COVID-19 and the Snake, Pangolin and Bat: Who Did it?

The snake, the pangolin and more recently, the bat, have all been considered as the animal source of the new Coronavirus outbreak in humans, dubbed COVID-19. The theory at the moment is that the ongoing COVID-19 pandemic had to have had a zoonotic origin which, in layman’s terms, means it had to have started in animals. Which animals more exactly? Given the geographical origin of the outbreak, exact location nonetheless, the Huanan Seafood Wholesale market in the city of Wuhan, Hubei province in China, most likely animal sources that could have potentially started the spread of the novel Coronavirus were identified as the snake, the pangolin and the bat. But why these three in particular? And the biggest question on everyone’s minds: who did it?

  • Quick recap

In late 2019, presumably November or December, one of the very first cases of a novel respiratory infection were detected. In early 2020, more cases started to emerge and the situation was brought to the attention of the international community by media coverage in what would become the current COVID-19 pandemic. COVID-19 is also known as the 2019-2020 human Coronavirus infection, or Coronavirus 2 or SARS-CoV-2, given its semblance to the 2002-2003 SARS outbreak caused by a similar virus identified as Coronavirus strain SARS-CoV or SARS-CoV-1. COVID-19 causes a mild to severe, occasionally asymptomatic respiratory infection that has produced over 2,100,000 million cases as of April 16, 2020 and over 140,370 deaths. The infection is highly contagious and can evolve to severe outcomes in risk categories. Risk categories include the elderly (due to a naturally weakened immune system after the age of 60-65), anyone with chronic conditions (e.g. high blood pressure, various forms of heart disease, diabetes types 1 and 2, obesity, cancer), immuno-deficiencies (caused by  HIV, AIDS, cancer treatments, immune system suppression treatments in cases of autoimmune conditions) etc.

Coronavirus COVID-19 origin animal

  • Did the COVID-19 Coronavirus come from snakes?

When the novel COVID-19 outbreak first started, at the tipping point of the spread of the infection, serious efforts to identify the causative agent were made. A first theory proposed around January 2020 suggested that snakes might have caused the novel Coronavirus infection (see research). But Coronaviruses are specific to birds and mammals, not reptiles like snakes. In 2005, following the SARS epidemic of 2002-2003 and its resurgence in 2004, researchers identified bats as a natural source of Coronaviruses. Not only this, but bat Coronaviruses were fairly similar to the human Coronavirus that caused the 2002-2003 SARS epidemic. However, at the time, the source of the epidemic was found to be palm civets. It was then found that the strain of Coronavirus that caused the 2002-2003 SARS epidemic could cross species and is now known to have the ability to infect bats, civets and humans alike.

Building on research following the 2002-2003 SARS epidemic and its subsequent 2004 resurgence, Chinese researchers postulated that the novel Coronavirus responsible for the 2019-2020 Coronavirus pandemic, COVID-19, must have originated in an animal that is a natural host for Coronaviruses, one that was also found in the Huanan Seafood Wholesale market in the city of Wuhan, China at the start of the epidemic. Of all 200+ samples collected and studied, it was found that COVID-19 was most similar to strains of bat Coronavirus. It was then proposed as an explanation that the source Coronavirus evolved using genetic material from another species, theorized to be snakes, which gave it the ability to jump species and infect humans, resulting in the present pandemic.

Why snakes? Snakes were found to have the most similar codon usage bias and were thus the most likely source to allow for the genetic recombination that allowed the Coronavirus to acquire the ability to infect humans. As such, of all the animals that were being traded in the Huanan Seafood Wholesale market in the city of Wuhan, China for use as food and medicine, the Chinese cobra (Naja atra) and the many-banded krait (Bungarus multicinctus) were identified as the most likely hosts to provide the genetic coding information to account for present outcomes. Even so, the theory that a recombination of a bat Coronavirus and snake genetic coding could have created COVID-19 was soon refuted in favor of a different approach that builds on previous research and suggests an intermediate animal host that is a natural source for Coronaviruses.

Coronavirus and bats, pangolins and snakes

  • Did the pangolin start the COVID-19 outbreak?

After snakes, it was thought that pangolins had passed on the virus to humans based on preliminary studies showing a match between a strain of pangolin Coronavirus and the COVID-19 human Coronavirus strain (see source). But the bewildering 100%, 98.2%, 96.7% and 90.4% match was not correctly interpreted by the media as it was, in fact, an amino acid match in 4 genes (genes E, M, N and S) between the pangolin and human Coronavirus strains. But said match was enough to spark interest in the idea that the pangolin could have spread the new Coronavirus. Comparing the whole genomes of the pangolin and human Coronavirus strains showed an 86% to 92% match between the two which, officials say, is a strong indicator of the zoonotic origin of the new COVID-19 (see source), but does not definitively point at the pangolin as the source that started the infection. It would appear, at this point in the time, that the pangolin didn’t do it.

  • How did the pangolin supposedly spread the Coronavirus?

Supposedly through the handling of the animal for consumption. Although forbidden by law and harshly punished, the practice still manages to evade the law and law enforcement in some parts of Asia where the animal is sought after for use as food and in traditional medical practices dating back thousands of years. Virus shedding from the diseased animal host and improper handling of bodily evacuations as well as consumption as food or medicine are believed to have been the modes of transmission from the animal to humans. But there is no definitive proof the pangolin is the source of the COVID-19 infection in humans. Which brings us to the next question: if the pangolin did not start or spread the COVID-19 infection in humans, did the bat do it?

  • Did the bat spread the COVID-19 Coronavirus infection?

Since the 2002-2003 SARS outbreak caused by the notorious SARS-CoV-1 Coronavirus, there has been ample research on the matter in hopes that it would better prepare the world in case of a resurgence of the infection or more serious outcomes. The strategy proved foresightedness as the infectious agent resurged a year later. And now, with the emergence of the novel COVID-19, a SARS-Cov-1 upgrade in a manner of speaking, there is at least some valuable research to extrapolate from to help predict potential outcomes and maybe even help with a cure. One of the most valuable pieces of information set the tone for current research as it indicates the bat as one of the most likely potential sources. Full-length genome sequencing has shown the novel Coronavirus COVID-19 or SARS-Cov-2 to have 96.3% similarity to BatCoV RaTG13 sequence (find out more). This not only indicates the zoonotic origin of the current pandemic, but also strongly points to bats as the most likely source.

Even so, this is not irrefutable proof that the bat spread the COVID-19 Coronavirus. It may be the bat that is the origin animal in this Coronavirus outbreak or it may be another animal and that is for science to tell us for sure. The take on this is that Coronaviruses are not limited to humans – even though they are from the same family of viruses, most have evolved to infect select species and will stay like that for a long time. For example, our pets don’t catch the common cold from us, and the common cold is sometimes caused by a Coronavirus. Likewise, we don’t catch the feline Coronavirus from cats, and many other Coronaviruses that are specific to some animals. Species jump does not usually happen overnight, despite current events.

  • Conclusion

At this point in time, it is not yet irrefutably proven that snakes, pangolins or bats contributed to the start or spread of the novel COVID-19 and present outcomes. Even so, there is a strong suspicion that the current infection has zoonotic origins and, while the intermediate host responsible for the species jump has yet to be discovered, the aftermath suggests an urgent need for change in animal trade policies and regulations and consumption of animal foods as well as reinforces the idea that high population densities and poor hygiene remain two of the most challenging aspects with regards to human disease and epidemics development.

This post was updated on Saturday / August 15th, 2020 at 9:53 PM