Researchers discover over 30,000 hidden viruses in the DNA of single-celled organisms

Discovery of hidden viruses in DNA from an Alpine Lake

In 2021, Dr. Christopher Bellas and Prof. Ruben Sommaruga, researchers involved in the study, stumbled upon a new group of viruses in the Gossenköllesee water, sparking a research project. Although their initial goal was to trace the origin of the "Polinton-like viruses," they were unsure which organisms were typically affected, prompting a broader study of all microbes with known DNA sequences.

"Why so many viruses are found in the genomes of microbes is not yet clear," Bellas said in a statement. "Our strongest hypothesis is that they protect the cell from infection by dangerous viruses."

Despite consisting of several hundred gigabytes, the data set examined by researchers only contained DNA sequences, but state-of-the-art technology enabled them to find tiny virus sequences within it. They utilized the high-performance computer cluster "Leo" and the new Oxford Nanopore technology, which reads DNA sequences by passing them through tiny pores in a membrane, generating a signal from each base - A, G, C, or T - that interrupts an electric current.

According to the study, numerous protist EVEs are not only remnants in the genome but active viruses, forming an antivirus mechanism for the host.

The study was published in the Proceedings of the National Academy of Sciences.

Study Abstract:

Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be “genomic fossils.” Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.