The discovery of at least 2,800 dead pigs in a major Shanghai river that is one of the city’s main water sources has alarmed residents and triggered fresh public health concerns in China amid an on-going debate about food and water safety.

Authorities said on Monday they had found a pig virus (porcine circovirus) in water samples in the Huangpu river, adding that the thousands of carcasses had likely been dumped from villages upstream where farmers were thought to be grappling with an epidemic in recent weeks.

Photographs of carcasses of the more than 2,800 dead pigs were shared widely on social media sites over the weekend, triggering alarm among residents of China’s financial centre.

"This is the water we drink! Animals' dead bodies could easily be seen in the water conservation area and it stinks!," one blogger who posted one of the first photographs of eight dead pigs floating in the river was quoted as saying by the Shanghai Daily.

Authorities sought to calm the safety fears on Monday, saying that all tests for pig-borne diseases such as foot and mouth, cholera and epidemic diarrhoea had returned negative results. The Shanghai Animal Diseases Control and Prevention Centre said the pig virus that it had found in some of the samples would not have any affect on humans.

The Shanghai government in a statement said the city's tap water was still safe to drink. While the government stressed that water quality around the water plant had not been affected as the polluted stream did not directly run through it, many residents did not appear to share the government's belief in the quality of the water. "It seems incredible to suggest water quality is normal when 3,000 dead pigs are floating in a river!," said one journalist with a local newspaper.

But as details emerged on Monday of a possible pig epidemic that had been unreported for weeks – some reports online suggested tens of thousands of pigs had died in January and February in nearby Zhejiang and Jiangsu provinces – some online voices hit out at the government for not sharing information quickly enough. Bloggers pointed out that the government had responded and released information only after photographs had appeared online.

Officials fear further public outcry as the number of dead pigs is set to increase in coming days as authorities continue removing carcasses. “The number is expected to rise as there are still six barges that have not returned from collecting carcasses,” Xu Rong, director of Shanghai Songjiang District Environmental Protection Bureau, told the Global Times. “We have to act quickly to remove them all for fear of causing water pollution”.

China’s pollution problem has been at the centre of attention in recent months, with the new government that will take over this week promising to firmly deal with food, water and air pollution issues.

Only on Sunday, a major government restructuring plan announced at the on-going session of the National People’s Congress (NPC) or Parliament, which will formalise the leadership transition, proposed raising the status of the State Food and Drug Administration to a ministry-level general administration that will have more teeth to supervise food safety across the supply chain, from production to consumption.

“Overlapping of supervision from different departments and some supervision blind spots are weak links of the current food safety supervision system,” the State Council, or Cabinet, acknowledged in the plan.

The plan also specifically mentioned safety fears from pig slaughtering, underscoring the scale of the problem in China. Responsibility to ensure authorised slaughtering has been transferred from the control of the Commerce Ministry to the Agriculture Ministry, according to the plan. Supervising slaughtering has emerged as a difficult challenge for authorities. While farmers are allowed to slaugther pigs only in regulated and designated areas, supervision remains lax, as evident in the recent mass dumping of carcasses into local water bodies.

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