Out of the bat cave: China’s deadly Covid maze

In the monsoon season of August 2012 a small team of scientists travelled to southwest China to investigate a new and mysteriously lethal illness. After driving through terraced tea plantations, the scientists reached their destination: an abandoned copper mine, where — in white hazmat suits and respirator masks — they ventured into the darkness.

Instantly, they were struck by the stench. Overhead, bats roosted. Underfoot, rats and shrews scurried through thick layers of their droppings. It was a breeding ground for mutated microorganisms and pathogens deadly to human beings. There was a reason to take extra care. Weeks earlier, six men who had entered the mine had been struck down by an illness that caused an uncontrollable pneumonia. Three of them died.

Today, as deaths from the COVID-19 pandemic exceed half a million and economies totter, the bats’ repellent lair has taken on global significance.

Evidence seen by The Sunday Times suggests that a virus found in its depths — part of a faecal sample that was frozen and sent to a Chinese laboratory for analysis and storage — is the closest known match to the virus that causes COVID-19.

It came from one of the last droppings collected in the year-long quest, during which the six researchers sent hundreds of samples back to their home city of Wuhan. There, experts on bat viruses were trying to identify the source of the SARS — severe acute respiratory syndrome — pandemic 10 years earlier.

The virus was a huge discovery. It was a “new strain” of a SARS-type coronavirus that, surprisingly, received only a passing mention in an academic paper. The six sick men were not referred to at all.

What happened to the virus in the years between its discovery and the eruption of COVID-19? Why was its existence tucked away in obscure records, and its link to three deaths not mentioned? Nobody can deny the bravery of scientists who risked their lives harvesting the highly infectious virus. But did their courageous detective work lead inadvertently to a global disaster?

At the First Affiliated Hospital of Kunming, doctors were confounded by a mystery illness. The six men who had been working in the bat-infested mine had raging fevers above 39C, coughs and aching limbs. All but one had severe difficulty in breathing.

After the first two men died, the remaining four underwent a barrage of tests for haemorrhagic fever, dengue fever, Japanese encephalitis and influenza, but all came back negative. They were also tested for SARS, the outbreak that erupted in southern China in 2002, but also proved negative.

The Wuhan Institute of Virology (WIV), a renowned centre of coronavirus expertise, was called in to test the four survivors. These produced a remarkable finding: while none had tested positive for SARS, all four had antibodies against another, unknown SARS-like coronavirus.

Furthermore, two patients who recovered and went home showed greater levels of antibodies than two still in hospital, one of whom later died.

Researchers in China have been unable to find any news reports of this new SARS-like coronavirus and the three deaths. There appears to have been a media blackout. It is, however, possible to piece together what happened in the Kunming hospital from a master’s thesis by a young medic named Li Xu.

Li’s thesis was unable to say what exactly killed the three miners, but indicated the most likely cause was a SARS-like coronavirus from a bat. “This makes the research of the bats in the mine where the six miners worked and later suffered from severe pneumonia caused by unknown virus a significant research topic,” Li concluded. That research was already under way — led by the Wuhan virologist, Shi Zhengli, who became known as “Bat Woman” — and it adds to the mystery.

Coronaviruses are a group of pathogens that sometimes have the potential to leap species from animals to humans and appear to have a crown — or corona — of spikes when viewed under a microscope. Before COVID-19, six types of coronavirus were known to infect humans but mostly they caused mild respiratory symptoms such as the common cold.

The first outbreak of SARS — now known as Sars-Cov-1 to distinguish it from Sars-Cov-2, the virus that causes COVID-19 — is one of the deadly exceptions. It emerged in Guangdong, southern China, in November 2002 and infected 8096 people in 29 countries. It caused severe pneumonia in some and killed 774 people before petering out eight months later.

A race began to find out how a coronavirus had mutated into something so deadly and jumped from animals to humans. Shi and her team from the WIV began hunting among bat colonies in caves in southern China in 2004. In 2012 they were in the midst of a five-year research project when the call came to investigate the incident in the copper mine.

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