Anelloviruses (AV) were first found in the blood of a Japanese patient in 1997 [
1]. They have a small covalently closed single-stranded DNA genome. The complete DNA genome ranges from 2 to 3.9 kb in size [
2,
3]. AVs are a family of small circular ssDNA viruses with a vast genetic diversity [
3,
4]. The virus was first identified as the "TT virus" (TTV), meaning to the patient's initials. It was later called Torque teno virus after the Latin words “torques” (necklace) and “tenuis” (thin) referring to the organization of TTV DNA genome [
5]. Since AVs lack their own DNA polymerase, genome replication is entirely dependent on the machinery of the host cell [
6], where DNA polymerase forms a double-stranded DNA intermediate during the S (synthesis) process of the cell cycle [
7]. As a result, gene replication and ssDNA to dsDNA translation take place in the nucleus [
3]. The nucleotide sequence can be used to deduce two key open reading frames (ORFs), ORF1 and ORF2, as well as additional ORFs. These ORFs partly overlap, and their approximate sizes vary greatly among strains [
8]. Transfection of TTV DNA into cell cultures, as well as bone marrow cells originating from a TTV positive human, has been used to examine the transcriptional and protein profile of AVs [
6]. The study has shown that alternate translational initiation can be used to express at least 5–7 proteins with molecular weights ranging from 12 to 80 kDa [
9]. At present, AVs have been identified in several mammals [
10], such as pigs [
11], dogs [
12], masked palm civets [
13], rodents [
4,
14], bats [
15], sea lions [
16,
17] and primates [
3,
18]. These viruses are highly common, with a mostly stable global spread and a high level of genetic heterogeneity [
18]. Lupus, influenza, hematologic conditions, lung diseases, and myopathy are among the major diseases related to AVs [
19]. They can be transmitted by sexual routes, blood transfusions, and the fecal–oral pathway [
18,
20].
Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses [
4,
21]. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Furthermore, rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models [
22], and a history of pathogenic infections in these animals might directly affect the animal trial results. Viral metagenomics is an unbiased virus-detecting technique that is increasingly applied to non-specifically detect both already known and highly divergent viruses.
Although AVs have been identified in variety of mammal species, the pathogenicity of AV remains poorly understood owing to the lack of a suitable model cell line or animal to support the viral cycle. Here, using the viral metagenomic technique and bioinformatics analysis, we investigated the virome in the feces of experimental rats so as to finding possible AVs, which will be helpful for future establishing animal model for AV infection.