Kapusinszky Beatrix, Ardeshir Amir, Mulvaney Usha, Deng Xutao, Delwart Eric
Blood Systems Research Institute, San Francisco, California, USA.
Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA.
J Virol. 2017 Aug 24;91(18). doi: 10.1128/JVI.00952-17. Print 2017 Sep 15.
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, , , , , and , collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families and were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
腹泻是影响恒河猴供应且可能影响其对实验性治疗反应的非研究相关发病和死亡的主要原因。恒河猴特发性慢性腹泻（ICD）也类似于溃疡性结肠炎，这是人类炎症性肠病的一种形式。为了检测病毒病因，我们对32只健康动物、31只急性腹泻动物和29只患有ICD的动物的粪便病毒组进行了表征和比较。健康组真核病毒读数的总体比例为0.063%，急性腹泻组为0.131%，慢性腹泻组为0.297%。鉴定出属于6个病毒科的真核病毒以及众多环状Rep编码单链DNA（CRESS DNA）病毒基因组。最常检测到的序列来自小RNA病毒，占所有病毒读数的59%至88%，其次是CRESS DNA病毒序列，占9%至17%。其余5个病毒科，即 、 、 、 和 ，总共占病毒读数的1%至3%，但细小病毒除外，其在健康组中占病毒读数的23%。检测到的 科和 科成员高度多样化，由多个属、种和基因型组成。检测到多达六个病毒科成员的共感染。组装了完整和部分病毒基因组，并用于测量来自两个临床组和健康对照组的92只动物粪便中匹配短序列读数的数量。相对于健康动物，几种肠道病毒基因型和CRESS DNA基因组与ICD相关。相反，来自不同细小病毒的较高读数与健康动物相关。我们的研究揭示了圈养恒河猴群体中肠道病毒共感染的高水平，并鉴定出几种与ICD呈正相关或负相关的病毒。
