Transmission of zoonotic diseases

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.


Paralysis tick Ixodes holocyclus LEO Electron Microscopy Ltd.

Image: Sue Lindsay
© Australian Museum

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.

How animal viruses get into humans
More than 70 per cent of all new diseases emerging in humans are thought to have been caught from animals, some of which, such as bats, primates and rodents, might have lived with the viruses for thousands of years. Image: Matt Davidson
© The Age and The Sydney Morning Herald

Case study: Bats

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.

Grey-headed flying-fox

Grey-headed flying-fox (Pteropus poliocephalus) feeding on Eucalyptus blossom. As flying-foxes forage at night, transferring pollen and seeds between plants, they act as important short- and long- distance pollinators of Australia’s increasingly patchy native forests. Australian flying-foxes are known carriers of two viruses (ABLV and Hendra virus), however catching diseases directly from these animals is extremely unlikely.

Image: Mandi Griffith
© Australian Museum

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.

Grey-headed flying-fox
Grey-headed flying-fox feeding on blossom. Its face is covered in yellow pollen, which is transferred from tree to a tree, as the bat forages at night. Image: Mandi Griffith
© Mandi Griffith

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.

Illegal wildlife trade and risks to biosecurity

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:

The ACWG is often asked to identify bird eggs that have been smuggled into the country. Birds can carry many diseases that are a risk to native and domestic bird species, in addition to posing risks to humans, with the bird flu/avian influenza (H5N1) being one of the most well-known – there have been several outbreaks since its discovery in 1997. Knowing what species the eggs are and where they have come from can help authorities implement actions to stop the illegal movement of these animals into the country.

Another pathogen carried by birds that Australian authorities are concerned about is Newcastle Disease virus. Newcastle Disease is a viral disease in birds that impacts their gastrointestinal, respiratory and nervous systems. While no transmission to humans have been recorded, farms have had to destroy their entire poultry flocks to contain outbreaks of Newcastle Disease; thus if any large scale outbreak were to occur in Australia, it would have significant economic impacts to the Australian poultry industry.

Way Finder

Knowing what species the eggs are and where they have come from can help authorities implement actions to stop the illegal movement of these animals into the country.

Image: Carl Bento
© Australian Museum

The ACWG is often asked to help identify exotic species from all over the world that have been smuggled into the country, so that people can have unusual exotic pets. The ACWG works closely with other state agencies in NSW – such as the Department of Primary Industries (DPI), to better document the species coming into NSW and the threats they may pose to other wildlife and humans.

Red-eared turtle
Red-eared turtle in a pond in Kowloon park. Image: Lazlo-Photo

Examples of the species that have been found which may pose a health risk to people/wildlife/domestic animals, include red-eared slider turtles which can transmit various strains of Salmonella bacteria to humans. African hedgehogs are another example of a species known to carry disease and are periodically found in the illegal pet trade in Australia. Hedgehogs are known to carry foot-and-mouth disease, Salmonella, Q-fever and toxoplasmosis. While these pets may seem cute, the threats they pose to the Australian wildlife and potentially human health is not worth the risk. If you do spot any unusual exotic species in NSW you can report it to DPI via

Male Eastern Water Dragon, Intellagama lesueurii lesueurii

Salmonella can be widely carried by herptiles, including our pet lizards and snakes, not just illegal imports. This is an image of a Male Eastern Water Dragon, Intellagama lesueurii lesueurii. Water dragons are popular pets.

Image: Chris Hosking
© Australian Museum

Wet markets in Wuhan are being investigated as one of the possible places that allowed SARS-CoV-2 (the causative agent of COVID-19) to jump from wild animals to humans. The ‘wet market’ is a common overseas term for any market selling fresh produce and meat (often including both meat and seafood products) and which, in some countries, can include hunted wildlife, either legally and illegally – and maybe without the food handling standards we are used to here in Australia. The close proximity of many different animal species, raw meat and people provide ideal conditions for novel pathogen exposure and transfer between species. Primate meat products (part of a more general term ‘bushmeat’) are believed to have been the source of well-known infectious diseases that have jumped from animals to humans in the past, including Ebola and HIV. Most recently, Australian biosecurity agencies have been actively on the lookout for pork products coming into Australia because of the threat of African swine flu. While African swine flu has not been shown to cause symptoms in humans, its threat to the Australian pork industry is enormous and all efforts are being put in place to prevent its arrival in 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.

NSW Government, Health. Q fever fact sheet.

NSW Government, Health. Q fever control guideline.

Australian Museum Research Institute

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.

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