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JEREMY FARRAR BOOK EXTRACT

Burner phones and clandestine meetings: the inside story of Covid

exclusive

The first of our exclusive extracts from Sage adviser Jeremy Farrar’s new book, Spike — The Virus vs the People: The Inside Story

Jeremy Farrar: “It was clear that the Chinese authorities knew more than they were letting on.”
Jeremy Farrar: “It was clear that the Chinese authorities knew more than they were letting on.”
GETTY IMAGES; TOM JACKSON FOR THE TIMES
The Times

I was in an airport lounge on New Year’s Eve 2019 when my mobile rang. I was heading back to England from Rwanda and the Democratic Republic of Congo, where I had been visiting the ebola vaccination centres in Rwanda across the politically fraught border region of North Kivu. I was absolutely knackered and looking forward to a couple of days at home in Oxford before heading back to the office.

I was scanning my phone when I saw a report of a mystery pneumonia spotted by doctors at a hospital in China. I sent a short text message to George Gao, head of the Chinese Centre for Disease Control and Prevention (China CDC) in Beijing, and an old friend.

He phoned me back. Very soon, George told me, the world would be hearing about a cluster of cases of a new pneumonia from Wuhan in China. The cases had already been reported to the World Health Organisation. It was, essentially, a courtesy call from one scientist to another. I remember him telling me that we wouldn’t need to worry because it wasn’t severe acute respiratory syndrome (Sars), and that we must keep in touch.

The cases of unexplained and untreatable pneumonia in Wuhan kept growing, matched later by reports of crowded hospital wards and overflowing mortuaries. Social media and online chat rooms in China hummed with rumours of a strange new illness spreading in Wuhan, including among hospital workers; reports began filtering in of police crackdowns on those trying to get information out over the heavily monitored internet.

By the second week of January, I was beginning to realise the scale of what was happening. I was also getting the uncomfortable feeling that some of the information needed by scientists to detect and fight this new disease was not being disclosed as fast as it could be. I did not know it then, but a fraught few weeks lay ahead.

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In those weeks, I became exhausted and scared. I felt as if I was living a different person’s life. During that period, I would do things I had never done before: acquire a burner phone; hold clandestine meetings; keep difficult secrets. I would have surreal conversations with my wife, Christiane, who persuaded me we should let the people closest to us know what was going on. I phoned my brother and best friend to give them my temporary number. In hushed conversations, I sketched out the possibility of a looming global health crisis that had the potential to be read as bioterrorism.

“If anything happens to me in the next few weeks,” I told them nervously, “this is what you need to know.”

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The process of reporting a new disease to the wider world is quite informal and not at all glamorous. It often starts with a brief notice on ProMED-mail, an online repository collating short descriptions of outbreaks of animal and human diseases in different countries, as well as other news snippets relating to diseases, such as grant announcements. That is where I had picked up the information on the Wuhan cases that George Gao and I spoke about. The descriptions of outbreaks are clipped from official sources, such as health authorities, but also from social media and local newspapers. Every outbreak that becomes a global headline begins as a local rumour.

The ProMED alert that had caught my eye was dated December 30, 2019, next to a line reading simply: “Undiagnosed pneumonia – China (HU):RFI.” HU refers to Hubei, the central province in which the city of Wuhan is located; RFI signals a Request for Further Information.

Nobody knew it then, but that single line marked the debut of a new disease, one that would come to be called Covid-19 and cause the biggest upheaval to the global order since the Second World War. The line clicks through to an imperfect machine translation of a story relating to “an urgent notice on treatment of pneumonia of unknown cause” originally posted that evening by the Medical Administration of Wuhan Municipal Health Committee, concerning four patients with an unknown form of pneumonia.

A report appended underneath that urgent notice adds worrying detail gleaned on December 31: 27 people were in various hospitals in Wuhan with viral pneumonia or pulmonary (lung) infection. Two were recovering but seven were critical. All the patients apparently had links to the Wuhan South China Seafood Market (also known as the Huanan Seafood Wholesale Market). The report added, “At present, related virus typing, isolation treatment, public opinion control and terminal disinfection are under way.”

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On January 3, 2020, ProMED posted an update pulled from the South China Morning Post. The unexplained disease was spreading: 44 patients in Wuhan, up from 27; 11 seriously ill with breathing difficulties and lesions, or scarring, on both lungs. There was another unwelcome development: five people had shown up in Hong Kong with unexplained fever after visiting Wuhan.

Just a week into the new year, the unknown disease was no longer wreaking havoc just in Wuhan, a city of 11 million people and a major travel hub in central China. A lot of people were becoming anxious – and for good reason. A week is an unsettlingly long time in the world of infectious diseases.

By Friday, January 10, it was clear that the Chinese authorities knew more than they were letting on.

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Scientists track how viruses relate to each other by drawing family trees, in much the same way that people can trace their own origins back by following the trail of births, deaths and marriages. Instead of surnames and family records, viruses reveal their origins in their genetic sequences. Genetic overlap pinpoints the similarities between different viruses, signposting when they potentially share a common ancestor. Likenesses between human viruses and animal ones can also narrow down which animal might have transferred a virus across the species barrier to us.

Eddie Holmes is a British-born virologist and professor at the University of Sydney who does exactly this sort of viral detective work. He is, in my book, the outstanding evolutionary biologist of his generation, with an extraordinary brain when it comes to pattern recognition.

Since 2012, Eddie has worked closely with Yong-Zhen Zhang, a professor at Fudan University, Shanghai, on finding and identifying new animal viruses, and Wuhan is a familiar locale in their virus-hunting network.

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They don’t normally study samples from humans but genomic sequencing, the method used to place viruses in their family trees, can also be used as a diagnostic, to help identify mystery viruses found in hospital patients. On January 3, 2020, a sample taken from a pneumonia patient hospitalised in Wuhan on December 26, 2019, arrived at Zhang’s lab packed in dry ice in a metal box. By 2am on January 5, after a 40-hour shift in the lab, Zhang and colleagues had worked out its genetic sequence. It was a coronavirus that looked suspiciously like SARS-CoV-1, the virus responsible for the 2002-2003 outbreak.

Eddie still remembers the phone call (Sydney is two hours ahead of Shanghai). “We agreed that he should tell the Ministry of Health in China immediately. Zhang did it the same day.

“Zhang told them it was clearly very closely related to the first Sars virus and that it was very likely to be respiratory because of its relatedness. He also told the ministry that people should take precautions.”

That phrase – people should take precautions – was a direct warning that this new virus, like its dangerous predecessor, might be able to spread from one person to another. Eddie says this should have been interpreted back then as a warning of human-to-human transmission. In the end, China did not confirm this publicly until January 20, more than two weeks later.

While Zhang informed Beijing, some of the sequence was deposited on January 5, 2020, on GenBank, an online collection of publicly available gene sequences run by the National Institutes of Health in the US. But it takes a while for those deposited sequences to be checked, edited and put through the system in a way that others can use. There was an imperative to post the entire sequence more publicly. Anyone, anywhere, could then use that published information to develop a diagnostic test. The world would, at a stroke, have eyes on the virus.

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There was, though, a major hitch: Zhang was told in no uncertain terms not to publish anything. The gagging order, Eddie understood, came from Beijing. The warnings to stay silent were real – medics had already been disciplined by the Chinese Communist Party for discussing hospital cases online.

Eddie and Zhang hit on a loophole to get round the gagging order: the government ban on publishing information about the outbreak did not preclude them from writing and submitting a scientific paper. Holmes contacted the journal Nature; one of its editors urged them to submit something as soon as possible. By January 7, 2020, Zhang’s paper, with Eddie as one of the co-authors, reached Nature’s offices in London.

Things began moving quickly and chaotically. On January 8, rumours began circulating that the new virus was a coronavirus, putting it in the same family as Sars. A day later, the Chinese authorities confirmed the fact. But, otherwise, and especially on the genome sequence of the virus, they were silent.

Not only had Zhang contacted China’s Ministry of Health with details of the new virus, but Eddie was sure that, in doing so, Zhang had merely confirmed information that Beijing already knew. Eddie had screenshots of messages on WeChat, a social media platform in China, suggesting two private companies had already sequenced the virus in December 2019.

Eddie, disturbed at what was looking increasingly like a decision by China to hold back information on a new disease, rang me to tell me that he’d been trying to get the sequence released, with no luck. After that call, I realised that he and I were probably the only two people in the world outside China who knew there was this sequence in existence and what it was, with all the potential consequences.

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Eddie and I had a series of frantic calls between London and Sydney on the night of Thursday, January 9, which stretched into the early hours of Friday. We hatched a plan that Eddie would go back to his collaborators in China and I would go back to George Gao at China CDC. We would threaten to go public if they refused to disclose the information by Saturday morning GMT.

We decided to tell them, “If you don’t release the sequence in the next 24 hours, we will release it the next day.” By 9.18pm London time, and 8.18am in Sydney, Eddie and I had committed to the high-stakes pact to force China’s hand.

The world had to have access to that sequence because the world needed to be able to diagnose it. It was going to appear in Beijing, in Hong Kong and Singapore in the hours or days that followed. It was going to spread everywhere.

Eddie remembers the pressure-cooker atmosphere of those days too. Zhang deserved public credit for leading the consortium’s sequencing breakthrough – but Eddie also knew his colleague would be at the sharp end of Beijing’s displeasure for shattering the government’s code of silence.

“My big concern was not getting Zhang in trouble,” Eddie says now. “I called him and said, ‘There’s a lot of pressure to release the sequence. I think we have to do it.’ Zhang was on a plane going from Shanghai to Beijing, on the runway literally waiting to take off.”

Zhang asked his collaborator for a moment to think. It didn’t take long. Perhaps Zhang had already decided the world had waited long enough. Before the plane took to the skies, Zhang rang Eddie back with a simple message: “OK, let’s release it.” Eddie phoned me immediately.

By the time Zhang’s plane touched down just over two hours later, the information was out.

Coronavirus outbreak, China - 04 Feb 2020
Covid patients are wheeled into the newly built Huoshenshan Hospital in Wuhan, February 2020
REX/SHUTTERSTOCK

‘Chris Whitty wanted to be cautious — but the lesson is if you wait, you’re too late’

Sage has convened eight times since 2009 and I had sat on it before in 2014 during the Ebola epidemic in west Africa. The group is chaired by whoever is the UK government’s chief scientific adviser at the time. Patrick Vallance took on the role in 2018 and could never have dreamt he was signing up for the worst health crisis in living memory. He trained as a doctor and was a clinical scientist at University College London before heading research and development at GlaxoSmithKline. We have known each other for about eight years, as long as I have been director of the Wellcome Trust.

I had already texted both Patrick and Chris Whitty, the UK’s chief medical adviser, back in January to share my concerns: that this was a coronavirus related to Sars; that human-to-human transmission was possible, as well as asymptomatic transmission; and that there had already been geographical spread.

Patrick had arranged the very first “precautionary” meeting of Sage on 22 January 2020, to which I had dialled in. Neil Ferguson, who had also been involved in the early WHO response, had been quick off the mark in calculating the true size of the outbreak: by 16 January he had deduced, based on exported cases, that Wuhan was harbouring 1,000-plus cases by 6 January, more than ten times the official figure. A group of Mandarin-speaking PhD students at Imperial was scraping information from national and provincial government websites in China, and from preprint papers.

On Friday 24 January, Neil, who guessed that some infected travellers were slipping through the net, emailed me, Patrick and Chris to say that “NHS preparedness should be kicked up a gear”. We had also had that very important conference call on 27 January, launching UK research into vaccines and therapies into the so-called Wuhan coronavirus.

Patrick took our worries seriously because he knows my background in emerging infections. He knew I would not overplay something that was not worth worrying about. There was no human immunity to this new pathogen; this was a respiratory disease spreading, in some cases asymptomatically, in a big urban centre in winter; Chinese New Year was fast approaching and there were no diagnostic tests, treatments or vaccines. There were no vaccines for any member of the coronavirus family of viruses.

I’ve known Chris for years too: he also trained in infectious diseases and did a period of study in Vietnam. The global health and infectious disease community can sometimes adopt a slightly weary attitude of, “We’ve seen it all before and these things are never as bad as you think.” And that was Chris, initially: he wanted to be much more cautious, to wait and weigh everything before taking action. The lesson from every epidemic is that if you wait until you know everything, then you are too late. If you fall behind an epidemic curve, it is extraordinarily hard to get back in front of it.

The UK, meanwhile, was clocking up its first known cases in January 2020: a woman who returned from Hubei province on 23 January subsequently developed fever, sore throat and dry cough. A household contact later developed symptoms, suggesting person-to-person transmission. Both were hospitalised in Newcastle, in northeast England, on 31 January as a precaution and discharged after a mild illness. That friction, between waiting and wading in, led to a palpable tension between Patrick and Chris in the early weeks of 2020, particularly given the apparent absence of political leadership in that period. Boris Johnson, the prime minister, did not attend the first five Cobra meetings on coronavirus in January and February 2020.

Chris, though, had more experience than Patrick of operating in political circles: he was in government in 2009, during the H1N1 swine flu pandemic. It was projected to lead to 65,000 deaths; in the event, there were fewer than 300. Dame Sally Davies, then England’s chief medical officer, was unfairly criticised for overreacting. The UK stockpiled oseltamivir (sold as Tamiflu) and other measures at great expense.

That backlash possibly made Chris wary of the same happening this time round. He talked about the outbreak as a marathon not a sprint. In a sense, outbreaks are mara-thons but there are times in every long-distance race when you need to go fast. That go-slow outlook pervaded much of the thinking in January and February 2020 in the UK, even though all the information that had accumulated by the end of January should have set off the loudest of sirens.

Extracted from Spike — The Virus vs the People: The Inside Story by Jeremy Farrar with Anjana Ahuja, published on July 22 (Profile Books, £14.99)

Read the second instalment of our exclusive extracts tomorrow

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