On either side of the long straight road to La Gloria scrawny horses pull ploughs across flat sandy fields, sending up clouds of dust that mingle with the early morning mist. For the final mile, the tarmac turns to gravel as the road begins to wind on its way into the village in the southern Mexican state of Veracruz.

Here, in an unassuming little white house, lives Edgar Hernández Hernández. A neat five-year-old with a shy smile, he might just turn out to be key to understanding why swine flu is slowly shutting down Mexico and keeping health officials around the world locked in emergency meetings.

As the number of confirmed infections rose above 100 on four continents and anxiety gripped corners of the globe thousands of miles from La Gloria - from California, where officials last night said they were investigating two deaths, to Britain, where some tour operators said they were stopping flights to Mexico, Edgar told the Guardian about the illness that laid him up in bed for a week at the end of March: "My head hurt a lot ... I couldn't breathe."

Local nurses took a swab from Edgar's throat on 3 April and two weeks later this found its way into a batch sent to the Centres for Disease Control and Prevention in Atlanta, Georgia. By this time the Mexican government was getting increasingly concerned about a spike in atypical and fatal flu cases. Within hours they were informed that many of the samples tested positive for a new strain of swine flu and Edgar's was the earliest.

The authorities have not explained why the disease's first stop in Mexico should be a boy in La Gloria. But the villagers, who believe they suffered the disease before Edgar, blame a huge pig farm in the area belonging to a multinational, Smithfield Foods. "We are not doctors, but it is hard for us not to think the pig farms around here don't have something to do with it," says Anselma Amador. "The flu has pig material in it and we are humans, not pigs."

The pigs at the heart of the village's angst live in modules around the valley in long metal buildings with large rectangular tanks attached.

The closest one to La Gloria is a few miles back down the paved road and then a couple more down a cactus-lined track, where the wind whips up dust clouds that travel across the plain.

The tank lies open, apparently unattended, a putrid odour emanating from it - which is probably why the farmer herding his goats past is wearing a mask.

Residents in La Gloria say the prevailing wind invariably blows the fetid air their way, where it gets stuck because of the hills that rise just behind the village.

The company has vehemently denied that its pigs had anything to do with the outbreak and has shown journalists around pristine installations. The federal government has also said that it has no reason to believe there is any link.

"I think it is foolhardy to make such a link," the Mexican health minister, José Ángel Córdova, said on Monday. He added that the agricultural ministry had regularly tested the pigs and found nothing to indicate an association.

Córdova also insisted Edgar was the only case of swine flu in La Gloria - although residents say his illness came after weeks during which most of the village fell ill.

In February a seven-month-old baby died of pneumonia, and in early March a two-month-old died. The parents were told both children had died of bacterial pneumonia. Then, around 21 March, dozens of people started suffering high fevers, terrible aches and sore throats that led to trouble breathing.

Worried, Bertha Crisostomo, a local community leader, called the authorities in the city of Perote, and doctors were sent in with antibiotics and painkillers. But still the illnesses persisted.

"Eventually we began to get better, but it was truly terrible while it lasted," Crisostomo remembers, sitting in her living room surrounded by artificial flowers and china figurines of elephants and giraffes. "They told us that it was just an atypical cold that was nothing to worry about, that was probably caused by the flies from the pig farms, so they sent in fumigation teams to get rid of the flies."

Then she got ill and was out of action herself for more than a week.

The community was gradually beginning to put the illness behind them when they started seeing the outbreak of the flu that has brought Mexico City to a partial standstill, with schools and restaurants closed, and people being told to stay at home if they possibly can.

"I watch what is going on in Mexico City and we say to each other that is exactly what happened to us," says Rosa Jimenez, as she walks down the road holding her toddler's hand with a filthy mask around her neck. She notes that many families in La Gloria have relatives who work in Mexico City but came back to the village for the Easter week celebrations. "Could that be how it spread to the capital?" she asks.

Meanwhile, there is much fear in La Gloria; not so much that the illness will come back, but that the company will get angry at suggestions that it might have had something to do with it all. Many people will only talk on condition of anonymity, like one man raking rubbish outside his home.

"I was ill, my wife was ill, my children, my aunt. We were all in bed with exactly the same symptoms as we are now being told are swine flu," he says. "But I don't want to speak out, because I am afraid. This is a company with lots of power and lots of dollars. They have always been protected by the government and there is not much we can do about it."