Reports about rodents sold for food in markets and restaurants in Southeast Asia being infected with coronaviruses have heightened concerns about these animals transmitting the virus. During the COVID-19 lockdown, there have been many cases of rats and mice becoming bolder as their sources of food have disappeared—even turning to cannibalism—creating a risk of infestations. Homeowners have reported more sightings of rats, and callouts to pest controllers have increased. These reports of infected rats will only add to people’s concerns about keeping safe from the virus.

The three most recently discovered human coronaviruses, including the virus causing the current pandemic, SARS-CoV-2, have all caused epidemics with large numbers of serious infections and deaths. All three viruses have also been genetically traced to a bat origin that crossed over first to other animals and then to humans.

A number of wild animals hunted and sold for food have been found to be infected with coronaviruses—including bats, civet cats, rats, and pangolins—raising the fear of further infections passing to humans through the food chain. Here, we take a brief look at the connections between coronaviruses, animals, and humans, and show that the risks of infection are extremely low.

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The first coronaviruses found in humans only caused symptoms similar to the common cold. However, the first virulent human species to appear, SARS-CoV, led to an outbreak in Guangdong, China in 2002/3, spreading to 29 countries and causing around 8,000 deaths. The virus was also found in civet cats, raccoon dogs, ferret badgers, and domestic cats. Genetic analysis traced its origin to bats, the likely natural reservoirs. It is believed to have jumped species by infecting civet cats and then humans in a wildlife market.

The second outbreak, caused by MERS-CoV, was first detected in patients in Saudi Arabia and Qatar in 2012. Subsequent outbreaks occurred in 2015 and 2018, affecting 24 countries and resulting in over 500 deaths. This virus was traced genetically to an African bat but was also detected in isolated domestic herds of camels in Oman and the Canary Islands, suggesting it had been circulating in camels for several years.

The current outbreak of SARS-CoV-2 is the most serious, infecting over 9 million people (confirmed by testing) and causing over 500,000 deaths by the end of June 2020. This virus was linked to workers in a food market in Wuhan, and later, the pangolin was implicated as trafficked animals were found to have the virus. Genetic analysis shows the virus is most closely related to a bat coronavirus and was 96% similar to a bat virus collected from Yunnan province.

Are civet cats, rats, and pangolins to blame? 

During the first SARS outbreak, when the virus was found in civet cats in China, thousands were killed as a precaution.

No direct animal source of SARS-CoV-2 has been identified yet. It has been found in cats, dogs, tigers, hamsters, ferrets, macaques, and mink, but there’s no known case of direct infection from a wild animal. Mink on farms in the Netherlands were found to have been infected with coronavirus in April, and it had spread to 17 out of 130 farms in the country by 22 June.

The Dutch Minister of Agriculture, Nature, and Food Quality reported in May that "it was plausible" that two mink farm workers had been infected by the mink, based on genetic analysis of virus samples. Research is ongoing to trace the routes of infection of the mink, the workers, and three farm cats that tested positive for COVID-19 antibodies.

Several groups have identified a similar virus in pangolins seized from wildlife traders in China. This has focused attention on the illegal trade in these animals and the risk they might pose to food supplies in some countries.

An ongoing study has been sampling wild pangolins confiscated from smugglers en route to China or rescued from the wild in Malaysia. It has found that pangolins don’t carry the virus in the wild. The researchers noted that smuggled animals are often badly housed in groups of species from different sources where they can pick up infections from wild animals, domestic animals, and humans.

Rats are a popular source of meat in Southeast Asia. They’re caught in rice fields (Rattus sp. and Bandicota sp.), where they’re abundant, and in Vietnam, they’re also farmed. In Vietnam, the rats are often farmed with other wild animals such as primates, civets, wild boar, snakes, deer, crocodiles, porcupines, and turtles, alongside domestic farm animals. Additionally, bats are often provided roosts to collect their guano, creating a melting pot of potential infections and cross-overs of various diseases.

Coronaviruses were found in 50% of the wildlife farms. Six types of coronavirus were identified in rodents and bats, clustered in the Alpha, Beta, and Gammacoronaviruses. The proportion of infected animals increased from the farms to the food markets and was highest in the restaurants. While these are different species from human coronaviruses, the researchers concluded, "The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spill over to people." The trade in wildlife for food continues to add risks of introducing new viruses to humans. 

Implications for the food supply chain 

Many new diseases have emerged when humans have encroached on new land, increasing encounters with wild animals. Deforestation in the rainforests of West and Central Africa has been linked to the outbreak of the Ebola virus, as fruit bats, the suspected reservoir host, came into contact with humans at the edges of forest clearings. Similarly, HIV-AIDS and Zika have also been associated with human encroachment into natural forests. According to the US Centers for Disease Control and Prevention, three out of four new or emerging infectious diseases originate in animals.

The Directors of the Centre for International Forestry Research (CIFOR) and World Forestry have pioneered the concept that land health is fundamental to both human and environmental health. They proposed four steps for rebuilding planetary health and enhancing resilience in food production:

1. Change the Way Food is Produced

   Adopt regenerative agriculture using agroecology, agroforestry, and natural farming approaches. This would increase soil carbon, adding an estimated 3 billion tonnes of carbon to soils, protect soils, and stabilize production.

2. Restore Forests and Agricultural Lands

   Global forest restoration through assisted regeneration and planting could remove over 200 gigatonnes of carbon from the atmosphere, provide a buffer to protected forests, and produce goods and services for the local economy.

3. Make Supply Chains Sustainable

   Current supply chains often promote deforestation and land degradation. Paying a fair price to smallholder farmers, who produce 80% of food in Africa and Asia, and enforcing strict trade measures to prevent unsustainable practices, will help create a sustainable supply chain.

4. Value Natural Capital Correctly

   Properly valuing water, soil, viable land, food, air, and energy will incentivize their preservation and enhance the resilience of our food supplies. This will also lead to better diets, protection of pollinators, reduced use of agrochemicals, more efficient water use, low soil tillage, more cover crops protecting soil, and greater agro-ecological diversity.

These steps are essential for rebuilding planetary health and building resilience into food production.

Implications for rodent control