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A novel rodent Chapparvovirus in feces of wild rats.

ABSTRACT: Chapparvovirus, a recently determined new genus in the family Parvoviridae, can infect many species of animals including bats, chickens, and pigs. Here, using viral metagenomics method, we identified a novel Chapparvovirus from feces of wild rats and designated it as rat parvovirus 2 (RPV2). The nearly complete genome of RPV2 is 4222-nt long and includes two ORFs encoding a 654-aa nonstructural protein 1 (NS1) and a 472-aa capsid protein (VP), respectively. Phylogenetic analysis over the amino acid sequence of the NS1 showed that RPV2 clustered with Eidolon helvum parvovirus 2 (EHPV2), porcine parvovirus 7 (PPV7), and turkey parvovirus 1 (TP1), forming a separate clade. Sequence analysis indicated that the NS1 protein of RPV2 shared the highest amino acid sequence identity (51 %) with that of EHPV2. According to the genetic distance-based criteria, RPV2 identified here belongs to a novel species of Chapparvovirus.

SUBMITTER: Yang S

PROVIDER: S-EPMC4966819 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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A novel rodent Chapparvovirus in feces of wild rats.

Yang Shixing S Liu Zhijian Z Wang Yan Y Li Wang W Fu Xingli X Lin Yuan Y Shen Quan Q Wang Xiaochun X Wang Hua H Zhang Wen W

Virology journal 20160729

Chapparvovirus, a recently determined new genus in the family Parvoviridae, can infect many species of animals including bats, chickens, and pigs. Here, using viral metagenomics method, we identified a novel Chapparvovirus from feces of wild rats and designated it as rat parvovirus 2 (RPV2). The nearly complete genome of RPV2 is 4222-nt long and includes two ORFs encoding a 654-aa nonstructural protein 1 (NS1) and a 472-aa capsid protein (VP), respectively. Phylogenetic analysis over the amino a ...[more]

PMID: 27473724

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Project description:BackgroundRodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models, and a history of pathogenic infections in these animals will directly affect the animal trial results. The pathogenicity of Anellovirus (AV) remains poorly understood due to the lack of a suitable model cell line or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique.MethodsFecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline and two novel anelloviruses (AVs) were identified from fecal sample of experimental rats. The prevalence of these two viruses was investigated by conventional PCR.ResultsThe complete genomic sequence of these two AVs were determined and fully characterized, with strain name ratane153-zj1 and ratane153-zj2. The circular genomes of ratane153-zj1 and ratane153-zj2 are 2785 nt and 1930 nt in length, respectively, and both include three ORFs. Ratane153-zj1 closely clustered with members within the genus Wawtorquevirus and formed a separate branch based on the phylogenetic tree constructed over the amino acid sequence of ORF1 of the two AVs identified in this study and other related AVs. While the complete amino acid sequences of ORF1 of ratane153-zj2 (nt 335 to 1390) had the highest sequence identity with an unclassified AV (GenBank No. ATY37438) from Chinchilla lanigera, and they clustered with one AV (GenBank No. QYD02305) belonging to the genus Etatorquevirus from Lynx rufus. Conventional PCR with two sets of specific primers designed based on the two genomes, respectively, showed that they were detectable at a low frequency in cohorts of experimental rats.ConclusionOur study expanded the genome diversity of AVs and provided genetic background information of viruses existed in experimental rats.

Project description:Rodent species, such as Rattus rattus diardii and Rattus norvegicus are invasive species of wild rats that serve as potential reservoirs of important human's pathogens. Parasitic zoonosis accounts for over 60% of all human infectious diseases worldwide. This situation arises from the recent changes in the global climate and ecosystem composition, which led to the spread of rodents and rodent-borne pathogens globally. The aim of this study was to determine the occurrence of rodent's parasites and their zoonotic potentials in some selected areas in UPM. Rodents were captured using live-traps and euthanised for helminths and protozoan recovery. Intestinal parasites were detected and identified from stool samples using formalin ethyl-acetate concentration technique (FECT), while tissue parasites were identified by histopathological examination of selected tissue sections of the liver, brain, lungs, and muscle. In this study, a total of 89 wild rats were captured. Twelve species of intestinal and tissue parasites were recorded, of which, Taenia taeniaeformis accounts for the highest infection recorded (28%) followed by Hymenolepis nana (19.5%) and Capillaria hepatica (19.1%), while Toxoplasma gondii was the least parasite (6.7%) identified. Furthermore, other parasites species observed include, Cryptosporidium spp. (21.3%), Entamoeba histolytica/Entamoeba dispar and Moniliformis moniliformis (17.9%), Angiostrongylus cantonensis (16.8%), Hymenolepis diminuta (16.1%), Giardia spp. (14.6%), Trichuris spp. (12.3%), and Sarcocystis spp. (6.74). Based on the results obtained in the present study, 17.1% and 15.4% of the rodents captured were confirmed positive for at least one species of intestinal or tissue parasites, respectively. The presence of these zoonotic parasites in the wild rats suggests the potential risk of rodent-borne zoonotic disease transmission to humans. Hence, the need to improved rats control intervention and public health awareness among the populace.

Dataset Information

A novel rodent Chapparvovirus in feces of wild rats.

Publications

A novel rodent Chapparvovirus in feces of wild rats.

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