In December 2019, a cluster of patients suffering from an atypical pneumonia was reported in Wuhan city, Hubei province, China. Although the precise origins of this disease outbreak remain unknown, several of the early COVID-19 patients could be linked to a live animal market. During an outbreak of a disease that jumped from animals to humans (a so-called zoonotic disease), identifying the source of infection can allow health authorities to protect people by separating them from the animals posing an infection risk.
Related coronaviruses circulate in bats
The genome sequence of the virus causing atypical pneumonia in Wuhan was made available to the research community in early January 2020. It was quickly identified as a coronavirus similar to the virus that caused the 2003 SARS outbreak, which also began in China. The new coronavirus was given the formal name SARS-CoV-2 and is the cause of the disease called COVID-19. The hypothesis that COVID-19 was a zoonotic disease like MERS (Middle East respiratory syndrome) and SARS (severe acute respiratory syndrome) was supported by the observation that many of the early cases were associated with a “wet” food market in Wuhan where numerous live animals of different species were kept prior to sale.
Intensive genetic investigation of SARS-CoV-2 collected from a wide range of wild animals has shown that the new virus is most similar to viruses that naturally infect horseshoe bats – 96% of the genome sequence is identical. These bats are also thought to be the original host of the SARS virus and the bats support a community of coronaviruses that swap genetic material with each other. Comparison of genetic sequences suggests that SARS-CoV-2 split from the most similar known bat virus sequence 40–70 years ago, which suggests that SARS-CoV-2 has been circulating in bats unnoticed for decades. There are likely to be other closely related viruses infecting bats or other animals, which could also jump to humans.
There is also evidence of changes to the gene that codes for the spike protein in some kinds of bat coronaviruses. The spike protein sits on the surface coat of the virus – forming the distinctive “corona” or crown – and determines whether it can attach to and enter the cells of its hosts. Chance alterations in the spike protein could allow the virus to infect humans.
The role of other mammals during SARS-CoV-2 emergence
It is not yet known whether the new coronavirus spread directly from bats to humans, or via another animal. During the early stages of the current outbreak, it was suggested that human SARS-CoV-2 might have emerged from snakes. However, the analysis used to support this theory was flawed. More recently strong genetic similarities have been found between SARS-CoV-2 and several viruses infecting Malayan pangolins (scaly anteaters). Although the bat viruses are more similar to human SARS-CoV-2 than the pangolin viruses, there are several reasons why the pangolin link is receiving special attention. One is that the sequences of the spike protein genes in SARS-CoV-2 and in pangolin viruses are particularly close. Another is that pangolins are widely sold in live animal markets in China where they are more likely than bats to come into contact with humans.
In summary, current data indicate that SARS-CoV-2 originated directly or indirectly from a bat coronavirus, but these findings remain suggestive rather than conclusive because genetic and other investigations are still at a preliminary stage. There is substantial diversity among SARS-like coronaviruses circulating in bats and other animals and the identification of precisely where the virus originated will need further sampling and surveillance of animals.
After the emergence of SARS and MERS (and other zoonotic diseases) there were calls for restrictions on wildlife consumption by humans and the sale of wild animals in live markets. These recommendations are being restated during the current COVID-19 pandemic; whether they are justified on these grounds depends on knowing the animal origin of SARS-CoV-2 and how it entered the human population.