Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study

Circoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.

Members of the Circovirus (CV) and Cyclovirus (CyV) genera (Circoviridae family) have circular, single-stranded DNA genomes of 1.7-2.1 kb length enclosed in non-enveloped, icosahedral virions 1 . The replication-associated protein (rep) and capsid (cp) genes are transcribed bidirectionally 1 .The stem-loop structure at the 5' intergenic region has a role in the initiation of rolling-circle replication. Binding of the Rep protein near the origin of replication induces a nick in the nonanucleotide sequences of the stem-loop with its helicase and endonuclease activity supplying primer for the rolling circle amplification 1 . Circoviruses and cycloviruses could be distinguished based on the rep and cp position; the circoviral rep is located on the virion strand, while for cycloviruses this gene is encoded on the complementary strand 1,2 . The size of the intergenic region located between the stop codons of the two major ORFs could be also different and may be missing in some cycloviruses [1][2][3][4][5] .
A number of other circular, Rep-encoding single-stranded (CRESS) DNA viruses, which are currently not classified into these two genera, have been also characterized and may differ considerably in the genomic structure and gene orientation; for example, the genes of these viruses are either unidirectionally or bidirectionally oriented and the encoded rep and cp can be partially overlapping 1,[6][7][8] . With the development and general use of sequencing methods the amount of described CRESS DNA genomes have been rapidly expanded. To facilitate and reconsider the taxonomy of non-circoviral and non-cycloviral genomes, Rosario et al. established eight (I-VIII) types of genomes for grouping CRESS DNA viruses and made recommendations for reporting and classifying those 3 .
CRESS DNA viruses have been identified in terrestrial animals and marine organisms as well as environmental specimens collected in freshwater lakes, sewage or soil 1,[8][9][10][11][12][13][14][15] . Viruses of the Circoviridae family have been detected in domesticated, pet and wild birds. Some of these viruses (e.g., Beak and feather disease virus, Pigeon circovirus, or Goose circovirus) may cause serious infections and marked economical losses 1,16-18 . Furthermore, due to the provoked immunosuppression associated with circovirus infection the host bird may be predisposed to secondary infections by other microbes 16,19 .
In the present study we aimed at investigating the role of wild birds in the maintenance and transmission of pathogenic circoviruses. We applied a pan-circovirus PCR assay combined with sequencing of the amplified gene fragment. Based on the obtained gene sequences we performed whole genome sequencing on a subset of the identified circoviruses and other CRESS DNA viruses. Whole genome sequencing not only confirmed that the
Genomic diversity of cReSS DnA viruses. Because genomic fragments of CRESS DNA viruses have been commonly found in eukaryotic genomes as a consequence of ancient DNA integration events, it was important to verify that the amplified partial rep genes are parts of circular viral genomes 20 . Therefore, we performed whole genome amplification and sequencing. Back-to-back PCR amplicons were generated for nine specimens not analyzed earlier 6,21 and then subjected to next generation sequencing (Table 1). Five, three and one sequences showed similarities with the genome of DuACyV-1, GoCV, and GgaCV-1, respectively. The rep and cp genes, and control motifs typical for the reference genomes were readily identified in all viral genomes (Fig. 2).
The DuACyV-1 genomes encoded cp on the viral strand and rep on the complementary strand, with a 158 nt long non-coding region (NCR) between the 5' ends and a four nt long NCR between the 3' ends of the two genes. The nonanucleotide motif sequence in the NCR upstream of the cp was TAGTATTAC for all DuACyV-1 genomes 21 (Fig. 2). The 1902 nt long genomes of three strains (one sequence from great crested grebe or Podiceps cristatus and two sequences from mallards or Anas platyrhynchos) were near identical (99.7-99.8% genome-wide identity) with the same length of the rep and cp. Three newly determined DuACyV-1 genomes with a length of 1899 nt (two sequences from lesser white-fronted goose or Anser erythropus and one sequence from great crested grebe) were fully identical in their sequences ( Fig. 3 and Fig. 4). The cp genes derived from these shorter viral genomes were characterized by a three nt (i.e. one aa) deletion in the 5' region when compared with the cp genes of the variants with longer genome. The nt and aa identities of the Rep of strains DuACyV-1/1-1/5 (Table 1) ranged between 99.2-100% and 98.8-100%, while those for Cp it ranged between 72.1-100% and 73.4-100%, respectively. The genome wide identity was 88.6-100% for Hungarian DuACyV strains. DuACyV-1/1-1/5 showed 87.4-100% identity with viral sequences derived from fecal samples of diarrheic chickens (Gallus gallus) from Brazil 22 ( Fig. 3 and Fig. 4). In the phylogenetic tree of the Cp (Fig. 4) the strain DuACyV-1/4 and 1/5 grouped separately from the other known DuACyV sequences. On the other hand, in case of Rep, all DuACyV sequences clustered in a common branch (Fig. 3). To clarify this discrepancy, recombination analyses were carried out using the complete genomic sequences. Based on the RDP4 (with an average p-value between 2,023 ×10 −02 and 1.230 ×10 -23 as estimated by the different methods) and SIMPLOT analysis, putative recombination events were detected within the cp gene (Fig. 5). Unfortunately, due to the limited number of DuACyV sequences available currently in GenBank, it was not possible to infer the precise phylogenetic relationships and possible origins of the divergent capsid-coding regions within the DuACyV genomes.
The 1822 nt long GoCV genomes (n = 3) were characterized from cloacal swabs of wild mallard, wild greylag goose (Anser anser) and greater white-fronted goose (Anser albifrons). The GoCV genomes encoded an 882 nt long (nt 73-954) rep on the viral strand and a 783 nt long (nt 1791-1009) cp on the complementary strand with a 104 nt long NCR between the 5' ends, and a 54 nt long NCR between the 3' ends of the two major genes (Fig. 2). The nt and aa identities of the rep ranged between 97.3-97.7% and 99.3-99.8%, while those for the cap fell between 95.6-96.8% and 97.3-98.8%, respectively ( Fig. 3 and Fig. 4). The Hungarian genomic sequences showed 96.8-97.3% genome-wide identities. The Hungarian strains (strain GoCV-Hun1, -Hun2 and -Hun3) shared 97.0-99.4% genome-wide identities with the most closely related GenBank reference sequences collected from wild birds in Poland (Fig. 5) 19 . Recombination analysis using the RDP4 (with SiScan method, average p-value of 9.664 ×10 -08 ) and SIMPLOT software detected a common potential recombination event affecting the genomes of all three Hungarian GoCV strains and sequences from Poland (Fig. 5). In the phylogenetic analysis (Fig. 6), the Hun1 strain clustered together with a genotype VI strain (detected in wild greylag goose), while the Hun2 strain grouped with genotype V GoCV sequences. The strain Hun3 with a maximum of 96.9-97.1% whole genome sequence identity value was distinct from both genotype V and VI GoCVs and likely represents a novel genotype that we tentatively called genotype XVIII 19 .
The 1971 nt long genomes of the GgaCV-1 strains were identical (Figs. 3-4). The sequences were derived from distantly related bird species, the Eurasian jay and common teal (Table 1) 6 . These genomes coded for unidirectionally located, overlapping 891 nt long rep and 801 nt long cp on the viral strand with a 335 nt long NCR between the 5' end of the rep and 3' end of the cp, which encompassed the circovirus-like nonanucleotide motif of TAGTATTAC 6 (Fig. 2). Phylogenetic analyses placed both virus genomes in basal position when compared to CyVs and CVs.

Discussion
In this report we studied the occurrence of CRESS DNA viruses in cloacal samples of wild birds. Then we performed whole genomic analyses that permitted further insight into the genomic structure and evolutionary mechanisms of the identified viruses. A novel CRESS DNA virus, GgaCV-1, was uniquely identified in Hungary in two distantly related avian species, Eurasian teal and Eurasian jay 6 . Another newly described virus, DuACyV-1, since its first report 21 has been described in other waterfowls in Hungary and chickens in Brazil 22 . The question whether these two CRESS DNA viruses are pathogenic or innocuous viruses is open. A third group of CRESS DNA viruses, the GoCV, which is pathogenic to domestic geese, also shows a wider host spectrum than previously thought. Among bird species other than Anseriformes, GoCVs were detected in cormorant (Phalacrocorax carbo), grey heron (Ardea cinerea), European magpie (Pica pica), common buzzard (Buteo buteo) and Eurasian sea eagle (Haliaeetus albicilla) (Table 1). Furthermore, during the preparation of this manuscript, partial GoCV cp sequences became available in the DNA databases (unpublished GenBank records); these sequences derived from intestinal or other internal organ (liver, heart, kidney, gizzard) specimens of wild birds (including wild greylag goose, mallard, white stork (Ciconia ciconia), western jackdaw (Corvus monedula), European herring gull (Larus argentatus), brambling (Fringilla montifringilla), and rock dove (Columba livia)) collected in Poland between 2014 and 2017. Detection of GoCV in the internal organs may indicate active virus replication in distantly related wild bird species. This finding suggests that numerous wild bird species may serve as natural reservoirs for GoCV facilitating virus transmission among flocks of domestic geese. While analyzing the geographical data we observed that some CRESS DNA virus species were more common in a particular study area than in others (e.g., GoCV in Sárbogárd, DuACyV-1 in Mezőberény) raising the possibility that as yet unidentified factors may be more important in shaping the ecology and epizootiology of (potentially) pathogenic CRESS DNA viruses than the taxonomy, behavior or lifestyle of affected bird species. Nonetheless, an analytical evaluation of possible host species association with viral shedding was prevented by the low number of samples available for this study and by different sampling pattern of bird species at various study sites. Despite limitations that arose from the relatively low number of samples, our study provided new data on geographical distribution and genetic diversity of the identified CRESS DNA viruses. Wild birds, especially waterfowls, are able to carry low or high pathogenic avian viruses which can spread to geographically distant regions via their migration routes 23 . Influenza virus well exemplifies how long-distance migration birds contribute to the dispersal of highly pathogenic virus strains around the circumpolar region and help the virus to become globally spread within short period 23 . Hungary is a nesting area and a preferred resting place for wild greylag goose, greater white-fronted goose and mallard 24 . They migrate from North Europe to Middle and East Europe, and from the Carpathian Basin to South Europe and North Africa 24 . CRESS DNA viruses may be present in freshwater ecosystems and may have a role in virus circulation among distant freshwater habitats. This possibility on long-distance dispersal has now been demonstrated for GoCV and for DuACyV-1. Thus, for example, genetically closely related GoCVs were detected in Poland and Hungary. Additionally, DuACyV-1-like partial rep sequence was identified in human stool sample in Tunisia (GenBank acc.no. GQ404902) and DuACyV-1 genomes were detected in diarrheal chicken in Brazil 22 , suggesting a worldwide distribution of this virus species.
By analyzing the whole virus genomes from our sample archival we observed the following features with regard to the genetic variation of CRESS DNA viruses. (i) The genomic organization of the identified GoCVs, DuACyVs and GgaCVs strains was classified into CRESS DNA virus genome type 1, type 2 and type 5, respectively 3 . The main criteria that permit the classification into CRESS DNA virus genome types are the polarity and orientation of cp and rep genes, and the number of genes encoded by the genome 1,3,6,21 . (ii) Accumulation of point mutations resulted in limited genetic diversity among co-circulating CRESS DNA virus strains. This holds true even for GoCVs, which can be classified into XVII genotypes and one additional genotype described in the present study 19 . The three genotypes of GoCV were detected in the same Hungarian geographic area but from distinct host species. Similar findings were reported from Poland 19 . Despite the genetic diversity of GoCVs, low non-synonymous to synonymous substitution ratio was calculated (dN/dS, 0.0581 and 0.103 for the rep and cp, respectively; data not shown), implying that chiefly purifying selection acts on the genes of GoCVs. It needs to be monitored whether accumulation of mutations may help virus adaptation to novel hosts and could contribute to the selection of various genotypes in these novel host species over a long time. (iii) Recombination was found to shape the genomic evolution of the pathogenic GoCV as well as the DuACyV strains 19 . The recombination seen in GoCVs involved homologous viruses. In contrast, the parental strain that donated the cp gene for the recombinant DuACyVs is currently unknown and it is possible that the recombination event seen in these DuACyVs occurred between homologous or heterologous virus species. The relatively low cp gene sequence identity (nt, 72.1-72.4%; aa, 73.4-73.8%) in the two major variants of DuACyV might suggest that the recombination occurred between viruses belonging to different CyV species. Similar inter-virus-species recombination events  www.nature.com/scientificreports www.nature.com/scientificreports/ were reported for another group of CyVs, the dragonfly origin DfCyVs 25 . This possibility is further corroborated in the recent revision of CRESS DNA virus taxonomy where the authors claim that the 80% identity threshold established to demarcate distinct CV and CyV species generally holds true for pairwise comparisons of either the cp or rep gene sequences 1 .
In summary, our virus survey provides evidence of high detection rate of CRESS DNA viruses in wild bird samples around Hungarian lakes. More structured sampling that includes additional hosts and environmental specimens and extends the number of sites and duration of sample collection could help better understand the ecology and epizootiology of potentially pathogenic CRESS DNA viruses. New genome sequence data indicate that recombination among homologous and even among heterologous viral genomes contributes to the genetic diversity of CRESS DNA viruses highlighting the need for whole genome sequencing to become a routine approach when analyzing genetic diversity during virus surveillance studies.

Materials and methods
Samples. General considerations: Cloacal swabs and fecal samples were thought to serve as suitable materials to explore the diversity of (potentially) pathogenic CRESS DNA viruses 1 . The cloacal swabs were collected at variable country sites by veterinarians, hunters and ornithologists, who volunteered to contribute to the work of the national avian influenza virus surveillance network in Hungary. In terms of numbers and species of birds, sample collection was a fairly random process. Neither the minimum nor the maximum numbers of samples to be www.nature.com/scientificreports www.nature.com/scientificreports/ collected were defined. Consequently, at some study sites the prevailing wild bird species were sampled, whereas at other study sites the sampling better reflected the local bird species diversity. This random sampling resulted in differences in the host species composition of sample collections that prevented us from performing host species specific analysis of data.
The 90 cloacal swab specimens from 31 wild bird species were collected for compulsory seasonal influenza virus surveillance in November and December, 2013, at different lakes in Hungary near Sárbogárd  The barcoded samples were purified with Geneaid Gel/PCR DNA Fragments Extraction Kit, separated on a 2% precast gel (Thermo Fisher Scientific). Products between 300-350 bp were amplified with the PCR mixture of the NEBNext ® Fast DNA Fragmentation & Library Prep Set for Ion Torrent TM kit (NEB). The amplification protocol steps were initial denaturation at 98 °C for 30 sec, followed by 12 amplification cycles at 98 °C for 10 sec, 58 °C Figure 6. Maximum likelihood phylogenetic tree of goose circovirus complete genome sequences. Sequences identified in this study were highlighted by dots. The tree was generated by the PhyML online software with the best fitted TN93 + G + I model. SH-like support values <80 were not shown. Substitution per site is represented by the scale bar.