What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken

Abstract

We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies.

Keywords: Gyrovirus; Meat; Parvoviridae; Polyomaviridae; Viral metagenomics.

Fig. 1

Genome organization (A) and amino acid-based neighbor-joining analysis of BPyV2-SF (GenBank KM111535) (B). Genome organization of MCPyV and SV40 is included for comparison. The vertebrate hosts are shown for each taxon. BPyV2-SF taxa are labeled by a black diamond. Shaded area indicated the VP3-less polyomaviruses.

Fig. 2

The ORF map of MPCLV-SFBeef (GenBank KM111537) (A) and SFPorkNW2 (B).

Fig. 3

Genome organization (A) and amino acid-based neighbor-joining analysis of GyV-SF1 (GenBank KM111536) (B–D). Included with each taxon is the species in which each sequence was found. GyV-SF1 identified in this study is marked with black diamond.