Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China

Abstract

The emergence of COVID-19 since December 2019 has attracted great attention around the world and reminds the powerful pathogenic potential of viruses (Zhou et al. 2020). The subfamily Orthocoronavirinae of the family Coronaviridae contains four genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus, which are the largest group of positive-sense, nonsegmented, single-stranded, enveloped RNA viruses (Woo et al. 2012; Shi et al. 2016). The genus Gammacoronavirus currently has five species (https://talk.ictvonline.org/tax onomy/), which are primarily spread through birds (Woo et al. 2012). Infectious bronchitis virus (IBV) is the beststudied Gammacoronavirus, which can lead to economic losses to the global poultry industry by causing avian infectious bronchitis (a highly contagious viral respiratory disease) (Jackwood and de Wit 2020). Turkey coronavirus (TCoV), also a member of Gammacoronavirus, causes acute infectious diarrhea in domestic turkeys (Lin et al. 2002). Recently, a novel species of genus Gammacoronavirus was identified in a mass die-off of Canada and snow geese (Papineau et al. 2019). Birds, with more than 10,000 living species, are one of the most popular beings with global distribution (Prum et al. 2015), and are the reservoir of many emerging and reemerging viruses, such as avian influenza viruses and the West Nile virus (Reed et al. 2003; Olsen et al. 2006). With the capacity to fly long distances, birds play an important role in disseminating these emerging viruses to animals and/or humans (Woo et al. 2012). In the previous study, we have identified a new deltacoronavirus from birds of Qinghai-Tibetan Plateau in China (Zhu et al. 2020). In February–March 2019, migratory birds were livecaptured and kept in cages by professionals of migratory bird protection station under the permission from Jiangxi Province Department of Forestry. Feces of migratory birds were collected using non-invasive ways respectively, and then released. A total of 48 fecal samples were collected from two regions (Nanchang City and Jiujiang City) around Poyang Lake in Jiangxi Province of China. Total RNA was extracted from these samples using the QIAamp Viral RNA Mini Kit. Then, 15 out of 48 total RNA were randomly selected and pooled in equal amounts. Then, total RNA was used to construct the RNA sequencing library using Truseq stranded total RNA library prep gold kit and sequenced by the Illumina HiSeq2000 platform. After quality control, a total of 75,448,386 clean reads were obtained. The de novo assembled contigs were obtained using Trinity v2.10.0 (Grabherr et al. 2011) and annotated against the NCBI nr database with an E-value cutoff of 1 9 10. We identified a 28,466 nucleotide (nt) long contig annotated as coronavirus (CoV). The contig was verified, and a total of 1,346 reads were mapped to the CoV Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s12250021-00402-x.