Recombinant Goose Circoviruses Circulating in Domesticated and Wild Geese in Poland

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.

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.

Canine circovirus among dogs and cats in China: first identification in cats

Canine circovirus (CanineCV) is a virus associated with respiratory and digestive diseases in dogs and often occurs in coinfections with other pathogens, thereby aggravating the symptoms of infected dogs. CanineCV was first reported in the United States in 2012. Subsequently, it was reported among dogs in Europe, Asia, and South America. To investigate the prevalence of CanineCV in dogs in China, 331 dog samples were collected in this study. The PCR results showed that 9.06% (30/331, 95% CI = 6.2% ~ 12.7%) of the dog samples were CanineCV positive. CanineCV has also been detected in some carnivorous wild animals, indicating the potential risk of cross-species transmission of this virus. And, cats are also one of the most common pets in our daily lives, who is close contact with dogs. Thus, this study first investigated the prevalence of CanineCV in cats. The PCR results showed that 3.42% (14/409, 95% CI = 1.9% ~ 5.7%) of the cat samples were CanineCV positive. Moreover, 14 canine-derived CanineCV whole genomes and the first cat-derived CanineCV whole genome were obtained in this study. Rep and Cap are the major nonstructural proteins and structural proteins of CanineCV, respectively. In nucleic acid homology analyses, these 15 CanineCV strains showed a high degree of variation in Rep (85.9 ~ 99%) and Cap (85.6 ~ 100%). In phylogenetic analyses, the 15 CanineCV strains clustered into 3 different genotypes (genotypes 1, 3, and 4). Among them, the first cat-derived CanineCV belonged to CanineCV-3. In addition, 4 genetic recombination events were predicted in these 15 CanineCV strains, occurring in multiple regions of the genome. In conclusion, this study is the first to provide evidence of CanineCV infection in cats and successfully obtained the first whole genome of cat-derived CanineCV. The complex circulation and high prevalence of CanineCV among dogs and cats emphasize the importance of continuous monitoring of this virus in various animal species.

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.

Severe feather deformation in greater white-fronted goose (Anser alb. albifrons) goslings during hot summer period on Kolguev Island 2016

In summer 2016, we observed premature feather malformation among goslings of greater white-fronted goose (Anser alb. albifrons), between 7 and 10 weeks of age on family gathering areas on Kolguev Island, Russia, the most important breeding island in the Western Palearctic. Rarely reported in wild birds, to our knowledge, this phenomenon has not been recorded in wild geese of this species, despite continuous ringing and marking of thousands of wild geese across Northern Europe and Arctic Siberia. This feather malformations were documented in 36 unfledged goslings showing weak feather basis, deformed or unevenly grown wing feathers or even dead feather buds. Approximately about one-third of all chicks were affected. Feather malformations like this, causing flightless chicks as a result, have never been noticed in any other of our 12 study years since 2006. The lesion was characterised by soft feather buds, weak or incomplete wing feathers and lack of feather development. No other abnormalities were observed in the goslings, so goslings did not differ in weight or body sizes. Affected fledglings never became airworthy and were killed in large numbers by predators or at latest perished during the Arctic winter.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10344-022-01603-9.

Loop-Mediated Isothermal Amplification (LAMP) as a Promising Point-of-Care Diagnostic Strategy in Avian Virus Research

Simple Summary

Many of the existing screening methods of avian viruses depend on clinical symptoms and pathological gross examinations that still necessitate confirmatory microscopic testing. Confirmation of a virus is often conducted at centralized laboratories that are well-equipped with instruments for virus isolation, hemagglutinin inhibition, virus neutralization, ELISA, PCR and qPCR. These assays are known for their great accuracy and sensitivity, and hence are set as standard practices. Nevertheless, limitations arise due to the time, cost and on-site applicability. As the technology progresses, molecular diagnostics should be more accessible to isolated areas and even practicable for use by non-skilled personnel such as farmers and private breeders. One of the point-of-care diagnostic strategies to consider for such matters is loop-mediated isothermal amplification (LAMP).

Abstract

Over the years, development of molecular diagnostics has evolved significantly in the detection of pathogens within humans and their surroundings. Researchers have discovered new species and strains of viruses, while mitigating the viral infections that occur, owing to the accessibility of nucleic acid screening methods such as polymerase chain reaction (PCR), quantitative (real-time) polymerase chain reaction (qPCR) and reverse-transcription qPCR (RT-qPCR). While such molecular detection methods are widely utilized as the benchmark, the invention of isothermal amplifications has also emerged as a reliable tool to improvise on-field diagnosis without dependence on thermocyclers. Among the established isothermal amplification technologies are loop-mediated isothermal amplification (LAMP), recombinant polymerase amplification (RPA), strand displacement activity (SDA), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA) and rolling circle amplification (RCA). This review highlights the past research on and future prospects of LAMP, its principles and applications as a promising point-of-care diagnostic method against avian viruses.

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Porcine circovirus-like virus (PCLV) is a type of circular Rep-encoding single-stranded DNA virus and may be associated with the development of diarrheal symptoms in pigs. In this study, we retrospectively analyzed three years of past cases in Anhui, China, and reported a case of hemorrhagic enteritis and death in a pregnant sow possibly caused by PCLV. In addition, we analyzed the evolutionary characteristics of PCLV and found that mutation, recombination and selective pressure all played an important role in the evolution of PCLV. We identified N15D and T17S as well as L56T, T58R, K59Q, M62R, L75I and R190K mutations in two different branches, and we noted recombination events in the Rep of a group of Chinese strains. Analysis of selection pressure revealed that PCLV gained more positive selection, indicating that the virus is in a continuous evolutionary state. The PR2 plot, ENC-plot and neutrality analysis showed a greater role of natural selection than that of mutational pressure in the formation of codon usage patterns. This study is the first to identify PCLV in sows with hemorrhagic dysentery and death, and it provides new epidemiological information on PCLV infection in pigs in China.

Correlation between goose circovirus and goose parvovirus with gosling feather loss disease and goose broke feather disease in southern Taiwan

BACKGROUND

Goslings in several Taiwanese farms experienced gosling feather loss disease (GFL) at 21-35 days and goose broke feather disease (GBF) at 42-60 days. The prevalence ranges from a few birds to 500 cases per field. It is estimated that about 12,000 geese have been infected, the morbidity is 70-80% and the mortality is 20-30%.

OBJECTIVES

This study aims to investigate the pathogens that cause GFL and GBF. Focus on the study of the correlation between goose circovirus (GoCV) and goose parvovirus (GPV) with the goose feather loss in southern Taiwan. Furthermore, a phylogenetic tree was established to align the differences between southern and northern Taiwan and compare with virus strains from China and Europe.

METHODS

Samples were collected from animal hospitals. Molecular and microscopy diagnostics were used to examine 92 geese. Specific quantitative polymerase chain reaction (Q-PCR) assays are performed to evaluate GPV and GoCV viral loads and simultaneously evaluated the feather loss conditions in geese with the scoring method.

RESULTS

High prevalence of GoCV and GPV infection in geese showing signs of GFL and GBF. Inclusion body was detected in the feather follicles and Lieberkühn crypt epithelial cells. The Q-PCR showed the high correlation between feather loss and viruses during 3rd-5th week. However, the infection was not detected using the same test in 60 healthy geese.

CONCLUSIONS

Thus, GFL and GBF appear to be significantly closely related to GoCV and GPV. The geese feathers showed increasing recovery after being quarantined and disinfected.

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.

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.

Cellular p32 Is a Critical Regulator of Porcine Circovirus Type 2 Nuclear Egress

Circoviruses are the smallest DNA viruses known to infect mammalian and avian species. Although circoviruses are known to be associated with a range of clinical diseases, the details of circovirus DNA release still remain unknown. Here, we identified p32 as a key regulator for porcine circoviral nuclear egress. Upon porcine circovirus type 2 (PCV2) infection, p32 was recruited into the nucleus by the viral capsid (Cap) protein; simultaneously, protein kinase C isoform δ (PKC-δ) was phosphorylated at threonine 505 by phospholipase C (PLC)-mediated signaling at the early stage of infection, which was further amplified by Jun N-terminal protein kinase (JNK) and extracellular signal-regulated kinase (ERK) signaling at the late infection phase. p32 functioned as an adaptor to recruit phosphorylated PKC-δ and Cap to the nuclear membrane to phosphorylate lamin A/C, resulting in a rearrangement of nuclear lamina and thus facilitating viral nuclear egress. Consistent with these findings, knockout (KO) of p32 in PCV2-infected cells markedly reduced the phosphorylation of PKC-δ and impeded the recruitment of p-PKC-δ and Cap to the nuclear membrane, hence abolishing the phosphorylation of lamin A/C and the rearrangement of nuclear lamina. As a result, p32 depletion profoundly impaired the production of cell-free viruses during PCV2 infection. We further identified the N-terminal 24RRR26 of Cap to be crucial for binding to p32, and mutation of these three arginine residues significantly weakened the replication and pathogenesis of PCV2 in vivo In summary, our findings highlight a critical role of p32 in the activation and recruitment of PKC-δ to phosphorylate lamin A/C and facilitate porcine circoviral nuclear egress, and they certainly help understanding of the mechanism of PCV2 replication.IMPORTANCE Circovirus infections are highly prevalent in mammalian and avian species. Circoviral capsid protein is the only structural protein of the virion that plays an essential role in viral assembly. However, the machinery of circovirus nuclear egress is currently unknown. In this work, we identified p32 as a key regulator of porcine circovirus type 2 (PCV2) nuclear egress that forms a complex with the viral capsid (Cap) protein to enhance protein kinase C isoform δ (PKC-δ) activity; this resulted in a recruitment of phosphorylated PKC-δ to the nuclear membrane, which further phosphorylates lamin A/C to promote the rearrangement of nuclear lamina and facilitate viral nuclear egress. Notably, we found that the N-terminal 24RRR26 of Cap, a highly conserved motif among circovirus species, was required for interacting with p32, and that mutation of this motif markedly impeded PCV2 nuclear egress. These data indicate that p32 is a critical regulator of PCV2 nuclear egress and reveal the importance of this finding in circovirus replication.