Full?length and defective enterovirus G genomes with distincttorovirus protease insertions are highly prevalent on a Chinese pigfarm

AbstractRecombination occurs frequently between enteroviruses (EVs) which are classified within the same species of the Picornaviridaefamily. Here, using viral metagenomics, the genomes of two recombinant EV-Gs (strains EVG 01/NC_CHI/2014 andEVG 02/NC_CHI/2014) found in the feces of pigs from a swine farm in China are described. The two strains are characterizedby distinct insertion of a papain-like protease gene from toroviruses classified within the Coronaviridae family. According torecent reports the site of the torovirus protease insertion was located at the 2C/3A junction region in EVG 02/NC_CHI/2014.For the other variant EVG 01/NC_CHI/2014, the inserted protease sequence replaced the entire viral capsid protein regionup to the VP1/2A junction. These two EV-G strains were highly prevalent in the same pig farm with all animals sheddingthe full-length genome (EVG 02/NC_CHI/2014) while 65% also shed the capsid deletion mutant (EVG 01/NC_CHI/2014).A helper-defective virus relationship between the two co-circulating EV-G recombinants is hypothesized