Why COVID was first linked to bats

On the very last day of 2019, China reported an outbreak of a strange pneumonia in a cluster of people with links to the local Huanan live animal and seafood market. Two weeks later, the cause of the illness was identified as a new coronavirus, now named SARS-CoV-2, that causes the syndrome known as COVID-19. Since then, thousands of scientific papers have been published on the outbreak, including the genetic sequence of the new virus, which confirms its close relationship to coronaviruses carried by bats and therefore gives us clues of where this new coronavirus came from. Dennis Carroll heads the Global Virome Project, and explained to Chris Smith...

Dennis - The coronaviruses first and foremost are a family of viruses. We estimate there are between 4,000 - 5,000 different coronaviruses, and virtually all of the ones that we've discovered to date, about 200, we found in bats in different parts of the world; Asia, Africa, and in the Americas.

Chris - And why bats?

Dennis - We don't know why bats, except that bats are able to host viruses like coronavirus without themselves having any adverse effects, and they will periodically shed these viruses in their faeces or in their saliva. So they represent sort of an ideal host, because a virus... when it does infect another animal, the last thing it wants to do is to kill that animal off, it speaks to its own demise as well. So they've developed a very sympathetic relationship with bats over the millenia.

Chris - Are you saying that bats are the origin, and when you get coronaviruses in other species, it represents a jump from a bat into that species, at least at some point in time?

Dennis - Well first let's be very clear. We don't have a definitive answer as to how the COVID-19 virus entered the human population, but we've seen enough examples of the virus moving, either directly or indirectly, from bats, that it's the most reasonable explanation. There was some initial speculation, to be confirmed, that pangolin, another wildlife animal that is a food source in China, may have acted as a spillover agent; but more work needs to be done to really clarify exactly what the transmission route might've been.

Chris - One other avenue to pursue is: you read the genetic code of a virus, and then you go looking in the database to see what it's most closely related to, because that can sometimes point you in the right direction of where something came from. What story emerges when we do that sort of analysis?

Dennis - Many of the different coronaviruses circulating in these geographic areas do in fact have a strong genetic relatedness to the COVID-19 genetic profile. So it speaks to a pedigree, a shared pedigree.

Chris - If that's the case then, and you're making a case of the fact that these viruses are actually pretty common - you can find them across a very diverse patch of China - why would they emerge in Wuhan?

Dennis - Well the source is largely bats that are proximal to Wuhan City. And one of the things we know about bats first and foremost is that they have the ability to adapt and share a living space with human populations. What we've seen in Wuhan is an example of high interactive dynamics between bat populations; possibly, again, secondary intermediary hosts with human populations. If we don't bring a human in close proximity to these infected animals, you will not get a spillover.

Chris - So if that virus is present in Wuhan in the bat population there in the way that you're suggesting, surely the Chinese have already done sampling of the bats in Wuhan to try to find out if that's the case. If so, where is it then?

Dennis - Well let's first off acknowledge: going out and collecting bats, identifying viruses, is a very complicated exercise. So right now there isn't direct capture of a COVID-19 virus from a bat. But at some point it's inevitable that we will find it.