A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana.

Daniel A Truchado,Laura Benítez,Jonas Schmidt-Chanasit,Esperanza Gomez-Lucia,José Manuel Diaz-Piqueras,Borja Milá,Daniel Cadar,Javier Pérez-Tris,Ana Doménech

doi:10.3390/v11121148

Abstract

Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal–oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.

Highlights

An incomplete genome of a novel gyrovirus, named GyV11 (1855 b fragment) was assembled from one of the five cloacal pools subjected to deep sequencing
The findings suggest that this virus represents a novel member in the genus Gyrovirus, and we propose it as a new gyrovirus species or genotype, designated as GyV11 (GenBank accession number MH638372)
Owing to very low similarities with previously known gyroviruses, GyV11 could be designated as a novel gyrovirus species

Summary

Introduction

Numerous novel viruses and virus variants have been discovered by virus metatranscriptomics and metagenomics in different bird species, mainly in wild birds [1,2,3].there is still very little known about viruses that circulate in wild birds, especiallyViruses 2019, 11, 1148; doi:10.3390/v11121148 www.mdpi.com/journal/virusesViruses 2019, 11, 1148 in remote areas, and their possible interaction with domestic fowl or even their zoonotic potential. generation sequencing (NGS) technology allows the identification of, in principle, all the viruses present in a given sample, which improves our knowledge on the viral diversity and evolution in that area and helps estimate the potential risk to domestic fowl or humans [4].Gyroviruses (GyVs) are non-enveloped icosahedral viruses whose genome is a circular, single-stranded DNA molecule of approximately 2 Kb. Viruses 2019, 11, 1148 in remote areas, and their possible interaction with domestic fowl or even their zoonotic potential. Generation sequencing (NGS) technology allows the identification of, in principle, all the viruses present in a given sample, which improves our knowledge on the viral diversity and evolution in that area and helps estimate the potential risk to domestic fowl or humans [4]. Gyroviruses (GyVs) are non-enveloped icosahedral viruses whose genome is a circular, single-stranded DNA molecule of approximately 2 Kb. Gyroviruses (GyVs) are non-enveloped icosahedral viruses whose genome is a circular, single-stranded DNA molecule of approximately 2 Kb They are grouped in the genus Gyrovirus, which has been recently reclassified in the Anelloviridae family [5].

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