American intelligence officers knew a new contagion was sweeping Wuhan in November but they couldn't get the message through to the top, according to ABC News.

Spying is not just about secret agents and deep hacks. Intelligence agencies across the world also monitor the daily pulse of life across the planet.

How much has it rained? Are crops healthy? Are people following their usual behaviour patterns?

According to ABC News in the United States, a series of "red flags" began to appear over Wuhan in November.

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Behavioural patterns were changing — businesses were behaving differently, so too were local authorities. It all matched the profile for an emerging contagion.

Hospital staff wash the emergency entrance of Wuhan Medical Treatment Center, on January 22. Photo / AP
Hospital staff wash the emergency entrance of Wuhan Medical Treatment Center, on January 22. Photo / AP

So analysts delved deeper by tapping Chinese communications and accessing digital records and then initiated long-established protocols to get this early warning up the chain of command.

The ABC, citing four sources "briefed on the secret reporting", reports their message repeatedly hit brick walls.

"Analysts concluded it could be a cataclysmic event," one of the sources reportedly told the ABC.

"It was then briefed multiple times" to appropriate levels along the chain of command, extending from the Defense Intelligence Agency through to the Pentagon's Joint Staff – and the White House. However today the Pentagon denied such a report even exists.

Deaf ears

The US military's National Centre for Medical Intelligence (NCMI) was established to provide early warning of just such an incident as the coronavirus that began in Wuhan.

The Defence Intelligence Agency (DIA) subdivision knew a highly contagious disease could pose a "clear and present danger" to the US homeland. So it pulled together all the satellite imagery, behaviour mapping, wire and computer taps it had out of Wuhan into a comprehensive report.

The DIA's job is to ensure US soldiers, sailors and aircrew have the information they need to carry out their duties. And that includes staying healthy.

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A medical worker looks at CT scans at the Huoshenshan field hospital in Wuhan in central China's Hubei Province on March 17. Photo / AP
A medical worker looks at CT scans at the Huoshenshan field hospital in Wuhan in central China's Hubei Province on March 17. Photo / AP

"This was definitely being briefed beginning at the end of November as something the military needed to take a posture on," one source reportedly told the ABC.

Alert bulletins were circulated through confidential channels around Thanksgiving (November 26). From then through December, briefings were given to all levels of the US federal government and intelligence agencies.

The news eventually filtered its way through to President Donald Trump's Daily Brief in early January, the ABC reported.

The stark warnings this briefing carried has been the subject of reports by the Washington Post.

Donald Trump had initially been publicly downplaying the severity of the threat the virus presented. Photo / AP
Donald Trump had initially been publicly downplaying the severity of the threat the virus presented. Photo / AP

"Donald Trump may not have been expecting this, but a lot of other people in the government were — they just couldn't get him to do anything about it," one official told the Post last month. "The system was blinking red."

The New York Times has also reported Trump's trade adviser Peter Navarro sent an internal White House memo in late January warning of a "full-blown pandemic".

When asked at the weekend about receiving the intelligence briefing, US Defence Secretary Mark Esper told the ABC: "I can't recall." Asked if he recalled the NCMI presentation to the National Security Council in December, he replied: "I'm not aware of that".

After ABC News published its report, the Defence department gave a statement from Col. R. Shane Day, director of the NCMI who denied the report even exists.

"As a matter of practice the National Center for Medical Intelligence does not comment publicly on specific intelligence matters. However, in the interest of transparency during this current public health crisis, we can confirm that media reporting about the existence/release of a National Center for Medical Intelligence Coronavirus-related product/assessment in November of 2019 is not correct. No such NCMI product exists," the statement said.

ABC News said the White House National Security Council and the Office of the Director of National Intelligence declined to comment.

National security crisis

The pivotal National Security Council (NSC) has been in crisis for several years. Its most recent bloodbath was in September when National Security Advisor John Bolton quit.

He had replaced HR McMaster in April 2018. McMaster had replaced Lt Gen Michael Flynn, who was fired after less than a month in the job in January 2017.

But the specialist committee itself has also experienced a revolving door of staffers and members, all tasked with the job of turning intelligence agency data into informed advice for the President and his key staff.

According to the US ABC's sources, that intelligence was nevertheless provided.

It was comprehensive. It was detailed. It was clear.

Chinese police officers march past a checkpoint around the Wuhan Central Hospital April 4. Photo / AP
Chinese police officers march past a checkpoint around the Wuhan Central Hospital April 4. Photo / AP

"It's not surprising to me that the intelligence community detected the outbreak," former Department of Homeland Security undersecretary John Cohen said. "What is surprising and disappointing is that the White House ignored the clear warning signs, failed to follow established pandemic response protocols and were slow to put in place a government-wide effort to respond to this crisis."

Their warnings were handball to the NSC's Counter-proliferation and Biodefense directorate – generally tasked with analysing the threat of weapons of mass destruction.

Politico has revealed an NSC policy team began working around the clock on the implications of the virus through early January. They knew severe action was needed, fast.

By early March, more than 50 meetings and committee calls had been conducted and briefed.

Meanwhile, Trump had authorised restrictions of travel from China on January 31 while publicly downplaying the severity of the threat the virus presented.

Then, on March 19, he changed tack: "Nobody knew there'd be a pandemic or an epidemic of this proportion."