The AP’s investigation was based on interviews with Chinese and foreign scientists and officials, along with public notices, leaked emails and the unpublished documents from China’s State Council and the Chinese Centre for Disease Control and Prevention. It reveals a pattern of government secrecy and top-down control that has been evident throughout the pandemic.

“They only select people they can trust, those that they can control,” said an expert who works with the China CDC, declining to be identified out of a fear of retribution.

China’s foreign ministry said in a fax that “the novel coronavirus has been discovered in many parts of the world” and research should be carried out “on a global scale”.

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China’s leaders aren’t alone in politicising research into the pandemic’s origins. In April, President Donald Trump shelved a US-funded project to identify dangerous animal diseases across Asia. Although the World Health Organisation says it will send a team to China in January to investigate, its members and agenda had to be approved by China.

The probe into how the coronavirus first emerged started in the Huanan Seafood Market in Wuhan, a sprawling complex where many of the first human cases were detected.

In mid-December last year, Huanan vendor Jiang Dafa noticed people were falling ill, including a worker who helped clean carcasses at a stall who later died.

At first, the China CDC moved swiftly.

In mid-December last year, Huanan market vendor Jiang Dafa, pictured, noticed people were falling ill.

In mid-December last year, Huanan market vendor Jiang Dafa, pictured, noticed people were falling ill. Credit:AP

On January 1, the market was ordered shut, barring vendors from fetching their belongings, Jiang said.

In late January and early February, as the virus spread rapidly, Chinese scientists published a burst of research papers on COVID-19. Then one paper proposed without concrete evidence that the virus could have leaked from a Wuhan laboratory near the market. It was later retracted, but it raised the need for image control.

An internal notice from a China CDC lab issued on February 24 put in new approval processes to standardise publication under “important instructions” from Chinese President Xi Jinping. Other notices ordered CDC staff not to share any data, specimens or other information related to the coronavirus with outside institutions or individuals.

In early March, China’s cabinet, the State Council, centralised all COVID-19 publication under a special task force. The notice, obtained by the AP and marked “not to be made public,” was sweeping in scope, applying to all universities, companies and medical and research institutions. It said communication and publication of research had to be orchestrated like “a game of chess” under instructions from Xi.

After the secret orders, the tide of research papers slowed to a trickle. Though the China CDC returned to collect some 2,000 samples from the market over the following months, nothing was published.

On May 25, China CDC chief George Gao said no animal samples from the market had tested positive, ruling it out as the source.

With the market proving a dead end, scientist turned their attention to hunting for the virus at its likely source: bats.

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Nearly a thousand miles away from Wuhan, bats inhabit a maze of underground limestone caves in Yunnan province. The coronavirus’ genetic code is strikingly similar to bat coronaviruses, and scientists suspect COVID-19 jumped into humans from a bat or an intermediary animal.

Chinese scientists quickly started testing animals suspected of carrying the coronavirus. Records show scientist Xia Xueshan received a 1.4 million RMB ($277,000) grant to screen animals in Yunnan for COVID-19. In February, his team took samples from animals including bats, snakes, bamboo rats and porcupines.

But data on the samples has not been released.

Today, the caves in Yunnan home to the closest viral relative of the coronavirus are under close watch. Security agents stopped journalists from visiting the cave where researchers identified the bats responsible for SARS.

Chinese state media has instead aggressively promoted theories suggesting the virus originated elsewhere, such as via frozen seafood, a hypothesis WHO and others have dismissed.

The government is also limiting and controlling the search for the first human cases through the retesting of flu samples.

Villagers in Manhaguo in China's Yunnan province said a nearby cave had been used as a sacred altar presided over by a Buddhist monk - precisely the kind of contact between bats and people that alarms scientists.

Villagers in Manhaguo in China’s Yunnan province said a nearby cave had been used as a sacred altar presided over by a Buddhist monk – precisely the kind of contact between bats and people that alarms scientists.Credit:AP

Hundreds of Chinese hospitals collect samples from patients with flu-like symptoms, storing them for years. The samples could easily be tested again for COVID-19, although politics could determine whether the results are made public, said Ray Yip, the founding director of the China CDC.

Researchers in the US, Italy, France and elsewhere have already combed through some of their archived samples to identify the earliest cases of COVID-19 in late 2019. But in China, scientists have only published retrospective data from two Wuhan flu surveillance hospitals, out of at least 18 in Hubei province and more than 500 across the country.

The little information that has trickled out suggests COVID-19 was circulating beyond Wuhan in 2019, a finding that could raise awkward questions for Chinese officials about their early handling of the outbreak.

Peter Daszak of the EcoHealth Alliance said identifying the pandemic’s source should not be used to assign guilt.

“We’re all part of this together,” he said. “Until we realise that, we’re never going to get rid of this problem.”

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