COVID-19 and zoonotic diseases

Introduction – Zoonotic Diseases by Professor Kris Helgen, Chief Scientist and Director, Australian Museum Research Institute

The study of biodiversity—the richness of life on earth—is uniquely reliant on collections and specialized expertise housed within natural history museums. These museums, with large biodiversity collections that they house “behind the scenes”, are also one of the world’s most important resources for understanding the biology of pandemic diseases that arise from wild animals. What species of flea carries the bubonic plague? Which mosquitoes are the most important vectors of human disease? How many bat species live in south-east Asia, and which are the most important carriers of coronaviruses? Natural history museum collections have been used to research and answer these and many other related questions. Carefully studied and curated collections of organisms, like mosquitoes, fleas, worms, or bats, are one of the tools that scientists rely on initially to identify disease sources and vectors, and also to generate the molecular information that allows for their detection and surveillance. It is not well understood or appreciated that this is one of the fundamental scientific contributions made by natural history museums to society in general—something I would like to change.

The emergence of a new pandemic coronavirus has shown the world, across a matter of months, that an animal-borne disease can serve as a global disruptor on an almost unthinkable scale, bringing connections between wildlife, disease, environment, and our global society and economy into sharpest focus. The Australian Museum and its researchers have a history of playing an important part in studies examining connections between animals and human diseases, and we aim to become even more involved in the future. Here are just a few selected stories that tell of links between wildlife and disease. Emerging infectious diseases will continue to make their mark on our world--in the future, there will be more.

Zoonotic diseases or zoonoses (Greek, zoon – animal, -nosos – disease) are illnesses or infections that humans catch from animals, usually vertebrates. You have probably heard of quite a few zoonoses – recent studies estimate that about 75% of emerging infectious diseases in humans are zoonotic. Well-known zoonoses include: bubonic plague, Mediterranean fever (brucellosis), Q-fever, lyme disease, rabies, Ebola, SARS, MERS, COVID-19 and Creutzfeldt-Jacob disease (mad cow disease). Some of the most infamous diseases in history, such as the plague, malaria and typhus are caught from animals. Closer to home, pet owners can be infected by Salmonella bacteria, Toxoplasma (the protozoan causing toxoplasmosis), tape-worms from pet droppings, and several kinds of parasitic worms from raw or undercooked meat and fish. Zoonotic diseases can be caused by all kinds of pathogens, ranging from viruses and bacteria, to parasitic worms, and even inanimate particles called prions (which cause mad cow disease).

Although all zoonoses are caught from animals, not all work in the same way. Often, the pathogen is harmless to an animal but causes disease when passed to humans – a kind of direct one-way transmission. Examples include the malaria parasite and dengue virus carried by mosquitoes; these pathogens are harmless to the host mosquito, but when passed to humans by bites, cause illness. On the other hand, some zoonoses cause illness in both animals and humans. These include rabies, anthrax and even some forms of influenza. Some diseases can pass in both directions, so-to-speak, with important implications for wildlife conservation (especially in captive zoo animals and threatened species regularly visited by tourists). In addition to direct transmission from one species to another, zoonoses can be transmitted via an intermediate species, called a vector. The coronavirus, SARS-CoV-1, which caused the outbreaks of severe respiratory illness in 2002–2004, originated in bats but infected humans via civets as an intermediate vector. Similarly, the current coronavirus pandemic (COVID-19), caused by SARS-CoV-2, is believed to have come from bats but reached humans, possibly via pangolins (which are known to naturally harbour coronaviruses). Indeed, a number of emerging human diseases are zoonoses transmitted by an intermediate vector – and some important human diseases, such as AIDS, smallpox and measles, are thought to originally have been zoonotic.

The expanding human impact on the planet, including increased urbanisation and agriculture, human-mediated destruction and degradation of wildlife habitat, climate change and the wildlife trade are all increasingly bringing humans, domestic animals and wildlife species into novel interactions and contact. These factors increase opportunities for zoonoses to emerge and spread.

The transmission of zoonotic diseases requires a pathogen (usually a virus or bacterium) found in one species to be passed onto a human host. Transmission of these infectious agents can occur by various means through either direct or indirect contact pathways.

Direct contact occurs when pathogens from an animal are passed to a human through direct exposure for example, contact with bodily fluids such as saliva, mucus, blood, urine and faeces. This can occur through physical contact (e.g. petting animals), contaminated food, as well as bites and scratches from infected animals. Notably, modes of transmission will vary according to the innate biological features of that pathogen. For instance, a respiratory pathogen like the influenza virus inhabits the respiratory tract and consequently is passed on through infected droplets from a cough, sneeze or saliva; but a blood-borne parasite, such as Plasmodium (causing malaria) must enter the bloodstream, as during a mosquito bite.

Indirect contact pathways for transmission of infectious agents do not require close contact between an infected animal and an uninfected human. Rather, areas inhabited or visited by an infected animal provide the means for pathogen transmission, including farms and wildlife habitats. Transmission most likely occurs through contaminated surfaces. In an agricultural setting, this may include barns, stables and chicken coops. Domestic settings can also be a source of infection and may include fish aquariums, food and water dishes and pet litter boxes. Indirect transmission can also occur via exposure to alternative mediums such as contaminated drinking water and food products sourced from animals (e.g., unpasteurised dairy products like milk and cheese).

It is also important to note disease vectors in transmission. A disease vector is an organism or object that can carry and transmit infectious agents. Organisms like biting insects (mosquitoes and ticks) are typical examples, but inanimate objects such as those described above within indirect contact transmission pathways and others can also be regarded as vectors.

As the world is working together to limit the spread of the COVID-19 pandemic, scientists are still trying to determine its precise origins. At present, the leading theory is that COVID-19 (or at least a closely related) virus originated in horseshoe bats (from the genus Rhinolophus), with another species (possibly pangolins) acting as the intermediate host for the virus to infect humans.

In fact, many wildlife species are natural hosts of viruses, which may not typically cause them any illness. Globally, bats are hosts to a number of recently emerging viruses, including the Japanese encephalitis, Ebola and Marburg viruses. In Australia, bats are natural hosts of two known viruses: Australian Bat Lyssavirus (ABLV) and Hendra virus, both of which can be life-threatening to humans. ABLV is a virus similar to rabies (found in other parts of the world), and a very small proportion of bats (both smaller ones and larger flying-foxes) in the bat populations are thought to be infected at any one time. Sick bats are likely to behave abnormally (e.g. can be aggressive, unable to fly, hang low in the tree, etc.) and are therefore more likely to be encountered by people, who then may potentially get scratched or bitten by the bat, and contract the virus. Contact or exposure to bat faeces, urine or blood do not pose an ABLV risk to people, nor does living, playing or walking near bat roosting trees. Since it was identified some 25 years ago, there have been three fatalities from the ABLV in Australia. If scratched or bitten by a bat, people should seek immediate medical attention to receive a post-exposure rabies virus vaccine, to prevent the potential for the disease to develop.In contrast to ABLV, Hendra virus is present in flying-foxes only (not all Australian bats) and is one of those viruses that requires an intermediate host, in this case a horse, for humans to get infected. Hendra virus causes no particular symptoms in flying-foxes, and horses are most likely infected by eating grasses that flying-foxes may have urinated on. When humans (or other horses) come in contact with sick horses, they may become infected too. In Australia, since the virus was first described in 1994, seven people have contracted Hendra, with four cases proving fatal. Fortunately, a Hendra vaccine for horses was developed in late 2012 and there have been no more reported cases in humans. Still, it is important to continue vaccinating horses to prevent potential outbreaks of the virus, which would increase the risk of people becoming infected.

Owing to these links to some known viruses, bats are unfortunately getting a pretty bad reputation globally. Yet, bats are some of the most extraordinary animals on Earth. They are found on every continent, except Antarctica, and account for about ¼ of all mammal species. This means there are over 1,400 species of these flying mammals adorning the skies at night, with over 80 found in Australia alone! Bats are incredibly important for the health of the ecosystems they inhabit. For example, many bats eat insects, and in rather large quantities – up to about ½ of their body weight each night! This keeps insect populations in check, and alone can save the agricultural industries billions of dollars in pest management of crops each year. Other bats, like Australian flying-foxes, are vital long-distance plant pollinators and seed dispersers, without which the increasingly patchy native forests would lose genetic diversity. The Australian endemic grey-headed flying-fox (Pteropus poliocephalus), for example, can cover 25km foraging at night and even more impressively, can fly from Sydney to Melbourne (some 700km) in just over two days.

What people often do not realise is that many of the bat species are actually in decline. As anthropogenic land-use expands, and natural habitats are degraded and modified, many bat species are forced into closer proximity with humans. Seeing bats (particularly flying-foxes) in their gardens, makes some people think that bats are everywhere, and often in ‘plague’ numbers. In Australian cities and towns, for instance, we are increasingly seeing permanent flying-fox roosting sites, which is an unusual behaviour for these nomadic species. Their year-round presence creates a false sense of a rise in numbers. Instead, flying-foxes are losing their natural habitat, leading them to live and forage in the riskier urban landscapes, where they face increased mortality from causes such as: netting, electrical power lines and collisions with vehicles and planes. In addition, as a direct result of climate change, the incidence of mass mortality in flying-foxes has been on the rise, as thousands of animals can die in a single day in a roosting camp when the daily temperatures exceed 40°C. There is evidence that these additional pressures on bat populations can lead to increased stress levels amongst individual animals, which can in turn promote viral shedding in bats, increasing the risk of viruses spreading to other species. Consequently, we should focus on promoting healthy bat populations, through restoration and preservation of native habitat, and move away from portraying them in negative light in the press.

As we find ourselves in these unique times, it is important to remember that COVID-19 is now a human disease, spreading from direct human-to-human contact. Therefore, people living close to flying-foxes, other bats, or wildlife in general, should not be worried of getting the virus from these animals, but instead develop a deeper appreciation for our remarkable wildlife and nature in general. It is also important for people to avoid direct contact with wild animals (including bats), and if they see an injured animal, contact the Wildlife rescue groups, who are trained in handling and helping animals.

The illegal wildlife trade is a driver of international environmental change. Unregulated movement of live animals and plants, as well as their parts, is not only a direct threat to the long-term survival of these species in the wild but can have wider ranging impacts. One of the most important is the introduction of species into environments/ecosystems where they should not be (we all know how bad the cane toad and fox have been to Australia!). With the movement of these species also come the potential diseases they carry; while this mostly affects native species that have not encountered them before, it could also provide a transmission route or intermediate vector for a novel pathogen similar to SARS-CoV-2 that causes COVID-19.

The Australian Centre for Wildlife Genomics (ACWG) works closely with Australian government departments that protect Australia’s environment and biosecurity at both the state and federal level, via laws protecting animal health, trade restrictions, and enacting quarantine requirements and inspections. The ACWG is an accredited wildlife forensic laboratory and is often called upon to provide evidence in instances where these laws/provisions have been breached and investigations have been instigated. The evidence we provide assists with enforcement actions brought against the people perpetrating these crimes. By identifying the species that are involved (and where they come from) it helps the Australian authorities in directing their efforts to stop the illegal trade of animals, and animal parts, entering Australia.

Below are some select examples of risks to Australia:

Q-fever (bacterium: Coxiella burnetii) is a zoonotic disease that can cause severe flu-like symptoms in humans. Q-fever (the q stands for query) was first described in 1937 and although thought to be an Australian disease, it has since been found across the globe. Both an acute and chronic disease, Q-fever is predominantly spread to humans from sheep, goats and cattle but can be found in a range of domestic and wild animals (including camels, bandicoots, kangaroos, and more). Infected animals are usually asymptomatic. The bacteria can also be present in manure, soil and in wool, and can survive for a long time in the environment. Ticks are the most important vector of Q-fever in wildlife, but the most common way humans contract Q-fever is by inhaling bacteria in the air or contaminated dust.

Although Q-fever can be transmitted in a number of ways, including inhalation of bacterial spores, contact with infected animal tissue and drinking unpasteurised milk from infected animals, the disease is rarely transmitted from person to person. Q-fever is largely an environmental or occupational risk for people working in abattoirs, with livestock, breeding cats/dogs, agriculture and those working with Australian wildlife (including some types of museum specimens).

The good news is that Q-fever can be treated with antibiotics and we have an effective vaccine.

The Australian Museum Research Institute (AMRI) brings together teams of research scientists, collection scientists, collection officers, associates, fellows and students.

Our research focuses on some of today’s major challenges including climate change impacts on biodiversity; the detection and biology of pest species; and, understanding what constitutes and influences effective biodiversity conservation. Our deep knowledge of biodiversity and geodiversity, combined with our integrative, collections-based approaches give us a unique perspective on understanding the evolution of our environment and on the path to a better future. We discover and document the biodiversity of our backyards and beyond, identify potentially environmentally and economically devastating pests, and use molecular techniques (DNA) to solve wildlife forensic mysteries and to understand the origins of Australia’s unique fauna.

For more information on COVID-19 and zoonotic diseases, please refer to the recent Sydney Morning Herald article: Identify host animal carrying COVID-19 or risk future outbreaks, says top scientist.

https://www.smh.com.au/national/identify-host-animal-carrying-covid-19-or-risk-future-outbreaks-says-top-scientist-20200726-p55fhh.html