Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China

Zhibin Shi,Xijun He,Zaisi Liu,Hua Liu,Yan Chen,Lili Wei,Chunguo Liu,Huanliang Yang,Yongping Jiang,Jingfei Wang

doi:10.1007/s12250-020-00232-3

Abstract

Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.

Highlights

Zhibin Shi and Chunguo Liu have contributed to this work.Electronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.Many viruses with circular DNA genomes, including circular replication-associated protein (Rep)-encoding singlestranded (CRESS) DNA viruses, have been reported in both human and animal virome studies (Sikorski et al 2013a; Tan le et al 2013; Cui et al 2017; Kaszab et al 2018; Kraberger et al 2018; Varsani and Krupovic 2018)
Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)encoding single-stranded (CRESS) DNA virus that has been detected in mammals
We report for the first time the identification of FSfaCVs in pigs in Anhui Province, China

Summary

Introduction

Many viruses with circular DNA genomes, including circular replication-associated protein (Rep)-encoding singlestranded (CRESS) DNA viruses, have been reported in both human and animal virome studies (Sikorski et al 2013a; Tan le et al 2013; Cui et al 2017; Kaszab et al 2018; Kraberger et al 2018; Varsani and Krupovic 2018). A convincing causal relationship between the animal-associated viruses from other CRESS DNA viral families (e.g., Smacoviridae and Genomoviridae) and any disease, has yet to be documented (de Rezende et al 2018; Steel et al 2016; Walters et al 2017) Infections with these viruses may play a Virologica Sinica role in disorders of the host immune system and become an indirect factor for diseases caused by other pathogens (Shulman and Davidson 2017)

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