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Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan

Our take —

In this report, the authors describe a sarbecovirus related to SARS-CoV-2 in Rhinolophus cornutus bats from Japan. The virus is more distantly related to SARS-CoV-2 than other viruses from bats and pangolins within the same phylogenetic group. Experiments suggest that the virus is only able to infect cells of R. cornutus and not human cells. These findings expand the geographic and host range of SARS-CoV-2-related viruses, but should be regarded as preliminary due to the very limited sample size.

Study design

Other

Study population and setting

The paper describes the characterization of a novel coronavirus detected in feces from captured Rhinolophus cornutus bats in Iwate prefecture, Japan. The samples were originally collected in 2013 and partial genetic fragments were sequenced from two samples. The new analysis of RNA sequences captured a full genome from one fecal sample. The authors also assess the ability of the novel coronavirus they characterized to enter human or bat cells.

Summary of Main Findings

Phylogenetic analysis placed the novel coronavirus (Rc-o319) from R. cornutus into the subgenus Sarbecovirus and within the clade that includes SARS-CoV-2. Nucleic acid similarity between Rc-o319 and SARS-Cov-2 was 81.5% and there was no evidence of genetic exchange (recombination) between Rc-o319 and other coronaviruses. Analysis of the receptor binding motif of the spike protein of Rc-o319 shows that the virus has a unique deletion in one region of the protein important to binding the human angieotensin-converting enzyme receptor 2 (ACE2) prior to cell entry. Since this deletion was unique compared to other bat coronaviruses with and without the ability to enter human cells, the authors could not infer the ability of Rc-o319 to enter human cells from genetic data alone. By using a combination of pseudotyped vesicular stomatitis virus (VSV) containing spike protein from Rc-o319 and other sarbecoviruses, the authors showed that Rc-o319 pseudotyped VSV could enter cells expressing ACE2 from R. cornutus but not from another Rhinolophus species (R. ferrumequinum) or from humans.

Study Strengths

No specific strengths were noted other than the use of full genome sequencing and the experiments assessing binding ability of Rc-o319 to human ACE2.

Limitations

The very small number of samples prevents assessment of the prevalence and phylogenetic diversity of SARS-CoV-2-related viruses in R. cornutus in Japan. There are two other Rhinolophus species in Japan, so the possibility of virus sharing among species cannot be fully evaluated from these results.

Value added

This study increases the number of sarbecoviruses identified within the SARS-CoV-2 clade, as well as the host and geographic range of the SARS-CoV-2 clade. The results also provide information on additional deletions in the spike receptor binding domain that may predict the potential of viruses to infect human cells.

This review was posted on: 19 December 2020