Despite the conspiracy theories you're hearing, or the misinformation that's spreading on social media, it's clear that this coronavirus came from wildlife.

By looking at the genome of SARS-CoV-2 — the virus that causes COVID-19 — it is clear it has signatures that are closely related to other viruses that are present in wildlife, said evolutionary biologist Jemma Geoghegan of the University of Otago.

"There is a virus in bats, as well as a virus in pangolins, that shares similarities with the new virus that has appeared in humans," said Dr Geoghegan, who studies the emergence and evolution of viruses.

We don't need to manufacture this virus, it exists in nature as it is, said veterinarian and environmental scientist Hume Field from the EcoHealth Alliance, who was also part of the original team that determined the SARS-CoV-1 virus, which caused the SARS outbreak in China in 2003, originated in bats.

"From a scientific point of view, that argument that it's a manufactured virus has been totally discredited," Dr Field said.

But when it comes to how exactly this new coronavirus jumped the species barrier to us, and from which animal, that's a lot less clear.

So let's take a look at what scientists do and do not know about the origins of this coronavirus.

What happened at Wuhan's live animal market?

We know that a lot of the early cases of COVID-19 were connected to a live animal market, or wet market, in the Chinese city of Wuhan.

However, we don't know this market was the actual source of the virus or the place where it jumped the species barrier from another animal to humans.

"To be honest, I'm not sure if we'll ever know that because the wet market has now been cleared and been decontaminated," Dr Geoghegan said.

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Scientists never had the opportunity to sample the animals to see whether there were viruses in the live animals being sold at the market.

Having these samples would have helped to better understand SARS-CoV-2, Dr Geoghegan said.

"Obviously if it was from a live animal market, then we can use this as an argument to prevent this from happening by having fewer of these live animal markets around."

Bats have 'an impressive array of' coronaviruses

Bats are likely a reservoir host for many coronaviruses. ( Getty Images: Elena Bolshakova / EyeEm )

Research over recent years has revealed bats are hosts to quite "an impressive array of" coronaviruses.

Part of this is because there are so many bat species, they make up about a fifth of the world's mammalian species.

"[Due to] the sheer diversity of bats around the world," said infectious disease ecologist David Hayman from Massey University, "they have a diverse range of viruses."

But it's also about the way bats live.

"They're really like humans in cities," Professor Hayman said.

"They form very dense colonies with thousands in a small space. So that's ideal for infections to be able to transmit from one individual to another."

Social distancing is not a behaviour seen in bat colonies.

This also suggests bats are most likely a reservoir host for many coronaviruses, meaning the viruses are living and reproducing in the bats, but not necessarily causing any disease in the animals.

SARS-CoV-2 is 96 per cent similar genetically to a bat coronavirus.

And both SARS-CoV-1, the virus which caused the SARS outbreak in 2003, and MERS‐CoV, the virus that causes MERS, are found in bats.

Both these viruses jumped to humans via an intermediate, in the case of SARS via civet cats, and with MERS a couple of times via camels.

"It's likely that this new SARS virus has a similar route," Dr Geoghegan said.

How did coronavirus make its way from bats to humans?

"Human interactions with live animals make a host jump more likely to occur," Dr Geoghegan said, and live animal markets are a massive source of these interactions.

"These locations can act as mixing pots, and you can have animals defecating, urinating, they're stressed maybe, you're bringing together the different species that may not be together," Professor Hayman said.

"And if hand hygiene and stuff like that isn't optimal, then this is where you have the opportunity for an infection to go from one species to another, and that includes humans."

Dr Field said live animal markets are an absolute recipe for that kind of thing to happen.

"You've got this mixing of species and this potential mixing of viruses in these animals that are under stress, sick and dying as they've gone from their wild environment to the market."



"We don't know pangolins are the intermediate [between bats and humans], but it's clear they obviously have a similar virus," Dr Geoghegan said.

And this coronavirus going from bats to humans via an intermediate could provide a more direct route than going directly from bats to humans.

Let Dr Geoghegan explain:

"For the reservoir host, say it's bats, the virus is happily circulating among bats, so in the virus sense it's extremely fit," she said.

"There's no actual pressure for the virus to change because it's already happily circulating in bats."

To get to humans it would have to cross a metaphorical valley, to genetically adapt to be transmissible between humans.

"But when it's in the middle of this valley, it's kind of not suited for either host," Dr Geoghegan said.

It's not great for bats because it's changed from its optimal genetic structure, and it hasn't got to wherever it needs to get to, to be good for human transmission.

Going via an intermediate host, particularly one that is more closely related to us, is an easier way of getting across that valley.

Where did bats get the virus from?

Viruses found in fish could be the ancestors of viruses that infect us. ( Unsplash CC: Francesco Ungaro )

If bats are the reservoir hosts of this coronavirus, it probably co-evolved with them over millions of years of their evolutionary history, Dr Geoghegan said.

Dr Field said recent research has found that coronaviruses and bats had been coexisting for at least 10,000 years, probably for hundreds of thousands of years, and possibly millions of years.

"These are very robust and sort of long-term evolutionary relationships of these viruses with these bats," he said.

Dr Geoghegan is now doing a lot of work looking at fish viruses.

"Fish are at the sort of base of the vertebrate evolutionary tree, they evolved about 500 million years ago and all vertebrates have come from that lineage," she said.

"So fish viruses tend to be the ancestors of viruses that today infect all the rest of the vertebrates, like birds, and mammals and reptiles."

So far, Dr Geoghegan and her colleagues haven't found any coronaviruses in fish, but they are finding the deep ancestors of many other virus families.

"For example, Ebola virus which we thought only infected sort of bats and primates and humans, we found Ebola virus genetic relatives in fish."

Where to from here?

To better understand how SARS-CoV-2 is spreading in human populations and how it's evolving, scientists around the world are doing whole genome sequences of the virus.

These are being shared in a global repository of over 2,800 genomes, showing both the evolutionary tree of the virus and a map of where all these genomes are coming from.

"That can tell us a lot about how the virus spreads and evolves through time and space," Dr Geoghegan said.

"And the importance of using genomic information to be able to inform the effect of things like lockdowns, and how that affects the spread of the virus."