Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis.
The application of viral metagenomic techniques and a series of PCRs in a human fecal sample enabled the detection of two novel circular unisense DNA viral genomes with 92% nucleotide similarity. The viruses were tentatively named circo-like virus-Brazil (CLV-BR) strains hs1 and hs2 and have genome lengths of 2526 and 2533 nucleotides, respectively. Four major open reading frames (ORFs) were identified in each of the genomes, and differences between the two genomes were primarily observed in ORF 2. Only ORF 3 showed significant amino acid similarities to a putative rolling circle replication initiator protein (Rep), although with low identity (36%). Our phylogenetic analysis, based on the Rep protein, demonstrated that the CLV-BRs do not cluster with members of the Circoviridae, Nanoviridae or Geminiviridae families and are more closely related to circo-like genomes previously identified in reclaimed water and feces of a wild rodent and of a bat. The CLV-BRs are members of a putative new family of circular Rep-encoding ssDNA viruses. Electron microscopy revealed icosahedral (~23 nm) structures, likely reflecting the novel viruses, and rod-shaped viral particles (~65-460 × 21 × 10 nm in length, diameter, and axial canal, respectively). Circo-like viruses have been detected in stool samples from humans and other mammals (bats, rodents, chimpanzees and bovines), cerebrospinal fluid and sera from humans, as well as samples from many other sources, e.g., insects, meat and the environment. Further studies are needed to classify all novel circular DNA viruses and elucidate their hosts, pathogenicity and evolutionary history.
Department of Respiratory Diseases, Adolfo Lutz Institute, Av. Dr. Arnaldo, 355, CEP 01246-902, São Paulo, SP, Brazil. Electronic address: silbc@uol.com.br.
Silvana Beres
SB
Castrignano
Teresa Keico
TK
Nagasse-Sugahara
Jonas José
JJ
Kisielius
Marli
M
Ueda-Ito
Paulo Eduardo
PE
Brandão
Suely Pires
SP
Curti
D001938:Brazil; D018136:Circoviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000648:ultrastructure*; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D005243:Feces / Q000821:virology; D005260:Female; D016679:Genome, Viral; D006801:Humans; D008854:Microscopy, Electron; D008875:Middle Aged; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014771:Virion / Q000648:ultrastructure*
D004279:DNA, Viral
Circular Rep-encoding ssDNA virus; Complete genome; Electron microscopy; ICTV; International Committee on Taxonomy of Viruses; Metagenomics; Novel circo-like virus; ORF; RCR; Rep; Rep gene; SISPA; TEM; open reading frame; rolling circle replication; rolling circle replication initiator (protein/gene); sequence-independent single primer amplification; transmission electron microscopy.