Friday, 7 October 2016

The Mystery "Mystery Virus" is Still a Mystery

Last week, Bellingen put on a show. The Bellingen Turtle Festival was a symbol for a community concerned about its turtle and a community ready to do something about it. But where are we at since the outbreak of a mystery disease in February 2015. The community shared their theories at the festival, and they were diverse - from meth lab chemicals - to impacts of various agricultural practices - to road construction processes. 

Speculation can thrive because it was an August 31st, 2015, press release from the member for Oxley, Melinda Pavey, that reported a mystery disease wiped out the Bellinger River Snapping Turtle. 14 months on, nothing else about this 'Mystery Virus' has been released or subject to scientific peer review, thus we still do not know what caused the die off 18 months ago. 

Going forward, a plan on whether the species can recover with or without human intervention will be developed (in my next blog, I will discuss some options). This will be part of a recovery plan when/if it gets listed as critically endangered by the federal government. So for recovery planning by government agencies and researchers, you would think details of the virus would be important to know. But is it?

In this blog (and my next one on a recovery plan), I suggest that the virus is one of many catastrophic events that could have affected the turtle and in planning for the recovery of the species, we need to treat it that way- just one of many factors that could affect the turtle population.

From a logistics perspective (ie. quarantine procedures etc), the virus is important, but from a conservation planning perspective, the virus is likely to be the spectacular culmination of a series of ecological or biological perturbations that affected turtles well before the outbreak. 

Going forward, we need to address issues 'further up the chain', before investing too much into a 'Mystery Virus'. We have all heard the expression "prevention is better than a cure"- We don't need a cure- there are currently no sick turtles alive- so understanding the processes that let a 'Mystery Virus' proliferate is of far greater relevance and importance for planning the recovery of a species that is on the brink of extinction.

(Photo credit: Ricky Spencer)

So what do we know. It is worth a recap.
1. Over a three week period from mid February 2015, around 500 turtles were recovered dead or displaying external symptoms of a disease and were subsequently euthanased (Spencer 2015). Many more decomposing dead turtles were collected and rapidly disposed without counting. 

2. The disease presented symptoms of lesions throughout the body, but particularly around the eyes, making the turtle blind (Britton 2015).

3. 17 turtles were retrieved from the upper reaches of the River as a captive insurance population before the disease had reached these upper catchment populations (ABC News 2015).

4. The disease appeared to be travelling at ~2km per day from downstream to upstream populations (Moloney 2015).

5. A press release suggested the disease was a 'Mystery Virus' in August/September 2015. It was announced by the member for Oxley, Melinda Pavey (Pavey Vimeo 2015), who said that scientists from NSW Department of Primary Industries (DPI) Elizabeth MacArthur Agricultural Institute had recently made a significant breakthrough and detected a new virus, the cause of a mystery illness that killed the turtles.

6. In October 2015, NSW Department of Primary Industries (DPI) Elizabeth MacArthur Agricultural Institute released a report (hosted on the Bellingen Council Website) that described the epidemiology of the disease, but did not name the virus (Moloney 2015). No other public statements, reports or scientific publications have been released since that time.

7. 20 juveniles were collected in limited surveys of the River in November 2015 (Bellingen Courier 2015)

8. A much larger survey in March 2016 confirmed that the remaining turtles in the River are predominantly juveniles (Bellingen Courier 2016). Only two adult female turtles were found in the wild during these surveys and the health of one of these animals was questionable (ARWH Annual Report)

What does it mean?
Basically, a 'Mystery Virus' appears associated with the die off of the adult population, leaving juveniles almost unaffected in the River and no other species has been obviously affected. More than 12 months have passed since the announcement of a 'Mystery Virus', but the identity of the virus has not been released to the public or been subject to scientific peer review. 

The recovery of a species will rely primarily on a handful of adult females rescued before they became victims of the disease and a population of juveniles. It is equivalent to leaving the planet to a small number of young kids to eventually repopulate the planet. The likelihood of extinction is very high without intervention; the path to recovering the species is complex and has little room for error, but this will be discussed in a separate blog.

The 'Mystery Virus'
Can a disease be that virulent and target-specific to travel upstream at ~2km per day and affect only a portion of the population of single species?  If the carrier was traversing upstream and were consumed by primarily adult Snapping Turtles, then possibly. 

Intraspecific differences in diet are generally related to size with juveniles consuming very little plant material, ephemeropteran larvae and odonate lymphs compared to adult Bellinger River Snapping Turtles (Allanson and Georges 1998). Items like fish, a prime candidate for this type of transmission, are not common food items because short-necked turtles are unable to catch them (Spencer et al. 1998) and probably consume them as carrion. 

All turtle species and all size-classes in the River consume fish as carrion. No dead fish were observed during the February/March 2015 emergency surveys. Ephemeropteran or odonate nymphs are also unlikely to be a source for a disease spread through consumption. The closely related species, Emydura macquarii, is a generalist and would have also been consuming similar foods (Spencer et al. 2014).

A suggested hypothesis for the spread of the disease is associated with faster moving eels, as the spread rate during the event occurred upstream at a rate faster than turtles are able to move and eels are one of the few species in that waterway that would routinely move upstream (Moloney et al. 2015). Eels could have spread the disease, but you would still expect turtles other than adult turtles from a single species to be affected. Juveniles are found in the same waterholes as adults, eels, catfish, other species of turtle. The big question is why were primarily adults from a single species affected if many other organisms had been exposed to the virus, including juveniles of the same species?

The Epidemiological Triad
Identifying the cause of wildlife diseases is difficult because rarely can a single factor be identified as responsible, a concept commonly termed the ‘epidemiological triad’. In addition to immune suppression related to exceeded stress responses and pollutant exposure, environmental change can impinge directly on wildlife health and survival and, consequently, affect the viability of their populations in various intricate ways. For example, climate-related shifts in pathogen and host ranges and pathogen spillover from humans and domestic animals can both increase exposure to new diseases (reviewed in Smith et al. 2009). 

Similarly, changes in habitat size or quality might lead to a reduction in prey population sizes and increased competition for resources (Ryall & Fahrig 2006), which in turn might augment starvation and lead to disease and/or death. Effects will be further complicated if the genetic makeup of the affected populations has been compromised owing to reduced gene flow or inbreeding, as low levels of genetic diversity tend to be correlated with reduced fitness and lowered evolutionary potential (Spielman et al. 2004).

All three aspects of the triad apply here to varying degrees. Given that the epidemiological triad relies on external factors such as environmental parameters, changes in habitat quality and the genetic makeup of the populations, the disease itself becomes irrelevant (to a significant extent). It is relatively unusual for infectious diseases to be the sole cause of endangerment for a species (Smith et al. 2006). Disease can wipe out an entire species. Rats native to Australia's Christmas Island fell prey to "hyperdisease conditions" caused by a pathogen that led to the rodents' extinction. This was classic exposure of a species to a novel pathogen. Ship-jumping black rats carried a protozoan known as Trypanosoma lewisi (ABC News 2008). On this Island population, it appears that the population was driven low enough to become prone to extinction.

"Not every rat would have to be infected. If you push a population down to an unsustainable number then it will collapse. In addition, if a substantial number of reproducing individuals became infected and ill, even if they survived the infection, their reproduction rate may be lowered and lead to a population crash."

The case of the Bellinger River Snapping Turtle is likely to be very different in that the disease has not driven a healthy stable population to the brink of extinction, the turtle population was possibly already in decline and the 'Mystery Virus' proliferated through an immune challenged population. If a virus proliferated through a healthy population, then you would expect the population to be decimated, but the virus would not selectively target any cohort or sex, even if the genetic makeup of the population exhibited low levels of genetic diversity. 

However, if we look at the population structure between 2007 and the dead turtles collected in 2015, it is clear that the juvenile population escaped the effects of the disease. At first, small turtles may have simply been missed in the collection of sick or dead animals in 2015, but the November 2015 and March 2016 surveys clear demonstrate that turtles less than 100mm plastron length (probably aged 3-5yo) survived the outbreak and those older than that did not (Bellingen Courier 2016). What this means is that <10% of the population remains.

Fig. 1. Population changes in body size. Histograms (percentage of animals) of turtles captured in 2007 (light grey) and 2015 during the disease outbreak (dark grey). Not all turtles were measured during the die-off because of biosecurity and health concerns ie. those that were decomposing were disposed of immediately (Maher pers. com.), however the recent surveys indicate that juveniles are still present, with only two adult female turtles found in the wild during March 2016 surveys and the health of one of these animals was questionable (ARWH Annual Report) .

The novel virus hypothesis/low genetic diversity argument is important and may help explain the difference in mortality between the Snapping turtles and the introduced Emydura macquarii, but it does not explain the difference in mortality between adults and juveniles, if anything, juveniles from the same cohort are likely to have lower genetic diversity than the adult population, because the juveniles are likely to have come from a limited number of nests. Remember, these turtles can produce more than 20 eggs per nest (Cann 1998) and if a nest survives, it is a good chance that most of the hatchlings from the same nest would emerge. Similarly, the 2-5yo turtles are coming from mothers and fathers that did not survive the pathogen.

Stop Worrying- Nothing to See Here?

The 'Mystery Virus' is likely to be a spectacular end of a chain that has many broken links and I argue, we need to focus on where the links are broken, rather than concentrate on a 'Mystery Virus', particularly if we want to prevent a die-off of this magnitude occurring in other catchments and to eventually repopulate the River with Bellinger River Snapping Turtles. 

The 'Mystery Virus' press coverage in August 2015 came over as a great breakthrough, but there was no detail provided. Community communication and consultation is important, but this press release did not relieve community concerns about the state of the River, going by the Bellingen community Facebook site, attending community group meetings, and having well respected members of the community expressing cynicism at the announcement. 

It failed in the scientific community too. There has been no data presented to the scientific community about the virus or to recovery teams involved in the conservation and management of this species or the captive breeding population. 

A respected colleague who has a long history working on impacts of mining practices on river biota wrote after the press announcement

"I'd like to see the isolated viral RNA/DNA in a peer-reviewed paper before accepting this.  As written, it reads very much as a "we can't find anything else, so it must be a virus" by process of elimination, especially since it says "no confirmed diagnosis".

"The ecotoxicological logic presented here is also extremely flawed.  Water samples alone are insufficient to demonstrate the absence of contaminants- they could be taken up into the biota and simply not be present at high concentrations in water and/or microbiota.  I'm not saying there are contaminants in the Bellinger, just that water sampling alone isn't sufficient to make the claim that there aren't."

The initial announcement from local member of the NSW legislative council, Melinda Pavey.

"It does not mean that there is something wrong with our beautiful River"-  (Pavey Vimeo). 

I truly believe that the local member was sincere in this statement because the information in the press release was structured to sound like the cause of death was discovered and that sampling for a contaminant turned up negative results (Bellingen Shire Council). 

All this may be true, but none of this data is available. Yes turtles may have died, possibly from a virus; yes limited tests for contamination may have come back negative- None of this data has been made available or subject to peer review. But from my perspective, we cannot accept that there is nothing wrong with a River based on these two pieces of information, with no data presented. We need to delve a little more forensically into things. 

"It does not mean that there is something wrong with our beautiful River".
Does the discovery of a virus mean that there is nothing wrong with the river? and what does "wrong" actually mean?

Discovery of a novel virus killing turtles does not mean that there is nothing "wrong" with the River. Just go to any country where you cannot drink the tap water to realise that. Surface waters and tap water qualities of both developed and developing countries have continued to deteriorate. Enterovirus bearers are in sewage, sewage sediments, rivers receiving sewage , as well as treated sewage. The sources of enteroviruses may be groundwaters, coastal river waters, coastal marine waters, aerosols emitted from sewage treatment plants and from solid waste landfills, soils and insufficiently treated drinking water (see Kocwa-Haluch 2001). 

So the discovery of a disease killing turtles should not stop us continuing to question whether there is something "wrong" with the River. If anything, it should make us question it a little more- question why a novel "Mystery Virus" could become so pathogenic so quickly.

"Wrong" is largely defined by what we classify as water quality. For the general public, to which Melinda Pavey was addressing, a turtle virus probably means that there has been no large isolated toxic chemical spill. We could deduce that without looking for a virus or even doing a one off test for standard toxins- no other organism seemed affected. But as the Epidemiological Triad suggests above, "In addition to immune suppression related to exceeded stress responses and pollutant exposure, environmental change can impinge directly on wildlife health and survival and, consequently, affect the viability of their populations in various intricate ways." So perhaps we need to broaden the definition of "wrong" to evaluate environmental factors (abiotic and biotic) that may have led to immune suppression in the particular cohorts of turtles affected.

There is strong evidence that the turtles were underweight at the time of the disease breakout. Turtles were described as "emaciated" (Moloney et al. 2015). Hence it is worth investigating environmental parameters from that area since that time.

It's a Dry Heat
I am now going to get into the data on long and short-term water and temperature data, because "The Epidemiological Triad" suggests that climate-related shifts in pathogen and host ranges can increase exposure to new diseases (reviewed in Smith et al. 2009), as well as, increase stress levels of the host. 

Average water course levels at Thora were well below average for the last three years (Fig. 2), with water levels almost 30% below average in 2014. Deaths were recorded less than a week after a minor-moderate flood in February 2015 (Fig. 3). Over the 32 year period, average water course height at Thora was ~2m, however from Spring 2011-April 2015, water course levels average ~1.5m (Fig. 3). During this period, only one moderate-major flood occurred in the River until the flood surrounding the disease outbreak in February 2015. It is likely that low River levels negated two minor flood levels in 2013/2014 (Fig. 3).
Fig. 2. Annual changes from the mean in water course levels from 1983 to 2014 in the Bellinger River at Thora

Fig. 3.Monthly averages of water course levels at Thora from 1982-2015. Solid black line is average levels over the same time period. Dotted lines represent minor (3m), moderate (4.5m) and major (5.8m) flood levels in the River. Deaths we first observed just after a minor-moderate flood in February 2015.

Significant warming has occurred in the region since 1965. Cumulative differences from mean daily maximum temperatures were calculated for each decade and the degree of warming in the region has been 8-9 times greater in the last decade compared to 1965-1974 (Fig. 4a). Mean daily minimum temperatures demonstrated similar trends, with warming occurring even earlier. Looking specifically at the last five years, the degree of heating in the region in 2014 was almost twice as large as compared to 2010.

Fig. 4. Cumulative differences from mean daily maximum temperatures over the last five decades- South West Rocks  BOM Site number: 059030 (~60km from Thora).

So What Does It Mean?
Bottom-line. There has been a significant warming event occurring for several decades and this was magnified over the two years prior to the disease outbreak. The water levels in the River have not fully reflected rainfall trends and have been declining since 2012. There was the long period without a flood event in the River. The outbreak of the "Mystery Virus" coincided with significant rain and a minor flood over a three week period. Prior to February 2015, there had not been a flood in the River since 2011/2012, which is a significant period without a flood for the River (Fig. 3).

The region's temperatures are changing and combined with the River's abnormal flow patterns over the last few years- it is a classic pattern of broad-scale environmental patterns interacting (directly or indirectly) with local patterns to create extreme conditions- ie. Climate Change. 

This blog is not a debate of the validity of human induced climate change, but it does help put data to what people have been saying about the River over the last decade. The Banana farmers in the region will testify to this too. They can no longer compete with NQ growers because of the hotter drier climate experienced in NE NSW and SEQ (Banana Growers Report). Blueberry crops are rapidly taking over the region.

But back to the turtles and the River. There are two possible effects of these sort of climatic changes on the River. Firstly, reduced flow and heating could dramatically change the habitat of the River, a well as it's ecosystem. Flowing parts of the River could become stagnant, further magnifying the heating event- increasing algal growth, reducing clarity and reducing oxygen levels. The Bellinger River Snapping Turtle is a bum breathing clear water specialist- cool, clear and well oxygenated water is very important for it. Heating and drying could also directly impact the timing of breeding for fish and insects, as well as plant growth- common food sources for these turtles.

These are the links in the chain that I am talking about. All are connected and can be broken at any part. At the end of the chain was the spectacular conclusion- the disease outbreak.

Changing climatic conditions can influence the spread of novel viruses and perhaps the chain may have repaired itself if a new pathogen did not proliferate through the population, however, the key to population recovery lies central to understanding the broken parts of the chain and whether turtles can display future resilience. That will rely on understanding ontogenetic changes in their ecology and identifying threats to their survival 

Clearly our climate is changing, but the last 3-4 years in the Bellinger River may have been the tipping point for the turtles. Any cause (or combination of causes) is likely to have been chronic rather than acute. These turtles have survived the last mass extinction, so they are adaptable, but we are driving species like this to the 6th mass extinction?

Next I will explore how we can recover the species. Turtles are survivors, so it is not all doom and gloom.

Published reports for further reading

Data here were presented at the World Congress of Herpetology in Hangzhou, China in August 2016, but they have not been subject to peer review and thus should not be used until published in a scientific journal.

R-J Spencer. 2016. Profiling a disease that may have driven a species of turtle from Australia to extinction over a three week period. WCH8. Symposium talk. Hangzhou August 2016.


  1. A point on the impacts of warming if I may. The family chelidae are a group of turtles that evolved and entered Australia from Antarctica. Antarctica at the time it supported reptilian fauna was significantly warmer than it is now, but was still a relatively cool place. In general chelids have a high tolerance for cold, as compared to many other turtle groups. Even tropical species can tolerate cold spells for short periods. Myuchelys is an extremely ancient linneage and for the most part are only found in southern Australia, the only exception being Myuchelys latisternum, even among fossils. As such the genus is well adapted to cooler climates. Increasing the climate that species adapted this way are exposed to creates stress. This can be seen across a range of animals not just turtles. Environmental stresses such as increasing climate has an immunological effect on cold climate specialists, increasing susceptibility to disease. Coupled with this is the effect that warmer climates permit previously unknown in the locality diseases, particularly viruses to become established. We have seen in recent years the latitudinal expansion of some tropical human viruses. So an overall increase in the local climate in the Bellingen could have had the dual effect of range expansion of viruses, and a reduction in the immune system health of the turtles.

    1. Excellent point. Puts a historical context to what we are seeing with the ecology of this species.

      Cool, clear water with lots of dissolved oxygen is preferred.