The new coronavirus that has claimed nearly 3,000 lives and spread to almost 50 countries was sequenced in Chinese labs -- and found to be similar to SARS -- weeks before officials publicly identified it as the cause of a mysterious viral pneumonia cluster in Wuhan, a Caixin investigation has found.

Test results from multiple labs in December suggested there was an outbreak of a new virus. However, the results failed to trigger a response that could have prepared the public, despite being fed into an infectious disease control system that was designed to alert China's top health officials about outbreaks.

The revelations show how health officials missed opportunities to control the virus in the initial stages of the outbreak, as questions mount about who knew what and when, and what, if any, actions helped the disease to spread.

As early as Dec. 27, a Guangzhou-based genomics company had sequenced most of the virus from fluid samples taken from the lung of a 65-year-old deliveryman who worked at the seafood market where many of the first cases emerged. The results showed an alarming similarity to the deadly SARS coronavirus that killed nearly 800 people between 2002 and 2003.

Around that time, local doctors sent at least eight other patient samples from hospitals around Wuhan to multiple Chinese genomics companies, including industry heavyweight BGI, as they worked to determine what was behind a growing number of cases of unexplained respiratory disease. The results all pointed to a dangerous SARS-like virus.

That was days before China notified the World Health Organization on Dec. 31 about the emergence of an unidentified infectious disease, two weeks before it shared the virus' genome sequence with the world, and crucially, more than three weeks before Chinese authorities confirmed publicly that the virus was spreading.

Concerns about the new disease were initially kept within a small group of medical workers, researchers and officials. On Dec. 30, Dr. Li Wenliang was one of several in Wuhan who sounded the first alarms and released initial evidence online. Li, who was punished for the disclosure, would perish from the disease five weeks later, after contracting it from a patient.

On Jan. 1, after several batches of genome sequence results had been returned to hospitals and submitted to health authorities, an employee of one genomics company received a phone call from an official at the Hubei Provincial Health Commission, ordering the company to stop testing samples from Wuhan related and destroy all existing samples. The employee, who spoke on condition of anonymity, said they were told to immediately cease releasing test results and related information, and report any future results to authorities.

Then on Jan. 3, China's National Health Commission, the nation's top health authority, ordered institutions not to publish any information related to the unknown disease, and ordered labs to transfer any samples they had to designated testing institutions, or destroy them. The order, which Caixin has seen, did not specify any testing facilities.

It was Jan. 9 when Chinese authorities finally announced that a novel coronavirus was behind Wuhan's viral pneumonia outbreak. Even then, the transmissibility of the virus was downplayed, leaving the public unaware of the imminent danger.

Bruce Aylward of the World Health Organization attends a news conference of the WHO-China Joint Mission on COVID-19 on Feb. 24 about the organization's investigation of the coronavirus. © Reuters

Finally, on Jan. 20, Zhong Nanshan, a leading authority on respiratory health who came to public prominence for his role in fighting SARS, confirmed in a TV interview that the disease was spreading from person to person.

Two days later, Wuhan, a city of 11 million, was placed in lockdown. It remains quarantined today.

Social media provide clues

The earliest results came from a 65-year-old deliveryman who worked at the Wuhan seafood market. These were returned on Dec. 27 by Vision Medicals, a genomics company based in the Huangpu district of Guangzhou in Guangdong Province.

The patient was admitted to the Central Hospital of Wuhan on Dec. 18 with pneumonia and his condition quickly deteriorated. On Dec. 24, doctors took fluid samples from his lungs and sent them to Vision Medicals for testing, according to Zhao Su, head of respiratory medicine at the hospital.

In an unusual move, the company did not send back results, but instead telephoned the doctor on Dec. 27. "They just called and said it was a new coronavirus," Zhao said.

Vision Medicals confirmed the tests took place in a post it published on social media late last week. The post said the company was involved in early studies of the new coronavirus and had contributed to an article published in the English version of the Chinese Medical Journal. That article makes specific mention of a sample collected on Dec. 24 from a 65-year-old patient who had contact with the seafood market.

A different social media post, believed to have been made by a Vision Medicals employee, sheds more light on the company's early work. The author of the Jan. 28 post said only that they worked at a private company based in Huangpu, Guangzhou, where Vision Medicals is located.

The author said they noticed a close similarity with the SARS coronavirus in test results of a sample collected on Dec. 24, but decided to study the results more closely before returning them, due their significance. The company did, however, share the data with the Chinese Academy of Medical Sciences, according to the article in the Chinese Medical Journal.

By Dec. 27, the lab had sequenced most of the virus' genome and confirmed it was a coronavirus similar to the SARS virus, the article said.

In the following days, company executives visited Wuhan to discuss their findings with hospital officials and disease control authorities, the article said. "There was an intensive and confidential investigation underway, and officials from the hospital and disease control center had acknowledged many similar patients," it said.

Little information about this early study has been officially released. The patient, who was transferred to Wuhan Jinyintang Hospital, later died.

The Wuhan Institute of Virology under the Chinese Academy of Sciences: Not qualified to do coronavirus tests? (Photo by Ding Gang/Caixin)

Revelations triggered by 'small mistake'

While researchers at Vision Medicals considered their findings, the Central Hospital of Wuhan sent swabs from another patient with the mysterious pneumonia to CapitalBio Medlab, a Beijing-based lab, for study.

The sample came from a 41-year-old man who had no history of contact with the seafood market and who was admitted to the hospital on Dec. 27.

Test results showed a false positive for SARS. It was a "small mistake," a gene sequencing expert told Caixin, which may have occurred due to a limited gene database or lack of retesting.

But it was this mistake that triggered the first concerns heard by the public, recalling painful memories of the cover-up that defined the SARS outbreak 17 years before.

On the evening of Dec. 30, several doctors in Wuhan, including the late Li Wenliang, privately shared CapitalBio's results as a warning to friends and colleagues to take protective measures. Their warnings circulated widely online and sparked an uproar from a public demanding more information. Several people, including Li and two other doctors who sent the warnings, were later reprimanded by authorities for "spreading rumors."

Zhang Jixian, head of the respiratory department at Hubei Xinhua Hospital, noticed on Dec. 26 that he had received a growing number of patients with symptoms of pneumonia from the neighboring seafood market. The next day, he reported the situation to the hospital, which passed the information on to city and provincial health authorities.

Following the reports, disease control authorities in Wuhan and Hubei on Dec. 30 issued an internal notice warning of the emergence of pneumonia patients with links to the seafood market and requiring hospitals to monitor similar cases.

The notice, later leaked online, offered the public its first glimpse of official acknowledgment of the outbreak.

Silenced alarms

Several other genomics companies also tested samples from patients in Wuhan with the then-unidentified virus in late December, Caixin learned.

BGI received a sample from a Wuhan hospital on Dec. 26. Sequencing was completed by Dec. 29 and showed that, while it was not the SARS virus, it was a previously unknown coronavirus that was about 80% similar to the SARS virus.

A BGI source told Caixin that when they undertook the sequencing project in late December, the company was unaware that the virus had sickened so many people. "We take a lot of sequencing commissions every day," the source said.

Caixin has learned that the Wuhan hospital sent BGI at least 30 samples from different pneumonia cases for sequencing in December, of which three were found to contain the new coronavirus. In addition to the Dec. 26 case, the second and third positive samples were received on Dec. 29 and Dec. 30. They were tested together and the results were reported to the Wuhan Municipal Health Commission as early as Jan. 1.

On Jan. 1, gene sequencing companies received an order from Hubei's health commission to stop testing and destroy all samples, according to an employee at one such company. "If you test it in the future, be sure to report it to us," the person said they were told over the phone.

Two days later on Jan. 3, the National Health Commission issued its gag order and said the Wuhan pneumonia samples needed to be treated as highly pathogenic microorganisms, and that any samples needed to be moved to approved testing facilities or destroyed.

One virologist told Caixin that even the Wuhan Institute of Virology under the Chinese Academy of Sciences was not qualified to do the tests and was told to destroy any samples it had.

But that day, professor Zhang Yongzhen of Fudan University in Shanghai received biological samples packed in dry ice in metal boxes and shipped by rail from Wuhan Central Hospital. By Jan. 5, Zhang's team had also identified the new SARS-like coronavirus.

Zhang reported his findings to the Shanghai Municipal Health Commission as well as China's National Health Commission, warning the new virus was like SARS, and was being transmitted through the respiratory system. This sparked a secondary emergency response within the Chinese Center for Disease Control and Prevention on Jan. 6.

On Jan. 9, an expert team led by the Chinese CDC made a preliminary conclusion that the disease was caused by a new strain of coronavirus, according to Chinese state broadcaster CCTV.

On Jan. 11, Zhang's team became the first to publish the genome sequence of the new virus on public databases Virological.org and GenBank, unveiling its structure to the world for the first time. The NHC shared the virus genomic information with the World Health Organization the next day.

Also on Jan. 11, the Wuhan Municipal Health Commission resumed updating infection cases caused by the virus after suspending reports for several days. But the government repeated its claim that there had been no medical worker infections and that there was no evidence of human transmission.

Meanwhile, the commission reported that the number of confirmed cases had dropped to 41.

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Caixinglobal.com is the English-language online news portal of Chinese financial and business news media group Caixin. Nikkei recently agreed with the company to exchange articles in English.