A novel rodent Chapparvovirus in feces of wild rats
- Shixing Yang†1,
- Zhijian Liu†1,
- Yan Wang1,
- Wang Li1,
- Xingli Fu1,
- Yuan Lin2,
- Quan Shen1,
- Xiaochun Wang1,
- Hua Wang1 and
- Wen Zhang1, 3Email author
© The Author(s). 2016
Received: 16 June 2016
Accepted: 25 July 2016
Published: 29 July 2016
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.
KeywordsWild rat Chapparvovirus Genome structure Viral Metagenomics
Parvoviruses can infect many species of animals and cause illness through individual or together with other viruses [1–3]. The virion of parvovirus is icosahedral and non-enveloped package, whose core is a linear single-stranded DNA genome of approximately 5 Kb long. The family Parvoviridae is divided into the subfamilies Parvovirinae and Densovirinae , which infect vertebrates and invertebrates, respectively. The subfamily Parvovirinae is divided into 8 genera: Dependoparvovirus, Copiparvovirus, Bocaparvovirus, Amdoparvovirus, Aveparvovirus, Protoparvovirus, Tetraparvovirus, and Erythroparvovirus. Recently two other genera of Marinoparvovirus and Chapparvovirus were identified. The genus of Marinoparvovirus only has one member named sesavirus which was discovered from the feces of a California sea lion pup suffering from malnutrition and pneumonia . The genus of Chapparvovirus have been detected from chicken feces samples, Eidolon helvum feces samples, and porcine multiple tissue samples including serum, rectal swab, nasal swab, and lung lavage [6–8]. Chapparvovirus, as a novel genus of parvovirinae, still have unclear species. Here, using viral metagenomics and PCR amplification, we identified a novel species of Chapparvovirus from the feces of wild rats and characterized its nearly complete genome.
In the present study, we investigated 40 fecal samples from wild rats captured by the Chinese Center for Disease Control and Prevention in Taizhou City from three districts of Taizhou City including Taixing (n = 15), Gaogang (n = 15), and Hailing (n = 10) from June to August in 2004. All of the wild rats were adults and the exact age was unknown.
Viral metagenomics method was used to characterize viral sequences in the fecal samples. Fecal samples were suspended in DPBS, vortexed for 10 min, and then centrifuged at 12,000 × g for 10 min. The stool suspensions were collected in 1.5 ml centrifuge tubes. Three pools were randomly generated, each of which contained 10 fecal suspensions. After low speed centrifugation and filtration, the samples were treated with DNase and RNase, to reduce levels of mink nucleic acids while viral genomes are protected from digestion within viral capsid [9, 10]. Three libraries were then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag for each pool. Resulting raw reads were trimmed for quality and primer, and de novo assembled into contigs. Sequences and contigs were compared to the GenBank non-redundant protein database using BLASTx with an E-value cutoff of <10−5.
To determine the relationship between RPV2 and the other members of the subfamily Parvoviridae, phylogenetic analysis over the NS1 protein of 48 members in the Parvovirinae was performed. Amino acid sequences of NS1 were aligned by ClUSTAL W, and phylogenetic trees were constructed with MEGA 6.0 software using the Neighbor-Joining statistical method based on the Jones-Taylor-Thornton matrix-based model. Result showed that RPV2 clustered with EHPV2, PPV7, and TP1, forming a separate clade (Fig. 1, panel b). Among them, RPV2 has the closest relationship with EHPV2, which was identified from fecal samples of Eidolon helvum .
To investigate the prevalence of RPV2 in wild rats, viral nucleic acid was extracted from all the 40 individual samples using TaKaRa MiniBEST Universal Genomic DNA Extraction Kit Ver.5.0 (TaKaRa, Japan). A set of nested primers designed basing on the NS1 nucleotide sequence of RPV2 was used to perform PCR screening in the 40 rat fecal samples. Primer RPV2 F1 (5′-TGGGTTCAGGCTACACAGGGTGG-3′) and RPV2 R1 (5′-CAGTCGCCCCTCTCAGGGCT-3′) were used for the first round of PCR, and RPV2 F2 (5′-AGCTGTACCCTGGGGAGAAATTGT-3′) and RPV2 R2 (5′-CGGGTTGTTGTCCTCTCGGCA-3′) for the second round, the expected length of amplified fragment was 419 bp. Our results indicated 17.5 % (7/40) of the fecal samples were positive. The PCR amplicons were T-A cloned and sequenced by Sanger method. Sequence analysis showed that the seven amplicons shared >98 % nucleotide identity, indicating a single virus strain was prevalent in the wild rats in this area.
In summary, we detected a novel rodent Chapparvovirus in wild rats and characterized its nearly complete genome. Phylogenetic analysis indicated that the RPV2 clustered with EHPV2, PPV7, and TP1, forming a separate clade. According to the genetic distance-based criteria, RPV2 belonged to a novel species of Chapparvovirus. Our epidemiologic data indicated RPV2 was prevalent in the wild rats in this area.
BLAST, basic local alignment search tool; DPBS, Dulbecco’s phosphate buffered saline; EHPV2, eidolon helvum parvovirus 2; NS1, nonstructural protein 1; ORF, open reading frame; PCR, polymerase chain reaction; PLA2, phospholipase A2; PPV7, porcine parvovirus 7; RPV2, rat Ch ap p arvo v irus 2; VP, capsid protein
This work was supported by the Natural Science Foundation of Jiangsu Province No. BK20130502 and BK20140537, the National Natural Science Foundation of China No. 31302107, the Professional Research Foundation for Advanced Talents of Jiangsu University No. 12JDG085 and 13JDG087, the Postdoctoral Foundation of Jiangsu Province No. 1302058C and 1302057C, the China Postdoctoral Foundation No. 2014 M561597 and China Postdoctoral Special Foundation No. 2015 T80503.
WZ and SY conceived the study. SY and ZL performed all the experiments. SY wrote the paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Ethics approval and consent to participate
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