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Questions Remain About the Swine Flu Infection of Canadian Pigs and the Origin of Outbreak

Canadian scientists today clarified that they still think it’s “highly probable” that a farm worker infected the Alberta pig herd found to have the virus now causing the outbreak of swine flu in humans around the globe. But so far, they have no lab evidence that the man suspected of transmitting the H1N1 virus to pigs—the first pigs yet found to harbor the virus—was himself infected or even had influenza. Several other questions remain, including the number of pigs infected and whether any people living there or studying the outbreak have become infected.

Veterinarian Jim Clark of the Canadian Food Inspection Agency (CFIA) spoke with ScienceInsider today at length about the Alberta farm, clarifying several points that were imprecisely reported here and elsewhere. CFIA and the Public Health Agency of Canada (PHAC) also provided more details about the pig herd at a press conference this morning.

The confusion begins with the infected pigs. On 2 May, CFIA revealed that it had found the virus in a herd of 2200 swine in Alberta. Although a World Health Organization food safety scientist said at a 3 May press conference that 220 animals had shown symptoms, Clark says that vastly underestimates the spread through the herd. “The actual number of infections is in the 75% to 80% range,” Clark estimates. This is based on 20 pig samples tested for the virus, 16 of which were positive.

From the outset, Canadian officials focused on a farm worker as the likely source of transmission to the pigs, which are in a “closed” herd. “There hasn’t been any introduction of pigs into this herd for an exceedingly long time,” explains Clark. The farm worker who became the suspected “index case” of this outbreak in pigs returned from Mexicali, Mexico, on 12 April and went back to the farm on 14 April. At that time he had an influenza-like illness. Subsequent analysis of two-thirds of the genome in the 2009 A (H1N1) isolated from more than a dozen pigs shows that it closely matches the human version of the virus. “The viruses are highly related to what’s circulating in Mexico,” says Francis Plummer, head of PHAC’s National Microbiology Laboratory in Winnipeg, which played a central role in identifying the virus. “I don’t know how else it could have got there.”

But a report released yesterday by the European Centre for Disease Prevention and Control revealed that the worker had “tested negative” for the virus, with no explanation. Clark and Plummer explained today that although tests showed that the worker did not harbor the virus, that may reflect when he had a nasopharyngeal swab, the standard way to obtain a viral sample from people suspected of having influenza. “As I understand it, the time when this individual who had returned from Mexico was swabbed was a significant  time period after he was actually, clinically ill,” says Clark. “The anticipation from the public health end is they likely weren’t going to find any virus anyway, but they had to take the opportunity to test him.”

Plummer says it may be possible to determine whether the man has antibodies to the novel H1N1 virus, which his lab is now looking for in blood samples. “We think we probably will be able to make a call based on the antibody levels in this individual,” says Plummer. He noted that the antibody response elicited by the novel H1N1 virus of swine origin “is quite a bit different” from the response to common “seasonal” H1N1 of human origin. If that fails, Plummer says his lab still may be able to answer the question by looking at the man’s T cells and analyzing whether they have any immunologic memory of having see the new virus.

As a final dizzying twist to the story, people living on the farm and CFIA investigators recently developed influenza-like illness, says Clark. All of them tested negative for the novel H1N1, but again, some may have been tested too late to find the virus, says Clark. “The individuals in the farm family who had any illness after this individual returned, it could have been as a result of exposure to him, but again it may have been a seasonal influenza A virus that had absolutely no relationship to the worker returning from Mexico,” says Clark. “Or it may have been due to some transmission from the swine back to the on-farm family.”

So for now, no lab evidence connects the worker who went to Mexico to the infection in the pigs. “Saying something definitely with corroborating laboratory information can’t be done,” says Clark. “All we can talk about is how we understand the situation in terms of the events and when they occurred and probability. Making definitive statements about whether this individual was the source of the virus, it’s highly probable, but definitively, no we can’t say that.”