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Please do not take it out on the snakes. Photo: Getty
Please do not take it out on the snakes. Photo: Getty

ScienceJanuary 24, 2020

Is this… snake flu?! What we know about the source of the Wuhan coronavirus

Please do not take it out on the snakes. Photo: Getty
Please do not take it out on the snakes. Photo: Getty

The world is on edge over a coronavirus outbreak that started in early December in Wuhan City, China. The virus is thought to have first infected people working at a seafood and live animal market. So what could the original source have been? Siouxsie Wiles explains.


Update, January 27: Soon after the “snakeflu” paper was released, scientists took to social media expressing doubts, raising the fact that it’s pretty rare for the codon usage of a virus to closely match its reservoir host. Others criticised the way the authors prepared their codon usage tables.


There’s no official word yet, but that’s not surprising. Sources like this can be incredibly difficult to track down. Especially in a market selling so many different kinds of animals. I can’t even begin to imagine how many samples scientists would have to test.

The coronaviruses that cause SARS and MERS are thought to have originated in bats and crossed to humans via civet cats (SARS) and camels (MERS). Now researchers in China have published a study suggesting that this new virus also originated in bats and that it could have crossed to humans from infected snakes.

Snakeflu?!

Thanks to the Chinese quickly putting the full genetic sequence of the new virus online, Wei Ji and colleagues were able to compare it to 271 other coronavirus sequences. They’ve just published their results in the Journal of Medical Virology.* They started by using the sequences to make a family tree and the new virus came out as most closely related to the viruses isolated from bats in the city of Nanjing, China between 2015 and 2017.

Next, they studied the new virus’s genetic code to see which nucleotides it uses to make its proteins. Proteins are strings of amino acids, and each amino acid is encoded by three nucleotides, called a codon. All the proteins in the world are made from a pool of 20 amino acids. But there are 61 codons, so most amino acids are coded for by more than one codon. Take the amino acid valine. It can be made from the codons GUU, GUC, GUA, or GUG.

Most creatures have a bias for which codons they prefer to use to encode their amino acids. So the researchers compared which codons the new coronavirus uses with the ones preferred by humans and a bunch of other animals: marmots, hedgehogs, the Sunda pangolin, the Chinese rufous horseshoe bat, the Red junglefowl – and two species of snake, the many-banded krait (Bungarus multicinctus) and the Chinese cobra (Naja atra).

The closest match was with a bat coronavirus, but next best match was to the krait and cobra. From that, they’ve concluded that the “snake is the most probable wildlife animal reservoir responsible for the current outbreak”.

This isn’t the strongest of evidence so please don’t start killing any snakes. The source could just have easily been bats. Don’t kill them, either. Please.

Numbers of cases and deaths continue to rise

As for the outbreak itself, it’s clear person-to-person transmission is happening, though it’s still not clear how infectious the virus is or when people are likely to be infectious. As of Thursday, there are reports of well over 500 confirmed cases in the current outbreak and 17 deaths. There have also now been confirmed cases in Hong Kong, Japan, Macau, South Korea, Taiwan, Thailand, and the US.

The person in Brisbane suspected to have the virus has now been cleared. Given its winter in the northern hemisphere and the symptoms of this infection are very similar to other respiratory infections, there are likely to be plenty of false alarms.


* The article is behind a paywall that is asking me to pay $18 just to read it. Luckily my university has a subscription, so I was able to access it, but if there was ever a time for scientific knowledge to NOT BE HIDDEN BEHIND A FUCKING PAYWALL it is during an outbreak of a new potentially deadly virus. If you agree and you live in or are from the USA, please consider signing this letter saying you endorse a national policy that would ensure that Americans are no longer denied access to the results of research their tax dollars paid for.

Keep going!
A helicopter drops fire retardant to protect a property in New South Wales. (Photo by PETER PARKS/AFP via Getty Images)
A helicopter drops fire retardant to protect a property in New South Wales. (Photo by PETER PARKS/AFP via Getty Images)

ScienceJanuary 22, 2020

Scientists hate to say, ‘I told you so.’ But Australia, we warned you

A helicopter drops fire retardant to protect a property in New South Wales. (Photo by PETER PARKS/AFP via Getty Images)
A helicopter drops fire retardant to protect a property in New South Wales. (Photo by PETER PARKS/AFP via Getty Images)

Bushfire conditions will become more severe. We call on Australians, particularly our leaders, to heed the science, writes Will Steffen of the Australian National University

Those who say “I told you so” are rarely welcomed, yet I am going to say it here. Australian scientists warned the country could face a climate change-driven bushfire crisis by 2020. It arrived on schedule.

For several decades, the world’s scientific community has periodically assessed climate science, including the risks of a rapidly changing climate. Australian scientists have made, and continue to make, significant contributions to this global effort.

I am an Earth System scientist, and for 30 years have studied how humans are changing the way our planet functions.

Scientists have, clearly and respectfully, warned about the risks to Australia of a rapidly heating climate – more extreme heat, changes to rainfall patterns, rising seas, increased coastal flooding and more dangerous bushfire conditions. We have also warned about the consequences of these changes for our health and well-being, our society and economy, our natural ecosystems and our unique wildlife.

Today, I will join Dr Tom Beer and Professor David Bowman to warn that Australia’s bushfire conditions will become more severe. We call on Australians, particularly our leaders, to heed the science.

The more we learn, the worse it gets

Many of our scientific warnings over the decades have, regrettably, become reality. About half of the corals on the Great Barrier Reef have been killed by underwater heatwaves. Townsville was last year decimated by massive floods. The southeast agricultural zone has been crippled by intense drought. The residents of western Sydney have sweltered through record-breaking heat. The list could go on.

All these impacts have occurred under a rise of about 1℃ in global average temperature. Yet the world is on a pathway towards 3℃ of heating, bringing a future that is almost unimaginable.

How serious might future risks actually be? Two critical developments are emerging from the most recent science.

First, we have previously underestimated the immediacy and seriousness of many risks. The most recent assessments of the Intergovernmental Panel on Climate Change show that as science progresses, more damaging impacts are projected to occur at lower increases in temperature. That is, the more we learn about climate change, the riskier it looks.

For Australia, a 3℃ world would likely lead to much harsher fire weather than today, more severe droughts and more intense rainfall events, more prolonged and intense heatwaves, accelerating sea-level rise and coastal flooding, the destruction of the Great Barrier Reef and a large increase in species extinctions and ecosystem degradation. This would be a tough continent to survive on, let alone thrive on.

The city I live in, Canberra, experienced an average seven days per year over 35℃ through the 1981-2010 period. Climate models projected that this extreme heat would more than double to 15 days per year by 2030. Yet in 2019 Canberra experienced 33 days of temperatures over 35℃.

Second, we are learning more about ‘tipping points’, features of the climate system that appear stable but could fundamentally change, often irreversibly, with just a little further human pressure. Think of a kayak: tip it a little bit and it is still stable and remains upright. But tip it just a little more, past a threshold, and you end up underwater.

Features of the climate system likely to have tipping points include Arctic sea ice, the Greenland ice sheet, coral reefs, the Amazon rainforest, Siberian permafrost and Atlantic Ocean circulation.

Heading towards ‘Hothouse Earth’?

These tipping points do not act independently of one another. Like a row of dominoes, tipping one could help trigger another, and so on to form a tipping cascade. The ultimate risk is that such a cascade could take the climate system out of human control. The system could move to a “Hothouse Earth” state, irrespective of human actions to stop it.

Hothouse Earth temperatures would be much higher than in the pre-industrial era – perhaps 5–6℃ higher. A Hothouse Earth climate is likely to be uncontrollable and very dangerous, posing severe risks to human health, economies and political stability, especially for the most vulnerable countries. Indeed, Hothouse Earth could threaten the habitability of much of the planet for humans.

Tipping cascades have happened in Earth’s history. And the risk that we could trigger a new cascade is increasing: a recent assessment showed many tipping elements, including the ones listed above, are now moving towards their thresholds.

Time to listen

Now is the perfect time to reflect on what science-based risk assessments and warnings such as these really mean.

Two or three decades ago, the spectre of massive, violent bushfires burning uncontrollably along thousands of kilometres of eastern Australia seemed like the stuff of science fiction.

Now we are faced with more than 10 million hectares of bush burnt (and still burning), 29 people killed, more than 2,000 properties and several villages destroyed, and more than one billion animals sent to a screaming, painful death.

Scientists are warning that the world could face far worse conditions in the coming decades and beyond, if greenhouse gas emissions don’t start a sharp downward trend now.

Perhaps, Australia, it’s time to listen.The Conversation

Will Steffen is emeritus Professor at the Australian National University

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