Here is Aish's translation of the pertinent section:
They informed Rav Yehudah: There is a deadly plague affecting the pigs. He decreed a fast. Do we say that Rav Yehudah holds that a plague which affects one [animal] species is likely to affect all species (and therefore, kosher farm animals were threatened also)? No. Pigs are different since their digestive tracts are similar to those of humans.Adds the Meiri (13th century commentary on the Talmud)
Since both pigs and humans lack a certain abdominal organ (the rumen), there was reason to fear that epidemics that affect pigs may also affect humans.In under 8 seconds I came up with the following objections to the claim that Rav Yehuda and the Meiri are discussing swine flu.
1. The strain of influenza currently affecting humans did not exist in the time of the Talmud. The type of swine flu that infects humans is believed to have resulted from the seasonal reassortment of two different strains of swine influenza.
2. The Meiri's suggestion that the absence of a rumen makes pigs and humans susceptible to the same diseases is unverified, and has no backing. The only mammals with rumens are the cud-chewers. No other type of mammal has one. If the Meiri is right every non-ruminant mammal (including rodents, canines, felines, etc.) is at risk for swine flu. There is no evidence this is true.
3. Human susceptibility to swine flu has little if anything to do with any similarity between the swine and human digestive tracks. In fact, the strain of swine influenza sickening humans is not the same strain that sickens pigs. They contain common genetic elements, but they are different. To date, the human strain has not been isolated in pigs. (Wikipedia)
Afterthought: Perhaps Rabbi Yehuda observed a different, earlier strain of swine flu? This is certainly possible, and I concede the liklihood, but why find it astounding? Wouldn't you expect any agriculturalist to notice if livestock and people were coming down with similar illnesses? If Rav Yehuda is discussisng swine flu, this is merely a routine observation and no evidence of his superior torah-based wisdom.
*Link to CoolJew via @gruven_reuven @ashleyroz and @jtowncrier on Twitter. I have no reason to think these three fine Tweeters endorse the idea that swine flu is discussed in BT Taanis.