Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins
Authors: Wei-Jun Xie
Zhipeng Zhang
Fanfan Shu
Yaoyu Feng
Na Li
Xiaobing Li
Kangpeng Xiao
Yu Li
Yaqiong Guo
Shi-Ming Peng
Yongyi Shen
Rui-Ai Chen
Fang-Hui Hou
Xuejuan Shen
Lihua Xiao
Jie-Jian Zou
Wanyi Huang
Xu Zhang
Junqiong Zhai
Mian Huang
Wu Chen
Niu Zhou
Ziding Zhang
Ya-Jiang Wu
Qin-Hui Cai
Journal: Nature (2020)
Discipline: Multidisciplinary
Keywords: coronavirus; COVID-19; SARS-CoV-2; pangolin-CoV; host species
Affiliations: Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China., Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China., Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China., Guangdong Provincial Wildlife Rescue Center, Guangzhou, China., State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China., Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China., Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China. ., Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China. ., Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China. .

Abstract:  The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled. 

Retracted: No

PubPeer comments:
 The methods of this paper is extremely vague, despite taking almost 3 moths from submission to online publication. Apparently the animals died on their own, including the ones that where not virus positive:  These animals were sent to the wildlife rescue center, and were mostly inactive and sobbing, and eventually died in custody despite exhausting rescue efforts.  Main text states:  furthermore, 14 of the 17 pangolins that tested positive died within a time-interval of 1.5 month. When did the other pangolins die? From what I can understand, the pangolins died sometime in spring 2019 and their serum was then tested early 2020 for SARS-COV2 antibodies. How was the samples stored? also there is no description in the methods section of taking serum samples, only tissue samples. The full methods section for the RT-PCR appears to be:  Viral RNA was extracted from the lung tissue using the QIAampu00ae Viral RNA Mini kit (Qiagen) following the manufacturer-recommended procedures, and examined for CoV by RT-PCR using a pair of primers (F: 5u2019-TGGCWTATAGGTTYAATGGYATTGGAG-3u2019, R: 5u2019-CCGTCGATT GTGTGWATTTGSACAT-3u2019) designed to amplify the S gene of u03b2 CoV. What machine was used and what CT-value was required ? Methods like these may be acceptable in a pre-print, but should not pass peer review... ,