Until now, viruses have been difficult to classify. The International Committee on the Taxonomy of Viruses recognized seven orders of viruses, based on their shapes and sizes, genetic structure and means of reproducing.
Only 26 (of 104) viral families have been assigned to an order, and the evolutionary relationships of most of them remain unclear.
Part of the confusion stems from the abundance and diversity of viruses. Less than 4,900viruses have been identified and sequenced so far, even though scientists estimate there are more than a million viral species. Many viruses are tiny - significantly smaller than bacteria or other microbes - and contain only a handful of genes. Others, like the recently discovered mimiviruses, are huge, with genomes bigger than those of some bacteria.
The researchers chose to analyze protein folds because the sequences that encode viral genomes are subject to rapid change; their high mutation rates can obscure deep evolutionary signals, author said. Protein folds are better markers of ancient events because their three-dimensional structures can be maintained even as the sequences that code for them begin to change.
The researchers analyzed all of the known folds in 5,080 organisms representing every branch of the tree of life, including 3,460 viruses. Using advanced bioinformatics methods, they identified 442 protein folds that are shared between cells and viruses, and 66 that are unique to viruses.
The data suggest "that viruses originated from multiple ancient cells ... and co-existed with the ancestors of modern cells," the researchers wrote. These ancient cells likely contained segmented RNA genomes, author said.
The data also suggest that at some point in their evolutionary history, not long after modern cellular life emerged, most viruses gained the ability to encapsulate themselves in protein coats that protected their genetic payloads, enabling them to spend part of their lifecycle outside of host cells and spread. The protein folds that are unique to viruses include those that form these viral "capsids."