Description of the first isolates of Guinea fowl corona and picornaviruses obtained from a case of Guinea fowl fulminating enteritis.

Guinea fowl fulminating enteritis has been reported in France since the 70s. In 2014, a coronavirus was identified and appeared as a possible viral pathogen involved in the disease. In the present study, intestinal content from a guinea fowl involved in a new case of the disease in 2017 was analyzed by deep sequencing, revealing the presence of a guinea fowl coronavirus (GfCoV) and a picornavirus (GfPic). Serial passage assays into the intra-amniotic cavity of 13-day-old specific pathogen free chicken eggs and 20-day-old conventional guinea fowl eggs were attempted. On chicken eggs, isolation assays failed, but on guinea fowl eggs, both viruses were successfully obtained. Furthermore, two GfCoV and two GfPic isolates were obtained from the same bird but from different sections of its intestines. This shows that using eggs of the same species in which the virus has been detected can be key for successful isolation.The consensus sequence of the full-length genomes of both GfCoV isolates were highly similar, and correlated to those previously described in terms of genome organization, ORF length and phylogenetic clustering. According to full-length genome analysis and the structure of the Internal Ribosome Entry Site, both GfPic isolates belong to the <i>Anativirus</i> genus and specifically the species <i>Anativirus B</i>. The availability of the first isolates of GfCoV and GfPic will now provide a means of assessing their pathogenicity in guinea fowls in controlled experimental conditions and to assess whether they are primary viral pathogens of the disease ‘guinea fowl fulminating enteritis’. RESEARCH HIGHLIGHTS First isolation of guinea fowl coronaviruses and picornaviruses Eggs homologous to the infected species are key for isolation Isolates available to precisely evaluate the virus roles in fulminating enteritis First full-length genome sequences of guinea fowl picornaviruses