SARS-CoV-2 Coronavirus Didn’t Come from Pangolins, Scientists Say

by johnsmith

A team of researchers from China and the United States has sequenced the genome of pangolin-CoV-2020, a coronavirus isolated from sick Malayan pangolins (Manis javanica), and found that this virus is genetically similar to SARS-CoV-2 but isn’t its precursor.

A Malayan pangolin (Manis javanica) climbing a lychee tree. Image credit: Jinping Chen.

A Malayan pangolin (Manis javanica) climbing a lychee tree. Image credit: Jinping Chen.

In December 2019, there was an outbreak of pneumonia with an unknown cause in Wuhan, Hubei province, China. Through deep sequencing on the lower respiratory tract samples of patients, a novel coronavirus named as SARS-CoV-2 was identified.

Epidemiological study suggested SARS-CoV-2 was associated with the Huanan Seafood Wholesale Market, a live animal and seafood market in Wuhan.

Soon after the release of the SARS-CoV-2 genome, scientists sequenced the full genome of Bat-CoV-RaTG13, a coronavirus isolated from a bat species called Rhinolophus affinis. This virus was 96% identical at the whole genome level to SARS-CoV-2, suggesting the latter could be of bat origin.

However, because direct human-bat contact is rare, it seems to be more likely that SARS-CoV-2 jumped to humans from an intermediate host rather than directly from bats, as was the cases with both SARS-CoV-1 and MERS-CoV viruses.

“To effectively control the disease and prevent new spillovers, it is critical to identify the animal origin of SARS-CoV-2,” said Dr. Jinping Chen from the Guangdong Institute of Applied Biological Resources and colleagues.

In the new study, the researchers assembled the complete genome of the pangolin-CoV-2020 coronavirus identified in three individuals from two groups of sick Malayan pangolins, which were likely to be smuggled for black market trade.

Their results showed that pangolin-CoV-2020 is genetically associated with both SARS-CoV-2 and a group of bat coronaviruses.

However, phylogenetic analyses and a special amino acid sequence in the S gene of SARS-CoV-2 did not support the hypothesis of SARS-CoV-2 arising directly from pangolin-CoV-2020.

“Although our study does not support the idea that pangolins are an intermediate host directly responsible for the emergence of SARS-CoV-2, it is possible that other coronaviruses could be circulating in pangolins,” the scientists said.

“Wildlife conservation and limited exposure to wildlife will be important to minimize the risk that coronaviruses will spill over from wild animals to humans.”

The study was published in the journal PLoS Pathogens.


P. Liu et al. 2020. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? PLoS Pathog 16 (5): e1008421; doi: 10.1371/journal.ppat.1008421

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