Enteric Viruses Nucleic Acids Distribution along the Digestive Tract of Rhesus Macaques with Idiopathic Chronic Diarrhea

Abstract

Idiopathic chronic diarrhea (ICD) is a little understood common clinical problem in captive rhesus macaques claiming 33% of medical culls unrelated to research. The eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD was characterized using viral metagenomics. We compared the distribution of viral reads in tissues and mucosal scrapings from the stomach, duodenum, jejunum, ileum, and the proximal, transverse, and distal colons. In situ hybridization (ISH) using viral probes were performed on fixed tissues. Deep sequencing revealed multiple viruses in the Parvoviridae and Picornaviridae family. Tissues and mucosal scraping from the same locations showed closely related viral reads contents while different gut tissues from the same animal varied widely. ISH showed punctuated staining for both RNA and DNA viruses in the distal colon. Parvovirus staining was also detected in the stomach/duodenum/jejunum in distinct oval-shaped structures. The location of enteric viral nucleic acid differed widely between different viral families and along the length of the digestive tract.

Keywords: biogeography; idiopathic chronic diarrhea; viral metagenomics; virome.

Figure 1

Viruses detected and their abundance in RPM in tissue and mucosal scrapings from the stomach, duodenum, jejunum, ileum, proximal colon, transverse colon, and distal colon of nine macaques with ICD.

Figure 2

Abundance of viral reads in RPM along length of the digestive tract. Top panel: Abundance of eukaryotic viral reads from tissues along the intestinal tract for all animals. Bottom panel: Abundance of eukaryotic viral reads from mucosal scrapings along the intestinal tract for all animals. Blue shading represents different enteroviruses, while shades of pink or purple represent different parvoviruses.

Figure 3

Abundance of picornavirus and parvovirus reads in RPM along the length of the digestive tract. Top panel: Abundance of eukaryotic viral reads from tissues along the intestinal tract for all animals. Bottom panel: Abundance of eukaryotic viral reads from mucosal scraping along the intestinal tract for all animals. Shades of blue represent different enteroviruses, while shades of pink or purple represent different parvoviruses.

Figure 4

MDS plot of a Bray-Curtis dissimilarity matrix. The large intestine tissues are represented in shades of blue, the small intestine tissues are in shades of pink, and the stomach is in orange. Circles represent mucosal scrapings, while triangles represent tissue samples.

Figure 5

Representative positive microscope fields of different gut tissues hybridized with RNAScope viral probes. (A) Erythroparvovirus probes hybridized with 46526 tissues. (B) Quantitation of fluorescent signal of erythroparvovirus RNA in 46526 (left frame) and protoparvovirus RNA probe in 46700 (right frame). (C) Enterovirus 19 probe hybridized with 46636 tissues. (D) Quantitation of RNAScope signal for enterovirus 19 RNA in 46636 (left frame), 46774 (middle frame), and 57210 (right frame).