Tuesday 24 April 2012 to Saturday 30 November 2019
In a sense, the world had been waiting for this moment. The possibility that a deadly virus might one day emerge from the zoological melting pots in temperate climes had been foreshadowed in a series of outbreaks in which animals had passed viruses to humans over the last 20 years. It seemed only a matter of time before one of these killers would acquire the potency to leap easily from human to human and cause destruction to lives and livelihoods in a way that had not been witnessed since the Spanish flu pandemic more than a hundred years ago. But like other natural disasters such as earthquakes, volcanos and rising sea levels, it appeared to be mostly a distant problem to governments in the West. This was especially true in Britain. In 2019 the UK was still suffering from an extreme form of myopia, which had left the government unable to see beyond the domestic drama of Brexit. A pandemic virus was listed as the top threat to the country on paper for the purposes of emergency planning, but it had slipped to the bottom of the government’s list of actual concerns. It had been many years since an emerging virus from across the globe had severely impacted on Britain and there was an insular self-confidence – some might say arrogance – that our island nation with its sea borders had the best pandemic plan in the world.
There was no such complacency in China. The Communist-controlled country had experienced a tragically painful wake-up call 17 years earlier. The 2002 Severe Acute Respiratory Syndrome (Sars) pandemic had infected 5,300 people in China and killed 349 after first surfacing in the wild-animal markets in the south of the country. Sars was a coronavirus – from a group of viruses that look like they have a crown (corona) when viewed under a microscope because of the spikes protruding from their surface. Before Covid-19 appeared in 2019 there were six types of coronavirus known to infect humans, but mostly they caused mild respiratory symptoms with the exception of the Middle East Respiratory Syndrome in 2012 and Sars, which were both killers.
Covid-19 is from the same evolutionary branch as Sars, which is why the virus causing the disease is named Sars-CoV-2. The original Sars virus – or Sars-CoV-1 as it is now officially called – is thought to have been passed to humans by masked palm civets, which are eaten in China as a delicacy. The animal’s flesh in combination with snake meat are the main ingredients of an exotic wildlife dish called ‘dragon-tiger-phoenix soup’, which is flavoured with chrysanthemum petals and sells at expensive restaurants in Guangdong province, southern China. Sars, first emerged in Foshan, a city south-west of Guangzhou in Guangdong province, in the middle of November 2002. It went on to reach 29 countries across the world and caused a major outbreak far away in Toronto, Canada. There were four suspected cases in the UK. By the time the virus fizzled out in 2004, it had infected 8,096 people in 29 countries and killed 774.
The Chinese authorities did not cover themselves in glory when the virus was first discovered. There were several reports about a ‘strange disease’ made by regional health officials to the central government over the following months, but there was a blanket of secrecy placed over the news. The authorities are alleged to have ordered doctors to downplay the scale of the epidemic to a team from the World Health Organization (WHO). At one stage, 30 patients with the virus are claimed to have been driven around Beijing in ambulances while another 40 were moved out of a hospital into a hotel in order to hide their existence from WHO scientists.1
The WHO would not be officially informed about the outbreak until the beginning of April 2003 – five months after its emergence. Stung by criticism that it had allowed the virus to flourish, the Chinese government beefed up public health surveillance by increasing its network of centres for disease control and laboratory systems.
One of the main challenges for the scientists was to hunt down the original source of the Sars virus to try to prevent such an outbreak happening again. In 2004 this task fell on the slim shoulders of a 39-year-old virologist called Dr Shi Zhengli, who would later earn the nickname ‘Bat Woman’. Her work would be inextricably linked to the discovery of the Covid-19 virus, which was, in effect, a new supercharged and much more lethal version of Sars. Courageous and dedicated, she has provided the biggest leads so far to one of the most pressing questions facing humankind today: where and how did our current pandemic come into existence? And yet, Shi’s research has also sparked great controversy because of the secrets she and her colleagues have kept back from the world.
As a young student Shi had taken a degree in hereditary biology at Wuhan University in the central Chinese city of that name. She was hired by the city’s virology institute in the early 1990s and went on to gain a doctorate from the Montpellier II University in France. Following the Sars outbreak, Shi took a leading role in the virology institute’s investigation into the theory that the virus may have originated in one of south China’s many bat caves. The Sars virus might have passed from a bat to a civet to humans, according to the theory. Shi was dispatched to the subtropical south of China along with an international team to see whether they could find any evidence to support this hypothesis. Later, in the course of this work, she would find the best clue to the origins of the Covid-19 pandemic – years before it began.
When the Wuhan Institute’s south China work on Sars began in 2004, there was developing research that would link bats to many viruses that affected humans, including the world’s most deadly, Ebola, which took its name from the river in the Democratic Republic of Congo where it was found. These types of viruses were usually transmitted via an intermediary animal. The Hendra virus that broke out in Australia in 1994 and the Nipah virus that first hit Malaysia in 1998 were both shown to have originated in bats. The Hendra virus – which was relatively rare, killing only four people – had passed from bats to horses to humans. The Nipah virus spread widely through South East Asia and had caused hundreds of fatalities after being passed on to humans by pigs, which had probably caught it from bats. Four different species of bat had been found to be carrying Sars-like viruses by 2004.
Bats are the second most common order of mammal in the world after rodents and are known to carry a diverse range of viruses that spread quickly in their crowded cave habitats, where they mingle with other animals. The caves are breeding grounds for viruses that can pass from species to species and mutate into hundreds of new forms that might randomly become infectious to humans. As bats can contract more than one strain at a time, they become mammalian blenders for viruses. As the only flying mammal, they are also ideal hosts to disperse diseases far beyond the caves where they are incubated.
In an interview with Scientific American
magazine, Shi described how the team scoured the mountainous terrain of Guangxi autonomous region, on China’s border with Vietnam, seeking out bat caves. When they found bats, they placed a net across the entrance to the cave at dusk and captured the animals as they flew out to find food. Faecal samples were then taken from the bats and sent back in frozen containers to the laboratories in Wuhan for testing. The first eight months of the search proved fruitless and the team were on the brink of giving up. ‘Eight months of hard work seemed to have gone down the drain,’ Shi told the magazine.2
‘We thought maybe bats had nothing to do with Sars.’ But the breakthrough came when they were given a diagnostic test kit for Sars antibodies in humans that they could use on the bats. These tests were able to determine whether the bats had been infected with the virus at some point in the past – whereas previously they had been forced to rely on discovering an infection in the animal at the very moment they were tested. It therefore significantly increased the scope of the scientists’ surveillance programme. The new technique proved a success. Three samples from horseshoe bats were found to have Sars antibodies. ‘It was a turning point for the project,’ said Shi.
Shi’s team then used the antibody test to narrow down the list of locations that her team would target. By 2010 they had decided to concentrate on a cave called Shitou in remote mountains south-west of Yunnan’s capital Kunming, on the far eastern edge of the Himalayas. They began a five-year study that would find a strain of coronavirus with similar genetic building blocks to Sars. Evidence gathered there would later be used as clinching proof that Sars began in bats. However, it was while they were conducting this research that they were called upon to investigate an incident in a copper mine 200 miles away. Their findings have major ramifications for the Covid-19 pandemic, but at the time they were hushed up even though three people died from a mysterious pneumonia-type illness with links to bats. It all began with an extraordinary series of admissions to a hospital near to the caves where Shi and her team were searching for the origin of Sars.
The sprawling high-rise buildings of the First Affiliated Hospital tower over the ancient city of Kunming, which is known as ‘the city of eternal spring’ because its unique climate encourages flowers to bloom all year. On Tuesday 24 April 2012, a 45-year-old man with the surname of Guo was admitted to the hospital’s intensive care unit suffering from severe pneumonia. The next day a 42-year-old man with the surname Lv was taken to the hospital with the same life-threatening symptoms, and by Thursday three more cases – Zhou, 63, Liu, 46, and Li, 32 – had joined him in intensive care. A sixth man called Wu, 30, was taken into intensive care the following Wednesday.
All of the men were linked. They were part of a group of 10 miners who had been tasked with clearing out piles of bat faeces in the abandoned copper mine in the hills south of the town of Tongguan in the Mojiang region. Some had worked for two weeks before falling ill, and others just a few days. The illness confounded the doctors. The men had raging fevers of above 39°C, coughs and aching limbs. All but one had severe difficulty breathing.
The first man to die, on 7 May 2012, was Zhou – the oldest of the group. Zhou had been admitted to the hospital 11 days earlier, after working in the mine for a fortnight. Lv, who had been clearing out the mine alongside Zhou, also lost his life to the mystery illness days later. The remaining four men were given a barrage of tests for haemorrhagic fever, dengue fever, Japanese encephalitis and influenza, but they all came back negative. They were also tested to check whether they had the Sars virus, but that also proved negative.
Initially, a respiratory specialist from another hospital suggested that the cause might be an infection from fungus in the mine and the men were treated with antifungal drugs, but the evidence was inconclusive as to whether this was effective. So the doctors sought the opinion of Professor Zhong Nanshan, a British-educated respiratory specialist and a former president of China’s medical association who had spearheaded his country’s efforts to combat the Sars pandemic nine years earlier. Aware the men might be suffering from another Sars-related coronavirus, he advised they be tested for antibodies against Sars, which would have shown whether the men had previously contracted the virus.
These tests were undertaken on the remaining four of the patients. The doctors also wanted to carry out tests on the bodies of the two dead men, but their families were unwilling to give permission to carry out autopsies. The four tests, however, produced remarkable findings. While none of the men tested positive for Sars itself, all four had antibodies against another, previously unknown Sars-like coronavirus. Furthermore, the two patients who recovered and went home showed greater levels of antibodies to this novel coronavirus than the two who were still patients in hospital at the time of the tests. This led the doctors to conclude that the deaths were likely to have been caused by the coronavirus. By September 2012, three out of six of the miners had died and three were discharged. Two of the men who recovered had spent more than a hundred days in hospital and would still be reporting symptoms resulting from the damage to their lungs more than a year later.
News of this emergence of a potentially deadly Sars-like coronavirus would have rung alarm bells across China if it had been allowed to get out. But there was a news blackout. There is no known contemporaneous reporting in the national or local media of the tragedy in the mine and its aftermath. We have, however, pieced together what little is known about these cases from two pieces of academic research that were produced shortly after the incident. The most detailed is a master’s thesis by a young medic at the Kunming Hospital called Li Xu, which we had translated into English. Li Xu’s thesis supervisor was Professor Qian Chuanyun, who headed the emergency department that treated the men. The other is a doctoral thesis by a student of the director of the Chinese Centre for Disease Control and Prevention, which was on constant watch for the emergence of a new threatening virus. There has been no official acknowledgement of the incident by the Chinese authorities to date.
Both pieces of research accept that it is difficult to be conclusive as to the actual cause of the miners’ illness given the available evidence. But Li Xu’s thesis argues that it was most likely to have been a Sars-like coronavirus that the men had caught from a bat while working in the cave. ‘This makes the research of the bats in the mine where the six miners worked and later suffered from severe pneumonia caused by an unknown virus a significant research topic,’ Li concluded. That research was already underway, led by ‘Bat Woman’. It would lead to the discovery of the virus that is now recognised to be the closest known relative of Sars-CoV-2, which caused the pandemic.
Monsoon season had arrived by the time the small team of scientists from the Wuhan Institute of Virology travelled to investigate the mine. They were already familiar with the region as they were in the midst of their five-year research project monitoring the Shitou caves a little over two hundred miles away searching for the origin of Sars. The last leg of their journey by car took them through the fertile lands south of the town of Tongguan where the famous green terraces of the tea plantations flow across the contours of rolling hills, which had been made more verdant by the daily downpours. The team were fully equipped with their best protective equipment, as they were aware that whatever was lurking in the murky crevices of the mine had already claimed three lives.
When the scientists cautiously ventured into the darkness of the mine – dressed from head to toe in white suits, respirator face masks and thick gloves – they were instantly struck by the repellent stench. Before them was a breeding ground crawling with mutated and as yet undiscovered microorganisms. In its derelict state, the former copper mine had been taken over by a large colony of roosting bats, which mingled with the rats and shrews that scurried along man-made floors made soft underfoot with thick layers of foul-smelling guano. It was the perfect environment for the intermingling of dangerous pathogens that might one day make the leap to human hosts. The scientists set about sampling the animals in the cave.
Between August 2012 and July 2013 they visited the mine four times. Shi led a team of six scientists from the Wuhan Institute, who were aided by researchers from the local Yunnan and Mojiang Centres for Disease Control. The bats were captured in large nets, as was now routine practice for Shi’s team. In total they took faecal samples from 276 different bats, which were quickly stored at –80°C in liquid nitrogen and were then dispatched in small freezer containers back to Wuhan where the molecular study work and analysis were conducted in the virology institute’s laboratories. The analysis work found that the fetid mine was infested with viruses – especially coronaviruses. Exactly half the bats carried coronaviruses and several were carrying more than one virus at a time – an illustration of just how easy it was for potentially harmful new strains to develop within the bloodstream of a single bat.
The first public mention of the mine was in a scientific paper by Shi and her team three years later in 2016 entitled ‘Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft’. The paper reported on the coronaviruses found during the one-year investigation in the mine by her team. One of the most striking things about the paper is that there is not a single mention of the reason that the Wuhan scientists went there in the first place. There was no reference at all to the deaths of the miners. This was puzzling because her team’s main work had been to discover the source of Sars – a pneumonia-type illness caused by a coronavirus. Yet the paper ignored the fact that the miners suffered from a pneumonia illness and had been exposed to multiple coronaviruses. This may well have been because there was still a news blackout imposed by the Chinese government over the tragedy. It was certainly very odd.
The paper says that a total of 152 genetic sequences of coronavirus were found in the six species of bats in the mineshaft and two were of the strand that had caused Sars. One of them stood out because it was a ‘new strain’ of coronavirus, which, while being far from an exact match for Sars, came from the same family as the 2003 killer. The small faecal sample of this new strain had been collected from a Rhinolophus affinis, commonly known as a horseshoe bat, during the scientists’ last visit to the mine on 24 July 2013. It was listed in the storage vaults as RaBtCoV/4991 – not a catchy name, but this would later become important when the worldwide significance of this virus strain became clear.
It is not known what happened to the mine after the scientists left in 2013. Neither the Chinese authorities nor the Wuhan Institute have ever said what became of it. Were the infected bats allowed to continue breeding viruses in the mine or were they evicted? Was the mine boarded up? These would become important questions. Meanwhile, RaBtCoV/4991 would apparently remain just an interesting discovery in a scientific paper until January 2020, when the Sars-CoV-2 pandemic began in Wuhan – the same city where it was being stored in the virology institute’s vaults. It would then be identified as the closest known match in the world to the new killer virus.
Today Wuhan is a modern metropolis – a ubiquitous skyline of concrete. To the casual onloo...