A TaqMan-based real-time PCR assay for specific detection of novel duck reovirus in China

Development of an RT-qPCR Assay for the Detection of an Emerging Duck Egg-Reducing Syndrome

Duck egg-reducing syndrome virus (DERSV) is a novel Avihepatovirus and is responsible for a gradual decline in the laying rate of ducks, decreasing from a peak of 90% to 50%. The development of a rapid detection method for DERSV is crucial for the identification and control of virus infections. In this study, we developed a quantitative reverse transcription PCR (RT-qPCR) assay for detecting DERSV. Specific primers and a probe were designed to target a conserved region of the 3D gene. The assay demonstrated high specificity, with no cross-reactivity to other non-target duck viruses. It had a detection limit of 102 copies and a linear range from 102 to 109 copies per reaction. The assay's efficiency was 92.59%, with a regression coefficient (R2) of 0.999. The coefficient of variation for both intra-and inter-assays was less than 2.00%. Among the 153 clinical samples collected from 2016 to 2023, the RT-qPCR detected a DERSV positive ratio of 47.06% (72/153). In conclusion, the utilization of the real-time RT-qPCR assay holds potential for the detection of DERSV in epidemiological and pathogenesis studies.

Simultaneous detection of novel goose parvovirus and novel duck reovirus by SYBR Green I-based duplex real-time quantitative polymerase chain reaction

Co-infection with novel goose parvovirus (NGPV) and novel duck reovirus (NDRV) is common, significantly impeding duck growth and resulting in considerable economic losses within the duck farming industry. To facilitate rapid and accurate diagnosis and differentiation of these two viruses, this study developed a SYBR Green I-based duplex real-time quantitative polymerase chain reaction (qPCR) assay. This assay enabled the simultaneous detection of NGPV and NDRV by exploiting their distinct melting temperatures (Tm): 78.5 ± 0.50 °C for NGPV and 84.5 ± 0.50 °C for NDRV. No amplification was observed for other prevalent non-target duck viruses. The intra- and inter-assay coefficients of variation were less than 1.75%. The assay showed good performance with the same detection limit of 102 copies/μL for both NGPV and NDRV. The results of the clinical testing indicated that 45.3% (34/75) of the samples tested positive for NGPV, while 38.7% (29/75) were positive for NDRV. Notably, 13.3% (10/75) exhibited co-infection. These results revealed that the sensitivity of the developed method exceed that of conventional polymerase chain reaction (PCR). The developed method for the identifying of NGPV and NDRV shows good specificity, sensitivity, and repeatability, rendering it an effective tool for the simultaneous detection of co-infection with NGPV and NDRV.

A rapid simultaneous detection of duck hepatitis A virus 3 and novel duck reovirus based on RPA CRISPR Cas12a/Cas13a

The mixed infection of duck hepatitis A virus 3 (DHAV-3) and novel duck reovirus (NDRV) has caused significant losses to the global duck farming industry. On-site point-of-care testing of viruses plays a crucial role in the early diagnosis, prevention, and disease control. Here, we proposed an RPA-CRISPR Cas12a/Cas13a one-pot strategy (DRCFS) for rapid and simultaneous detection of DHAV-3 and NDRV. This method integrated the reaction of RPA and CRISPR Cas12a/Cas13a in a single tube, eliminating the need to open the lid during the intermediate processes and thereby avoiding aerosol contamination. On this basis, we proposed a dual RPA-CRISPR strategy coupled with a lateral flow analysis platform (DRC-LFA). This circumvented the necessity for complex instruments, enabling direct visual interpretation of results, making the test more accessible and user-friendly. Our findings demonstrated that the DRCFS method could detect DHAV-3 and NDRV at concentrations as low as 100 copy/μL, while DRC-LFA achieved limit of 101 copies/μL within 35 min. Furthermore, when DRCFS, DRC-LFA, and qPCR were employed collectively for clinical samples analysis, all three methods yielded consistent results. The specificity, sensitivity, and user-friendly of these methods rendered them invaluable for on-site virus detection.

Recombinant linear multiple epitopes of σB protein protect Muscovy ducks against novel duck reovirus infection

Infection by the novel duck reovirus (NDRV) in ducklings causes high mortality, which leads to substantial economic losses in the duck industry in China. To date, no commercial vaccine is available for this disease. In this study, linear B cell epitopes of the σB protein of the NDRV were predicted and recombinant multiple linear B cell epitopes (MLBEs) were constructed through linkers. The recombinant MLBEs were then expressed and purified. One-day-old Muscovy ducklings were immunized with different doses of MLBEs and challenged with 5 × 104 ELD50 of the virulent CHY strain of NDRV 14 days after immunization. The ducklings vaccinated with 20 and 40 μg of MLBE performed no clinical signs or gross or histopathological lesions, indicating 100% protection against infection. The viral load in the liver and spleens of these birds was significantly lower than that in the control group. Additionally, these ducklings exhibited positive seroconversion at 7 days after vaccination on enzyme-linked immunosorbent assay. These results indicate that MLBE of σB could be used as a candidate for developing vaccines against NDRV infection.

Development and application of a multiplex PCR method for the simultaneous detection of goose parvovirus, waterfowl reovirus, and goose astrovirus in Muscovy ducks

A multiplex polymerase chain reaction (PCR) method was developed to detect and distinguish goose parvovirus (GPV), waterfowl reovirus (WRV), and goose astrovirus (GAstV). Three pairs of primers were designed based on conserved regions in the genomic sequences of these enteric viruses and were used to specifically amplify targeted fragments of 493 bp from the viral protein 3 (VP3) gene of GPV, 300 bp from the sigma A-encoding gene of WRV, and 156 bp from the capsid protein-encoding gene of GAstV. The results showed that the primers can specifically amplify target fragments, without any cross-amplification with other viruses, indicating that the method had good specificity. A sensitivity test showed that the detection limit of the multiplex PCR method was 1 × 103 viral copies. A total of 102 field samples from Muscovy ducks with clinically suspected diseases were evaluated using the newly developed multiplex PCR method. The ratio of positive samples to total samples for GPV, WRV, and GAstV was 73.53% (75/102) for multiplex PCR and was 73.53% (75/102) for routine PCR. Seventy-five positive samples were detected by both methods, for a coincidence ratio of 100%. This multiplex PCR method can simultaneously detect GPV, WRV, and GAstV, which are associated with viral enteritis, thereby providing a specific, sensitive, efficient, and accurate new tool for clinical diagnosis and laboratory epidemiological investigations.

Multiplex digital PCR: a superior technique to qPCR for the simultaneous detection of duck Tembusu virus, duck circovirus, and new duck reovirus

Duck Tembusu virus (DTMUV), duck circovirus (DuCV), and new duck reovirus (NDRV) have seriously hindered the development of the poultry industry in China. To detect the three pathogens simultaneously, a multiplex digital PCR (dPCR) was developed and compared with multiplex qPCR in this study. The multiplex dPCR was able to specifically detect DTMUV, DuCV, and NDRV but not amplify Muscovy duck reovirus (MDRV), Muscovy duck parvovirus (MDPV), goose parvovirus (GPV), H4 avian influenza virus (H4 AIV), H6 avian influenza virus (H6 AIV), and Newcastle disease virus (NDV). The standard curves showed excellent linearity in multiplex dPCR and qPCR and were positively correlated. The sensitivity results showed that the lowest detection limit of multiplex dPCR was 1.3 copies/μL, which was 10 times higher than that of multiplex qPCR. The reproducibility results showed that the intra- and interassay coefficients of variation were 0.06-1.94%. A total of 173 clinical samples were tested to assess the usefulness of the method; the positive detection rates for DTMUV, DuCV, and NDRV were 18.5, 29.5, and 14.5%, respectively, which were approximately 4% higher than those of multiplex qPCR, and the kappa values for the clinical detection results of multiplex dPCR and qPCR were 0.85, 0.89, and 0.86, indicating that the two methods were in excellent agreement.

Isolation and Pathogenicity Analysis of a Novel Orthoreovirus Caused the Outbreak of Duck Viral Arthritis in China

Novel duck orthoreovirus can infect various hosts, mainly causing spleen necrosis and hemorrhagic necrotizing hepatitis, leading to immunosuppression and growth impairment. Infectious diseases characterized by swollen hock joints, movement disorders, and impaired growths have recently occurred in significant duck breeding areas in China. Infected ducks from Shandong Province were selected, and N-DRV-LY20 was isolated from the swollen joints. Next-generation sequencing (NGS) of N-DRV-LY20 and homology analysis showed that all ten fragments had the highest homology to N-DRV and the closest affinity to Duck/N-DRV-XT18/China/2018. After artificial inoculation with N-DRV-LY20 virus solution, Cherry Valley ducks showed the same symptoms of leg swelling and hock joint deformation, which were not explored in previous studies. A long history of evolution has led to significant variation in DRV and altered its pathogenicity. In this study, we confirmed the ability of N-DRV to cause viral arthritis in ducks and clarified this isolate's genetic characteristics and level of variation, providing a basis for the control and variation detection of N-DRV.

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.

Genomic characteristics, pathogenicity and viral shedding of a novel DVEV variant derived from goose

Duck virus enteritis (DVE), caused by the DVE virus (DVEV), is an acute, septicemic, and contagious disease affecting ducks of different breeds, ages, and sexes. In late spring and summer 2019, several outbreaks of DVE were reported in areas with large waterfowl industries in central and southern China. A goose farm located in Jining County, Shandong Province, was impacted by an acute DVE outbreak in July 2019. The causative DVEV field strain (Goose/DVEV/SDJN/China/2019) was subsequently isolated from the liver specimens collected from acute cases of dead geese, which showed severe hemorrhagic lesions on the esophageal mucosal membranes of specimens collected from all the postmortem cases. Comparison of the genome sequence of this newly isolated field strain (Goose/DVEV/SDJN/China/2019) with the common DVEV strains revealed insertions or mutations in the gB and gC genes, which possibly caused the observed high morbidity and mortality in this acute outbreak. We conducted a trial among geese to evaluate the pathogenicity of this strain. Healthy experimental goslings aged 15 d old were inoculated with 10^-5.53 ELD₅₀/0.2 mL doses orally or through intramuscular injection. Clinical signs and esophageal erosion appeared in infected geese. Necropsy revealed hemorrhage and necrosis of the cloacal mucosa and liver. Detection of the virus using real-time PCR in the liver, brain, and spleen indicated that they were the hotspots of DVEV infections. One day after the DVEV infection, virus release and seroconvert were observed in infected geese. Thus, our studies demonstrate that DVEV is highly pathogenic and contagious in geese. To the best of our knowledge, this is the first study on the pathogenicity of mutant duck viral enteritis virus in goslings. This study serves as a foundation for further investigations into the pathophysiology of the recently identified variant DVEV strains.

Identification and Pathogenicity Analysis of the Pathogen Causing Spotted Spleen in Muscovy Duck

Since September 2020, the clinical symptoms of Muscovy duck spleen spots have appeared in Guangdong, Guangxi, Jiangxi, Hunan, Hubei, and other provinces, resulting in a large number of Muscovy duck deaths and great economic losses. The absence of the typical clinical symptoms caused by pathogenic microorganisms makes the cause of the spotted spleen a mystery. High-throughput sequencing results suggested that Riemerella anatipestifer (R. anatipestifer) may be the pathogen. Then, R. anatipestifer was regarded as the research target for isolation, identification, and pathogenicity assessment. After biochemical test, PCR amplification, and serotype determination, it was confirmed that the isolated strain CZG-1 was serotype 15 R. anatipestifer. Typical spotted spleen symptoms were observed after CZG-1 infection. Furthermore, drug sensitivity assays showed the similar drug-resistant spectrum of R. anatipestifer serotype 15 to other serotypes; for example, all test strains were resistant to polymyxin, gentamicin, and neomycin. The CZG-1 strain has high pathogenicity, and its lethal dose of 50% (LD50) is 35.122 CFU/ml. Virulence gene determination showed that the CZG-1 strain had at least five virulence genes, bioF, TSS9-1, TSS9-2, PncA, and 0373Right. Above all, this study identified and proved that the pathogen of spotted spleen in ducks was R. anatipestifer serotype 15, which caused death of ducks without the typical symptoms of bacterial infection. The results of this study enriched the knowledge of symptom after R. anatipestifer infection, provided a reference to the identification of the pathogen of spotted spleen, and provided theoretical basis for prevention and control of spotted spleen.

DDX1 from Cherry valley duck mediates signaling pathways and anti-NDRV activity

Novel duck reovirus (NDRV) causes severe economic losses to the duck industry, which is characterized by hemorrhagic spots and necrotic foci of the livers and spleens. DEAD-box helicase 1 (DDX1) plays a critical role in the innate immune system against viral infection. However, the role of duck DDX1 (duDDX1) in anti-RNA virus infection, especially in the anti-NDRV infection, has yet to be elucidated. In the present study, the full-length cDNA of duDDX1 (2223 bp encode 740 amino acids) was firstly cloned from the spleen of healthy Cherry valley ducks, and the phylogenetic tree indicated that the duDDX1 has the closest relationship with Anas platyrhynchos in the bird branch. The duDDX1 mRNA was widely distributed in all tested tissues, especially in the duodenum, liver, and spleen. Overexpression of duDDX1 in primary duck embryo fibroblast (DEF) cells triggered the activation of transcription factors IRF-7 and NF-κB, as well as IFN-β expression, and the expression of the Toll-like receptors (TLR2, TLR3, and TLR4) was significantly increased. Importantly, after overexpressing or knocking down duDDX1 and infecting NDRV in DEF cells, duDDX1 inhibits the replication of NDRV virus and also regulates the expression of pattern recognition receptors and cytokines. This indicates that duDDX1 may play an important role in the innate immune response of ducks to NDRV. Collectively, we first cloned DDX1 from ducks and analyzed its biological functions. Secondly, we proved that duck DDX1 participates in anti-NDRV infection, and innovated new ideas for the prevention and control of duck virus infection.