A virus is attacking koalas’ genes. But their DNA is fighting back

Keith Chappell, The University of Queensland

A virus that infects koalas is steadily integrating itself into their DNA, ensuring that it is passed down from generation to generation. But the koala genome is defending itself, revealing that DNA has its own immune system to shut down invaders.

The virus, called koala retrovirus (KoRV), is linked to weakened immunity, cancer, and chlamydia infection in koalas. All retroviruses hijack the DNA in some cells of their host’s body, but not all of them manage to be transmitted to the host’s offspring.

Your DNA is 8% virus

Over the millions of years of evolutionary history, retroviruses have at one time or another made their way into the genomes of all species of vertebrates that we have studied.

We know about these ancient infections because retroviruses sometimes infect the animal’s sperm or egg cells, which means the virus incorporates its own DNA sequences into the genome that is passed from generation to generation.

---

Read more:
An ancient retrovirus has been found in human DNA – and it might still be active

---

These viral sequences can contribute to disease, but have also been “co-opted” by the host animals for processes that are essential to normal development. As much as 8% of the human genome is made up of the remnants of infectious viruses.

While we know that retroviruses have frequently appeared during evolutionary history, we don’t know much about how retroviral sequences infiltrate sperm and egg cells, or how these cells react.

Catching a retrovirus in the act

Almost all known retrovirus genome invasions happened millions of years ago. However, KoRV is a recently identified exception. The virus spreads between individuals, but is also infecting sperm and egg cells, so many koalas are born with this pathogen as part of their genome.

My colleagues and I at the University of Queensland are collaborating with scientists from the University of Massachusetts Medical School to analyse how koala sperm and egg cells respond to KoRV-A infection.

Our findings, published today in Cell, suggest these cells mount a novel “innate genome immune response” to viral infection, which may help control the spread of infectious KoRV.

Within this project, the team analysed DNA and RNA from different tissue samples from deceased wild koalas from South East Queensland. (Like DNA, RNA also contains genetic information about the koalas – but it is also what KoRV’s own genome is made of.)

The team specifically looked for short sequences of RNA, between 23 and 35 nucleotides long, known as PIWI Interacting RNAs (piRNAs). Clusters of piRNA sequences are retained within the genome and serve as a kind of memory bank of undesirable sequences – signatures of invading viruses – to be targeted.

An immune system for the genome

Based on our new findings, we suggest that there is a specialised immune system to defend against retroviral genome invasion. Like the ordinary immune system, this one includes an innate response – a sort of general-purpose defence against attackers – and an adaptive response, which learns to recognise specific pathogens and take them down.

At the early stages of egg or sperm infection, the altered DNA sequence results in a “molecular pattern” that is recognised by an innate genome immune system, which stops the activity of the virus and starts producing signature piRNA sequences to recognise the invader.

---

Read more:
Koalas sniff out juicy leaves and break down eucalypt toxins – it’s in their genome

---

The innate immune response works until a memory of the genome invader is created and a sequence-specific adaptive response kicks in.

We propose a framework through which a sequence from an invading retrovirus can first have its genes “silenced”, and then through targeted processes it eventually becomes an integral part of the host genome.

This “genome immune system” changes our understanding of what shapes the genomes of all animals. No more can we view the genome as a defenceless entity governed purely by natural selection – it fights back.

Keith Chappell, Senior Research Fellow, School of Chemistry and Molecular Biosciences, The University of Queensland

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Advertisement

Explainer: what is Murray Valley encephalitis virus?

Ana Ramírez, James Cook University; Andrew Francis van den Hurk, The University of Queensland; Cameron Webb, University of Sydney, and Scott Ritchie, James Cook University

Western Australian health authorities recently issued warnings about Murray Valley encephalitis, a serious disease that can spread by the bite of an infected mosquito and cause inflammation of the brain.

Thankfully, no human cases have been reported this wet season. The virus that causes the disease was detected in chickens in the Kimberley region. These “sentinel chickens” act as an early warning system for potential disease outbreaks.

What is Murray Valley encephalitis virus?

Murray Valley encephalitis virus is named after the Murray Valley in southeastern Australia. The virus was first isolated from patients who died from encephalitis during an outbreak there in 1951.

The virus is a member of the Flavivirus family and is closely related to Japanese encephalitis virus, a major cause of encephalitis in Asia.

Murray Valley encephalitis virus is found in northern Australia circulating between mosquitoes, especially Culex annulirostris, and water birds. Occasionally the virus spreads to southern regions, as mosquitoes come into contact with infected birds that have migrated from northern regions.

---

Read more:
After the floods come the mosquitoes – but the disease risk is more difficult to predict

---

How serious is the illness?

After being transmitted by an infected mosquito, the virus incubates for around two weeks.

Most people infected don’t develop symptoms. But, if you’re unlucky, you could develop symptoms ranging from fever and headache to paralysis, encephalitis and coma.

Around 40% of people who develop symptoms won’t fully recover and about 25% die. Generally, one or two human cases are reported in Australia per year.

Since the 1950s, there have been sporadic outbreaks of Murray Valley encephalitis, most notably in 1974 and 2011. The 1974 outbreak was Australia-wide, resulting in 58 cases and 12 deaths.

It’s likely the virus has been causing disease since at least the early 1900s when epidemics of encephalitis were attributed to a mysterious illness called Australian X disease.

Traditional monitoring of mosquito-borne diseases relies on the collection of mosquitoes using specially designed traps baited with carbon dioxide.
Cameron Webb

Early warning system

Given the severity of Murray Valley encephalitis, health authorities rely on early warning systems to guide their responses.

One of the most valuable surveillance tools to date have been chooks because the virus circulates between birds and mosquitoes. Flocks of chickens are placed in areas with past evidence of virus circulation and where mosquitoes are buzzing about.

Chickens are highly susceptible to infection so blood samples are routinely taken and analysed to determine evidence of virus infection. If a chicken tests positive, the virus has been active in an area.

The good news is that even if the chickens have been bitten, they don’t get sick.

Mosquitoes can also be collected in the field using a variety of traps. Captured mosquitoes are counted, grouped by species and tested to see if they’re carrying the virus.

This method is very sensitive: it can identify as little as one infected mosquito in a group of 1,000. But processing is labour-intensive.

---

Read more:
How Australian wildlife spread and suppress Ross River virus

---

How can technology help track the virus?

Novel approaches are allowing scientists to more effectively detect viruses in mosquito populations.

Mosquitoes feed on more than just blood. They also need a sugar fix from time to time, usually plant nectar. When they feed on sugary substances, they eject small amounts of virus in their saliva.

This led researchers to develop traps that contain special cards coated in honey. When the mosquitoes feed on the cards, they spit out virus, which specific tests can then detect.

We are also investigating whether mosquito poo could be used to enhance the sugar-based surveillance system. Mosquitoes spit only tiny amounts of virus, whereas they poo a lot (300 times more than they spit).

This mosquito poo can contain a treasure trove of genetic material, including viruses. But we’re still working out the best way to collect the poo.

Mosquito poo, shown here after mosquitoes have fed on coloured honey, can be used to detect viruses like Murray Valley encephalitis.
Dagmar Meyer

Staying safe from Murray Valley encephalitis

There is no vaccine or specific treatment for the virus. Avoiding mosquito bites is the only way to protect yourself from the virus. You can do this by:

• wearing protective clothing when outdoors

• avoiding being outdoors when the mosquitoes that transmit the virus are most active (dawn and dusk)

• using repellents, mosquito coils, insect screens and mosquito nets

• following public health advisories for your area.

The virus is very rare and your chances of contracting the disease are extremely low, but not being bitten is the best defence.

Ana Ramírez, PhD candidate, James Cook University; Andrew Francis van den Hurk, Medical Entomologist, The University of Queensland; Cameron Webb, Clinical Lecturer and Principal Hospital Scientist, University of Sydney, and Scott Ritchie, Professorial Research Fellow, James Cook University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Tandem virus cocktail kills pest rabbits more effectively

Tagged European rabbit kitten infected with myxoma virus, but that died from rabbit haemorrhagic virus disease (RHDV).
Photo by David Peacock, Biosecurity South Australia, CC BY-NC-SA

Corey Bradshaw, Flinders University; Louise Barnett, Flinders University, and Thomas Prowse, University of Adelaide

Farmers, landowners and conservationists across Australia are benefiting from an unexpected, combined effect of two biological controls that target feral populations of European rabbits (Oryctolagus cuniculus), according to our research, published in the Journal of Applied Ecology.

---

Read more:
Explainer: how ‘biocontrol’ fights invasive species

---

Pest rabbits cost the Australian economy over A$200 million each year in lost production, and millions more in pest control. They compete with livestock for food and cause enormous environmental damage.

Rabbits previously reached plague numbers in much of agricultural and outback Australia, until the introduction of two rabbit-specific viruses and insect vectors.

Myxoma virus was first introduced in 1950, followed by European rabbit fleas in the 1960s to help spread the virus, and then Spanish rabbit fleas in the 1990s to increase spread into arid areas.

Then, in 1995, rabbit haemorrhagic disease virus (RHDV) escaped from quarantine, before an official release in 1996. These biocontrols have reduced rabbit numbers by an estimated 75-80% (see references in our paper) in South Australia alone since the 1950s.

Rabbits around a waterhole at the myxomatosis trial enclosure on Wardang Island in 1938.
National Archives of Australia/Wikimedia Commons

Together, myxoma virus and RHDV saved the Australian economy an estimated A$70 billion by 2011.

But managing rabbits’ growing immunity to these virus biocontrol agents is now presenting new challenges for Australian land managers.

---

Read more:
Controlling rabbits: let’s not get addicted to viral solutions

---

This is why our new discovery of a positive interaction between the two main viruses is great news for the Australian environment and economy.

Our study represents the first solid evidence that a combination of these two rabbit diseases is more effective in reducing rabbits’ abundance, providing agencies and landowners with more bang for their buck during rabbit control programs.

Our findings were made possible by one of the longest-running monitoring programs in disease ecology: the 21-year (and ongoing) Turretfield Rabbit Research Project north of Adelaide.

Roughly every two months for more than two decades, PIRSA Biosecurity South Australia has counted, tagged, virus-tested, and released rabbits of all ages from the isolated sentinel rabbit population.

Analysing this unrivalled dataset, we discovered that the probability of dying from rabbit haemorrhagic disease was 10% higher than expected when an individual rabbit had previously been exposed to myxoma virus. These means that rabbits that are now immune to the myxoma virus (Australia’s first rabbit biocontrol) are nevertheless more susceptible to RHDV (Australia’s second rabbit biocontrol).

In other words, the two diseases (a poxvirus and a calicivirus) interacted to give a population-level effect that resulted in more rabbit deaths overall.

Such an interaction between biocontrol agents is rare; in fact, it is the first discovery of its kind in the world.

Tagged rabbit from Turretfield (photo taken September 8, 2014). This individual had no antibodies against RHDV or myxoma virus, but was found dead from haemorrhagic disease two hours later.
David Peacock/Biosecurity SA

The knowledge that the two viruses combine as a potent weapon against rabbits has major implications for land owners and farmers around the world who battle pest rabbits. Disease outbreaks could potentially be timed to ensure that the death rate of pest rabbits is as high as possible.

In Australia, rabbits are a dietary mainstay for two other damaging invasive species: feral cats and red foxes. A large rabbit population can keep the two predator species at high densities, thus promoting their high predation rates on native wildlife.

---

Read more:
Invasive predators are eating the world’s animals to extinction – and the worst is close to home

---

Keeping rabbit numbers low can therefore benefit our environment. In fact, the rate of native vegetation cover has increased since RHDV began to spread in 1995, and there have been documented increases in the numbers of small native mammal species since that time.

Ecologically informed biocontrol is therefore just another smart way to manage invasive species.

Our discovery also has implications right across the world. European rabbits cause environmental and agricultural damage in places as diverse as the United Kingdom, New Zealand, and in parts of South America.

Our findings will also help researchers and conservationists to safeguard the rabbit in its natural range in Europe, and support Australia’s search for other biocontrols in the future.

Corey Bradshaw, Matthew Flinders Fellow in Global Ecology, Flinders University; Louise Barnett, Adjunct researcher, Flinders University, and Thomas Prowse, Postdoctoral research fellow, School of Mathematical Sciences, University of Adelaide

This article was originally published on The Conversation. Read the original article.

Are Australia’s native pigeons sitting ducks?

These migratory pied imperial-pigeons in Far North Queensland, like many of Australia’s 22 species of native pigeons and doves, play an important role in our ecosystems but may be at risk from emerging viruses in domestic pigeons.
Dejan Stojanovic, CC BY-SA

Andrew Peters, Charles Sturt University

The word “pigeon” evokes thoughts of gentle cooing, fluttering in rafters, and poo-encrusted statues. The species responsible for the encrustation is deeply familiar to us, having ridden waves of European expansionism to inhabit every continent, including Australia. First domesticated thousands of years ago, urban pigeons have turned feral again.

Less familiar are the native species that are not your stereotypical pigeons: a posse of pointy-headed crested pigeons in a suburban park, or a flock of topknot pigeons feeding in a camphor laurel.

Crested pigeons (left), brush bronzewings (centre) and pied imperial-pigeons (right) are amongst the 22 species of native pigeons and doves in Australia. Their charm and beauty belies the important functions they play in ecosystems.
Author provided

Australia and its neighbouring islands are the global epicentre of pigeon and dove (or “columbid”) diversity with the highest density of different columbids – an impressive 134 species – found in the region. Twenty-two of these native species are found in Australia alone, in just about every habitat.

These native species play an important role in ecosystem functioning: they forage for and disperse seeds, concentrate nutrients in the environment, and are a source of food for predators. Fruit doves for example, are zealous fruitarians, and the region’s tropical rainforests depend on them for tree diversity. Where fruit-doves have disappeared in the South Pacific, numerous plant species have lost an effective dispersal mechanism.

The rose-crowned fruit-dove is not only beautiful but also plays an important role in dispersing seeds in Australian rainforests.
Author provided

The future of Australia’s native pigeons however, may depend on our domestic pigeons. Australia’s domestic pigeon population — both feral and captive – is large and interconnected by frequent local and interstate movements. Pigeon racing, for example, involves releasing captive birds hundreds of kilometres from their homes only so they may find their way back. While most birds do navigate home, up to 20% will not return, of which some will join feral pigeon populations. Birds are also traded across the country and illegally from overseas. These movements, together with poor biosecurity practices, mean that captive pigeons can and do mingle with feral domestic pigeons.

And here’s a paradox. Could Australia’s feral domestic pigeons become the vector for a dramatic decline of columbids – native species on which Australian ecosystems rely?

Emerging viral epidemics

In recent years, two notable infectious diseases have been found to affect our captive domestic pigeons: the pigeon paramyxovirus type 1 (PPMV1) and a new strain of the pigeon rotavirus (G18P). These diseases are notable because in captive domestic flocks they are both spectacularly lethal and difficult to control.

PPMV1, although likely to have originated overseas, is now endemic in Australia. This virus has jumped from captive to feral domestic pigeon populations on several occasions, but fortunately has yet to establish in feral populations.

Domestic pigeons suffer high mortality rates after being infected with either pigeon paramyxovirus ‘PPMV1’ or pigeon rotavirus ‘G18P’.
Dr Colin Walker

G18P is thought to have spread to Victoria and South Australia from a bird auction in Perth in 2016. PPMV1 also spread rapidly to multiple states following its first appearance in Melbourne in 2011.

The movements of captive pigeons, and their contact with their feral counterparts, can be the route through which virulent and lethal diseases – such as the PPMV1 and the G18P – may spread to Australia’s native columbids.

Pigeon paramyxovirus and pigeon rotavirus are known to have escaped from captive domestic pigeons into feral domestic pigeons (black arrow). The risk is that these viruses will establish in feral pigeon populations and cause epidemics in our diverse and ecologically important wild native columbids (red arrow).
Author provided

What have we got to lose?

Fortunately, neither PPMV1 nor G18P has crossed over to Australia’s native columbids. We can’t say how likely this is, or how serious the consequences would be, because we have not previously observed such viral infections among our native pigeons.

If the viruses prove equally lethal to native columbids as they are to domestic pigeons, we could see catastrophic population declines across numerous columbid species in Australia over a short period of time.

Should these viruses spread (via feral domestic pigeons), the control and containment of losses among our native pigeon species would be near impossible. Such a nightmare scenario can only be avoided by predicting if and how these viruses might “spill over” into wild columbids so that we can prevent this in the first place.

Maps of Australia showing the overlapping distribution of our 22 native pigeon and dove species (left) and the distribution (in orange) and verified individual records (red dots) of introduced feral domestic pigeons (right).
Atlas of Living Australia, Birdlife International

Protecting our pigeons

Agricultural poultry is routinely screened to check their vulnerability to threats like the PPMV1 and G18P. Such screening is an appropriate response to protect our agricultural industry.

For our native pigeons and doves however, no such similar testing is planned. Based on progress in veterinary vaccine development and advancements in understanding of feral pigeon control, the knowledge and technology required to mitigate this threat should be relatively inexpensive. The threat for these species can be actively managed, now, by improving our biosecurity and vaccination programs for captive domestic pigeons, and eradicating feral domestic pigeons.

The protection of our native columbids however, ultimately relies on valuing their ecosystem functions in the first place.

Andrew Peters, Senior Lecturer in Veterinary Pathology, Charles Sturt University

This article was originally published on The Conversation. Read the original article.

USA: Alaska – Virus Infecting Wildlife

The link below is to an article reporting on growing concern over a possible virus that is spreading through wildlife off Alaska, infecting Walruses, Seals and Polar Bears.

For more, visit:
http://www.independent.co.uk/environment/nature/walruses-seals-and-polar-bears-hit-by-mystery-virus-7626990.html

Australia: Koalas Face Chlamydia Wipeout

The link below is to an article reporting on how the Koala population in Queensland is threatened by the Chlamydia virus.

For more visit:
http://www.nytimes.com/2012/02/21/science/queensland-koalas-hit-by-chlamydia-infections.html