Identification, genotyping, and molecular evolution analysis of duck circovirus

Epidemiology and genotypic diversity of feline bocavirus identified from cats in Harbin, China

Feline bocavirus (FBoV) is a globally distributed linear, single-stranded DNA virus infect cats, currently classified into three distinct genotypes. Although FBoV can lead to systemic infections, its complete pathogenic potential remains unclear. In this study, 289 blood samples were collected from healthy cats in Harbin, revealing an overall FBoV prevalence of 12.1%. Notably, genotypes 1 and 3 of FBoV were found co-circulating among the cat population in Harbin. Additionally, recombination events were detected, particularly in the newly discovered NG/104 and DL/102 strains. Furthermore, negative selection sites were predominantly observed across the protein coding genes of FBoV. These findings suggest a co-circulation of genetically diverse FBoV strains among cats in Harbin, indicate that purifying selection is the primary driving force shaping the genomic evolution of FBoV, and also underscore the importance of comprehensive surveillance efforts to enhance our understanding of the epidemiology and evolutionary characteristics of FBoV.

Interactions between avian viruses and skin in farm birds

This article reviews the avian viruses that infect the skin of domestic farm birds of primary economic importance: chicken, duck, turkey, and goose. Many avian viruses (e.g., poxviruses, herpesviruses, Influenza viruses, retroviruses) leading to pathologies infect the skin and the appendages of these birds. Some of these viruses (e.g., Marek's disease virus, avian influenza viruses) have had and/or still have a devasting impact on the poultry economy. The skin tropism of these viruses is key to the pathology and virus life cycle, in particular for virus entry, shedding, and/or transmission. In addition, for some emergent arboviruses, such as flaviviruses, the skin is often the entry gate of the virus after mosquito bites, whether or not the host develops symptoms (e.g., West Nile virus). Various avian skin models, from primary cells to three-dimensional models, are currently available to better understand virus-skin interactions (such as replication, pathogenesis, cell response, and co-infection). These models may be key to finding solutions to prevent or halt viral infection in poultry.

Simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting analysis

Birds infected with duck circovirus (DuCV) can potentially cause immunosuppression by damaging lymphoid tissues, causing great losses in the duck breeding industry. Duck circovirus can be divided into two genotypes (DuCV-1 and DuCV-2), but simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting (HRM) analysis is still lacking. Here, we designed specific primers according to the sequence characteristics of the newly identified ORF3 gene and then established a PCR-HRM method for the simultaneous detection and differentiation of DuCV-1 and DuCV-2 via high-resolution melting analysis. Our data showed that the established PCR-HRM assay had the advantages of specificity, with the lowest detection limits of 61.9 copies/μL (for DuCV-1) and 60.6 copies/μL (for DuCV-2). The melting curve of the PCR-HRM results indicated that the amplification product was specific, with no cross-reaction with common waterfowl origin pathogens and a low coefficient of variation less than 1.50% in both intra-batch and inter-batch repetitions, indicating the advantages of repeatability. We found that the percentage of DuCV-2-positive ducks was higher than that of DuCV-1-positive ducks, with 8.62% rate of DuCV-1 and DuCV-2 coinfection. In addition, we found DuCV-2-positive in geese firstly. In conclusion, this study provides a candidate PCR-HRM assay for the detection and accurate differentiation of DuCV-1 and DuCV-2 infection, which will help us for further epidemiological surveillance of DuCVs.

From obscurity to urgency: a comprehensive analysis of the rising threat of duck circovirus

Duck circovirus (DuCV) is a small, nonenveloped, single-stranded DNA virus with immunosuppressive effects on ducks that leads to slow growth and elevated mortality following mixed infections. Its infection manifests as feather loss, slow growth, swelling of respiratory tissue, and damage to immune organs in ducks. Although single infections with DuCV do not cause noticeable clinical symptoms, its ability to compromise the immune system and facilitate infections caused by other pathogens poses a serious threat to duck farming. Given the prevalence of this disease and the increasing infection rates in recent years, which have resulted in significant economic losses in duck farming and related sectors, research and control of DuCV infection have become especially important. The aim of this review is to provide a summary of the current understanding of DuCV, serving as a reference for subsequent research and effective control of the virus. We focus mainly on the genetics and molecular biology, epidemiology, clinical symptoms, and pathology of DuCV. Additionally, topics such as the isolation and culture of the virus, vaccines and antiviral therapies, diagnostics, and preventative measures are discussed.

Molecular Detection and Genetic Characterization of Vertically Transmitted Viruses in Ducks

To investigate the distribution and genetic variation in four vertically transmitted duck pathogens, including duck hepatitis B virus (DHBV), duck circovirus (DuCV), duck hepatitis A virus 3 (DHAV-3), and avian reoviruses (ARV), we conducted an epidemiology study using PCR and RT-PCR assays on a duck population. We found that DHBV was the most prevalent virus (69.74%), followed by DuCV (39.48%), and then ARV (19.92%) and DHAV-3 (8.49%). Among the 271 duck samples, two, three or four viruses were detected in the same samples, indicating that the coinfection of vertical transmission agents is common in ducks. The genetic analysis results showed that all four identified DuCV strains belonged to genotype 1, the DHAV-3 strain was closely clustered with previously identified strains from China, and the ARV stain was clustered under genotype 1. These indicate that different viral strains are circulating among the ducks. Our findings will improve the knowledge of the evolution of DuCV, DHAV-3, and ARV, and help choose suitable strains for vaccination.

Epidemiology and genotypic diversity of canine circovirus identified in pet dogs in Harbin, China

Canine circovirus (CanineCV) is a single-stranded DNA virus that circulates in dogs and wild carnivores around the world. It has been suggested to be associated with diseases of respiratory and gastrointestinal systems, though its pathogenic potential remains unclear. Currently, CanineCV is divided into six genotypes (genotype 1-6), and genotypes 2, 3, and 4 have been described in China. In this study, 359 blood samples from pet dogs with or without clinical signs were collected in Harbin city. After PCR screening, a total of 34 samples were tested positive for CanineCV, and nine full-length genome sequences were recovered from positive samples. Pairwise sequence comparison showed that they shared 82.4-99.3% genome-wide identity with other CanineCVs available in GenBank. Additionally, recombination events were detected, all of which were determined to be associated with sequences obtained in China. The reconstructed phylogenetic tree based on the recombination-free complete genome sequences revealed that the complete genome sequences generated herein were clustered into genotypes 1 and 3. Furthermore, purifying selection was the dominant evolutionary pressure acting on the genomes of CanineCV. These results expand the knowledge about the genetic diversity of CanineCV circulating in China, and also promote us to better understand the evolution of CanineCV.

Development and application of a multiplex qPCR assay for the detection of duck circovirus, duck Tembusu virus, Muscovy duck reovirus, and new duck reovirus

A multiplex qPCR assay was developed to simultaneously detect duck circovirus (DuCV), duck Tembusu virus (DTMUV), Muscovy duck reovirus (MDRV), and novel duck reovirus (NDRV), but it did not amplify other viruses, including duck virus enteritis (DVE), infectious bursal disease virus (IBDV), avian reovirus (ARV), H5 avian influenza virus (H5 AIV), H7 avian influenza virus (H7 AIV), H9 avian influenza virus (H9 AIV), Newcastle disease virus (NDV), and Muscovy duck parvovirus (MDPV), and the detection limit for DuCV, DTMUV, MDRV, and NDRV was 1.51 × 10¹ copies/μL. The intra- and interassay coefficients of variation were less than 1.54% in the repeatability test with standard plasmid concentrations of 1.51 × 10⁷, 1.51 × 10⁵, and 1.51 × 10³ copies/μL. The developed multiple qPCR assay was used to examine 404 clinical samples to verify its practicability. The positivity rates for DuCV, DTMUV, MDRV, and NDRV were 26.0%, 9.9%, 4.0%, and 4.7%, respectively, and the mixed infection rates for DuCV + DTMUV, DuCV + MDRV, DuCV + NDRV, MDRV + NDRV, DTMUV + MDRV, and DTMUV + NDRV were 2.7%, 1.2%, 1.2%, 1.0%, 0.5%, and 0.7%, respectively.

Duck Circovirus genotype 2 ORF3 protein induces apoptosis through the mitochondrial pathway

Duck circovirus genotype 2 (DuCV2) belongs to the genus Circovirus, family Circoviridae. It can generally cause lymphocyte atrophy and necrosis in ducks, which leads to immunosuppression. The function of the DuCV2 open reading frame 3 (ORF3) protein in viral pathogenesis in host cells remains unclear. Therefore, a series of studies based on ORF3 of the isolate DuCV GH01 strain (belonging to DuCV2) were carried out in duck embryo fibroblasts (DEFs) in this study. The results showed that the ORF3 protein could induce nuclear shrinkage and fragmentation in DEFs. Chromosomal DNA breakage was observed by TUNEL assay. The expression levels of caspase-related genes showed that ORF3 primarily promoted caspase 3 and caspase 9 expression. Furthermore, the protein expression levels of cleaved caspase 3 and cleaved caspase 9 in DEFs were enhanced by ORF3. Thus, ORF3 may activate the mitochondrial apoptosis pathway. When the 20 amino acid residues at the C-terminus of ORF3 (ORF3ΔC₂₀) were deleted, the apoptosis rates were decreased. Moreover, compared to ORF3, ORF3ΔC₂₀ downregulated the mRNA levels of cytochrome c (Cyt c), poly ADP-ribose polymerase (PARP) and apoptosis protease activating factor 1 (Apaf-1), which are the key molecules in the mitochondrial apoptotic pathway. Further study showed that ORF3ΔC₂₀ could reduce the mitochondrial membrane potential (MMP). This study suggested that the DuCV2 ORF3 protein may primarily activate apoptosis through the mitochondrial pathway in DEFs, and this function is ORF3 C₂₀ dependent.

Duck circovirus in northern Vietnam: genetic characterization and epidemiological analysis

In the present study, tissue samples collected from 130 ducks from clinically suspected commercial flocks and diseased birds in six provinces of northern Vietnam were tested for duck circovirus (DuCV) infection. The DuCV genome was detected in 56 out of 130 (43.08%) duck samples by PCR. Of 38 tested farms, 26 (68.42%) were positive for the DuCV genome. The rate of the DuCV genome detection in ducks at 3-4 weeks of age (54.17%) was significantly higher (p < 0.05) than that at <3 (32.43%) and >7 (33.33%) weeks of age and insignificantly higher than that at 5-7 weeks of age (43.33%) (p = 0.11). The genomes of six Vietnamese DuCV isolates were determined. They ranged in length from 1,988 to 1,995 nucleotides, and their nucleotide sequences were 83.24% to 99.69% identical to each other. Phylogenetic analysis based on the complete genome sequences indicated that the DuCV strains circulating in northern Vietnam can be divided into two main genotypes (I and II) and several subgenotypes. The Vietnamese DuCV isolates were closely related to Chinese, Taiwanese, and Korean strains. One positively selected site was detected in the capsid protein.

Effects of duck circovirus on immune function and secondary infection of Avian Pathogenic Escherichia coli

Duck circovirus (DuCV) infection occurs frequently in ducks in China and is generally believed to lead to immunosuppression and secondary infection, though there has been a lack of detailed research and direct evidence. In this study, one-day-old Cherry Valley ducklings were artificially infected with DuCV alone and co-infected with DuCV and Avian Pathogenic Escherichia coli (APEC). The immune indexes at 32 d old were systematically monitored, including immune organ weight, lymphocyte transformation rate, IL-10, IL-12, soluble CD4 (sCD4), soluble CD8 (sCD8), IFN-γ, viral loads in each organ, APEC colonization, and so on. The results showed the development of immune organs in ducklings was affected, resulting in a decrease in the lymphocyte transformation rate (LTR), IL-12, sCD4, sCD8, IFN-γ and an increase in IL-10 content at 8 to 32 d postinfection (dpi). In the detection of virus loads in some organs, it was found that 8 dpi, DuCV existed stably in various organs, suggesting the importance of preventing and controlling the virus in the early stage of culture. The results of exploring the DuCV infection that shows some influence on secondary infection by APEC. The results showed that DuCV infection could significantly enhance the pathogenicity of APEC and the colonization ability of APEC in vivo. DuCV can induce more serious APEC infection in 24 dpi than in 14 dpi. Based on the above results, it can be concluded that DuCV infection will affect the immune system, cause immunosuppression, and lead to more serious secondary infection.

Establishment of TaqMan-based real-time PCR assay for rapid detection of duck circovirus

Duck circovirus (DuCV) is widespread across the world and causes feather disorders in young ducks. It was identified as the causative pathogen of duck beak atrophy and dwarfism syndrome and primary sclerosing cholangitis. In this study, we aimed to establish a TaqMan-based real-time PCR assay to detect DuCV. The primers and probe were designed based on the conserved region of the DuCV Rep gene. After optimizing the reaction conditions, the minimum virus detection limit of the designed PCR technique was 39.4 copies/μL, 100 times that of conventional PCR (cPCR). No cross-reaction with six other common duck viruses was observed. The intra- and inter-assay variations were less than 1%. The detection rate of DuCV-positive clinical samples using TaqMan-based real-time PCR was higher than that using SYBR Green-based real-time PCR and cPCR. Collectively, these results showed that the established TaqMan-based real-time PCR detected DuCV with high sensitivity and specificity, and significant repeatability, making it suitable for clinical use. Hence, it may be used as a novel tool for the diagnosis and epidemiological investigation of DuCV.

Development of a dual-labeled, hydrolysis probe-based, real-time quantitative PCR assay for detection of both genotypes of duck circovirus-1 (DuCV-1) and DuCV-2

In this study, we developed a real-time quantitative polymerase chain reaction (qPCR) assay based on a dual-labeled hydrolysis probe to simultaneously detect both duck circovirus (DuCV) 1 and DuCV-2. The reproducibility, sensitivity and specificity of the primer set and probe were evaluated using other duck pathogens. The detection limit was 20 copies per µL. The intra-assay coefficients of variation (CVs) were ≤ 0.73% and the inter-assay CVs were ≤ 1.89%. No cross-reaction occurred with other duck pathogens. In addition, the qPCR assay was successfully applied to the simultaneous detection of DuCV-1 and DuCV-2 in clinical field samples. Therefore, this assay will be useful for laboratory diagnosis and epidemiological field studies of DuCV.

Apoptosis Triggered by ORF3 Proteins of the Circoviridae Family

Apoptosis, a form of the programmed cell death, is an indispensable defense mechanism regulating cellular homeostasis and is triggered by multiple stimuli. Because of the regulation of apoptosis in cellular homeostasis, viral proteins with apoptotic activity are particular foci of on antitumor therapy. One representative viral protein is the open reading frame 3 (ORF3) protein, also named as apoptin in the Circoviridae chicken anemia virus (CAV), and has the ability to induce tumor-specific apoptosis. Proteins encoded by ORF3 in other circovirus species, such as porcine circovirus (PCV) and duck circovirus (DuCV), have also been reported to induce apoptosis, with subtle differences in apoptotic activity based on cell types. This article is aimed at reviewing the latest research advancements in understanding ORF3 protein-mediated apoptosis mechanisms of Circoviridae from three perspectives: subcellular localization, interactions with host proteins, and participation in multiple apoptotic signaling pathways, providing a scientific basis for circovirus pathogenesis and a reference on its potential anticancer function.

Isolation and characterization of a duck-origin goose astrovirus in China

In 2019, a new type of infectious disease characterized with haemorrhage and swellings of kidneys, occurred on commercial duck farms in Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AstV-SDTA strain and was isolated from a diseased duckling using LMH cells. Similar clinical symptoms were reproduced by experimental infection using the AstV-SDTA strain. The complete genome sequencing characterization of AstV-SDTA was conducted using next-generation sequencing (NGS) technique on Illumina HiSeq platform, and used polymerase chain reaction method to verify the NGS results for the obtained whole sequences. Phylogenetic analysis revealed that AstV-SDTA strain belongs to a novel goose astrovirus (GoAstV) branch of avian astroviruses, and the nucleotide homology based on the complete genome sequences among AstV-SDTA and other GoAstV strains deposited in Genbank was 97.2–98.8%. Taken together, these results suggest that the cross-species transmission of novel GoAstV between domestic waterfowl is possible. Further surveillance of novel GoAstV in poultry are needed in order to gain a better understanding of both the molecular and evolutionary characteristics of novel GoAstV.

Molecular characteristics of a novel duck circovirus subtype 1d emerging in Anhui, China

The frequency of infection of duck circovirus (DuCV) in Anhui province, China is not well-characterized. Therefore, in this study, we collected 69 samples from sick ducks and tested them for the presence of DuCV by conventional polymerase chain reaction (PCR) analysis. The complete viral genomes of five DuCV strains from five different cities were randomly selected, amplified via PCR, sequenced, and subjected to recombination analysis. The five DuCV genomes were named as AHAU9, AHAU25, AHAU28, AHAU37, and AHAUHQ. We found that 36.2 % of the ducks were infected with DuCV. The five DuCV strains had genome lengths ranging from 1987 to 1995 nucleotides, with a sequence similarity of 81.8-98.2 %. Among them, AHAU28, AHAU37, and AHAUHQ were closely related to the reference strain YF180403, GX1105 strain, and wd2015028 of DuCV, respectively. AHAU9 and AHAU25 were found to belong to a new DuCV subtype, DuCV-1d. Moreover, recombination analysis showed that the DuCV-1d subtype strains had the same recombination pattern. These results improve the understanding of the frequency of DuCV infection in Anhui province. Our findings may be useful for preventing and controlling the spread of DuCV.

Simultaneous detection of duck circovirus and novel goose parvovirus via SYBR green I-based duplex real-time polymerase chain reaction analysis

Beak atrophy and dwarfism syndrome (BADS) is commonly caused by co-infection with duck circovirus (DuCV) and novel goose parvovirus (NGPV). Therefore, concurrent detection of both viruses is important for monitoring and limiting BADS, although such a diagnostic test has not been reported. In this study, we developed a duplex, SYBR Green I-based real-time polymerase chain reaction (PCR) assay to enable the simultaneous detection of DuCV and NGPV. The assay readily distinguished between the two viruses, based on their different melting temperatures (Tm), where the Tm for DuCV was 80 °C and that for NGPV was 84.5 °C. Other non-target duck viruses that were tested did not show melting peaks. The detection limit of the duplex assay was 10¹ copies/μL for both viruses. This method exhibited high repeatability and reproducibility, and both the inter-assay and intra-assay variation coefficients were <1.6%. Thirty-one fecal samples were collected for clinical testing using real-time PCR analysis, and the results were confirmed using sequencing. The rate of co-infection was 6.5%, which was consistent with the sequencing results. This duplex real-time PCR assay offers advantages over other tests, such as rapid, sensitive, specific, and reliable detection of both viruses in a single sample, which enables the quantitative detection of DuCV and NGPV in clinical samples. Using this test may be instrumental in reducing the incidence of BADS and the associated economic losses in the duck and goose industries.

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SYBR Green based PCR to simultaneously detect duck circovirus and goose parvovirus.

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The assay had specificity, sensitivity and reproducibility.

Novel genotype definition and genome characteristics of duck circovirus in central and Eastern China

To explore genetic variations in duck circovirus (DuCV) and the molecular epidemiology of its infection, tissue samples were collected from 219 dead ducks from 20 farms in the central and eastern regions of China. All farms tested positive for DuCV, with duck-origin goose parvovirus, reovirus and Tembusu virus having co-infection rates of 100%, 0% and 0%, respectively. A total of 20 strains from the DuCV-positive flock were sequenced. The total sequence length was 1987-1996 nt, and the sequences shared 82% (JX499186, DuCV2 from Sichuan province, China) to 99.7% (KY328304, DuCV1 from Shandong Province, China) sequence identity with DuCV sequences available in GenBank. Hyper-variable regions were mainly located in open reading frame (ORF)2, ORF3 and intergenic regions. The tertiary structure of ORF2 from four provinces (Henan, Anhui, Zhejiang and Fujian) in China showed a canonical viral jelly roll and the antigenic epitope of ORF2 located in the bulge of the protein surface. Overall, 15 of the 20 DuCV strains are possibly derived through inter-genotypic and intragenotypic recombination. Based on sequence and phylogenetic analyses, six strains from Fujian Province clustered into a novel genotype-DuCV-1d. These findings may enrich our understanding of DuCV evolution and circulation and lay the foundation for vaccine strain selection.

Molecular survey of duck circovirus infection in poultry in southern and southwestern China during 2018 and 2019

Background

Duck circovirus (DuCV) is a potential immunosuppressive virus that causes feather disorders in young ducks. In this study, DuCV obtained from various species of ducks was investigated by polymerase chain reaction (PCR) in southern and southwestern China (Guangdong, Guangxi and Yunnan provinces) from 2018 to 2019.

Results

A total of 848 bursa samples were collected from dead Mulard, Cherry Valley Pekin, Muscovy and Mallard ducks from duck farms. The positivity rate of DuCV in the total sample was approximately 36.91%. We found that the prevalence of DuCV in Yunnan (43.09%) was higher than those in Guangxi (34.38%) and Guangdong (34.4%). However, the positivity rates of DuCV in the four duck species were not significantly different (P > 0.05). Nineteen randomly selected complete viral genomes were sequenced. The complete genomes of the DuCV were 1987 to 1995 nt in length, and were 81.7–99.3% homologous to the other 57 sequences in GenBank. Phylogenetic analyses based on the complete genomes of 76 DuCVs showed that the 19 novel DuCV sequences from Guangdong and Guangxi provinces mainly belonged to the DuCV-1 and DuCV-2 genetic groups, respectively. However, the two genotype groups coexisted in Yunnan Province. In addition, recombination analysis showed putative recombination sites in 3 strains in Yunnan that originated from strains Guangdong and Guangxi. Interestingly, the epidemiological investigation showed that Mulard ducks, Cherry Valley Pekin ducks and Muscovy ducks more than 4 weeks old were more susceptible to infection with the novel DuCV than ducks less than 4 weeks old.

Conclusions

These data provide insight into the molecular epidemiology and genetic diversity of DuCVs circulating in southern and southwestern China for the first time.

Pathogenesis of duck circovirus genotype 1 in experimentally infected Pekin ducks

Ducks infected with duck circovirus (DuCV) exhibit feathering disorder, growth retardation, and low body weight. The virus can induce immunosuppression and increase rates of infection caused by other pathogens. The purpose of the present study was to investigate the pathogenesis of DuCV in experimentally infected Pekin ducks. At postmortem examination, gross lesions were observed in the immune organs including bursa of Fabricius (BF), thymus, and spleen. Hemorrhage, lymphocytic depletion, necrosis, and degeneration were observed in the bursal tissues by histological examination. The TUNEL assay was performed with bursal tissue. There was a significant difference of the apoptosis rate between the negative and DuCV-infected ducks. The earliest time point for detection of DuCV DNA in sera, cloacal swabs, and organs was 1 wk post-infection (WPI). Viral shedding was persistent and detectable at the end of the experiment (10 WPI). The findings provide evidence that horizontal transmission and persistent infection are the characteristics of DuCV. The organ with the highest mean viral load was the spleen, followed by BF, cecal tonsil, lung, thymus, liver, and kidney. We successfully established an experimental DuCV genotype 1 (DuCV-1) infection in Pekin ducks and demonstrated the pathogenicity and persistence of DuCV-1. In conclusion, DuCV-1 caused extensive damage to the immune organs that may have resulted in immunosuppression. Pathobiological characteristics of DuCV-1 include systemic infection, persistent infection, and horizontal transmission. These features allow DuCV-1 to circulate more easily in farms and increase the susceptibility of ducks to other diseases.

Genetic variation analysis of PCV1 strains isolated from Guangxi Province of China in 2015

Background

Porcine circovirus type 1 (PCV1) was discovered in 1974 as a contaminant of a porcine kidney (PK-15) cell line and was generally accepted to be nonpathogenic. But recently it was shown to cause lesions in experimentally infected pig fetuses. Serological evidence and genetic studies suggested that PCV1 was widespread in domestic pigs. Thus, the molecular epidemiology and genetic variation of PCV1 are still necessary to understand.

Results

Here 247 tissue samples were collected from piglets in Guangxi Province, China and performed whole-genome sequencing of the PCV1 genome. Thirteen PCV1 strains were sequenced from the samples. Similarity analysis showed that there were 97.8% to 99.6% nucleotide similarity to each other and 97.1% to 99.8% nucleotide similarity to the 40 reference strains. Besides, based on sequence analysis, we found one putative recombinant virus named GXdx84 strain contained the open-reading frame 1 (ORF1) of PCV1 and the ORF2 of PCV2d-2, which was consistent with the results of phylogenetic analysis that compared PCV1 and PCV2 strains. Variation analysis of the amino acids of the capsid protein revealed that the GXyl224 strain, which encoded 235 amino acids, had two amino acids more than other strains. This is the first study to report that a cap gene mutation resulted in lengthening of in the gene sequence.

Conclusions

These data contribute to the understanding of PCV1 evolution and molecular epidemiology that will facilitate programs for its control and prevention.

Duck "beak atrophy and dwarfism syndrome" disease complex: Interplay of novel goose parvovirus-related virus and duck circovirus?

As a newly emerged infectious disease, duck "beak atrophy and dwarfism syndrome (BADS)" disease has caused huge economic losses to waterfowl industry in China since 2015. Novel goose parvovirus-related virus (NGPV) is believed the main pathogen of BADS disease; however, BADS is rarely reproduced by infecting ducks with NGPV alone. As avian circovirus infection causes clinical symptoms similar to BADS, duck circovirus (DuCV) is suspected the minor pathogen of BADS disease. In this study, an investigation was carried out to determine the coinfection of NGPV and DuCV in duck embryos and in ducks with BADS disease. According to our study, the coinfection of emerging NGPV and DuCV was prevalent in East China (Shandong, Jiangsu and Anhui province) and could be vertical transmitted, indicating their cooperative roles in duck BADS disease.

Genome Sequences of a Novel Recombinant Duck Circovirus in China

In this study, YN26/2013, a novel recombinant duck circovirus (DuCV), was isolated from a Muscovy duck in Yunnan Province, southern China. The whole genome of YN26/2013 consists of 1,987 nucleotides (nt), the same genomic size as that of the DuCV-2 genotype. However, YN26/2013 shares 91.5 to 94.3% nucleotide identity similarity with previously reported type I (DuCV-1) viruses. Importantly, a novel putative recombinant event between DuCV-1 and DuCV-2 was identified as occurring within the 987- to 1111-nt region of the YN26/2013 genome.

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

Background

The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca).

Results

In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses.

Conclusions

In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.

A new duck circovirus sequence, detected in velvet scoter (Melanitta fusca) supports great diversity among this species of virus

BACKGROUND

The aim of this study was to investigate the presence of circoviruses in wild bird populations, in Poland. Circoviruses possess immuno-suppressive properties and might interfere with the health of wild birds.

METHOD

83 birds, which belonged to 23 species, were tested with broad-range, nested PCR. The obtained PCR products were sequenced and new primers designed, to analyse the full-length, viral genome. A phylogenetic analysis was conducted, to find any relationship to known circoviruses.

RESULTS

The circovirus DNA sequence was found in 4 birds. All samples originated from the velvet scoter (Melanitta fusca) a marine duck from the Merginae sub-family. Birds which tested positive for the circovirus were found dead in fishing nets, off the Baltic coast. During post-mortem examination, carcasses of two of the scoters showed only light emaciation, while the two other birds appeared healthy. The obtained, full-length, circovirus sequence revealed 1,988 nucleotides and the presence of typical features (i.e. Cap, Rep and ORF3). Nucleotide similarity to other duck circoviruses was 84 to 86 %. Phylogenetic analysis of the complete genome and cap gene, indicated that the new circovirus is related to known duck circoviruses, especially to sub-types sometimes referred to as duck circovirus genotype 1, but not genotype 2.

CONCLUSIONS

In this study, we have reported a new duck circovirus sequence detected in the velvet scoter, a species of marine duck. Sequence comparison and phylogenetic analysis of the new virus sequence support previous reports that duck circovirus (DuCV) is a species with a high degree of diversity. The viral sequence obtained from the velvet scoter suggests that DuCV may infect birds from the Anatinae sub-family. More studies are needed to prove if the velvet scoter and other marine ducks act as a reservoir for DuCV.

Genome Sequence of a Diverse Goose Circovirus Recovered from Greylag Goose

A diverse goose circovirus (GoCV) genome was recovered from a wild hunted greylag goose (Anser anser) in Poland. The genome shares 83% pairwise identity with other GoCV genomes recovered from various geese from China, Germany, and Taiwan.

Rescue of a duck circovirus from an infectious DNA clone in ducklings

Background

Duck circovirus may predispose the host to immunosuppression and may serve as an immunological trigger for further complicated disease progression. Due to the lack of a cell culture system for propagating DuCV, little is known regarding the molecular biology and pathogenesis of DuCV. The aim of this study was to describe the construction and initial in vivo characterization of full-length DNA clones of DuCV (pIC-Mu2DuCV) and its infectivity under in vivo conditions.

Method

The constructed pIC-Mu2DuCV contained two copies of the whole DuCV genome and an introduced Xho I restriction enzyme site. Eighty-one 10-day-old conventional ducklings that were free of DuCV were randomly divided equally into three groups (1, 2 and 3). The ducklings in groups 1, 2 and 3 were inoculated intramuscularly with pIC-Mu2DuCV, wild-type virus GH01 and PBS, respectively. Subsequently, all of the ducklings were examined clinically, which were each given a physical condition score, and their rectal temperatures were taken daily during the experimental period. DuCV genomes in serum samples and in various tissues from all of the ducklings at 0, 1, 3, 5, 7, 10, 15, 21 and 28 DPC were detected by PCR and real-time quantitative PCR, respectively.

Results

The average daily weight gain (ADWG) of group 3 was significantly higher than those of groups 1 and 2, and the temperature of all ducklings was stable between 41.7 °C and 42.2 °C. The clinical values (physical condition scores) of groups 1, 2 and 3 were 12.5, 15.6 and 0, respectively. In addition, viremia occurred at 15 and 10 days post-challenge (DPC) in groups 1 and 2, and antibodies could be detected in these ducklings at 21 and 15 DPC. Proliferation ability analysis showed that the viral titers of group 1 were lower than those of their parental viruses in group 2.

Conclusion

This study shows that the rescued viruses are not significantly different but exhibit lower pathogenicity and proliferation ability compared with the parental virus. The results will facilitate future studies on DuCV pathogenesis and biology.

Evidence of possible vertical transmission of duck circovirus

To test the hypothesis that duck circovirus (DuCV) may be vertically transmitted from infected breeder ducks to their ducklings, we investigated 120 newly hatched ducklings, 30 dead duck embryos and 80 non-embryonated duck eggs with the duplex polymerase chain reaction (PCR). DuCV DNA was present in 15 newly hatched ducklings, 4 duck embryos and 3 non-embryonated eggs. Four ducklings from two flocks were co-infected by DuCV-1 and DuCV-2, three ducklings from three flocks were DuCV-1 single infection, and eight ducklings from six flocks were DuCV-2 single infection. One duck embryo and one non-embryonated egg were positive for both DuCV-1 and DuCV-2 DNAs, one embryo for DuCV-1 DNA, and two embryos and two non-embryonated eggs for DuCV-2 DNA. The findings provide evidence of possible vertical transmission of DuCV and simultaneous transmission of DuCV-1 and DuCV-2 from breeder ducks to ducklings.