Patient-derived mutations impact pathogenicity of SARS-CoV-2

Hangping Yao; Xiangyun Lu; Qiong Chen; Kaijin Xu; Yu Chen; Linfang Cheng; Fumin Liu; Zhigang Wu; Haibo Wu; Changzhong Jin; Min Zheng; Nanping Wu; Chao Jiang; Lanjuan Li

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.14.20060160 doi: medRxiv preprint 34 SPAdes (Bankevich et al., 2012) (v3.1.3) using an iterative short-read genome assembly 512 module for pair-end reads. K-values were selected automatically at 33nt, 55nt and 77nt 513 for these samples. After assembling, contigs was blasted to nt database (20190301) to 514 confirm their origins, and only contigs belonging to coronavirus were retained for base 515 correction. Next, filtering reads of each sample were mapped back to retained assembled 516 contigs and bam-readcount was applied (--min-mapping-quality=5, other parameter was 517 set default) to calculate the base frequency of every post of each assemble contigs. 518 Meanwhile, Haplotypecaller of gatk was applied to call snp/indel based on the assembled 519 contigs with reads quality higher than 20. Finally, bam files were inspected in igv 520 manually to verify each mutation based on the number of reads mapped, the balance 521 between reads mapped to plus and minus strands of the reference genome, and the 522 relative positions of the mutations on these reads. 523 524 Phylogenetic analysis 525 We acquired 725 high quality and high coverage SARS-CoV-2 genomes from GISAID 526 (downloaded on 3/21/2020), including the Yunnan RaTG13 viral strain and the 527 Guangdong pangolin viral strain as the outgroup. We aligned the 736 genomic sequences 528 All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity.