It may hardly seem like news, but here’s the latest: raw sewage is loaded with viruses. That’s the
part you may have already guessed. The more astounding aspect of a study published in mBio this week is the diversity those viruses represent. Biologists have described only a few thousand different viruses so far, but this latest study reveals that raw sewage is home to the most diverse array of viruses ever found. Apparently, a vast world of unseen viral diversity exists right under our noses.
Viruses are everywhere: every moment of every day, humans are exposed to viruses on surfaces, in foods, and in water. However, our knowledge of the viral universe is limited to a tiny fraction of those that likely exist. A quick calculation bears this out: there are roughly 1.8 million species of organisms on planet Earth, and each one is host to untold numbers of unique viruses, but only about 3,000 have been identified to date.
To explore this diversity and to better gauge the numbers of unknown viruses that are out there, the researchers applied a metagenomics approach to raw sewage samples from North America, Europe, and Africa. (Unfortunately, in my mind, they lumped the results from these three locations together. How do sewage viruses in Addis Ababa differ from those in Pittsburg?) Cantalupo et al. concentrated and purified the virions in their samples, then isolated DNA and RNA and reverse transcribed it. Deep sequencing resulted in a total of 897,647 high-quality reads (approximately 278 Megabases), which were compared to databases by a series of BLAST searches.
The authors detected signatures from 234 known viruses that represent 26 different “families”, or types, of viruses. Known viruses included human pathogens like Human papillomavirus and norovirus. Also present were several viruses belonging to those familiar denizens of sewers everywhere: rodents and cockroaches. Bacteria are also plentiful in sewage, so it was not surprising that the viruses that prey on bacteria dominated the known genetic signatures. Finally, a large number of the known viruses found in raw sewage came from plants, probably owing to the fact that humans eat plants and plant viruses outnumber other types of viruses in human stool.
Raw sewage contains more mysteries than answers, however: the vast majority of viral genetic signatures belong to unknown viruses. This fact is significant, says the study’s editor, Michael Imperiale of the University of Michigan. Unknown viruses like those found in sewage probably play many roles in human health and environmental processes that we simply do not appreciate yet, he says.
Of the unknown sewage viruses that come from humans, some of them may be opportunists that lie in wait for the human host’s immune system to break down and provide an opening, he says.
Other viruses may be benign or even helpful. “There’s a theory out there that we may be infected with viruses that don’t cause any disease and may have beneficial effects,” says Imperiale. There are examples of animal viruses that bear this out, he says, including a herpes virus in mice that makes them somewhat resistant to bacterial infections.
The study’s authors plan to follow up their examination of sewage viruses with studies of other environments around the world where viruses are likely to thrive.
Michael Imperiale expects more discoveries to come. “I think this is going to be the tip of the iceberg of how many viruses are out there,” he says. “I think the ocean is going to top raw sewage by orders of magnitude,” although they won’t be found in such densities as they are in sewage, he concedes.
[The study's lead author is James Pipas of the University of Pittsburgh. Coauthors are affiliated with Pitt, the University of Barcelona, and Washington University in St. Louis.]