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 investigate whether these deletions described above are random mutations occasionally identified in a strain or would commonly occur after cell passages, we performed whole genome sequencing on the other 21 SARS-CoV-2 viral strains collected after 2 rounds of cell passage in Vero-E6 or Vero cells (Supplemental Table) . The corresponding original samples for these strains were collected between 19 th January and 28 th February 2020. Multiplex-PCR combined with the nanopore sequencing was used, following the general protocol as described in (https://artic.network/ncov-2019). The ARTIC pipeline was applied to trimmed primers and generated the bam files, which included all reads mapping to the SARS-CoV-2 reference genome (MN908947.3). Variant sites were called by using iVar 7 with depth >=20 as a threshold. With this method, 10 of 21 cell isolate strains have different ratios of variants (>10%) with deletion at the flank of the polybasic cleavage site (deletion at 23585-23599) ( Figure C) . One has the variant with deletion on the polybasic cleavage site (deletion at 23596-23617). To find out whether the deletion on 23585-23599 was restricted in a specific genetic lineage, we next investigated the phylogenetic relationship of these strains and first 014 strain described above. As shown in Figure D , the strains with a relative higher ratio of this deletion were dispersed in the phylogenetic tree suggesting the deletion mutation was not restricted to a specific genetic lineage of SARS-CoV-2 viruses.