Covid-19 may have originated from recombined bat, pangolin coronaviruses
A coronavirus isolated from Malayan pangolins by a team of Chinese scientists showed 100%, 98.6%, 97.8% and 90.7% amino acid identity with Sars-CoV-2 in 4 genes.Updated: May 11, 2020 08:34 IST
A new study has suggested that the Sars-CoV-2, the virus that causes Covid-19, might have originated from a recombination of coronaviruses in a bat and pangolin. The findings strengthen the theory that pangolins could be the intermediate host for transmission of Sars-CoV-2 to humans.
The paper, published in the journal Nature by researchers from College of Veterinary Medicine, South China Agricultural University, also flags that pangolins, being the most trafficked mammal in the world, could be a future threat to public health if wildlife trade is not controlled because they harbour Sars-CoV-2-like viruses.
A coronavirus isolated from Malayan pangolins by a team of Chinese scientists showed 100%, 98.6%, 97.8% and 90.7% amino acid identity with Sars-CoV-2 in 4 genes.
The Malayan pangolin coronavirus was found to be particularly identical to Sars-CoV-2 in its receptor binding domain of the spike protein (which SARS-CoV-2 uses to bind to its host’s cells).
Genome sequencing found that the pangolin-CoV was very similar to both SARS-CoV-2 and Bat Sars-CoV RaTG13 (from which SARS-CoV-2 is suspected to have originated) but the only difference was the spike or S gene.
Further analysis of S gene sequences has suggested recombination events on May 8.
For this study, the team used lung tissues from four Chinese pangolins and 25 Malayan pangolins in a wildlife rescue center during March-August 2019. RNA from 17 of the 25 Malayan pangolins were found to be positive for Sars-CoV-2 like viruses and they gradually showed signs of respiratory disease, including shortness of breath, emaciation, inactivity, and crying.
Out of 17, 14 pangolins later died.
Generally, a natural reservoir host does not show severe disease, while an intermediate host may have clinical signs of infection, the authors said.
Pangolins and bats are both nocturnal animals, eat insects, and share overlapping ecological niches which make pangolins the ideal intermediate host for some Sars-related coronaviruses.
The paper recommended more systematic and long-term monitoring of coronaviruses in pangolins and a complete ban on illegal pangolin trade, international cooperation and strict regulation against consumption of game meat and wildlife trade.
“Of particular interest here is that the entire genome of the pangolin coronavirus is not similar to the Sars-CoV-2 but they’re almost identical in the receptor-binding area (which the virus uses to bind to its host’s cells). Interestingly, the genome of Sars-CoV-2 is 96% similar to the bat coronavirus RaTG13 (found in the intermediate horseshoe bat) but differs in the receptor-binding site (which means that the RaTG13 cannot directly infect human lungs because its receptor cannot bind to human lung cells). Put these two pieces of information together and you arrive at the hypothesis that has the most amount of support so far,” said Rohit Chakravarty, wildlife biologist and PhD student at the Leibniz Institute for Zoo and Wildlife Research in Berlin, Germany who read the paper.
“Which is, a bat coronavirus jumped from a bat to a Malayan pangolin (either in the wild or in captivity), the virus recombined in the pangolin and incorporated the pangolin coronavirus’s receptor-binding region, and then it evolved into Sars-CoV-2 that causes Covid-19 in humans,” he added.
Pangolins are trafficked because it is believed that their scales and blood have medicinal properties, and their flesh is considered a delicacy in some parts of southeast Asia.
“As many reports have shown, pangolins are now the most trafficked wild animal species in the world. As with all wildlife trade, the answer to how it can be controlled is quite complicated, because the flow chain goes through several layers of society. Ultimately, we are all culpable because the scale of operations is directly correlated to wealth in consumer countries. It is very easy to say that the eating habits of the Chinese are responsible for all the current problems we face. However, it is much harder for us to acknowledge, that actually the consumerist lifestyles of all developed and developing economies is actually the engine that’s driving this thriving trade,” said Abi Tamim Vanak, Fellow, Wellcome Trust/DBT India Alliance Program and senior fellow at Ashoka Trust for Research in Ecology and the Environment.