A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene

PLoS Pathog. 2016 Sep 27;12(9):e1005883. doi: 10.1371/journal.ppat.1005883. eCollection 2016 Sep.

Abstract

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3'-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.

Grant support

This work was supported by the National Natural Science Foundation of China (NSFC) Grant No. 81290342 and 81461168030 (to GFG), and Grant No. 81373141 and 81401312 (to WJL), the China National Grand S&T Special Project Grant No. 2014ZX10004-001-006 (to YW), and GFG is a leading principle investigator of the NSFC Innovative Research Group Grant No. 81321063. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.