Phylogenetic analysis of VP1 gene sequences of waterfowl parvoviruses from the Mainland of China revealed genetic diversity and recombination

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

Epidemiological investigation of infectious diseases in geese on mainland China during 2018-2021

Geese play an important role in agricultural economics, with China producing the vast majority of goose meat consumed worldwide annually. The variations in the avian viruses and co-infections result in substantial economic losses to the goose industry in China. To understand the evolutionary characteristics and co-infections of viruses, a broad epidemiological investigation of epizootic viruses of goose was carried out in nine provinces of China during 2018-2021. Here, the results indicated that, among the 1970 clinical samples, 50.81% (1001/1970) were positive for goose astrovirus (GAstV), 18.22% (359/1970) for avian orthoreovirus, 12.74% (251/1970) for goose parvovirus, 11.02% (217/1970) for H9N2 subtype avian influenza virus, 4.01% (79/1970) for Newcastle disease virus, and 2.08% (41/1970) for fowl adenovirus. Among the six viruses, co-infections comprised a large proportion (66.37%) in the field, of which the dual infection was more common. Additionally, phylogenetic analysis of GAstVs indicated that Chinese GAstVs had formed two distinct groups, that is, GAstV-1 and GAstV-2. GAstV-2 sub-genotype II-c had arisen as the dominant genotype in the whole country. Notably, all the H9N2-AIV isolated strains harboured the mammalian adaptation markers I155T, H183N, and Q226L (H3 numbering) in the HA gene, which promotes preferential binding to human-like α2-6-linked sialic acid receptors. And beyond that, we determined that the goose-origin Muscovy Duck Reovirus isolates, showing 51.7%-96% similarities to that of other waterfowl-origin orthoreovirus isolates in sequence homology analysis of the representative part of σC, are a new variant of waterfowl-origin orthoreovirus. These data provide valuable information about the prevalence of infectious diseases in geese on mainland China.

Epidemiological Analysis and Genetic Characterization of Parvovirus in Ducks in Northern Vietnam Reveal Evidence of Recombination

In total, 130 tissue-pooled samples collected from ducks in some provinces/cities in north Vietnam were examined for waterfowl parvovirus genome identification. Twenty-six (20%) samples were positive for the parvovirus infection, based on polymerase chain reaction analysis. Of the 38 farms tested, 14 (36.84%) were positive for the waterfowl parvovirus genome. The rate of the parvovirus genome detection in ducks aged 2−4 weeks (37.04%) was significantly (p < 0.05) higher than that at ages <2 weeks (9.09%) and >4 weeks (16.30%). The positive rate on medium-scale farms (9.36%) was significantly (p < 0.05) lower than for small-scale (31.03%) and large-scale (29.73%) farms. The lengths of the four Vietnamese waterfowl parvovirus genomes identified were 4750 nucleotides. Among the four Vietnamese parvovirus genomes, nucleotide identities were from 99.29% to 99.87%. Phylogenetic analysis of the near-complete genomes indicated that the waterfowl circulating in northern Vietnam belonged to the novel goose parvovirus (NGPV) group. The Vietnamese NGPV group was closely related to the Chinese group. Recombination analysis suggested that the Vietnam/VNUA-26/2021 strain was generated by a recombination event. One positive selection site of the capsid protein was detected.

Molecular Characterization and Pathogenicity of the Novel Recombinant Muscovy Duck Parvovirus Isolated from Geese

Simple Summary

Waterfowl parvoviruses are important pathogens that cause severe disease in young waterfowl. Waterfowl parvoviruses can be divided into goose parvovirus (GPV)- and Muscovy duck parvovirus (MDPV)-related groups. New variant strains can be generated from genomic recombination between different waterfowl parvoviruses and result in new epidemics. Recently, a novel recombinant MDPV (rMDPV) derived from recombination between GPVs and MDPV was reported. This virus caused high morbidity and mortality rates in ducklings and was circulating in waterfowl in mainland China. In this study, a novel rMDPV was isolated in Taiwan from a goose flock that experienced a high mortality. The complete genome of this goose-origin rMDPV was sequenced. Phylogenetic and recombination analyses were performed to elucidate its molecular characteristics. The virulence of this rMDPV was evaluated using experimental infection goose embryos and goslings. This study was the first report showing the pathogenicity of rMDPV in geese.

Abstract

Goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) are the main agents associated with waterfowl parvovirus infections that caused great economic losses in the waterfowl industry. In 2020, a recombinant waterfowl parvovirus, 20-0910G, was isolated in a goose flock in Taiwan that experienced high morbidity and mortality. The whole genome of 20-0910G was sequenced to investigate the genomic characteristics of this isolate. Recombination analysis revealed that, like Chinese rMDPVs, 20-0910G had a classical MDPV genomic backbone and underwent two recombination events with classical GPVs at the P9 promoter and partial VP3 gene regions. Phylogenetic analysis of the genomic sequence found that this goose-origin parvovirus was highly similar to the circulating recombinant MDPVs (rMDPVs) isolated from duck flocks in China. The results of experimental challenge tests showed that 20-0910G caused 100% mortality in goose embryos and in 1-day-old goslings by 11 and 12 days post-inoculation, respectively. Taken together, the results indicated that this goose-origin rMDPV was closely related to the duck-origin rMDPVs and was highly pathogenic to young geese.

Detection and Molecular Characterization of Two Genotypes of Goose Parvoviruses Isolated from Growing Period Geese and Cherry Valley Ducks in China

Goose parvovirus (GPV) is the etiologic pathogen of Derzsy's disease, causing great economic losses in the waterfowl industry. A novel GPV-related virus (NGPV), which caused short beak and dwarfism syndrome, has occurred in China since 2015. In this study, two GPV strains (RC45 and RC70) were isolated from diseased growing period geese (45 days old and 70 days old), and one NGPV strain GXN45 was isolated from a 45-day-old Cherry Valley duck in China. To better understand the genetic diversity between GPVs isolated from growing period waterfowls and other classical waterfowl parvoviruses, the complete genomes and main genes were sequenced and analyzed. Full-length genomic sequence alignments demonstrated that both RC45 and RC70 showed the highest identity with classical GPVs YZ99-6 and SHFX1201, whereas GXN45 shared the highest identity with NGPV SDLC01. Sequence alignment of the inverted terminal repeat region showed that GXN45, RC45, and RC70 had two 14-nucleotide (nt) deletions compared with the classical GPV virulent B strain and one 14-nt deletion compared with mule duck-origin NGPV M15 strain. Phylogenetic tree analysis of nonstructural and VP1 genes showed that GXN45 was clustered into a branch with NGPV QH15 strain except for the VP1 amino acid tree. Although both RC45 and RC70 formed one separate branch distinct from classic GPV isolates, they were in one large phylogenetic tree branch. This study will contribute to a better understanding of the genetic diversity and molecular characterization of three isolated parvoviruses and lay the foundation to further study the relationship between mutations of virus genome and viral pathogenicity.

Screening of tea saponin-degrading strain to degrade the residual tea saponin in tea seed cake

Although tea seed cake (TSC) possesses high nutritional value, its high content of tea saponin (TS) limits its potential as feed. This study aimed to degrade TS in TSC by saponin-degrading strain and used a multistrains fermentation method to improve its nutritional value and palatability. Three saponin-degrading strains were isolated from Oleum Camelliae mill soil and identified as Citrobacter sp. FCTS301, Pantoea sp. FCTS302, and Enterobacter sp. FCTS303. Single-factor experiment showed that Citrobacter sp. FCTS301 had the highest degradation rate of TS. Response surface analysis for Citrobacter sp. FCTS301 indicated that the optimum culture conditions were as follows: initial pH of 7.2, culture temperature of 34.2 °C, inoculation amount of 7.3%, the agitation rate of 150 rpm, and the TS concentration of 10.0 g/L. Under these conditions, the maximum degradation rate was 82.6%. The fermentation process of TSC was obtained by a multistrains fermentation experiment. Considering the protein content, crude fiber degradation rate, and TS degradation rate of each group, the optimum inoculum amount of strains included Citrobacter sp. FCTS301, Aspergillus oryzae NCUF414, Saccharomyces cersvisiae NCUF306.5, and Lactobacillus plantarum NCUF201.1(5%, 0.5%, 1.0%, and 1.5%). After TS was degraded efficiently, fermented TSC can be presumed a potential feed raw material.

Molecular evidence of goose-parvovirus-related abnormal molting in Pekin ducks

Since January 2019, abnormal molting has been observed frequently in approximately 40-day-old Pekin ducks in China. To investigate the possible involvement of a virus, we tested the prevalence of duck circovirus (DuCV), goose hemorrhagic polyomavirus (GHPyV), and goose parvovirus (GPV) in 11 molt cases in two provinces. GPV was detected in all cases, particularly in all samples collected from the feather area. The complete genome sequences of three GPV strains were determined and found to have 52 nucleotide changes relative to GPVs associated with short beak and dwarfism syndrome of Pekin ducks. These data will enhance our understanding of GPV diversity and outcomes of GPV infection in Pekin ducks.

Development of a duplex SYBR Green I-based quantitative real-time PCR assay for the rapid differentiation of goose and Muscovy duck parvoviruses

Background

Waterfowl parvoviruses, including goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV), can cause seriously diseases in geese and ducks. Developing a fast and precise diagnosis assay for these two parvoviruses is particularly important.

Results

A duplex SYBR Green I-based quantitative real-time PCR assay was developed for the simultaneous detection and differentiation of GPV and MDPV. The assay yielded melting curves with specific single peak (Tm = 87.3 ± 0.26 °C or Tm = 85.4 ± 0.23 °C) when GPV or MDPV was evaluated, respectively. When both parvoviruses were assessed in one reaction, melting curves with specific double peaks were yielded.

Conclusion

This duplex quantitative RT-PCR can be used to rapid identify of GPV and MDPV in field cases and artificial trials, which make it a powerful tool for diagnosing, preventing and controlling waterfowl parvovirus infections.

Comparative genetic analysis and pathological characteristics of goose parvovirus isolated in Heilongjiang, China

BACKGROUND

Goose parvovirus (GPV) causes acute enteritis, hepatitis, myocarditis and high morbidity and mortality in geese and ducks. GPV H strain was isolated from a Heilongjiang goose farm where the geese were showing signs of hemorrhage in the brain, liver, and intestinal tract. In this study, we explored the genetic diversity among waterfowl parvovirus isolates and the pathological characteristics of GPV H in Shaoxing ducklings.

METHODS

The complete capsid protein (VP) and non-structural (NS) sequences of the isolated H strain were sequenced, and phylogenetic trees of VP and NS were constructed in MEGA version 5.05 using the neighbor-joining method. Three-day-old Shaoxing ducklings were inoculated with GPV and were euthanized at 1, 2, 4, 6, and 8 days post-inoculation (PI), and their organs were removed and collected. The organs of 6-day PI ducklings were fixed in formalin, embedded in paraffin, sectioned for histology, stained with HE and analyzed for pathological lesions. The distribution of the GPV H strain in the tissues of the inoculated ducklings was detected using the polymerase chain reaction (PCR) method.

RESULTS

Genetic analysis of the NS and VP genes indicated that the H strain was closely related to strains circulating in China during 1999-2014, and the nucleic acid identity of those strains was 98%-99%. Classical symptoms were observed in the inoculated ducklings. GPV remained in many tissues and replicated in a majority of the tissues, leading to histopathological lesions in four tissues.

CONCLUSIONS

We first reported the distribution and histopathological lesions of a Chinese strain of GPV in infected shaoxing ducklings. This H strain was moderate pathogenic for Shaoxing ducklings.

Genomic and pathogenic analysis of a Muscovy duck parvovirus strain causing short beak and dwarfism syndrome without tongue protrusion

In 2008, clinical cases of short beak and dwarfism syndrome (SBDS) caused by Muscovy duck parvovirus (MDPV) infection were found in mule duck and Taiwan white duck farms in Fujian, China. A MDPV LH strain causing duck SBDS without tongue protrusion was isolated in this study. Phylogenetic analysis show that the MDPV LH strain was clustered together with other MDPV strains, but divergent from GPV isolates. Two major fragment deletions were found in the inverted terminal repeats (ITR) of MDPV LH similar to the ones in the ITR of MDPV GX5, YY and SAAS-SHNH strains. To investigate the pathogenicity of the MDPV LH strain, virus infection of young mule ducks was performed. The infected ducks showed SBDS symptoms including retard growth and shorten beaks without tongue protrusion. Atrophy of thymus, spleen and bursa of Fabricius was identified in the infected ducks. The results show that MDPV LH strain is moderately pathogenic to mule duck, leading to occurrence of SBDS. As far as we know, it is the first study showing that SBDS without tongue protrusion, and atrophy of thymus, spleen and bursa of Fabricius possibly associated with immunosuppression were found in the MDPV-infected ducks. The established duck-MDPV-SBDS system will help us to further work on the virus pathogenesis and develop efficacious vaccine against MDPV infection.

Isolation and characterization of a distinct duck-origin goose parvovirus causing an outbreak of duckling short beak and dwarfism syndrome in China

Many mule duck and Cherry Valley duck flocks in different duck-producing regions of China have shown signs of an apparently new disease designated "short beak and dwarfism syndrome" (SBDS) since 2015. The disease is characterized by dyspraxia, weight loss, a protruding tongue, and high morbidity and low mortality rates. In order to characterize the etiological agent, a virus designated SBDSV M15 was isolated from allantoic fluid of dead embryos following serial passage in duck embryos. This virus causes a cytopathic effect in duck embryo fibroblast (DEF) cells. Using monoclonal antibody diagnostic assays, the SBDSV M15 isolate was positive for the antigen of goose parvovirus but not Muscovy duck parvovirus. A 348-bp (2604-2951) VP1gene fragment was amplified, and its sequence indicated that the virus was most closely related to a Hungarian GPV strain that was also isolated from mule ducks with SBDS disease. A similar disease was reproduced by inoculating birds with SBDSV M15. Together, these data indicate that SBDSV M15 is a GPV-related parvovirus causing SBDS disease and that it is divergent from classical GPV isolates.