Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces

Abstract

Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named "Cyclovirus" whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.

FIG. 1.

Phylogenetic analysis of the translated Rep sequences amplified by pan-Rep PCR. Sequences derived from human stool samples (red), chimpanzee stool samples (purple), and farm animal meat samples (green) are indicated. Cycloviruses in the same species are defined as having >85% identity in Rep region and are labeled by vertical bars 1 to 25. The scale bar labeled 0.05 at the bottom of the figure represents 5% estimated phylogenetic divergence. The countries of origin are Pakistan (PK), Nigeria (NG), Tunisia (TN), and the United States (US).

FIG. 2.

Genomic organizations of circoviruses (A) and cycloviruses (B). The 2 major ORFs, encoding the putative replication-associated protein (Rep) and the putative capsid protein (Cap), and other ORFs with a coding capacity greater than 100 amino acids are shown. The locations of the stem-loop structures are marked.

FIG. 3.

Phylogenetic analysis of 15 Circoviridae replicase proteins from 12 human stool samples and 3 chimpanzee stool samples. Outlier taxa are non-Circoviridae Rep proteins. Sample designation is the same as in Fig. 1. CyCV, cyclovirus.

FIG. 4.

(A) Stem-loop of Cyclovirus prototype CyCV1-PK5006 and (B) nonamer sequences and stem lengths of the stem-loop structures for circoviruses and cycloviruses.