Pangolin homology associated with 2019-nCoV

Tao Zhang; Qunfu Wu; Zhigang Zhang

To explore potential intermediate host of a novel coronavirus is vital to rapidly control 2 continuous COVID-19 spread. We found genomic and evolutionary evidences of the 3 occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan 4 Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 5 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common 6 ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more 7 closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the 8 interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019- 9 nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has 10 similar pathogenic potential to 2019-nCoV, and would be helpful to trace the origin and 11 probable intermediate host of 2019-nCoV. 12 . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 org/10. /2020 which is close on the outbreak of COVID-19. From their published results, all virus contigs 1 assembled from 2 lung samples (lung07, lung08) showed not high identities ranging from 2 80.24% to 88.93% with known SARS coronavirus. Hence, we conjectured that dead 3 Malayan pangolin may carry a new coronavirus close to 2019-nCoV. 4 To confirm our assumption, we downloaded raw RNA-seq data (SRA accession 5 number PRJNA573298) of those two lung samples from SRA and conducted consistent 6 quality control and contamination removing as described by Liu's study (7) . We found 1882 7 clean reads from lung08 sample mapped upon 2019-nCoV reference genome (GenBank 8 Accession MN908947)(3) with high genome coverage of 76.02%. We performed de novo 9 assembly of those reads and totally obtained 36 contigs with length ranging from 287bp to 10 2187bp with mean length of 700bp. Blasting against proteins from 2845 coronavirus 11 reference genomes including RaTG13, 2019-nCoVs and other known coronaviruses, we 12 found 22 contigs can be best matched to 2019-nCoVs (70.6%-100% aa identity; average: 13 95.41%) and 12 contigs matched to Bat SARS-like coronavirus (92.7%-100% aa identity; 14 average: 97.48%) (Table S1 ). These results indicate Malayan pangolin indeed carries a 15 novel coronavirus (here named as Pangolin-CoV) close to 2019-nCoV. 16 Using reference-guided scaffolding approach, we created Pangolin-CoV draft 17 genome (19,587 bp) based on the above 34 contigs. Remapping 1882 reads against the draft 18 genome resulted in 99.99% genome coverage at a mean depth of 7.71 X (range: 1X-47X) 19 ( Figure 1A) . Based on Simplot analysis, Pangolin-Cov showed highly overall genome 20 . 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 org/10. /2020 sequence identity throughout the genomes to RaTG13 (90.55%) and 2019-nCoV (91.02%) 1 ( Figure 1B) , although there is greatly high identity 96.2% between 2019-nCoV and 2 RaTG13(3). Another SARS-like coronavirus more similar to Pangolin-Cov were Bat 3 SARSr-CoV ZXC21(85.65%) and Bat SARSr-CoV ZC45 (85.01%). These results indicate 4 Pangolin-Cov may be the common origin of 2019-nCoV and RaTG13. 5 The viral genome organization of Pangolin-Cov was characterized by sequence 6 alignment against 2019-nCoV (GenBank