We're still a long way off developing new drugs to combat them, but scientists have finally cracked the code used by a major group of virus to spread infections such as the common cold, Ebola, hepatitis C, HIV, and polio around the body.

This newly discovered code has been hiding inside the sequence of ribonucleic acid (RNA) - a nucleic acid involved in the coding, decoding, regulation, and expression of genes - that makes up the genome of the single-stranded RNA viruses group, which is considered one of the most potent and debilitating of groups of infectious pathogens. And once the scientists found it, they were able to decipher it.

“We have understood for decades that the RNA carries the genetic messages that create viral proteins, but we didn’t know that, hidden within the stream of letters we use to denote the genetic information, is a second code governing virus assembly,” one of the team, biophysicist Roman Tuma from the University of Leeds in the UK, told Laura Donnelly at The Telegraph. “It is like finding a secret message within an ordinary news report and then being able to crack the whole coding system behind it.”

Single-stranded RNA viruses are the most simple type of viruses known to science, and it’s thought that they were probably one of the first to evolve. And being around for a long time means they’re super-effective at what they do. Rhinovirus, which is the predominant cause of the common cold, is responsible for 1 billion infections per year - in the US alone.

The discovery has taken the team several years to complete, the first big step occurring in 2012, when Tuma and his colleagues published the first observations taken at a single-molecule level of how a single-stranded RNA virus fit its core into its outer shell. And it’s not just a case of stuffing it in like vacation wear into a suitcase - the core has to be very precisely folded in order to fit within the shape of the shell, made from a protective protein coating, and the virus has figured out how to do this in mere milliseconds. But how?

The next step involved mathematicians at the University of York in the UK, who worked with the Leeds group to come up with algorithms that could read the encrypted code that controls the complex folding process. Computer models were then built to replicate this coding system so the team had a better chance of cracking it.

The team compared these computer models to the Enigma machine, used famously during the 20th century to encipher and decipher secret messages, particularly during World War II.

Now, publishing in the Proceedings of the National Academy of Sciences, the team reports that they’ve finally done it. Using a visualising technique called single-molecule fluorescence spectroscopy, they watched the common plant disease - a single stranded RNA plant virus called the tobacco necrosis virus - use the code to replicate itself.

“The Enigma machine metaphor is apt,” says one of the team, Reidun Twarock from the University of York, in a press release. "The first observations pointed to the existence of some sort of a coding system, so we set about deciphering the cryptic patterns underpinning it using novel, purpose-designed computational approaches. We found multiple dispersed patterns working together in an incredibly intricate mechanism and we were eventually able to unpick those messages. We have now proved that those computer models work in real viral messages.”

Not only can the team read these coded messages within the genomes of the viruses, but they now know how to jam them and stop the spread of the virus in its tracks. The way to do this, says Tuma, is by designing molecules that can interfere with this secret code and scramble it, so the virus cannot fold its core properly and replicate. The team plans to work on this and start testing the method out on animal viruses.

Source: The Telegraph