What animal did the coronavirus come from?

When the coronavirus was first identified at the end of 2019 as something new and dangerous, there were a lot of questions. What actually is this disease? And where did it come from? These are especially difficult when you know almost nothing and your target is essentially invisible. Arinjay Banerjee at McMaster University in Canada has been researching coronavirses in bats for six years before this new one came along and his skills became extremely relevant. I asked him how he and other scientists have been answering these questions…

Arinjay - When Covid-19 cases showed up in Canada one of the first cases in the province of Ontario showed up at Sunnybrook hospital. I instantly offered my skillset and I think I knew I could contribute in understanding this new outbreak. One of the priorities was to get the virus out of these patients so we can use it to develop vaccines, drugs. So I acquired swabs from the patient's nose and I put them on cells in a high containment lab and we were able to get lots of virus onto these cells.

Phil - Like a lot of people I would expect that if the virus exists in your country or in this person across the room from you, it's not actually that hard to get it, but it sounds like it's actually a whole process.

Arinjay - Yes. If you think about it, humans have lots of different viruses. We have the common cold. You may have the flu and there are other viruses that you may not develop symptoms for. The trick is to separate out the one virus that you're interested in, which for us was the new coronavirus and we used a treatment that enhances coronavirus infection in the cells.

Phil - How do you keep yourself safe and stop yourself getting infected?

Arinjay - So these are not regular labs. These are some of the best high containment labs that exist on the planet. A containment level three lab is, it's essentially you're working inside of a cabinet that's negatively pressurised. So all the air comes into the lab and gets sucked out and that's just the facility. We also have PPE, very expensive, very fancy PPE that we wear working with the virus.

Phil - Okay, so you have your special equipment to keep you safe. You have your special treatment to take out only the coronavirus. Did it work first time?

Arinjay - Yes and no. We started with three samples and it worked for two samples and it didn't work for the one sample. Now we don't know if the sample that didn't work had very low amounts of virus in it and the samples that did work may have had lots of virus in it. We really did get lucky.

Phil - For the two that it did work, you've now got the virus’ total genetic code?

Arinjay - Yes.

Phil - Now we've seen a lot of stuff in the news that's trying to explain what animal the virus originally came from. Can you tell that from the genetics?

Arinjay - Yes and no. So for you to be able to find a good match with an animal source, somebody would have had to sample that animal sequence, the virus and that animal and submit it that sequence in the database. Now for bats - bats have been looked into extensively since SARS-1, and the closest match to the SARS-2 coronavirus with the 96% identity is a bat coronavirus. But are bats responsible for direct transmission to humans? We don't know. I think that data is very anecdotal on this. We're not sure if the virus went bats to humans or somewhere mixed up with the pangolin coronavirus.

Phil - Why pangolin? Where's this bat versus pangolin confusion?

Arinjay - If you look at the virus, there's a protein that's critical for infection - it's called the spike protein. Now that sits on top of the virus, it interacts with cells in the human body and infects human cells. Now within the spike protein, there's a small portion that's called receptor binding domain, but this small portion is critical for that entry into human cells. Now the small portion within the spike protein is almost a hundred percent identical with a pangolin coronavirus. The rest of the virus is not, but this tiny little small fragment is almost a hundred percent identical. So all of these questions and observations raise a bunch of questions like, where did the virus come from? Was it bats? Was it pangolins? Or is there a third species of animal missing?

Phil - So if the way that people even figure this out is just by matching the genetics to see what looks most similar, how close are we? Is it like putting the two of diamonds against the three of diamonds or is it like putting the two against the King and going, well, I dunno, they both have a diamond on them?

Arinjay - I think at this point in time we are really trying to find the third piece of diamond. You know, it's a great question and you can only answer this question if we could have extensively sampled all the animals that existed in the seafood market. Now this is assuming that the outbreak started from an animal in the seafood market. It's possible that an infected individual walked into that market and spread it to other individuals. I think we can say with some certainty that the virus did evolve in bat. What we cannot say with any amount certainty is that the virus jumped into humans directly from bats. How did pangolins get involved? What we don't understand is like the logical interactions that really went on.

Phil - So ultimately it's probably from bats, but a bat could have weed on something and then that animal went to something else and then it could have been this whole huge wacky chain of animals that we don't know about?

Arinjay - Yes, it is possible that we might never know which animal directly transmitted this virus to humans.