Hepatitis C: Closing in on its viral origins

The virus behind Hepatitis C has been the target of virologists, epidemiologists and geneticists for years, in a bid to find out the animal host from which it likely came. But Prof Jonathan Ball, a virologist at the University of Nottingham, UK, says early indications that bats are the culprit may yet be proven wrong.

The omnipresent bat represents around one fifth of mammal species, yet remains strangely enigmatic.

Known to be the source of a range of human viral infections such as Sars and ebola, a recent study published in PNAS suggests that bats are a large natural reservoir to groups of viruses similar to the hepatitis C virus (HCV).

HCV is a life-threatening infection affecting more than 150 million people worldwide and its origin has eluded scientists for years.

To define if bats were a possible source for HCV-like viruses, Phenix-Lan Quan from Columbia University in New York and her colleagues analysed the blood from hundreds of bats living in South America, Africa and Asia.

To expose any infectious payload that the bats carried, the team used a method called high-throughput sequencing, which surveys all of the genetic material - nucleic acids - present in their blood.

In amongst the bat DNA, in approximately 5% of the animals tested, they discovered novel genetic sequences that were similar to nucleic acid present in viruses belonging to two groups - or genera - called pegiviruses and hepaciviruses. HCV is a member of the hepacivirus genus.

To determine the evolutionary history and relatedness of these viruses, they performed computer analyses to build what is called a phylogenetic tree.

Unlike a family tree, which is built using archive records of significant events like births, deaths and marriages, phylogenetic trees use the historic record written into the sequence of information stored in nucleic acids.

During replication, virus genetic material changes, or mutates, and these mutations accumulate over time allowing the virus to evolve.

Determining the number of genetic differences that exist between viruses gives an idea of how related they are - the fewer the changes, the more closely related - and phylogenetic trees represent this genetic relationship.

Viruses located on connecting branches are most related and the shorter the branches, the more related they are.

In the pegivirus and hepacivirus tree constructed by Dr Quan, the branches leading to clusters of bat virus sequences were numerous and long, indicating that bats have long been infected by a great variety of strains; more so than humans.

The branching pattern of the phylogenetic tree can also provide a clue to the origins of HCV.

If bats are the source of this virus, then the HCV sequences should nestle amongst the branches of the bat hepaciviruses - and at first sight they do.

But before we designate the much-maligned bat as public enemy number one, is there sufficient evidence to suggest that these vital pollinators and insect predators are the direct source of deadly HCV?

Equine enigma

Scientists have used phylogenetic trees to identify the source of many viral infections.

A 2005 paper in Science showed that Sars passed from bats to civet cats then on to humans, and a 2010 Royal Society journal article reported that HIV arose following transmission from African primates.

Initial studies suggested that the bat was responsible, but other suspects have now entered the line-up

The evidence supporting these particular animal-human transmissions - or zoonoses - is strong.

For example, in trees of virus sequences derived from extensive sampling of wild primate and monkey species, HIV is embedded firmly on the branch of the tree containing chimpanzee viruses. Genetically, HIV is most closely related to its chimpanzee counterparts and they are the most likely source.

In the hepacivirus tree, research in Emerging Infections Diseases has shown that HCV is more related to viruses found in horses and dogs than it is to those present in bats, but the branch leading to HCV is very long - it contains lots of genetic change and therefore long evolutionary timeframe.

A virus could have made the jump into humans millennia ago, but this unlikely.

The key to it all is in the virus sampling.

Just as an identity parade is only useful if the guilty party is present, phylogenetic analysis can only identify the cause of a virus outbreak if the most probable source is included.

Although Dr Quan's analysis includes far more viral sequences than has been possible before, the hepacivirus and pegivirus line-up still contained very few suspects.

"Our findings shed new light on the deep evolutionary history of those viruses that ultimately resulted in HCV," Dr Quan explained.

"We show that all known hepaciviruses and pegiviruses - including primates, horses and dogs - fall within the phylogenetic diversity of the bat-derived viruses, suggesting a longer evolutionary history of these viruses in bats than in primates, horses or dogs."

Whilst Dr Quan believes that bats harbour the greatest array of these important viruses, she stops short of arguing that her data prove that bats are the source of HCV.

"With our current data, we cannot conclude whether or not bats are the 'ultimate' reservoir of hepaciviruses and pegiviruses, nor whether HCV came from bats," she said. "To be truly able to answer this question, you would need to study a far larger sample of potential reservoir hosts."

Of mice and men

And to prove this point, a related study published in the journal mBio by a team led by Prof Amit Kapoor, also from Columbia University in New York, reported that numerous species of rodents also harbour hepacivirus and pegiviruses.

Just like the bat viruses, these too exhibited a large degree of genetic variability, hinting at an enduring history of infection.

Future studies could see rodents emerge as the confirmed source of the virus

None of the rodent sequences was more related to HCV than the horse hepaciviruses, but one of the co-authors of this study, Prof Peter Simmonds from the University of Edinburgh, thinks that the large degree of variability observed in these rodent viruses might prove significant.

"It seems as though different bat and rodent species carry a remarkably diverse range of HCV-like viruses," he said.

"None of these are very close genetically to HCV, but with such limited sampling, it certainly remains possible that other variants exist in other species that match HCV more closely."

Although leaving open the possibility that other animals might be the source of HCV, he added: "My prediction is that we will find a range of bat and/or rodent species to be infected with viruses that represent the immediate source of human infections in those parts of Africa and South Asia where HCV seems to have originated. It's difficult to know what those species are, when and how such species jumps occurred."

So, despite recent growth spurts, the hepacivirus and pegivirus phylogeny is still more of a sapling than a fully grown tree.

Extensive virus sampling from global mammalian species will add further branches and bring us closer to understanding the origin of HCV.

Bats and rodents have been around for more than 50 million years, so it's no surprise they've picked up one or two viruses in their travels.

Some of these, driven by habitat encroachment and human activity, have undeniably passed into humans.

But whether HCV arose from bats or rodents remains to be seen.