Are pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ?

Ping Liu; Jing-Zhe Jiang; Xiu-Feng Wan; Yan Hua; Xiaohu Wang; Fanghui Hou; Jing Chen; Jiejian Zou; Jinping Chen

In March of 2019, we detected Betacoronavirus in three animals from two sets of smuggling Malayan pangolins (Manis javanica) (n=26) intercepts by Guangdong customs [11] . All three animals suffered from serious respiratory diseases and failed to be rescued by the Guangdong Wildlife Rescue Center [11] (Table S2) . Through metagenomic sequencing and de novo assembling, we recovered 38 contigs ranging from 380 to 3,377 nucleotides, and the nucleotide sequence identities among the contigs from these three samples were 99.54%. Thus, we pooled sequences from three samples and assembled the draft genome of this pangolin origin coronavirus, so called pangolin-CoV-2020 (Accession No.: GWHABKW00000000), which was approximately 29,380 nucleotides, with approximately 84% coverage of the virus genome ( Figure 1a ). Strikingly, genomic analyses suggested the pangolin-CoV-2020 has a high identity with both 2019-nCoV and Bat-CoV-RaTG13, the proposed origin of the 2019-nCoV [10] (Figure 1b; Figure 1c ). The nucleotide sequence identity between pangolin-CoV-2020 and 2019-nCoV was 90.23% whereas the protein sequence identities for individual proteins can be up to 100% (Table S3; Table S4 ). The nucleotide sequence between pangolin-CoV-2020 and Bat-CoV-RaTG13 was 90.15%