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Metagenomic Sequencing Uncovers Seal Virus Related to Hepatitis A

NEW YORK (GenomeWeb) – In a study appearing online today in mBio, a Columbia University-led team described a new seal virus that's closely related to the human hepatitis A virus (HAV).

Columbia University Center for Infection and Immunity Director Ian Lipkin and colleagues sequenced RNA in organs from three harbor seals that died of avian influenza in 2011. The outbreak killed more than 150 harbor seals on the coast of New England and the group was keen to find co-occurring viruses in the animals, if any.

Indeed, the harbor seal samples contained an almost 7,500-nucleotide-long virus dubbed "phopivirus" that shared genetic and other similarities with HAV. And follow-up testing on diverse samples from dozens more juvenile harbor seals, harp seals, and grey seals from the same region uncovered 11 more harbor seals and six harp seals carrying the phopivirus, which doesn't cause any obvious symptoms in the animals.

"Our findings show that these so-called 'hepatoviruses' are not in fact restricted to primates, and suggest that many more may also exist in other wildlife species," first author Simon Anthony, an epidemiology, infection, and immunity researcher affiliated with Columbia and EcoHealth Alliance, said in a statement.

HAV affects well over a million people a year, leading to liver problems that range from relatively mild to severe. Its origins are poorly understood, the team explained, with some past studies pointing to Old World non-human primates as a potential source of the human form.

With the unexpected new phopivirus finding, the study's authors hope to start inching closer to understanding HAV history and relationships to viruses circulating in the wild. Several such viruses, many of which may be closer to HAV than phopivirus, could exist in wildlife, meaning that "the evolutionary history of HAV may be far more complex than previously considered," they noted.

Using the Ion Torrent PGM platform, the researchers sequenced RNA from lung, liver, spleen, and mouth mucus samples obtained from the harbor seals that died from avian influenza.

They then tracked down and assembled the phopivirus with the help of nucleotide and viral protein databases, using a combination of PCR and Sanger sequencing to confirm the 7,476-base sequence.

The team found that new virus shares between almost 45 percent and 75 percent amino acid sequence identity with its closest known relative, HAV, depending on the region in question.

Likewise, the phopiviruses showed a preference for liver cells, though the researchers have not yet found any consequences for phopivirus-infected seal livers — potentially because the juvenile seals tested for the study were too young to show disease symptoms.  

While all of the phopiviruses isolated from New England harbor seals were genetically identical, the harp seal viruses were 97 percent identical, hinting at the possibility of species-specific phopivirus strains.

Based on these and other features such as secondary structure and codon use patterns, which also resembled those in HAV, the study's authors argued that the seal virus is a distinct species descended from an ancestor shared with human pathogen.

"Our data suggest that hepatitis A and this new virus share a common ancestor, which means that a spillover event must have occurred at some point in the past," Anthony said. "It raises the question of whether hepatitis A originated in animals, like many other viruses that are now adapted to humans."

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