Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Tommy Tsan-Yuk Lam; Marcus Ho-Hin Shum; Hua-Chen Zhu; Yi-Gang Tong; Xue-Bing Ni; Yun-Shi Liao; Wei Wei; William Yiu-Man Cheung; Wen-Juan Li; Lian-Feng Li; Gabriel M Leung; Edward C. Holmes; Yan-Ling Hu; Yi Guan

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.13.945485 doi: bioRxiv preprint GX/P2V, GX/P3B, GX/P4L, GX/P5E and GX/P5L. Based on these genome sequences, we 176 designed primers for qPCR to confirm the positivity of the original tissue samples (Extended 177 Data Table S4 ). This revealed an original lung tissue sample that was also qPCR positive, in 178 addition to the six original samples with coronavirus reads. We further tested an addition 19 179 samples (nine intestine tissues, ten lung tissues), from 12 smuggled pangolins sampled RNA-seq raw files on the SRA database (https://www.ncbi.nlm.nih.gov/sra). We screened 199 these raw read files using BLAST methods and found that five (SRR10168374, 200 SRR10168376, SRR10168377, SRR10168378 and SRR10168392) contained reads that 201 mapped to 2019-nCoV. These reads were subjected to quality assessment, cleaning and then 202 de novo assembly using MEGAHIT 12 and reference assembly using BWA 13 . These reads 203 were then merged and curated in a pileup alignment file to obtain the consensus sequences. sequence. Since their genetic difference is so low, for the recombination analysis we merged 208 author/funder. All rights reserved. No reuse allowed without permission.