Is factory farming to blame for coronavirus?

Where did the virus causing the current pandemic come from? How did it get to a food market in Wuhan, China, from where it is thought to have spilled over into humans? The answers to these questions are gradually being pieced together, and the story they tell makes for uncomfortable reading.

Let’s start at the beginning. As of 17 March, we know that the Sars-CoV-2 virus (a member of the coronavirus family that causes the respiratory illness Covid-19) is the product of natural evolution. A study of its genetic sequence, conducted by infectious disease expert Kristian G Andersen of the Scripps Research Institute in La Jolla, California, and colleagues, rules out the possibility that it could have been manufactured in a lab or otherwise engineered. Puff go the conspiracy theories.

The next step is a little less certain, but it seems likely that the original animal reservoir for the virus was bats. Andersen’s team showed – like the Chinese before them – that the sequence of Sars-CoV-2 is similar to other coronaviruses that infect bats.

Since other bat coronaviruses have transited to humans via an intermediate animal host, it seems likely that this one did too. That animal was probably one that some Chinese people like to eat, and that is therefore sold in “wet” markets (those that sell fresh meat, fish, seafood and other produce). This animal may have been the scaly mammal called a pangolin. That can’t be conclusively proved, but several groups have found sequence similarities between Sars-CoV-2 and other coronaviruses that infect pangolins.

If this is indeed the route the virus took to humans, it has two critical interfaces: one between us and the intermediate host, possibly a pangolin, and one between that host and bats. Most of the attention so far has been focused on the interface between humans and the intermediate host, with fingers of blame being pointed at Chinese wet markets and eating habits, but both interfaces were required for the pandemic to ignite. So where and how did the spillover from the bat to the pangolin – or other wild or semi-wild intermediate host – occur?

“Our study does not directly shed light on the geographical origin of the virus,” says Andersen. “However, all the available evidence shows that it was inside China.”

Case closed then, and President Trump is right to call Sars-CoV-2 the “Chinese virus”. Well, no, because if you want to understand why this pandemic happened now and not, say, 20 years ago – since Chinese people’s taste for what we in the west consider exotic fare is not new – you have to include a number of other factors. “We can blame the object – the virus, the cultural practice – but causality extends out into the relationships between people and ecology,” says evolutionary biologist Rob Wallace of the Agroecology and Rural Economics Research Corps in St Paul, Minnesota.

The closed Huanan Seafood Wholesale Market in Wuhan, in China’s Hubei Province, in January. Photograph: Noel Celis/AFP via Getty Images

Starting in the 1990s, as part of its economic transformation, China ramped up its food production systems to industrial scale. One side effect of this, as anthropologists Lyle Fearnley and Christos Lynteris have documented, was that smallholding farmers were undercut and pushed out of the livestock industry. Searching for a new way to earn a living, some of them turned to farming “wild” species that had previously been eaten for subsistence only. Wild food was formalised as a sector, and was increasingly branded as a luxury product. But the smallholders weren’t only pushed out economically. As industrial farming concerns took up more and more land, these small-scale farmers were pushed out geographically too – closer to uncultivable zones. Closer to the edge of the forest, that is, where bats and the viruses that infect them lurk. The density and frequency of contacts at that first interface increased, and hence, so did the risk of a spillover.

It’s true, in other words, that an expanding human population pushing into previously undisturbed ecosystems has contributed to the increasing number of zoonoses – human infections of animal origin – in recent decades. That has been documented for Ebola and HIV, for example. But behind that shift has been another, in the way food is produced. Modern models of agribusiness are contributing to the emergence of zoonoses.

Take flu, a disease that is considered to have high pandemic potential, having caused an estimated 15 pandemics in the past 500 years. “There is clearly a link between the emergence of highly pathogenic avian influenza viruses and intensified poultry production systems,” says spatial epidemiologist Marius Gilbert of the Université Libre de Bruxelles in Belgium.

The reasons, many of which were documented in Wallace’s 2016 book Big Farms Make Big Flu, include the density with which chickens, turkeys or other poultry are packed into factory farms, and the fact that the birds in a given farm tend to be near genetic clones of one another – having been selected over decades for desirable traits such as lean meat. If a virus gets introduced into such a flock, it can race through it without meeting any resistance in the form of genetic variants that prevent its spread. Both experimental manipulations and observations in the real world have demonstrated that this process can result in a ratcheting up of the virus’s virulence. If it then spills over into humans, we are potentially in trouble.

In a paper published in 2018, Gilbert’s group reviewed historical “conversion events”, as they call them – when a not-very-pathogenic avian flu strain became much more dangerous, and found that most of them had occurred in commercial poultry systems, and more frequently in wealthy countries. Europe, Australia and the US had generated more of them than China.

That doesn’t let China off the hook. Two highly pathogenic forms of avian flu – H5N1 and H7N9 – have emerged in that country in recent decades. Both infect humans, though not easily (yet). The first human cases of H7N9 were reported in 2013, and there were small annual outbreaks thereafter. But, says Gilbert, “nothing was done until the virus turned out to be pathogenic for chickens as well. Then it became an important economic issue and China started to mass-vaccinate its poultry against H7N9, and that ended the transmission to humans.”

A banner reading ‘We are all pangolins’ hangs on a balcony in Bordeaux, France. The entire country has been on coronavirus lockdown since 16 March. Photograph: Nicolas Tucat/AFP via Getty Images

China is one of the world’s major exporters of poultry, but its poultry industry is not wholly Chinese-owned. After the recession of 2008, for example, New York-based investment bank Goldman Sachs diversified its holdings and moved into Chinese poultry farms. So if China has its share of responsibility for spillover events, it isn’t alone. That is why Wallace insists on talking about relational geographies rather than absolute geographies, when it comes to identifying the causes of disease. Or as he puts it: “Follow the money.”

Not everybody sees a straightforward link between factory farming and new and dangerous forms of flu. Michael Worobey, an evolutionary biologist at the University of Arizona, points out that before they were brought into factory farms, poultry were kept outside. The factory model may ramp up virulence, he says, but it probably protects a flock from being infected by a virus in the first place.

Still, Worobey doesn’t doubt that farming and other human-animal interactions have shaped our disease ecology. His group collects the sequences of flu viruses from a range of animal hosts, including humans, and plots them on a family tree to try to understand how flu has evolved over time. Flu is constantly mutating – that’s the reason the seasonal flu vaccine has to be updated each year – but it mutates at different rates in different hosts, which means that his flu family tree is informative both about the parentage and intermediate host of each strain and about the approximate timing of past spillover events.

It’s possible – though by no means certain – that flu first became a disease of humans after the Chinese domesticated ducks about 4,000 years ago – drawing that animal reservoir into human communities for the first time. But humans can also catch flu from, and give flu to, pigs – another animal we have lived alongside for millennia. A few years ago, Worobey suggested – controversially – that birds might not always have been the main intermediate host for human flu viruses. Until about a century ago, he reported, people may have caught flu from horses. Around the time that motor vehicles supplanted horses as transport, poultry farming was expanding in the western hemisphere, and it’s possible, Worobey argued, that birds then took over as the main intermediate host of flu for humans.

Not everyone buys that scenario. Wendy Barclay, a virologist at Imperial College London, says that if horses were once the main intermediate host for flu, “most avian viruses would contain the mammalian adaptation”, and they don’t. David Morens of the US National Institute of Allergy and Infectious Diseases in Bethesda, Maryland, thinks that it is more likely that the horse was a temporary detour, and that the main intermediate host of flu for humans has always been birds – especially wild ones. But all agree that humans have shaped these host-pathogen relationships, through our use of land and other animal species. And as Worobey points out, the sheer size of the human population today means that in the 21st century, we are doing so on an unprecedented scale. He estimates, for example, that domesticated ducks probably outnumber wild ones by now.

And we’re not just talking about birds. Gilbert believes a ratcheting up of viral virulence is happening in pig herds, too. Porcine reproductive and respiratory syndrome (PRRS), a disease of pigs that was first described in the US in the late 1980s, has since spread to herds across the world and strains detected recently in China are more virulent than the early American ones. A 2015 study carried out by Martha Nelson of the US National Institutes of Health and colleagues mapped the genetic sequences of swine flu viruses and found that Europe and the US – the largest global exporters of pigs – are also the largest exporters of swine flu.

There have been claims on social media, sometimes posted by vegans, that if we ate less meat there would have been no Covid-19. Interestingly, some of these have been blocked by mainstream news organisations as “partly false”. But the claims are also partly true. Though the links they draw are too simplistic, the evidence is now strong that the way meat is produced – and not just in China – contributed to Covid-19.

It is clear that to prevent or at least slow the emergence of new zoonoses, as Fearnley and Lynteris have argued, China’s wet markets will need to be better regulated. But we also need to look behind those markets, at how our food is produced globally.

Though it may not feel like it now, Wallace says, we have been lucky with Sars-CoV-2. It appears to be far less lethal that either H7N9 – which kills around a third of those it infects – or H5N1, which kills even more. This gives us an opportunity, he says, to question our lifestyle choices – because chicken isn’t cheap if it costs a million lives – and vote for politicians who hold agribusiness to higher standards of ecological, social and epidemiological sustainability. “Hopefully,” he says, “this will change our notions about agricultural production, land use and conservation.”