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The copyright holder for this preprint (which was not peer-reviewed) is the .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 the GD/P1L and GD/P2S sequences into a single consensus sequence to minimize gap 209 regions within any sequences. Table S5 . potential recombination events, we implemented a window sliding approach to determine the 228 changing patterns of sequence similarity and phylogenetic clustering between the query and 229 the reference sequences, as well as a scanning of phylogenetic clusters performed directly 230 from the multiple sequence alignment. Maximum likelihood trees were estimated from each 231 window extraction (i.e. genome regions 1 to 8) using PhyML as described above. 232 author/funder. All rights reserved. No reuse allowed without permission. sequencing. We also thank Guangzhou Customs Technology Center, Guangzhou for re-274 examining their archived pangolin samples and providing the data. All the above persons 275 agree on the content of the study, authorship arrangement and publication. We thank the staff 276 of the Guangxi and Guangdong Custom Bureau for their laborious anti-smuggling operations. 277 We thank all the scientists who kindly shared their genomic sequences of the coronaviruses 278 used in this study. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi. org/10.1101 org/10. /2020 Data that support the findings of this study have been deposited in GenBank database with 302 the xxxx-xxxx accession codes and SRA database with xxxx-xxxx accession codes. 303 author/funder. All rights reserved. No reuse allowed without permission.