SARS-like bat coronaviruses are not only in China - Virology Hub

SARS-like bat coronaviruses are not only in China

It is well past the time to stop blaming a laboratory in China for the release of SARS-CoV-2. Such fallacies reflect an ignorance of scientific facts, including the recent finding of closely related coronaviruses in bats in Thailand.

The bat CoV RatG13, sampled in 2013 in Yunnan province, shares 96% whole genome identity with SARS-CoV-2, suggesting a likely bat origin of the pandemic virus. To identify other possible sources for highly related viruses, a colony of 300 bats in eastern Thailand, consisting only of one species, Rhinolophus acuminatus, was sampled in June 2020. Thirteen of 100 bat rectal swab samples were positive for a single PCR amplicon with 95.86% sequence identity to SARS-CoV-2 and 96.21% identity to bat CoV-RaTG13. This virus, named RacCS203, appears to be the dominant coronavirus circulating in this bat colony. Phylogenetic analyses indicate that RacCS203 is a new member of the SARS-CoV-2 related CoV lineage (SC2r-CoV).

Phylogenetic analyses of the spike receptor binding domain, and binding studies with purified recombinant proteins indicate that RacCS203 does not bind to ACE2 for entry into cells. This conclusion was confirmed by the finding that a pseudotyped VSV virus with the spike gene of RacCS203 cannot infect VeroE6 cells, while VSV with the spike gene of SARS-CoV-2 does infect these cells.

A surrogate virus neutralization test was used to measure antibodies in sera from the sampled bats that block binding of the SARS-CoV-2 receptor binding domain (RBD) to recombinant ACE2. Of 98 bat sera tested, four contained antibodies that block this ligand-receptor interaction. One of ten sera from pangolins also contained antibodies that block the SARS-CoV-2 RBD-ACE2 interaction. These pangolins were confiscated from illegal traders in Central and Southern Thailand are are of unknown origin.

The spike protein of RacCS203 is most similar to the same protein from the bat isolate RmYN02. Both share part of the furin cleavage site and the RBDs differ by just two amino acids. Sera from COVID-19 patients react strongly with the RBDs of SARS-CoV-2 and RaTG13, and weakly with RmYN02. Rabbit antibodies against the RBDs of RmYN02 and RaTG13 neutralized SARS-CoV-2.

These findings provide further support that SC2r-CoVs are not limited to China. Such viruses have also been detected in bats from the north of Japan, the eastern and southwestern parts of China, and Thailand, a distance of 4800 km. Many more SC2r-CoVs are likely to be found in Rhinolophus bats once surveillance in this region are increased. Such activities are likely to identify the immediate progenitor of SARS-CoV-2, the equivalent of the >99% identical SARS-CoV genomes found in palm civets in 2003.

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