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Pangolin Coronavirus Study Finds No Evidence of Direct Evolution to SARS-CoV-2

NEW YORK – A new analysis of Malayan pangolins by researchers in the US and China has found no evidence that the SARS-CoV-2 virus evolved directly from a pangolin coronavirus (pangolin-CoV-2020), seemingly contradicting a study published last week in Nature, which suggested pangolins may have served as an intermediate host for SARS-CoV-2.

In the Nature study published last week, a team led by researchers at South China Agricultural University searched for SARS-CoV-2-like viruses in the lung tissue of 25 Malayan pangolins (Manis javanica) that were confiscated by customs officials in March and August of 2019, as well as from four Chinese pangolins (M. pentadactyla). The investigators said they isolated a pangolin virus in 17 of the Malayan pangolins that shared a high amino acid identity with SARS-CoV-2, including at the receptor-binding domain of the S protein.

"The isolation of a coronavirus that is highly related to SARS-CoV-2 in pangolins suggests that they have the potential to act as the intermediate host of SARS-CoV-2," SCAU's Yongyi Shen and colleagues wrote in their paper.

Now, however, another team of researchers said it has come to a different conclusion based on its own results. In a study published in PLOS Pathogens on Thursday, a team led by Jinping Chen of the Guangdong Institute of Applied Biological Resources assembled the complete genome of a coronavirus identified in three sick Malayan pangolins. But while the molecular and phylogenetic analyses showed that pangolin-CoV-2020 is genetically related to SARS-CoV-2, as well as a group of bat coronaviruses, the data did not support the theory that SARS-CoV-2 emerged directly from pangolin-CoV-2020, the researchers said.

Authors of the Nature study did not respond to a request for comment on the diverging results.

For the PLOS Pathogens study, the researchers conducted metagenomic sequencing and de novo viral genome assembly on samples from the three Malayan pangolins, recovering 38 contigs ranging from 380 to 3,377 nucleotides. The sequence identity among the contigs from the three samples was 99.54 percent. They then pooled sequences from the three samples and assembled the draft genome of the pangolin coronavirus, after which they conducted gap filling with amplicon sequencing to obtain a nearly full genome sequence. This pangolin-CoV-2020 genome was found to have 29,521 nucleotides.

Importantly, the researchers said, genomic analyses suggested that pangolin-CoV-2020 had high identity with both SARS-CoV-2 and Bat-CoV-RaTG13, which is the proposed origin of SARS-CoV-2 in bats. The nucleotide sequence identity was 90.32 percent between pangolin-CoV-2020 and SARS-CoV-2 and 90.24 percent between pangolin-CoV-2020 and BatCoV-RaTG13, but the sequence identity for the corresponding regions between SARS-CoV-2 and Bat-CoV-RaTG13 was 96.18 percent.

Further analyses found that pangolin-CoV-2020 and SARS-CoV-2 shared the same angiotensin-converting enzyme 2 (ACE2) receptor. However, the researchers also found that sequence similarities were not homogeneous across the S genes of pangolin-CoV-2020, SARS-CoV-2, Bat-CoV-ZXC21, and Bat-CoV-ZC45, which suggested that a recombination event could have occurred during the evolution of these coronaviruses.

"At the genomic level, SARS-CoV-2 was also genetically closer to Bat-CoV-RaTG13 than pangolin-CoV-2020," the authors wrote. "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 the pangolin-CoV-2020."

The researchers noted that although their study didn't support the hypothesis that pangolins are the intermediate hosts for the emergence of SARS-CoV-2, their results don't exclude the possibility that other coronaviruses could be circulating in pangolins. Therefore, they added, surveillance of coronaviruses in pangolins could elucidate the spectrum of coronaviruses in the wild and minimize the exposures of humans to these viruses.