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.Since the severe acute respiratory syndrome (SARS) outbreak in early 2003, many new viruses of the family Coronaviridae have been identified in diverse host species, including birds, humans, and other mammals (7, 12-14, 18, 25, 27, 28, 29). Of these hosts, bats have provided the highest genetic diversity of novel coronaviruses (CoVs) (23,29). Analyses of the genomic organization and phylogenetic relationships of CoVs from bats and other host species indicate that bats are the likely natural reservoirs for all known CoVs from other hosts (23,26). This research also suggests that CoVs resident in bats may be introduced into other animals and subsequently become established in these hosts.Interspecies transmission of CoV from its natural reservoir to another species might result in disease outbreaks in naive hosts. The emerging pathway of SARS CoV in humans and market civets is an example of this (4, 5). Accumulated information has demonstrated that many SARS-like CoVs are harbored in bat species (12,13,23). However, the cross homologies between civet and human SARS CoV and bat SARS-like CoVs are still relatively low (about 92%), even in the most conserved regions of the replicase gene (13). Phylogenetic analyses and divergence dates of these CoVs indicate that the likely interme...

Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats

“…The severe acute respiratory syndrome (SARS) outbreak in 2003 highlighted the potential health threat of coronaviruses to humans (Peiris et al, 2003). This prompted an intensive search for the precursor of SARS CoV in wildlife and the discovery of several novel CoVs in bats in China, including the viruses that are closely related to SARS CoV (Dong et al, 2007;Lau et al, 2005;Poon et al, 2005;Tang et al, 2006;Woo et al, 2006). Recently, the biological importance of bats for the ecology of coronaviruses was further reiterated by the discovery of novel bat CoVs (BtCoVs) in other continents (Dominguez et al, 2007;Muller et al, 2007).…”

Identification and Sequencing of a Novel Rodent Gammaherpesvirus That Establishes Acute and Latent Infection in Laboratory Mice

“…A total of 82 ORFs were identified in the RHVP genome, using the following criteria: (i) sequence similarity to known viral or cellular genes, (ii) prediction by two different gene prediction algorithms, fgenesV (SoftBerry, Mount Kisco, NY) (13,69) and GeneMark (6), and (iii) the presence of an initiating methionine and a stop codon. Translated sequences of these ORFs were analyzed by BLASTP, and those with significant similarity to conserved gammaherpesvirus ORFs were given ORF numbers according to the previously established convention for rhadinoviruses (2,65,84) and are shown as gray arrows in Fig.…”

“…Predicted ORFs were identified using Geneious (see above), fgenesV (SoftBerry, Mount Kisco, NY) (13,69), and GeneMark (6) and were analyzed using BLAST algorithms (3). ORFs that were predicted by both fgenesV and GeneMark and that contained canonical start and stop codons were annotated and queried against the GenBank nonredundant protein database, using BLASTP.…”

Infection with a pathogenic turkey coronavirus isolate negatively affects growth performance and intestinal morphology of young turkey poults in Canada

“…Group 3a includes viruses characterized by either induction of respiratory and urinary tract infections such as infectious bronchitis virus and pheasant coronavirus or by induction of enteric diseases such as TCoV and quail coronavirus (Pennycott, 2000;Cavanagh, 2001;Jonassen et al, 2005;Circella et al, 2007;Gomaa et al, 2008a;Woo et al, 2009). A unique coronavirus isolated from a whale (Mihindukulasuriya et al, 2008) is the only recognized member of Group 3b, while several recently described coronaviruses isolated from wild birds belong to Group 3c along with the coronavirus from Asian leopard cats (Dong et al, 2007;Woo et al, 2009).…”

“…This classification was developed to reflect the antigenic relationships among various coronaviruses as well as their genomic sequences and organizations (Lai & Cavanagh, 1997;Sawicki et al, 2007). With the exception of coronaviruses isolated from a dead Beluga whale (Mihindukulasuriya et al, 2008) and Asian leopard cats (Dong et al, 2007), all known Group 3 coronaviruses infect birds. Most Group 3 coronaviruses share a high degree of antigenic as well as genomic similarities based on sequencing data from full-length or partial genome sequences.…”