very strong conclusion” that E. gingival is the host, he adds. Additionally, Kinsella points out that using very different approaches, the two teams arrived at this discovery independently.
However, the identification of the host of these viruses does not yet make it possible to know if they play a role in the disease, or if their detection simply reflects the presence of the amoeba, whose role in the disease is itself same not clear. Even though E. gingival is indeed a contributing pathogen to periodontitis, “there is no reason at this time to believe that redondoviruses have any effect” on this pathogenesis, Bushman says. “But that’s not ruled out either.” For example, they could modify the amoeba so that it is more successful at infecting, as an unrelated virus Is with a parasitic protozoan.
Bushman points out that, considering that most studies on human virome focus on viruses that infect bacteria, this work highlights the potential of human-associated eukaryotic microbes to act as hosts for viruses present in the human body.