Ever since Canadian officials announced in May that pigs on an Alberta farm harbored the novel H1N1 virus causing the swine flu outbreak, scientists have struggled to explain its origins. Researchers had hoped a close look at virus isolates from the pigs would clarify matters, but new sequences posted on a public database yesterday had many unusual mutations that raised more puzzling questions.
Many mysteries remain about the origin of the pandemic in humans, and the Alberta pigs have received intense attention because they were the first swine found to harbor the virus. From the outset, the Canadian Food Inspection Agency (CFIA) dismissed the possibility that the pigs had spread the virus to humans, saying it was "highly probable” that the animals had become infected by a carpenter working on the farm who recently had returned from Mexico with a respiratory illness. But the carpenter, Adrian Blaak, told ScienceInsider on 24 June that he has tested negative for the virus on several tests, which Alberta health officials confirmed. Still, CFIA maintained that a human most likely infected the pigs, as that farm is isolated and does not introduce swine from other sources. (Pigs on a farm in Argentina recently tested positive for the virus, and officials there also suspect that it was human-to-swine transmission.)
On 14 May, CFIA sent GenBank, a public database, the sequence from one Alberta pig isolate. Evolutionary biologist Andrew Rambaut of the University of Edinburgh in the United Kingdom cofounded a wiki Web site about the evolution and origin of the new virus and noticed that it had an unusual number of mutations compared with human sequences. But with just one isolate, Rambaut had difficulty making sense of it. Then on 9 July, CFIA posted partial sequences from 10 more pig isolates; these, too, have many mutations not seen in the virus found in humans, he says.
Although Rambaut agrees that humans most likely infected the pigs, he says he has had difficulty understanding the evolutionary relationship between isolates from the Alberta swine and humans. “At first glance, it looks like these are quite genetically diverse, and my concern is that this might be interpreted as meaning the viruses are in some way ancestral to the human outbreak,” says Rambaut. But he suspects that the mutations are a laboratory artifact. Specifically, if the pig isolates are older than the human ones, they should share the same mutations, he says. But these pig isolates each have unique mutations seemingly scattered about willy-nilly. Rambaut has posted his preliminary analysis of the pig sequences on his wiki site.
Rambaut’s hunch is that the mutations may have been introduced when Canadian scientists prepared the isolates for sequencing. As a study published in 2000 in the Proceedings of the National Academy of Sciences found, growing influenza isolates in eggs before sequencing them can introduce mutations. CFIA’s John Pasick, who helped sequence the swine isolates, told ScienceInsider that the lab indeed did grow the isolates in eggs. “It could be these mutations might be adaptations from growing the virus in chicken embryos,” says Pasick, who grew them in eggs because he runs an avian influenza lab.
An alternate explanation, says Pasick, is that the swine-origin virus had adapted to humans, and when it went back into the Alberta herd, it mutated to readapt to pigs. “We do find the mutations a little unusual,” says Pasick, who added that his group is preparing a manuscript that discusses its findings. He says they also have the original swabs taken from the pigs and, “time and resources permitting,” will grow the viruses in a cell-based medium and resequence them to see if the mutations were introduced by growing them in eggs.