Genome analysis and epidemiological investigation of goose circovirus detected in eastern China

Codon usage bias of goose circovirus and its adaptation to host

Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.

TaqMan-probe-based multiplex real-time RT-qPCR for simultaneous detection of GoAstV, GPV, and GoCV

Goose astrovirus (GoAstV), goose parvovirus (GPV), and goose circovirus (GoCV) infections have similar symptoms, such as severe diarrhea, and cause serious economic losses to the goose industry globally. Therefore, it is necessary to develop a rapid and accurate method for the differential diagnosis of the 3 viruses. In this study, a TaqMan probe-based multiplex reverse transcription-qualitative polymerase chain reaction (RT-qPCR) method was established and optimized for simultaneous detection of the three viruses. Three pairs of specific primers and probes were designed considering the conserved sequences of ORF2, VP3, and Rep of GoAstV, GPV, and GoCV, respectively. Singleplex real-time RT-qPCR detected a minimum of 10 copies of these genes, while multiplex real-time RT-qPCR detected a minimum of 100 copies. The correlation coefficients exceeded 0.99, and the amplification efficiency was 80 to 100%. The assay had high sensitivity, specificity, and repeatability. In 85 tissue samples, GoAstV and GPV were the main pathogens and demonstrated co-infection. This assay provides a rapid, efficient, specific, and sensitive tool for the detection of GoAstV, GPV, and GoCV. This can facilitate disease management and epidemiological surveillance.

A TaqMan-based quantitative real-time PCR assay for identification of the goose circovirus

Goose circovirus (GoCV) is a potential immunosuppressive virus that poses a great hazard to the goose industry and has been shown to be widely distributed throughout China. We have established a fast, sensitive and highly specific TaqMan real-time quantitative PCR detection method for this virus. Specific primers and probes were designed against the conserved regions of the genomic GoCV Rep gene. The results showed that the assay was highly specific and sensitive for GoCV and did not cross-react with other non-targeted waterfowl viruses. The established method will be helpful for epidemiological detection and may be effective in the prevention and control of the disease.

Recombinant Goose Circoviruses Circulating in Domesticated and Wild Geese in Poland

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.

Epidemiological investigation of H9 avian influenza virus, Newcastle disease virus, Tembusu virus, goose parvovirus and goose circovirus infection of geese in China

To deepen the knowledge about epidemic prevalence in the goose breeding field, a triplex PCR assay was established, and 478 samples were collected from scaled goose farms in 11 provinces in China. The results of this epidemiological investigation showed that incidence rates of H9 avian influenza and goose circovirus were the highest among five infectious diseases that were evaluated. In addition, the triplex PCR assay established remarkable sensitivity, rapidity and versatility compared to other diagnostic methods. Dual infection comprised a large proportion of the co-infections in the field, of which the combinations of H9/Tembusu, H9/goose circovirus and goose circovirus/Tembusu co-infected cases were more common. Epidemics were more severe in winter and spring. Additionally, significant differences in the prevalence of these infectious diseases were observed in association with different age groups. In addition, phylogenetic analysis, determined by the neighbour-joining method, was carried out to investigate the evolution of these viruses during the study period. For the most part, virus strains isolated during the study were consistent with most goose-origin strains isolated from the Chinese mainland over the past few years. However, mutations were observed between isolated H9 avian influenza virus strains and sequences available from GenBank, which should draw much attention.

Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.

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.

Viral infections in goose flocks in Poland

The aim of this study was to determine the infectious agents isolated from infection - suspected geese sent for the diagnostic examination to National Veterinary Research Institute. The birds were sent from goose flocks localized in different parts of Poland. Totally, 1,013 birds from 122 flocks were examined. The presence of goose parvovirus (GPV), goose haemorrhagic polyomavirus (GHPV), and goose circovirus (GoCV) was detected by triplex PCR. The presence of GPV DNA was shown in 36 flocks. The disease was most frequently diagnosed in goslings aging 3.5 weeks (ten flocks), and 2.5 weeks (six flocks). The analysis of the nucleotide sequence of VP1 encoding region has shown close similarity of Polish GPV strains within the group which ranged from 92% to 100%. Moreover, the similarity level of these strains with GPV isolated in Europe was from 91.3% to 100%. The occurrence of GoCV DNA was shown in 25 goose flocks. The presence of GoCV DNA was found among geese aged from 2 to 6 weeks, but predominantly in those aging 3.5 (three flocks) and 5 weeks (five flocks). The sequence analysis of PCR products from the sequenced region of ORFC1 capsid protein of GoCV has shown that Polish isolates share from 85% to 91% similarity with the sequences of GoCV strains isolated in other countries. The presence of DNA of GHPV was found in 3-week-old geese. During the last 2 years the presence of GHPV was confirmed in three flocks of goslings at the age from 3 to 3.5 weeks. During the last 12 years the occurrence of co-infection with GPV and GoCV was detected in six flocks aging from 5 to 6 weeks.

Epidemiological investigation and genome analysis of duck circovirus in Southern China

Duck circovirus (DuCV), a potential immunosuppressive virus, was investigated in Southern China from March 2006 to December 2009 by using a polymerase chain reaction (PCR) based method. In this study, a total of 138 sick or dead duck samples from 18 different farms were examined with an average DuCV infection rate of ∼35%. It was found that ducks between the ages of 40∼60 days were more susceptible to DuCV. There was no evidence showing that the DuCV virus was capable of vertical transmission. Farms with positive PCR results exhibited no regularly apparent clinical abnormalities such as feathering disorders, growth retardation or lower-than-average weight. The complete genomes of 9 strains from Fujian Province and 1 from Zhejiang Province were sequenced and analyzed. The 10 DuCV genomes, compared with others genomes downloaded from GenBank, ranged in size from 1988 to 1996 base pairs, with sequence identities ranging from 83.2% to 99.8%. Phylogenetic analysis based on genome sequences demonstrated that DuCVs can be divided into two distinct genetic genotypes, Group I (the Euro-USA lineage) and Group II (the Taiwan lineage), with approximately 10.0% genetic difference between the two types. Molecular epidemiological data suggest there is no obvious difference among DuCV strains isolated from different geographic locations or different species, including Duck, Muscovy duck, Mule duck, Cheery duck, Mulard duck and Pekin duck.

Pathological observations of an experimental infection of geese with goose circovirus

There is so far no report describing the pathogenicity of goose circovirus (GoCV) following experimental infection. We report here an experimental inoculation of 21-day-old geese with a GoCV polymerase chain reaction (PCR)-positive sample of bursa of Fabricius (BF) homogenate, and the results of clinicopathological changes. Forty geese were randomly assigned to two groups: the inoculated group (n=30) receiving tissue homogenate and the uninoculated group (n=10) receiving a placebo (physiological saline). Tissue samples were collected for histopathological examination and GoCV detection. The main clinical signs in the GoCV-inoculated geese included diarrhoea at 17 to 30 days post inoculation, marked differences of growth rate and feather disorders in three of the geese. Viraemia was detected by PCR only at 14 days post inoculation. The BF, thymus, spleen, duodenum and liver of some inoculated geese were also PCR-positive. Real-time PCR showed that there was relatively more viral load in the BF. Histological examination revealed lymphocytic depletion and histiocytosis in the BF and inflammation characterized by lymphatic infiltration in the lung, liver and kidney. Immunohistochemistry applied to PCR-positive samples showed that in only three BF samples was GoCV antigen detected in lymphocytes in both the cortex and medulla. In situ apoptosis detection of all BF samples indicated that GoCV inoculation was associated with an increase in bursal lymphocytic apoptotic events.