Mutations, Recombination and Insertion in the Evolution of 2019-nCoV

Aiping Wu; Peihua Niu; Lulan Wang; Hangyu Zhou; Xiang Zhao; Wenling Wang; Jingfeng Wang; Chengyang Ji; Xiao Ding; Xianyue Wang; Roujian Lu; Sarah Gold; Saba Aliyari; Shilei Zhang; Ellee Vikram; Angela Zou; Emily Lenh; Janet Chen; Fei Ye; Na Han; Yousong Peng; Haitao Guo; Guizhen Wu; Taijiao Jiang; Wenjie Tan; Genhong Cheng

The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 To identify novel inherited mutations, we used SARS-CoV-2 strain (EPI_ISL_402125) as root to construct the phylogenetic tree for all 120 available complete genomes of the novel coronavirus from GISAID (updated February 18 th , 2020). Considering potential sequencing errors at both ends, the genome sequence variations among different strains of 2019-nCoV isolated from patients located in different cities were low considering only 5 several mutations in about 30kb genome per isolate. Based on the nucleotide positions 8517 and 27641, the 2019-nCoV strains can be divided into two major groups (Figs 2A and S2). All the group 1 strains have thymine at 8517 and cytosine at 27641, which are same as corresponding nucleotides in SARS, whereas the group 2 stains have cytosine at 8517 and thymine at 27641 (Figs 2A and S3) . Epidemiological data G1 and G2 strains 10 revealed that the collection date and location of the earliest G1 strain (EPI_ISL_406801) was January 5 th , 2020 in Wuhan, whereas the earliest G2 strain was isolated in December 24 th , 2019 in Wuhan (Fig 2A) . The existence of both genetic groups in the same city indicated co-circulation, but evolved convergently at the early outbreak. Within each group, we also observed additional shared mutations added to multiple strains. Based on 15 these potentially inheritable mutations and the identifying times and locations, we generated a mutation tree map to track individual shared mutations and show the relationships among different isolates (Fig 2A and S2 ). For example, five strains identified in Guangdong from Jan. 10-15 all share the same mutation in nucleotide position 28578 on the background of group 1 might be transmitted by the same person. The similar strain 20 may transmit to three patients identified in Japan on Jan. 29-31 with additional mutation at nucleotide position 2397 and to a patient identified in USA on Jan. 22 with additional mutation at nucleotide position 10818. The G10818T is very interesting as it is shared by author/funder. All rights reserved. No reuse allowed without permission.