A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds

Abstract

Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2-3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.

Keywords: Metagenomics; next-generation sequencing; picornavirus; poultry; runting-stunting syndrome; virome.

Figure 1.

MEGAN taxonomic analysis displaying a viral family comparison between all seven samples. VF14-181 A1 and B1 (*) represent unaffected samples. The “Viruses” and “dsDNA viruses, no RNA stage” categories contained viral contigs from the families Siphoviridae, Myoviridae, Podoviridae, Herpesviridae, Reoviridae, Retroviridae, Polyomaviridae, Inoviridae, Baculoviridae, and Poxviridae. These unassigned contigs were accounted for in Table 1. Bars located next to each taxon are proportional to the total number of contigs assigned to each category from sequencing runs.

Figure 2.

MEGAN taxonomic analysis displaying a viral genera comparison between all seven samples. VF14-181 A1 and B1 (*) represent unaffected samples. Bars located next to each taxon are proportional to the total number of contigs assigned to each category from sequencing runs.