“COVID-19 is a wake-up call... If we just carry on with business as usual, that will lead to the end of our species' tenure on planet Earth.”
--Jane Goodall
The 21st century has already witnessed three coronavirus outbreaks: Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and our current pandemic nightmare, Covid-19. All three coronaviruses originated in wild animals and then jumped to human hosts. Why is it that our historical moment is experiencing such a surge in coronaviruses that are virulent to human populations? Though not always viral, pandemics are a regular, if horrifying, part of human history. Is our contemporary moment any worse?
New research suggests that for zoonotic diseases (disease microorganism shared between humans and other animals) it is. Humans are creating conditions that make coronaviruses and other pathogenic diseases more common and more virulent. It turns out that the proliferation of novel coronaviruses is just one more devastating consequence of the industrial decimation of the natural world. But before we get to the ecological problems that greatly undermine our collective future, we need to understand a small bit of viral biology.
Like all life* forms, coronaviruses constantly evolve. In fact, they mutate with shocking speed, far faster than cellular life forms. Two mechanisms of that evolution create potentially lethal new variants. The first is point mutations, the change in one single nucleotide base. These small changes are often not significant, and coronaviruses do not readily mutate. But millions of human infections by billions of viral particles produces vast opportunities for potentially consequential changes.
A second evolutionary mechanism produces more profound changes to viral species. Homologous recombination is the novel combination of genetic material from two similar, “parent” strains of a virus. It is more fundamental change on a larger scale. Novel pathogenic coronaviruses – such as SARS-CoV and probably SARS-CoV-2 (the name of the virus responsible for Covid-19) – arose from the homologous recombination of two viruses co-infecting a single cell. So did HIV and classical swine fever virus.
The world is currently in a race against coronavirus mutations, pitting the struggle for herd immunity—the goal of mass vaccination—against novel and potentially lethal virus variants.
The race to reach immunity is vexed by the fact that coronavirus frequently shift hosts, jumping between different animal and human populations. That process may involve the virus changing the cells of its host organism, known as virus tropism. These shifts have created new diseases in both humans and animals.
What does all this mean for the potential for new coronavirus pandemics? An interesting new paper calculated the likelihood of homologous recombination creating novel coronaviruses. It found that such an event is much more likely than previously thought. The authors warn that:
“coronaviruses frequently undergo homologous recombination when they co-infect a host, and that SARS-CoV-2 is highly infectious to humans, the most immediate threat to public health is recombination of other coronaviruses with SARS-CoV-2. Such recombination could readily produce further novel viruses with both the infectivity of SARS-CoV-2 and additional pathogenicity or viral tropism from elsewhere in the Coronaviridae.”
In other words, there is a high likelihood that existing coronaviruses will interact and recombine to form new, potentially more virulent strains. The study predicted that 40 times as many mammal species as is now known may be infected with four or more different kinds of coronaviruses, making homologous combination much more likely. The model correctly predicted some already known associations between mammals and viruses.
One candidate to vector the next coronavirus to humans is the Asian Palm Civet (Paradoxurus hermaphroditus). According to the new model for calculating the likelihood of novel coronaviruses, the Palm Civet is “a potential host of 32…different coronaviruses (in addition to SARS-CoV-2).” Genetic analysis has already demonstrated that SARS-CoV-2 is closely related to coronaviruses derived from the Palm Civet. But—and this is the key point—it is not the Palm Civet, a marvelous, fascinating animal, that poses the threat. It is the way humans interact with the Palm Civet. It is our horribly destructive relationship with wild animals that makes the Palm Civet a likely disease vector more than any part of Civet biology. The problem is us, not them.
Palm Civets are hunted for bushmeat and, despite being wild, solitary and nocturnal animals, kept as pets. One investigation found Palm Civets widely available in wildlife markets throughout Indonesia. Most of the Civets for sale were young and in poor health, suggesting they were captured in the wild. In Indonesia, Palm Civets are increasingly popular pets, so much so that “civet lover” clubs are advertised widely on the internet. Many of these clubs are suspected of involvement in the wildlife trade. One member of a civet lover club was arrested for selling a Crested Serpent Eagle.
Second, Palm Civets are greatly affected by deforestation. They are not considered threatened because they are widespread and greatly adaptable, moving into parks and suburban environments, even making their homes in attics. But that adaptability brings them into contact with people, and with each new contact the chance for disease transmission.
Civets are also hunted then caged to produce Kopi Luwak coffee. Kopi Luwak is brewed from coffee cherries that have been consumed and partially digested by civets. This is not a problem if the coffee cherries are harvested from civet excrement collected in the wild. But such a labor-intensive methodology makes poor economic sense, so civets are now housed in battery cages—rows and columns of identical cages stacked upon each other—and force-fed coffee cherries. Factory farming—a nightmare for breeding infectious disease—has come for the Palm Civet. The proximity of cages, stress of conditions, and bacterial infections combine to make civet farms likely hot spots for the outbreak of pathogenic diseases.
Palm Civets are not the only potential vector species. Other species also house several coronaviruses and are thus likely sites for coronavirus recombination to occur. Signaled out by the researcher’s model are the lesser Asiatic yellow bat (Scotophilus kuhlii) already a known coronavirus carrier, as well as the greater horseshoe bat (Rhinolophus ferrumequinum)—predicted to host 68 different coronaviruses. The common hedgehog (Erinaceus europaeus), the European rabbit (Oryctolagus cuniculus) and the domestic cat (Felis catus) are also seen as likely hosts for SARS-CoV-2 and large numbers of other coronaviruses. Worryingly, the research also found that the common pig—"the most prominent result for a SARS-CoV-2 recombination” is a likely vector.
The paper forthrightly calls for disease monitoring of these species. Such monitoring is a commonsensical and necessary move but does not tackle the root problem, which is the human destruction of nature. That destruction is not just the caging of Palm Civets, but widespread deforestation and ecosystem abuse. Deforestation and habitat destruction not only bring humans into greater contact with wild animals and any diseases they may carry, but also makes pandemics more likely.
Research demonstrates that this happens because as humans destroy habitats, species go extinct, reducing biodiversity. Those species that survive and even thrive in such situations—think rats and bats (and some bird species)—are more likely to host the dangerous pathogens that might jump to humans. Known wildlife hosts of zoonotic diseases are comprising a greater proportion of species richness. Mammal species that host a greater number of pathogens are more likely to thrive in human dominated (agricultural or urban) ecosystems. Asian Palm Civets are one such animal. Not only are we caging them, but as they adjust to human landscapes, they bring their coronaviruses, and the opportunities for homologous recombination, with them. Our destruction of nature is a selective force for own destruction by disease.
But that risk is not shared equally. The most vulnerable will suffer the most. For example, one study found that rural agricultural workers in Southeast Asia are more likely to suffer from such pathogenic diseases as hookworm, malaria, scrub typhus and various kinds of spotted fevers. The problem is hardly confined to the Asian rural poor. We have seen that in greatly stratified countries like the United States, health disparities are themselves a kind of epidemic. Making matters even worse, those living in polluted environments—suffering from air pollution in the form of particulate matter and ozone smog—have chronic lung conditions and thus are more susceptible to Covid-19. The air in densely populated urban neighborhoods is often thoroughly polluted. Thus, these disparities are sure to worsen as deteriorating environmental conditions help bring about more novel pandemics.
There are other drivers of ecosystem destruction. Deforestation, the consumption of bushmeat and global pollution do not just happen, nor can they be seen solely as a feature of commodity capitalism, as immensely destructive as that economic system has proven to be. They result from human overpopulation. No matter how impactful any single individual is, the simple fact of seven and half billion mouths to feed means widespread environmental destruction. This topic is of primary importance. Suffice it say that I, for one, wish to maximize the number of people who live on planet Earth. I just understand that to achieve such a lofty goal, we cannot all be here at the same time.
In the short term we must understand that human health depends upon ecosystem health. We must enact policies that build from that profound truth. We are tied to palm civets. Their fate is ours.
*Are viruses alive? It is a fascinating question because life is extremely difficult to define. See Carl Zimmer’s “The Secret Life of A Coronavirus” if you have access to the New York Times behind its paywall.