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The copyright holder for this preprint (which was not peer-reviewed) is the .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 org/10. /2020 Based on these new genome sequences, we designed primers for qPCR detection to confirm 74 that the raw samples were positive for the coronavirus. We conducted further qPCR testing 75 on another batch of archived pangolin samples collected between May-July 2018. Among the 76 19 samples (nine intestine tissues, ten lung tissues) tested from 12 animals, three lung tissue 77 samples were coronavirus positive. 78 79 In addition to the animals from Guangxi, after the start of the 2019-nCoV outbreak the 80 Guangzhou Customs Technology Center re-examined their five archived pangolin samples 81 (two skin swabs, one unknown tissue, one scale) obtained in previous anti-smuggling 82 operations in March 2019. Following high-throughput sequencing the scale sample was 83 found to contain coronavirus reads, and from these data we were able to assemble a partial The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 2019-nCoV have only 89.2% amino acid similarity in RBD. Indeed, the Guangdong pangolin 108 coronaviruses and 2019-nCoV possess identical amino acids at the five critical residues of the 109 RBD, whereas RaTG13 only shares one amino acid with 2019-nCoV (residue 442, human 110 SARS-CoV numbering 9 ). Interestingly, a phylogenetic analysis of synonymous sites alone in 111 the RBD revealed that the phylogenetic position of the Guangdong pangolin is consistent 112 with that in the remainder of the viral genome, rather than being the closest relative of 2019-113 nCoV ( Figure 2b ). Hence, it is possible that the amino acid similarity between the RBD of 114 the Guangdong pangolin coronaviruses and 2019-nCoV is due to selectively-mediated 115 convergent evolution rather than recombination, although it is difficult to choose between 116 these scenarios on current data. Although the drivers of any convergent evolution are 117 unknown, its possible occurrence, as well as that of recombination, would further highlight Coronaviruses, including those related to 2019-nCoV, are clearly present in many wild 135 mammals in Asia 5,6,7,11 . Although the epidemiology, pathogenicity, interspecies infectivity 136 and transmissibility of coronaviruses in pangolins remains to be studied, the data presented 137 here strongly suggests that handling these animals requires considerable caution, and that Table S1 ). We obtained near complete genomes from these 174 samples (98%, compared to 2019-nCoV), with the virus genomes denoted as GX/P1E, 175 author/funder. All rights reserved. No reuse allowed without permission.