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

• Published in: Scientific reports Vol. 9; no. 1; p. 5045
• Main Authors: Anindita, Paulina D., Sasaki, Michihito, Gonzalez, Gabriel, Phongphaew, Wallaya, Carr, Michael, Hang’ombe, Bernard M., Mweene, Aaron S., Ito, Kimihito, Orba, Yasuko, Sawa, Hirofumi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.04.2019; Nature Publishing Group
• Subjects: 45/22; 45/23; 45/47; 45/77; 631/208/212/2306; 631/326/596/2554; Amino acids; Animals; Capsid protein; Deoxyribonucleic acid; DNA; DNA viruses; DNA Viruses - classification; DNA Viruses - genetics; DNA Viruses - isolation & purification; Genera; Genetic diversity; Genome, Viral; Genomes; Haplorhini; Host range; Humanities and Social Sciences; multidisciplinary; Open Reading Frames; Phylogeny; Primates; Recombination; Science; Science (multidisciplinary); Single-stranded DNA; Smacoviridae; Viral Proteins - genetics; Viruses; Zambia; Zambia
• DOI: 10.1038/s41598-019-41358-z
• ISSN: 2045-2322

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 c ircular r eplication-associated protein ( Rep ) e ncoding s ingle- s tranded (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.