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Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach

¹ Unité des Virus Emergents EA3292, Etablissement Français du Sang Alpes-Méditerranée, Service de Virologie Moléculaire, 13005 Marseille, France
² Unité des Virus Emergents EA3292, Faculté de Médecine, 13005 Marseille, France
³ Institute for Animal Health, Pirbright Laboratory, Department of Arbovirology, Pirbright GU24 0NF, UK

Correspondence
Philippe Biagini
pbiagini-ets-ap{at}gulliver.fr

A combined rolling-circle amplification (RCA) and sequence-independent single primer amplification (SISPA) approach was applied to four samples of human plasma and one sample of saliva from a cat. This approach permitted the characterization of nine anelloviruses. Most of them were identified as highly divergent strains that were classified into species of the genus Anellovirus. The smallest anellovirus described so far in humans was characterized (2PoSMA, 2002 nt; ‘small anellovirus’ species). Two highly divergent sequences belonging to the species Torque Teno Mini Virus (LIL-y1, 2887 nt; LIL-y2, 2871 nt), which clustered into a new phylogenetic branch, were also identified in human plasma samples. Finally, two genomes that are separated by a genetic divergence of 46 % were characterized in the cat's saliva, one of these creating a distinct phylogenetic branch (PRA1, 2019 nt). These results highlight the potential of RCA–SISPA for detecting circular (or circularized) genomes.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are EF538875–EF538883.

A figure showing the predicted genomic structure of isolates LIL-y3 and PRA4 and a table showing the selected DNA fragments and oligonucleotide primers used for sequence extensions are available with the online version of this paper.