Sequence and phylogenetic analysis identifies a putative novel gyrovirus 3 genotype in ferret feces

Abstract

The genomic sequence of a novel gyrovirus (GyV) 3 strain was detected from the fecal sample of a pet ferret.The length (2359 nt) and the basic genomic structure of this strain was very similar to that of the single known GyV3 reference strain, whereas the genome sequence identity between the two strains was only 76%. Similarly, moderate sequence homology was found within the predicted protein coding regions, VP1 (nt, 72%; aa, 76%), VP2 (nt, 84%; aa, 85%) and VP3 (nt, 85%; aa, 73%). Sequence identities were lower when comparing our strain with other GyV species (48-65% genome-wide nt identity). Phylogenetic analysis of the coding regions clustered the ferret origin GyV3 strain within Clade A. Although the available whole genomic sequence of novel GyVs permits limited conclusions to be drawn regarding the classification of the Hungarian GyV3 strain, our data indicate that this novel strain may be considered as a new genotype within GyV3. Further investigations are needed to reveal the genetic diversity and biological properties of newly described members of the Gyrovirus genus.

A new gyrovirus in human feces

“…The third gyrovirus species (GyV3) was found in feces of human diarrhea cases from Chile [9] and Hong Kong [10]. A second genotype of GyV3 was recently reported in feces of ferrets [11]. GyV4 was detected in the feces from unexplained cases of human diarrhea and in chicken meats and skin specimens in Hong Kong [10].…”

Genome sequence of a cluster A13 mycobacteriophage detected in Mycobacterium phlei over a half century ago

“…Phage particles were concentrated by CsCl equilibrium gradient centrifugation, and the phage DNA was extracted by the proteinase K-phenolchloroform method. The purified genomic DNA was processed to obtain a barcoded library compatible with the Ion Torrent PGM semiconductor sequencing system [4]. The BLAST engine was utilized to assign and compare putative ORFs of the Phlei phage genome to reference phage genes with known functions.…”

A gyrovirus infecting a sea bird

“…Many of these gyroviruses have been reported in chickens (CAV, HGyV1/ AGV2, GyV3, 4, and 7) [4, 36]. CAV shows high resistance to inactivation [34], and DNA from CAV, HGyV1/AGV2, GyV3 and 4 has also been reported in feces of humans and other mammals, indicating possible dietary sources from consuming chicken [4, 7, 8, 22, 24, 31, 37]. Testing for HGyV1/AGV2 DNA in human blood samples has yielded conflicting results [2, 17, 18, 22], possibly complicated by its detection on human skin [28].…”

“…The gyrovirus KM348009, recently described in ferret feces, shared 76 % genome-wide nucleotide sequence identity with GyV3, and both viruses were considered different variants/genotypes of the same species [7, 8, 24]. A species cutoff value of <75 % genome-wide nucleotide sequence identity was proposed [8].…”

“…A species cutoff value of <75 % genome-wide nucleotide sequence identity was proposed [8]. Using BLASTn, the genome of GyV8 only showed detectable nucleotide similarity to those of other gyroviruses over short regions totaling ~ 11 % of its genome, readily qualifying GyV8 as the prototype of a new gyrovirus species.…”