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Holy Influenza, New Flu Virus Found in Bats

NEW YORK (GenomeWeb News) – An influenza A virus with a new genetic lineage has been found infecting a fruit-eating bat species from Central and South America, researchers reported online yesterday in the Proceedings of the National Academy of Sciences.

A team from the US and Guatemala sampled several hundred bats from eight Guatemalan locations over two years. In one of the 21 bat species tested, investigators found an influenza A virus that appeared to be distinct from any characterized in the past. The virus, which has since been classified as influenza A sub-type "H17," turned up in three little yellow-shouldered bats captured at two different sites in 2009 and 2010.

Through genome sequencing and phylogenetic analyses, the team found that the bat flu virus is divergent from other influenza A viruses at a number of key genes. But while the virus could not be grown in traditional culture systems in the lab, it does appear to have the ability to replicate in human cells, sparking concerns that it could contribute to outbreaks of disease in humans or other animals.

"Despite its divergence from known influenza A viruses, the bat virus is compatible for genetic exchange with human cells," US Centers for Disease Control and Prevention researchers Charles Rupprecht and Ruben Donis, the study's co-corresponding authors, and colleagues wrote, "suggesting the potential capability for reassortment and contributions to new pandemic or panzootic influenza A viruses."

Though many of the influenza A viruses circulating in the wild are found in waterfowl, the study authors explained, some have turned up in mammals as well. Because these strains are predicted to be more prone to moving into humans and other mammalian hosts, they added, finding such flu viruses prior to this jump between species is key.

"Early prediction, detection, characterization, and risk assessment of viruses in their animals hosts, before they spread into the human population, are critical to protect public health," the team wrote.

For the current study, the researchers looked for flu viruses in bats — mammals that can migrate long distances, in some cases, and which have been found carrying a range of other pathogenic viruses.

Using RT-PCR, they tested rectal swab samples from 316 bats, testing for conserved polymerase gene sequences shared between influenza viruses. The bats represented 21 different species captured at eight sites in southern Guatemala in 2009 and 2010.

The search uncovered flu virus sequences in samples from the fruit-eating bat species Sturnira lilium, commonly known as the little yellow-shouldered bats.

Two of 15 S. lilium bats sampled in 2009 and one of the 14 S. lilium bats sampled at another site the following year all carried similar viruses, which had polymerase sub-unit sequences most similar to influenza A.

The virus was found in other tissues from one of the little yellow-shouldered bats, too, suggesting the animal was infected with influenza and had not just eaten something carrying the virus.

The team turned to genome sequencing to further characterize the three influenza A viruses. The 2010 isolate was sequenced using the Sanger strategy, while the 2009 isolates were sequenced with a combination of Illumina GAIIx and Roche 454 GS-FLX platforms.

For the viruses sequenced using high-throughput methods, researchers also shored up their sequence data by doing Sanger sequencing on amplicons representing the virus' eight segments.

While the two viruses collected in 2009 shared almost the same sequence, researchers reported, the 2010 virus was slightly less related, showing roughly 96 percent nucleotide identity with the other two genomes.

All three genomes contained segments and structural features that coincided with those found in other influenza A viruses, though some of their protein sequences diverged significantly from those found in other strains.

The researchers' phylogenetic analysis — a comparison between the bat viruses, 66 influenza A strains, six influenza B viruses, and a single influenza C virus — revealed different relationships depending on the gene segment considered.

For instance, they reported, the bat virus hemagglutinin gene falls squarely within influenza A HA group 1, earning it the H17 sub-type classification. Based on six internal gene sequences, meanwhile, the bat virus fell outside of the influenza A and B, but was closer to the influenza A viruses.

On the other hand, its neuraminidase gene sequence diverged a great deal from those found in both influenza A and B viruses — a pattern that researchers say might reflect an older ancestry for the NA gene or faster evolution of the gene due to distinct selective pressures.

"A better understanding of the evolutionary history of the bat influenza NA gene would be facilitated by identifying additional related viruses in bats," they explained.

Likewise, the team noted, more research is needed to determine how widespread the new influenza A virus is within bat populations, particularly since preliminary experiments hint that the bat virus likely has the genetic wherewithal to replicate in human cells.

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