Can A Viral Genome Be Made Of Both DNA And RNA?

Viruses typically store their genetic information encoded in molecules of either DNA or RNA — either one or the other but not both. In April of 2012, however, scientists at Portland State University discovered an unusual virus with a genome made from both RNA and DNA. No one knows whether this is a bizarre, single occurrence, or whether there are other similar viruses out there.

Virtually all living organisms carry hereditary information encoded in molecules of DNA. Viruses are an unusual exception. Admittedly, many biologists don't consider viruses to be a form of "life" since they can't reproduce on their own. While many viruses do have DNA genomes, others like HIV and the flu have genomes made from RNA instead. RNA and DNA are very similar: both are made from chains of chemical units stapled together by a specific type of chemical link called a phosphodiester bond. There are two important differences between RNA and DNA, however. RNA includes a chemical unit not found in DNA called uracil. In addition, the chemical units in RNA have one additional oxygen atom attached to the sugar part of each unit. This difference makes RNA more unstable and more prone to breaking down.

Scientists have long thought that viral genomes could be made from either DNA or RNA but not both. In April of 2012, however, scientists at Portland State University in Oregon announced the discovery of a virus they called RNA-DNA hybrid virus or RDHV in the waters of Boiling Springs Lake in the Lassen Volcanic National Park. The genome of this virus is made of DNA, but one of the genes in this genome is extremely similar to genes found only in RNA viruses, which strongly suggests that, at some point in the past, this virus had a hybrid genome made of both DNA and RNA. The virus was found in the lake water by running water through a filter to capture viruses for DNA sequencing, so scientists don't know what it does or what type of organism it infects, how abundant the virus is, or whether it can survive in other environments. At this time, RDHV is the only known instance of an RNA virus forming a hybrid with a DNA virus.

There are two ways that a gene from an RNA virus could have become part of the genome of a DNA virus. An RNA virus and a DNA virus could have infected the same cell at the same time; if one of the RNA genes was converted or translated into DNA, the resulting DNA could have been mixed up with the DNA viral genome, thereby creating the hybrid. Alternatively, a strand of DNA and a strand of RNA could have been glued together in a cell infected with both kinds of viruses. Based on what we know right now, scientists can't tell for sure which of these two scenarios gave rise to the hybrid in Boiling Lake. Nor do they know whether this type of hybrid would have any advantage over the competition.

There is a gigantic number of viruses in the world's oceans, most of which infect bacteria. The average milliliter of seawater contains an estimated several million viruses. The vast majority of ocean viruses have not been named, isolated or identified, although scientists have collected DNA sequence data for thousands of as-yet unidentified ocean viruses through a project called the Global Ocean Survey. The Portland State scientists tried searching Global Ocean Survey data for sequences similar to those in RDHV to determine whether there might be other RNA-DNA hybrid viruses out there, and they found several matching sequences, all from as-yet unidentified viruses. This tantalizing clue suggests there may be other RNA-DNA hybrid viruses somewhere in the world's oceans. Although scientists who study viruses aren't looking specifically for RNA-DNA hybrids, they are trying to learn more about the bewildering variety of viruses found in nature, and as this research progresses it's possible they may find other similar hybrids elsewhere.