These things constantly reassort, which is one reason for the US swine surveillance program.
You read "matched to" as "the same", but it is not. This is an H1N1 virus which is novel. The bulk of sequences are matched to NA and Eurasian swine viruses, but it is not the same virus. One of the major differences is that it is very easily transmittable between humans, which is not the case for most swine flu virus strains. Because of the way viruses replicate (RNA, sloppy) they exchange genes in bodies. So coinfection between two different viruses can produce a new virus very easily. That means that a high degree of similarity in gene sequences doesn't necessarily tell you the source of the infection.
Right now what little evidence we have points more to an NA source than a Mexican source, and it is very possible that when the Mexican authorities sent the medical team to La Gloria to check the outbreak of respiratory disease there that they brought this strain with them.
Since more Mexican samples are being typed, the number of Mexican deaths attributed to this virus keeps dropping, which makes sense of the earlier puzzle about why a virus that was mild in the US was killing people in Mexico. It's possible that the epicenter was Mexico City, and that it came in from Asia. It's also possible that this virus was circulating in the US for longer than we know. The CDC testing criteria were to test for Mexican-associated flu, so those are the initial samples they have been working on.
I very much doubt the point of the original article linked here, which is that factory farming causes epidemics. The reason is that modern factory farming cuts down the number of contacts between birds, swine and humans, and that is the interaction that produces these reassortments. Because most of these viruses originate in Asia in regions where small farming still predominates, there is more evidence to the theory that intensive agriculture on a small scale generates these viruses.
However, in this case there is no evidence at all that the Mexican farm generated the outbreak although I am sure there will be some genuine research done on the question. And one of the reasons I am bothering to post on this topic is that saying it did implies that Mexico is the source, when Mexico very well might not be the source.
There is an Alberta (CA) hog farm in which the pigs have already caught this new H1N1 virus from a human. Pigs and humans pass viruses very easily. There is actually more testing of viruses that cause illness in stock than in the human population, so it is possible that a human was the source of the Carolina detection. Humans frequently convey viruses from one farm to another. Sometimes they just do it by contact, but sometimes the human gets the virus and passes it that way.
Journalists who are not scientists frequently misunderstand what they are told. There has been a lot of misinformation in the press. I don't think it is intentional, but it is feeding calls to shut the border with Mexico, etc. This current frenzy is hurting the Mexican economy and feeding xenophobia. It also may hurt the international effort to track and control this thing, because if Mexico gets the idea that it is going to be quarantined and embargoed, it is going to stop sharing samples.
The first PCR primers are just being distributed, so in the next couple of weeks it will be possible to do far more testing. Whether some countries will be honest about what they find is questionable.
Here is another article which gives the timeline in even more detail. The first known case was in the US - CA. The girl who tested positive on 3/28 likely caught it from her cousin who became ill a few days earlier. Her brother got sick three days later:
http://online.wsj.com/article/SB124113696409275445.htmlQuote from article:
""This virus has been circulating around in the population for some time," said Gilberto Chavez, an epidemiologist with the California Department of Public Health. Its similar symptoms to a standard flu, he said, meant that "any cases that might have been around were probably seen, treated and diagnosed as regular flu."
You see, the US doesn't want to take credit for it either, and the Chinese press keeps publishing denials of the rumors that it originated in Fujian province in China. They are probably correct. There are always pigs dying there.
http://www.danwei.org/front_page_of_the_day/swine_flu_denied_by_china.phpThe cluster of detections on the CA peninsula indicate that Chavez may well be correct. On the other hand, it could be that the virus originated in Mexico and was not detected until it got to CA. Mexico does not have the same types of testing programs the US has.
Whatever the case, the virus appears "fixed" in its current form, which is why Chavez is saying that it has been circulating for a while. As time goes by, it will mutate, but detection right after the original jump would show considerable variation between the samples. It is possible the virus has been circulating for months. Right now everyone is only testing Mexican contacts, so of course that is what they are finding.