Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates

Paulina D Anindita,Kimihito Ito,Aaron S Mweene,Hirofumi Sawa,Michael Carr,Wallaya Phongphaew,Gabriel Gonzalez,Bernard M Hang’Ombe,Michihito Sasaki,Yasuko Orba

doi:10.1038/s41598-019-41358-z

Paulina D Anindita, Kimihito Ito + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-41358-z

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Journal: Scientific Reports	Publication Date: Apr 8, 2019
Citations: 8	License type: open-access

Affiliation: Hokkaido University, University of Zambia

Abstract

The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses. An increasing number of smacovirus genomes have been identified exclusively in faecal matter of various vertebrate species and from insect body parts. However, the genetic diversity and host range of smacoviruses remains to be fully elucidated. Herein, we report the genetic characterization of eleven circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses detected in the faeces of Zambian non-human primates. Based on pairwise genome-wide and amino acid identities with reference smacovirus species, ten of the identified CRESS DNA viruses are assigned to the genera Porprismacovirus and Huchismacovirus of the family Smacoviridae, which bidirectionally encode two major open reading frames (ORFs): Rep and capsid protein (CP) characteristic of a type IV genome organization. The remaining unclassified CRESS DNA virus was related to smacoviruses but possessed a genome harbouring a unidirectionally oriented CP and Rep, assigned as a type V genome organization. Moreover, phylogenetic and recombination analyses provided evidence for recombination events encompassing the 3′-end of the Rep ORF in the unclassified CRESS DNA virus. Our findings increase the knowledge of the known genetic diversity of smacoviruses and highlight African non-human primates as carrier animals.

Highlights

The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses
Small circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses have been discovered in a diversity of prokaryotes and eukaryotes[2]
The family Smacoviridae was recently assigned as a new viral family by the International Committee on Taxonomy of Viruses (ICTV)[3], which is further classified into six genera

Summary

Introduction

The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses. We report the genetic characterization of eleven circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses detected in the faeces of Zambian non-human primates. Based on pairwise genome-wide and amino acid identities with reference smacovirus species, ten of the identified CRESS DNA viruses are assigned to the genera Porprismacovirus and Huchismacovirus of the family Smacoviridae, which bidirectionally encode two major open reading frames (ORFs): Rep and capsid protein (CP) characteristic of a type IV genome organization. Despite the lack of evidence for a direct causal relationship, smacoviruses were identified in the faecal virome derived from human patients with diarrhea in France as well as in central and south American children with unexplained gastrointestinal disease negative for known pathogens[13,15] It remains, to be established whether smacovirus infect human cells, causes overt disease or not in humans and animals. This study extends the known genetic diversity of smacoviruses and the species range of NHPs which harbour these ssDNA viruses

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