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Pangolin Coronavirus Analysis Finds High Similarity to SARS-CoV-2

NEW YORK – Researchers have isolated a coronavirus from Malayan pangolins that is highly similar to SARS-CoV-2, suggesting pangolins may have served as an intermediate host for the virus.

While bats are thought to be the reservoir for a number of coronaviruses, and SARS-CoV-2 has high sequence similarity to the bat coronavirus RaTG13, it's unknown whether SARS-CoV-2 has other hosts, such as pangolins.

A team led by researchers at South China Agricultural University searched for SARS-CoV-2-like viruses in Malayan pangolins (Manis javanica) that were confiscated by customs officials in March and August of 2019. A pangolin virus they isolated shared a high amino acid identity with SARS-CoV-2, including at the receptor-binding domain of the S protein. As the scientists reported in Nature this week, about two-thirds of the Malayan pangolins they analyzed carried the pangolin SARS-CoV-2-like virus and displayed signs of infection.

"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.

For their study, the researchers obtained lung tissue samples from four Chinese pangolins (M. pentadactyla) and 25 Malayan pangolins and analyzed them for SARS-related coronaviruses using an RT-PCR-based assay. They recovered virus from 17 of the 25 Malayan pangolins, but none of the Chinese pangolins.

All of the infected Malayan pangolins, the researchers noted, were from the same seized transport, and all showed signs of respiratory disease. Histological examinations of infected animals uncovered diffuse alveolar damage in the lungs. Of the 17 animals that tested positive, 14 died within a month and a half.

The researchers then isolated a coronavirus from the lung tissue of a pangolin that died, and RT-PCR analysis targeting the spike and RdRp genes showed an 84.5 percent and 92.2 percent nucleotide sequence identity to the SARS-CoV-2 versions, respectively.

After assembling the genome of the coronavirus they isolated from the pangolin, dubbed Pangolin-CoV, they made additional comparisons to SARS-CoV-2. At the amino acid level, they noted that the S, E, M, and N Pangolin-CoV genes shared 90.7, 100, 98.6, and 97.8 percent identity with SARS-CoV-2.

At the whole-genome level, meanwhile, it shared 80 and 98 percent sequence identity with SARS-CoV-2 and Bat SARSr-CoV RaTG13 genomes, respectively, except for the S gene. 

The S gene instead exhibited signs of recombination: at the first 914 nucleotides, it was more similar to Bat SARSr-CoV ZXC21 and Bat SARSr-CoV ZC45, but the rest of the Pangolin-CoV S gene was more similar to SARS-CoV-2 and Bat-CoV-RaTG13. In particular, the receptor-binding domain of the S protein of Pangolin-CoV differed from that of SARS-CoV-2 by one amino acid.

This suggests that SARS-CoV-2 might have originated through the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus, the researchers said, a theory that is bolstered by additional analyses of the evolutionary relationships between the viruses.

These findings are in line with previous studies that also reported similarities between pangolin coronaviruses and SARS-CoV-2, especially in the receptor-binding domain, and additionally suggested that it may be the result of a recombination event between pangolin and bat coronaviruses.

Similar to one of the previous studies, the South China Agricultural University team suggested that pangolins may have been an intermediate host for SARS-CoV-2, while bats served as the native host. Further studies, they added, are needed to confirm the role of pangolins.

"Therefore, more systematic and long-term monitoring of SARSr-CoV in pangolins and other related animals should be implemented to identify the potential animal source of SARS-CoV-2 in the current outbreak," the researchers wrote.