Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence

Abstract

Over the last several decades, no emerging virus has had a profound impact on the world as the SARS-CoV-2 that emerged at the end of 2019 has done. To know where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated from and how it jumped into human population, we immediately started a surveillance investigation in wild mammals in and around Wuhan when we determined the agent. Herein, coronaviruses were screened in the lung, liver, and intestinal tissue samples from fifteen raccoon dogs, seven Siberian weasels, three hog badgers, and three Reeves's muntjacs collected in Wuhan and 334 bats collected around Wuhan. Consequently, eight alphacoronaviruses were identified in raccoon dogs, while nine betacoronaviruses were found in bats. Notably, the newly discovered alphacoronaviruses shared a high whole-genome sequence similarity (97.9 per cent) with the canine coronavirus (CCoV) strain 2020/7 sampled from domestic dog in the UK. Some betacoronaviruses identified here were closely related to previously known bat SARS-CoV-related viruses sampled from Hubei province and its neighbors, while the remaining betacoronaviruses exhibited a close evolutionary relationship with SARS-CoV-related bat viruses in the RdRp gene tree and clustered together with SARS-CoV-2-related bat coronaviruses in the M, N and S gene trees, but with relatively low similarity. Additionally, these newly discovered betacoronaviruses seem unlikely to bind angiotensin-converting enzyme 2 because of the deletions in the two key regions of their receptor-binding motifs. Finally, we did not find SARS-CoV-2 or its progenitor virus in these animal samples. Due to the high circulation of CCoVs in raccoon dogs in Wuhan, more scientific efforts are warranted to better understand their diversity and evolution in China and the possibility of a potential human agent.

Keywords: CCoV; SARS-related coronavirus; Wuhan; bats; raccoon dog.

Figure 1.

Sampling locations in Wuhan and its surrounding regions in Hubei province, China. SARS-CoV-related and SARS-CoV-2-related viruses identified in China are marked, corresponding to the three lineages in Supplementary Fig. S3. The scattered dots represent Chinese islands. Location abbreviations are as follows: AH, Anhui; FJ, Fujian; GD, Guangdong; GX, Guangxi; GZ, Guizhou; HuB, Hubei; HeB, Hebei; HeN, Henan; HK, Hong Kong; HN, Hunan; JL, Jilin; JX, Jiangxi; LN, Liaoning; SAX, Shaanxi; SC, Sichuan; SX, Shanxi; YN, Yunnan; ZJ, Zhejiang.

Figure 2.

ML phylogenetic trees were constructed based on the nt sequences of the whole genome and RdRp, S, M, and N genes of raccoon dog CoVs and other CoVs. Numbers (>70) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of substitutions per site.

Figure 3.

Schematic of the annotated GH8-2 genome in comparison to those of representative alphacoronavirus-1.

Figure 4.

ML phylogenetic trees were based on the nt sequences of the RdRp, S, M, and N genes of sarbecoviruses. Numbers (>70) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of substitutions per site. All viruses found in this study are labeled in red. SARS-CoV and SARS-CoV-related virus groups are labeled in red, and SARS-CoV-2 and SARS-CoV-2 related virus group are labeled in green. The GenBank and GISAID accession numbers are available in Supplementary Table S3.