Detection of a novel and highly divergent coronavirus from asian leopard cats and Chinese ferret badgers in Southern China

Abstract

Since an outbreak of severe acute respiratory syndrome (SARS) was averted in 2004, many novel coronaviruses have been recognized from different species, including humans. Bats have provided the most diverse assemblages of coronaviruses, suggesting that they may be the natural reservoir. Continued virological surveillance has proven to be the best way to avert this infectious disease at the source. Here we provide the first description of a previously unidentified coronavirus lineage detected from wild Asian leopard cats (Prionailurus bengalensis) and Chinese ferret badgers (Melogale moschata) during virological surveillance in southern China. Partial genome analysis revealed a typical coronavirus genome but with a unique putative accessory gene organization. Phylogenetic analyses revealed that the envelope, membrane, and nucleoprotein structural proteins and the two conserved replicase domains, putative RNA-dependent RNA polymerase and RNA helicase, of these novel coronaviruses were most closely related to those of group 3 coronaviruses identified from birds, while the spike protein gene was most closely related to that of group 1 coronaviruses from mammals. However, these viruses always fell into an outgroup phylogenetic relationship with respect to other coronaviruses and had low amino acid similarity to all known coronavirus groups, indicating that they diverged early in the evolutionary history of coronaviruses. These results suggest that these viruses may represent a previously unrecognized evolutionary pathway, or possibly an unidentified coronavirus group. This study demonstrates the importance of systematic virological surveillance in market animals for understanding the evolution and emergence of viruses with infectious potential.

FIG. 1.

Phylogenetic relationships of the RdRp genes of novel CoVs isolated from wild animals in China. The tree was generated by the neighbor-joining method in the PAUP* program. Analyses were based on 440 nucleotides of the RdRp. Values above branches are bootstrap values from 1,000 replicates. The tree was rooted to Okavirus (accession no. AF227196). Scale bar, 0.1 substitution per site. Red text indicates viruses characterized in this study. Abbreviations: LDV, lactate dehydrogenase-elevating virus; SHFV, simian hemorrhagic fever virus; PRRSV, porcine respiratory and reproductive syndrome virus; ToV, torovirus; IBV, infectious bronchitis virus; TGEV, transmissible gastroenteritis virus; FIPV, feline infectious peritonitis virus; PEDV, porcine epidemic diarrhea virus; MHV, murine hepatitis virus; PHEV, porcine hemagglutinating encephalomyelitis virus; BtCoV, bat coronavirus.

FIG. 2.

Schematic representation of the ORFs of Asian leopard cat/Guangxi/F230/2006 and representative group 1 and group 3 CoVs. Putative accessory proteins are indicated by gray boxes. For definitions of abbreviations, see the legend to Fig. 1.

FIG. 3.

Phylogenetic relationships of the spike (A), envelope (B), membrane (C), and nucleocapsid (D) protein genes of novel CoVs isolated from wild animals in China. Trees were generated by the neighbor-joining method in the PAUP* program. Values above and below branches are neighbor-joining bootstrap values from 1,000 replicates and Bayesian posterior probabilities, respectively. Analyses were based on 2,802, 339, 831, and 1,692 nucleotides of the spike, envelope, membrane, and nucleocapsid protein genes, respectively. The trees were midpoint rooted. Scale bar, 0.1 nucleotide substitution per site. Red text indicates viruses characterized in this study. For definitions of abbreviations, see the legend to Fig. 1.

FIG. 4.

Phylogenetic relationship of the complete HEL domain of the replicase gene of the novel CoVs isolated from wild animals in China. Trees were generated by the neighbor-joining method in the PAUP* program. Values above and below branches are neighbor-joining bootstrap values from 1,000 replicates and Bayesian posterior probabilities, respectively. Analyses were based on 1,797 nucleotides. The tree was midpoint rooted. Scale bar, 0.1 nucleotide substitution per site. Red text indicates viruses characterized in this study. For definitions of abbreviations, see the legend to Fig. 1.