Identification of a common deletion in the spike protein of SARS-CoV-2

Zhe Liu; Huanying Zheng; Runyu Yuan; Mingyue Li; Huifang Lin; Jingju Peng; Qianlin Xiong; Jiufeng Sun; Baisheng Li; Jie Wu; Ruben J.G. Hulswit; Thomas A. Bowden; Andrew Rambaut; Nick Loman; Oliver G Pybus; Changwen Ke; Jing Lu

To identify whether these deletions also occurred in original clinical samples, we screened the high through-put sequencing data from 149 clinical samples, which collected between 6 th February and 20 th March in Guangdong, China. These samples were sequenced as by using multiplex PCR combined with nanopore sequencing. There were 68 SARS-CoV-2 genomes with sequencing average depth >=20 at the sites neighboring 23585. As shown in Table 1 , the variants with the deletion at 23585-23599 were found in 3 (6%) of clinical samples with ratios ranging from 8.8-32.8% indicating this deletion may also occur in vivo infections even though the rate was extremely low compared to the results from in vitro ( Figure D ). To date, there are no genome sequences deposited in public dataset having this deletion. However, this did not mean this variant did not exist in currently released sequences since most of the variants with . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.015941 doi: bioRxiv preprint a lower ratio would be discarded when generating the final consensus sequences. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.015941 doi: bioRxiv preprint CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of this remarkable evolutionary tale. The deletion mutation identified in vitro should be also noted for current vaccine development.