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Viruses 2018, 10(3), 107; https://doi.org/10.3390/v10030107

Article
Recombinant Goose Circoviruses Circulating in Domesticated and Wild Geese in Poland
1
Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719 Olsztyn, Poland
2
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
3
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
4
The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287, USA
5
Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
*
Authors to whom correspondence should be addressed.
Received: 11 February 2018 / Accepted: 25 February 2018 / Published: 2 March 2018

Abstract

:
Circoviruses are circular single-stranded DNA (ssDNA) viruses that infect a variety of animals, both domestic and wild. Circovirus infection in birds is associated with immunosuppression and this in turn predisposes the infected animals to secondary infections that can lead to mortality. Farmed geese (Anser anser) in many parts of the world are infected with circoviruses. The majority of the current genomic information for goose circoviruses (GoCVs) (n = 40) are from birds sampled in China and Taiwan, and only two genome sequences are available from Europe (Germany and Poland). In this study, we sampled 23 wild and 19 domestic geese from the Gopło Lake area in Poland. We determined the genomes of GoCV from 21 geese; 14 domestic Greylag geese (Anser anser), three wild Greylag geese (A. anser), three bean geese (A. fabalis), and one white fronted goose (A. albifrons). These genomes share 83–95% nucleotide pairwise identities with previously identified GoCV genomes, most are recombinants with exchanged fragment sizes up to 50% of the genome. Higher diversity levels can be seen within the genomes from domestic geese compared with those from wild geese. In the GoCV capsid protein (cp) and replication associated protein (rep) gene sequences we found that episodic positive selection appears to largely mirror those of beak and feather disease virus and pigeon circovirus. Analysis of the secondary structure of the ssDNA genome revealed a conserved stem-loop structure with the G-C rich stem having a high degree of negative selection on these nucleotides.
Keywords:
circovirus; goose; diversity; recombination; ssDNA virus; secondary structure; selection

1. Introduction

Circoviruses (genus: Circovirus; family: Circoviridae) are non-enveloped, icosahedral viruses, with circular single-stranded DNA (ssDNA) genomes which are approximately 2 kb in length. Transcription is bidirectional with a replication-associated protein (Rep) encoded on the virion sense strand and a capsid protein (CP) on the complementary sense strand [1,2]. Circoviruses are known to infect various bird, mammal, and fish species [1]. The main consequence of circovirus associated infections in birds is immunosuppression which is associated with the apoptosis of lymphocytes [3,4,5,6]. This immunosuppression can predispose circovirus infected birds to secondary infections by pathogenic bacteria, fungi, and viruses [7].
Goose circovirus (GoCV) was firstly described by Soike, et al. [8] in a German commercial geese flock showing runting syndrome that was associated with a high degree of mortality. Subsequently, GoCV has been found infecting domesticated geese in other European and Asian countries [9,10,11,12,13] and, more recently, the virus has also been found in wild geese [14]. Based on published data, the prevalence of GoCV infections in domesticated geese (~20–56%) is similar to that noted for circovirus infections in pet/wild parrots (~20–64%) but generally lower than that for circoviruses infecting pigeons (~36–100% depending on age and health status) [9,12,15,16,17,18].
Geese infected with GoCV often shows non-specific clinical symptoms such as diarrhea and growth retardation [5]. Feather disorders, similar to those observed in circovirus-infected parrots [19], have also been observed in geese infected with GoCV [5]. Post-mortem examinations of infected birds frequently reveal both splenomegaly and enlargement of the thymus and liver while hemorrhages in the epi- and endocardium, the lungs, and the thymus have also been noted [5]. The most common histopathological changes are depletion of T-lymphocytes in lymphoid organs including the thymus, the spleen, and the bursa of Fabricius [5]. There have also been cases where GoCV has been found in co-infections with West Nile virus [11,12].
Although 42 full GoCV genomes are presently available in GenBank, all but one sequence from a domesticated goose in Germany and another from a wild graylag goose in Poland, have been obtained from two countries; China (n = 15) and Taiwan (n = 25). With the intention of determining the diversity of GoCV in Europe we screened wild and domestic geese in Poland for GoCV infections and, in birds when infections were detected we cloned and sequenced full GoCV genomes.

2. Materials and Methods

2.1. Sample Collection and Processing

Spleen and liver sections were collected during necropsy from 23 wild geese and one mallard duck that had been shot by sport hunters in the area around Gopło Lake in Kujawsko-Pomorskie District in Poland. Similar tissue types were also sampled from slaughtered domestic geese (n = 19) from farms located in the areas around Gopło Lake. Sample descriptions are provided in Table 1. Forty four tissue samples (each approximately 50 mg) were individually homogenized in 500 µL PBS using Tissuelyser II (Qiagen, Hilden, Germany). The supernatant from the homogenate (~200 µL) was used for DNA isolation using a Janus automated workstation (Perkin Elmer, Waltham, MA, USA) and NucleoMag Tissue Kit (Macherey-Nagel, Düren, Germany).

2.2. Screening and GoCV Genome Recovery

Each sample was prescreened with the broad-spectrum nested PCR method targeting the rep genes of various avian circoviruses in accordance with Halami et al. [20]. For each positive sample, circular DNA was amplified using 1 µL of total DNA and TempliPhi (GE Healthcare, Marlborough, MA, USA) as previously described [16,21]. Full GoCV genomes were recovered using the enriched DNA as a template with back-to-back primer pair GoCV-F 5′-CTSTCTCGWGCYCGGGGATCTGAC-3′ and GoCV-R 5′-CCAGGCTCTTCCTCCCAGCKWCTCTT-3′ using Kapa HiFI Hotstart DNA polymerase (Kapa Biosystems, Wilmington, DE, USA) with the following thermal cycling protocol: 96 °C for 3 min, 25 cycles (98 °C (20 s), 60 °C (30 s), 72 °C (2 min)), 72 °C for 3 min. Amplicons were resolved on 0.7% agarose gels and ~2 kb fragments were excised. Gel excised fragments were purified using a MEGA-spin Agarose Gel DNA Extraction Kit (iNtRON Biotechnology, Daejeon, Korea). Cleaned products were ligated into the plasmid pJET 2.1 (Thermo Fisher Scientific, Waltham, MA, USA) and transformed into DH-5α Escherichia coli competent cells. Recombinant plasmid DNA was isolated from single E. coli colonies using a DNA-spin Plasmid DNA Extraction Kit (iNtRON Biotechnology, Daejeon, Korea) and these were subsequently Sanger sequenced (Macrogen Inc., Seoul, Korea). Full genome coverage was obtained using primer walking. Sequence contigs were assembled into full genomes using DNA Baser V4 (Heracle BioSoft S.R.L., Pitesti, Romania).

2.3. Bioinformatic Analysis

The genetic diversity among the GoCV isolates was analyzed using SDT v1.2 [22]. Given that recombination has been detected in a range of other circoviruses, prior to phylogenetic analysis the 63 GoCV full genome sequences were aligned using MUSCLE [23] and analyzed for recombination using the seven detection methods implemented in RDP version 4.70 [24]. A maximum likelihood (ML) phylogenetic tree accounting for recombination was then constructed with PHYML 3.0 [25] using the full genome sequence alignment from which all recombinationally inherited genome segments had been removed. This tree was inferred with the best-fit substitution model GTR + G determined using jModelTest [26], with 1000 bootstrap replicates used to infer branch support and rooted with two swan circovirus sequences (EU056309, EU056310). Branches with less than 60% support were collapsed using TreeGraph2 [27].
The GoCV, PiCV, and BFDV gene sequences were all initially codon aligned within a singled data set so as to ensure that homologous codon sites could be accurately compared to one another following selection analyses. Gene sequences from each of the three species were then analyzed separately to identify codon sites evolving under either positive or negative selection using FUBAR [28] and under episodic positive selection using MEME [29]. We subsequently used the difference between the non-synonymous (dN) and synonymous (dS) rates (dN-dS) obtained from FUBAR and the locations of sites evolving under episodic selection from MEME to generate a selection map comparing the types and degrees of selection between the three circovirus datasets (GoCV; pigeon circovirus, PiCV; beak and feather disease viruses, BFDV) using the computer program SelectionMap (http://www.cbio.uct.ac.za/~brejnev/ComputationalTools.html).
Given that evidence of pervasive biologically relevant secondary structural elements has been found in other circovirus genomes, we used the computer program NASP [30] as previously described by Muhire, et al. [31] to identify and rank, in order of conservation, the secondary structural elements that are most likely present within the 63 GoCV genomes. Briefly, this was achieved using the minimum free-energy (MFE) approach implemented in the hybrid-ssmin component of UNAFold (with sequences treated as circular and folding carried out at 37 °C under 0.1 M magnesium and 1 M sodium ionic conditions) [32] to infer ensembles of secondary structural elements within ten GoCV genomes representing the known breadth of GoCV diversity (DQ192281, DQ192285, KP203866, KP229371, KT808650, KT808653, KT808656, KT808657, KT808663, KT808668) and ranking of structures based on the relative degrees to which inferred base-pairing interactions were conserved within them. From these ranked lists of plausible conserved structural elements, subsets of high-confidence structural elements—referred to as a high-confidence structure set (HCSS)—were identified using a nucleotide-shuffling permutation test (with 100 permutations and a p-value cutoff 0.05). In subsequent analyses, the only nucleotides considered as being paired within secondary structures were those identified by NASP as being base-paired within the HCSSs, while all other nucleotides were treated as unpaired sites. Structures were visualized with overlaid evolutionary data using the computer program DOOSS [33] and compared to similar structures in other circovirus genomes (namely beak and feather disease viruses (BFDV) and pigeon circovirus (PiCV), which were analyzed previously using identical methods [21].

3. Results and Discussion

3.1. GoCV in Domestic and Wild Geese in Poland

We recovered the genomes of GoCV from 14 domestic Greylag geese (Anser anser) and three wild Greylag geese (A. anser), three bean geese (Anser fabalis), and one white fronted goose (Anser albifrons) (Table 2; GenBank accession #s KT808650–KT808670). The 21 genomes share between 83% and 95% pairwise identities with other GoCV genomes available in GenBank (Figure S1). One of the GoCV genome sequences (GenBank accession # KT808657; Figure S1) from a domestic Greylag goose was most closely related to a divergent GoCV sequence recovered from a Polish wild Greylag goose (89%) [14] and, collectively, these two genomes share <84% genome-wide pairwise identity with all other known GoCV genomes.
In order to rationally categorize the presently known GoCV sequences, we determined the distribution of genome-wide pairwise identities (Figure 1). Owing to the trough in this distribution at 98% identity (indicating that there are very few sequences that share 98% genome-wide pairwise identity), we opted to use 98% as a threshold for assigning the genomes to different genotype groupings. According to this threshold, the 63 known GoCV genomes can be assigned to 17 genotypes (which we have simply named I through XVII; Figure 2; Table 2). Whereas the Polish sequences fell within nine of these genotype groupings (IV, V, VI, VII, XII, XIII, XIV, XVI, and XVII; Figure 2), the 15 GoCV genomes from China belong to four genotypes (III, VIII, IX, and X), the 25 from Taiwan to three genotypes (I, II, and XI), and the isolate from Germany to genotype XII (Figure 2).
It is noteworthy that the GoCV genotype assignments for the Polish isolates display a degree of host-structure (Figure 2; Table 2). Specifically, the isolates from wild geese belong mainly to the genotypes V, VI, and VII with a divergent Greylag goose isolate [14] falling within genotype XVII. Interestingly, the isolates obtained from the migratory bean and white fronted geese which do not nest in Poland, fall exclusively within genotype V. Conversely the genotype VI, VII, and XVII isolates were from wild Greylag geese which nest in the area of Gopło Lake. The genome-wide pairwise identities that are shared by GoCV isolates from wild migratory geese and those from local population geese are ~97%, whereas the isolates obtained from wild geese belonging to genotype V all share close to 100% pairwise identity with one another.
The GoCV isolates from wild geese were closely related to genotype IV isolates from domestic Greylag geese (94–95% identity). GoCV isolates assigned to genotypes XIII through XV are from domestic Greylag geese used for reproduction which share between 84% and 90% genome-wide pairwise identity with isolates from wild and domestic geese that have been slaughtered. The GoCV genotypes circulating in wild geese in the area of Gopło Lake therefore differ from those found in domestic geese kept in this area.
Seven unique recombination events were identified within 28 of the 63 GoCV sequences with a transferred fragment size spanning between 27% and 50% of the genome (Figure 2). Six of the nine polish genotypes were identified to be recombinant (IV, V, VI, VII, XIII, and XIV; Figure 1). As was suggested by the pairwise sequence analyses, the maximum likelihood phylogenetic tree that was constructed following the removal of recombinationally acquired genome segments displayed strong evidence of geographical structure.
We detected and compared natural selection signals within codon alignments of the GoCV rep and cp genes using two different codon-by-codon selection detection approaches (Figure 3; Supplementary data 1). In the BFDV cp there are three instances of positive selection, as opposed to none in PiCV and one in GoCV. The instances of episodic positive selection appears to largely mirror each other. The negative selection appears to be higher in the rep genes compared to cp (based on individual dN/dS values).

3.2. DNA Secondary Structure Analysis of GoCV Genomes

The stem-loop structures in GoCV and BFDV visualized in Figure 4A were both highly conserved among the plausible structural elements detected within the genomes of these two species (2nd out of 137 in GoCV and 9th out of 143 in BFDV). Despite sharing no obvious sequence similarity, the similar GC-rich, stable stem-loop conformation and genomic location of the structural elements in rep could indicate shared biological function across viral species. The excessively low synonymous substitution rates observable in the stem region of both structures (indicated by the blue coloring of the nucleotides) indicates a high degree of negative selection acting at the nucleotide-level for these particular sites.
Tests designed to determine whether the evolution of GoCV sequences was consistent with the selective preservation of biologically functional structural elements within their genomes were applied exactly as described by Muhire et al. [31]. These tests compared paired sites within the HCSS structures to unpaired sites with respect to degrees of evolutionary neutrality, synonymous substitution rate, and rates of complementary coevolution. Identical evolutionary analyses to those performed here on GoCV have been previously carried out on BFDV and PiCV [21], enabling the direct comparison of these three circovirus species.
At the whole-genome-scale, neutrality tests (which compare frequencies of minor/alternative allele frequencies at polymorphic paired sites with those occurring at unpaired sites) were used to test for elevated degrees of purifying selection at paired sites relative to unpaired sites. For all 3 datasets examined (GoCV, BFDV, and PiCV), minor allele frequencies were significantly lower at paired sites than at unpaired sites as indicated by lower D and F test static values (p < 0.01 in all cases), with the exception of GoCV (p = 0.66, Tajima’s D test) (Figure 4C). This finding is consistent with purifying selection being stronger at paired-nucleotide sites within the HCSS than at the remainder of unpaired genomic sites. This strong signal of purifying selection indicates that a substantial proportion of paired sites within the HCSS of the analyzed genomes are evolving in a manner that is consistent within many of the parent structures being evolutionarily preserved.
A very strong association between nucleotide sites that are complementary coevolving and nucleotide sites that are base-paired was detected in the BFDV dataset (p = 1.59 × 10−13) (Figure 4B). This provides compelling evidence that at least a subset of the structures in the BFDV genome likely provide a significant fitness advantage to the viruses, which suggests that these structures may have crucial, as yet undetermined biological functions. The lack of significant evidence of coevolution between paired-nucleotides within the GoCV HCSS may be due to the aforementioned high inter-cluster divergence of the GoCV species, or a lack of detectable biologically important structures.

4. Conclusions

The GoCV genome diversity in domesticated geese was found to be higher than that in wild geese. The domestic geese sampled in this study were slaughter birds which were from parental flocks (reproductive birds). Furthermore, a large number of these genomes are recombinant and this is likely due to the high density of birds in slaughter flocks, and in the herds of wild geese during migration, which facilitate recombination among GoCVs, similar to what has been noted for BFDVs in parrot breeding facilities [16]. The farming of geese in areas that are also inhabited by wild geese may enable the transfer of pathogens between domestic and wild geese populations. Although the GoCV variants from wild and domestic geese are in different genotype groupings, the detection of recombination between viruses assigned to the “wild” and “domestic” genotypes and suggests that may be at least a low degree of GoCV circulation between domestic and wild geese population—possibly even in the area of Gopło Lake. If there are indeed persistent low-levels of viral transmission between wild and domestic birds, this may expose both the domestic birds to pathogens from throughout the seasonal geographical ranges of the wild-birds (which include taiga areas of Scandinavia and that of Central to North Siberia, and the Siberian tundra), and the wild birds throughout those same geographical ranges to pathogens originating within the Polish domestic goose farming sector.
Taking into consideration the high diversity of GoCVs, which is typical for all avian circoviruses, and the fact that these viruses are highly recombinant and evolving at a significantly rapid rate [16,34], full genome analysis allows for the determination viral dynamics amongst local and migratory population of birds.

Supplementary Materials

The following are available online at https://www.mdpi.com/1999-4915/10/3/107/s1, Figure S1: Pairwise identity matrix of the 63 GoCV genomes.

Acknowledgments

We thank Grzegorz Pułkownik from a private veterinary practice in Janocin (Poland), who kindly collected samples included in this study. Publication is supported by KNOW (Leading National Research Centre) Scientific Consortium “Healthy Animal—Safe Food”, decision of Ministry of Science and Higher Education No. 05-1/KNOW2/2015 (Poland).

Author Contributions

Tomasz Stenzel and Daria Dziewulska collected the samples, processed the DNA and prescreened for GoCV with broad spectrum primers. Simona Kraberger amplified and cloned the full genomes of GoCV. Brejnev M. Muhire, Penelope Hartnady, Darren P. Martin and Arvind Varsani undertook all the bioinformatics analysis. Tomasz Stenzel, Daria Dziewulska, Brejnev M. Muhire, Penelope Hartnady, Simona Kraberger, Darren P. Martin and Arvind Varsani wrote the manuscript.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

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Figure 1. Distribution of pairwise identities of the 63 GoCV genomes. For the purpose of this study, a 98% pairwise identity was used as genotype threshold.
Figure 1. Distribution of pairwise identities of the 63 GoCV genomes. For the purpose of this study, a 98% pairwise identity was used as genotype threshold.
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Figure 2. (A) A summary of the seven recombination events detected using the RDP (R), GENECONV (G), BOOTSCAN (B), MAXCHI (M), CHIMAERA (C), SISCAN (S), and 3SEQ (Q) methods implemented in the computer program RDP4. Only detection methods with associated p-values < 0.05 are shown. The p-value is for the detection method shown in bold italics. (B) Recombination free Maximum likelihood phylogenetic tree (left) with a cartoon illustration of the associated recombination event. Genome sequences used in DNA secondary structure analysis are marked with *.
Figure 2. (A) A summary of the seven recombination events detected using the RDP (R), GENECONV (G), BOOTSCAN (B), MAXCHI (M), CHIMAERA (C), SISCAN (S), and 3SEQ (Q) methods implemented in the computer program RDP4. Only detection methods with associated p-values < 0.05 are shown. The p-value is for the detection method shown in bold italics. (B) Recombination free Maximum likelihood phylogenetic tree (left) with a cartoon illustration of the associated recombination event. Genome sequences used in DNA secondary structure analysis are marked with *.
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Figure 3. Patterns of natural selection acting at cp and rep codon sites in beak and feather disease viruses (BFDV), GoCV, and pigeon circovirus (PiCV) genomes. Presented here are schematic representations of aligned rep and cp codon sites where, for each site, absolute (Abs) values of inferred synonymous substitution rates subtracted from inferred non-synonymous substitution rates (dN-dS) are plotted (as determined by the FUBAR method). Significantly positive dN-dS values are indicated by a red bar (indicating the strength of positive selection), and significantly negative dN-dS values are plotted in grey, green, and blue (indicating the strength of negative selection). Whereas blue colors indicate sites at which negative selection favors the same encoded amino acid in multiple different species, green colors indicate sites where negative selection favors different encoded amino acids in different species. Grey colors indicate sites at which negative selection was only detectable in a single species. Sites in orange display evidence of evolving under positive selection within particular lineages of the various species (indicated by the MEME method). Missing bars indicates gaps in the BFDV, GoCV, and PiCV gene alignment.
Figure 3. Patterns of natural selection acting at cp and rep codon sites in beak and feather disease viruses (BFDV), GoCV, and pigeon circovirus (PiCV) genomes. Presented here are schematic representations of aligned rep and cp codon sites where, for each site, absolute (Abs) values of inferred synonymous substitution rates subtracted from inferred non-synonymous substitution rates (dN-dS) are plotted (as determined by the FUBAR method). Significantly positive dN-dS values are indicated by a red bar (indicating the strength of positive selection), and significantly negative dN-dS values are plotted in grey, green, and blue (indicating the strength of negative selection). Whereas blue colors indicate sites at which negative selection favors the same encoded amino acid in multiple different species, green colors indicate sites where negative selection favors different encoded amino acids in different species. Grey colors indicate sites at which negative selection was only detectable in a single species. Sites in orange display evidence of evolving under positive selection within particular lineages of the various species (indicated by the MEME method). Missing bars indicates gaps in the BFDV, GoCV, and PiCV gene alignment.
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Figure 4. (A) Conserved stem-loop structures within rep of GoCV and BFDV genomes. The structures presented are the consensus of all available genomes and were amongst the most highly conserved of all plausible structural elements detected within the genomes of these two species (2nd out of 137 in GoCV and 9th out of 143 in BFDV). The rank ratio indicates the actual conservation rank of the structure over the total number of predicted secondary structures. Nucleotide sequence variability is reflected by a sequence logo at each position, while overlaid synonymous substitution rate estimates are represented by the shading of each nucleotide (ranging from blue for low to green for high). Although these two structures have no obvious sequence similarity, something expected given that GoCV and BFDV groups are very divergent (sharing 58.5% sequence identity), they form within same genomic region in rep and have similar conformation consisting of a stable stem-loop structure with a GC-rich stem-region and with evidence of low synonymous substitution rates in codons occurring within the stem-region consistent with strong selection acting against synonymous substitutions at these sites. (B) Association between paired sites and complementarily coevolving sites. (C) Tajima’s D and Fu and Li F statistics for paired and unpaired genomic site alignments. (D) Comparison of synonymous substitution rates at paired- and unpaired-codon sites.
Figure 4. (A) Conserved stem-loop structures within rep of GoCV and BFDV genomes. The structures presented are the consensus of all available genomes and were amongst the most highly conserved of all plausible structural elements detected within the genomes of these two species (2nd out of 137 in GoCV and 9th out of 143 in BFDV). The rank ratio indicates the actual conservation rank of the structure over the total number of predicted secondary structures. Nucleotide sequence variability is reflected by a sequence logo at each position, while overlaid synonymous substitution rate estimates are represented by the shading of each nucleotide (ranging from blue for low to green for high). Although these two structures have no obvious sequence similarity, something expected given that GoCV and BFDV groups are very divergent (sharing 58.5% sequence identity), they form within same genomic region in rep and have similar conformation consisting of a stable stem-loop structure with a GC-rich stem-region and with evidence of low synonymous substitution rates in codons occurring within the stem-region consistent with strong selection acting against synonymous substitutions at these sites. (B) Association between paired sites and complementarily coevolving sites. (C) Tajima’s D and Fu and Li F statistics for paired and unpaired genomic site alignments. (D) Comparison of synonymous substitution rates at paired- and unpaired-codon sites.
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Table 1. Summary of all geese samples included in this study. Samples were prescreened by broad spectrum nested PCR by Halami, et al. [20].
Table 1. Summary of all geese samples included in this study. Samples were prescreened by broad spectrum nested PCR by Halami, et al. [20].
Sample IDSampling DateSpeciesCommon NameAgeHealth StatusBroad Spectrum Primer PositiveGoCV PositiveGenBank Accession #
G121 November 2014Anser fabalisBean gooseAHYesYesKT808664
G23 December 2014Anser fabalisBean gooseAHNoNoN/A
G33 December 2014Anser fabalisBean gooseAHYesNoN/A
G43 December 2014Anser albifronsWhite fronted gooseYHYesYesKT808665
G520 November 2014Anser anserWild Greylag gooseAHYesNoN/A
G620 November 2014Anser anserWild Greylag gooseYHYesYesKT808666
G720 November 2014Anser anserWild Greylag gooseAHNoNoN/A
G820 November 2014Anser anserWild Greylag gooseAHYesNoN/A
G920 November 2014Anser anserWild Greylag gooseAHYesYesKT808667
G1020 November 2014Anser albifronsWhite fronted gooseAHNoNoN/A
G1121 November 2014Anser albifronsWhite fronted gooseYHNoNoN/A
G1221 November 2014Anser fabalisBean gooseAHYesNoN/A
G1321 November 2014Anser fabalisBean gooseAHNoNoN/A
G1421 November 2014Anser fabalisBean gooseAHNoNoN/A
G1521 November 2014Anser fabalisBean gooseAHYesYesKT808668
G1621 November 2014Anser fabalisBean gooseAHYesYesKT808669
G1721 November 2014Anser fabalisBean gooseAHNoNoN/A
G1822 November 2014Anser anserWild Greylag gooseAHYesNoN/A
G1922 November 2014Anser anserWild Greylag gooseAHYesYesKT808670
G2022 November 2014Anser anserWild Greylag gooseAHYesNoN/A
G2123 November 2014Anser albifronsWhite fronted gooseAHYesNoN/A
G2223 November 2014Anser fabalisBean gooseAHNoNoN/A
G2323 November 2014Anser fabalisBean gooseAHNoNoN/A
G2423 November 2014Anas platyrhynchosMallard duckAHYesNoN/A
DG16 December 2014Anser anserDomestic gooseA *HYesYesKT808650
DG26 December 2014Anser anserDomestic gooseA *HYesNoN/A
DG36 December 2014Anser anserDomestic gooseA *HYesYesKT808651
DG46 December 2014Anser anserDomestic gooseA *HYesYesKT808652
DG56 December 2014Anser anserDomestic gooseA *HYesYesKT808653
DG66 December 2014Anser anserDomestic gooseA *HYesYesKT808654
DG76 December 2014Anser anserDomestic gooseA *HYesYesKT808655
DG86 December 2014Anser anserDomestic gooseA *HYesYesKT808656
DG95 December 2014Anser anserDomestic gooseA *HYesNoN/A
DG105 December 2014Anser anserDomestic gooseA *HYesNoN/A
DG115 December 2014Anser anserDomestic gooseA *HYesYesKT808657
DG125 December 2014Anser anserDomestic gooseA *HYesNoN/A
DG135 December 2014Anser anserDomestic gooseA *HYesYesKT808658
DG145 December 2014Anser anserDomestic gooseA *HYesYesKT808659
DG155 June 2015Anser anserDomestic gooseY **S ***YesYesKT808660
DG165 June 2015Anser anserDomestic gooseY **S ***YesYesKT808661
DG175 June 2015Anser anserDomestic gooseY **S ***YesYesKT808662
DG185 June 2015Anser anserDomestic gooseY **S ***YesYesKT808663
DG195 June 2015Anser anserDomestic gooseY **S ***YesNoN/A
A: Adult; Y: Young; H: Healthy; S: Sick; * Reproductive/parental flock; ** Slaughter flock; *** Aspergillosis.
Table 2. Details of 63 Goose circovirus (GoCV) genome sequences used in this study. GoCV sequences determined in this study are in bold font (GenBank accession #s KT808650–KT808670).
Table 2. Details of 63 Goose circovirus (GoCV) genome sequences used in this study. GoCV sequences determined in this study are in bold font (GenBank accession #s KT808650–KT808670).
AccessionDescriptionCountryHostGenotype
AF418552Goose circovirus isolate TWTaiwanAnser anserI
AF536931Goose circovirus isolate TW1/2001TaiwanAnser anserI
AF536932Goose circovirus isolate TW2/2001TaiwanAnser anserI
AF536933Goose circovirus isolate TW3/2001TaiwanAnser anserI
AF536934Goose circovirus isolate TW4/2001TaiwanAnser anserI
AF536935Goose circovirus isolate TW5/2001TaiwanAnser anserI
AF536936Goose circovirus isolate TW6/2001TaiwanAnser anserXI
AF536937Goose circovirus isolate TW7/2001TaiwanAnser anserI
AF536938Goose circovirus isolate TW8/2001TaiwanAnser anserXI
AF536939Goose circovirus isolate TW9/2001TaiwanAnser anserXI
AF536940Goose circovirus isolate TW10/2001TaiwanAnser anserI
AF536941Goose circovirus isolate TW11/2001TaiwanAnser anserI
AJ304456Goose circovirus isolate DEGermanyAnser sp.XII
AY633653Goose circovirus isolate yk1ChinaAnser anserIX
DQ192279Goose circovirus isolate yk2China: ZhejiangAnser anserIX
DQ192280Goose circovirus isolate yk3China: ZhejiangAnser anserIX
DQ192281Goose circovirus isolate yk4ChinaAnser anserVIII
DQ192282Goose circovirus isolate xs1ChinaAnser anserIX
DQ192283Goose circovirus isolate xs2ChinaAnser anserIII
DQ192284Goose circovirus isolate xs3ChinaAnser anserX
DQ192285Goose circovirus isolate xs4ChinaAnser anserIII
DQ192286Goose circovirus isolate xs5ChinaAnser anserX
DQ192287Goose circovirus isolate xs6ChinaAnser anserX
GU320569Goose circovirus isolate JX1China: JiangxiAnser anserIX
KP203866Goose circovirus isolate 1020111GBTaiwan: YunlinCoscoroba coscorobaXI
KP203867Goose circovirus isolate 1021024GTaiwan: YunlinCoscoroba coscorobaXI
KP203868Goose circovirus isolate GB20-13Taiwan: KaohsiungCoscoroba coscorobaXI
KP203869Goose circovirus isolate GB21-9Taiwan: PingtungCoscoroba coscorobaXI
KP203870Goose circovirus isolate GB25-8Taiwan: PingtungCoscoroba coscorobaXI
KP203871Goose circovirus isolate GB26-15Taiwan: ChanghuaCoscoroba coscorobaXI
KP203872Goose circovirus isolate GB27-20Taiwan: YunlinAnser cygnoidesI
KP229363Goose circovirus isolate CF13001Taiwan: YunlinCoscoroba coscorobaXI
KP229370Goose circovirus isolate CD13088Taiwan: ChiayiCoscoroba coscorobaXI
KP229371Goose circovirus isolate CPA13007-1TaiwanCoscoroba coscorobaII
KP229372Goose circovirus isolate CJ14010Taiwan: ChiayiCoscoroba coscorobaXI
KP229373Goose circovirus isolate CPA13007-2TaiwanCoscoroba coscorobaXI
KP229374Goose circovirus isolate CPA14012TaiwanCoscoroba coscorobaII
KR869727Goose circovirus isolate 2GKPolandAnser anserXVII
KT207809Goose circovirus isolate TD254-2014ChinaAnser anserIX
KT387277Goose circovirus isolate ShandongChinaAnser anserIX
KT443969Goose circovirus isolate TD227/2013ChinaAnser anserIX
KT443970Goose circovirus isolate TD265/2013ChinaAnser anserIX
KT808650Goose circovirus isolate DG1PolandAnser anserXIV
KT808651Goose circovirus isolate DG3PolandAnser anserXV
KT808652Goose circovirus isolate DG4PolandAnser anserXV
KT808653Goose circovirus isolate DG5PolandAnser anserXIII
KT808654Goose circovirus isolate DG6PolandAnser anserXV
KT808655Goose circovirus isolate DG7PolandAnser anserXV
KT808656Goose circovirus isolate DG8PolandAnser anserXV
KT808657Goose circovirus isolate DG11PolandAnser anserXVI
KT808658Goose circovirus isolate DG13PolandAnser anserXV
KT808659Goose circovirus isolate DG14PolandAnser anserXV
KT808660Goose circovirus isolate DG15PolandAnser anserIV
KT808661Goose circovirus isolate DG16PolandAnser anserIV
KT808662Goose circovirus isolate DG17PolandAnser anserIV
KT808663Goose circovirus isolate DG18PolandAnser anserIV
KT808664Goose circovirus isolate G1PolandAnser fabalisV
KT808665Goose circovirus isolate G4PolandAnser albifronsV
KT808666Goose circovirus isolate G6PolandAnser anserVII
KT808667Goose circovirus isolate G9PolandAnser anserV
KT808668Goose circovirus isolate G15PolandAnser fabalisV
KT808669Goose circovirus isolate G16PolandAnser fabalisV
KT808670Goose circovirus isolate G19PolandAnser anserVI

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