Detection of Novel duck reovirus (NDRV) using visual reverse transcription loop-mediated isothermal amplification (RT-LAMP)

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.

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.

Whole-genome sequence and pathogenicity of a fowl adenovirus 5 isolated from ducks with egg drop syndrome in China

Recently, fowl adenovirus (FAdV) infection has become widespread in poultry in China and may be asymptomatic or associated with clinical and other pathological conditions. In 2017, a severe egg drop syndrome outbreak in breeder ducks (45 weeks old) occurred in eastern Shandong province in China. The egg production rate declined from 93 to 41%, finally increasing to ~80% (did not reach complete recovery). The presence of the virus was confirmed by FAdV-5 specific PCR assay, and it was designated strain WHRS. Furthermore, next-generation and Sanger sequencing of genomic fragments yielded a 45,734 bp genome. Phylogenetic analysis showed that the genomic sequence of the WHRS strain was most homologous-(99.95%) to that of the FAdV-5 17/25,702 and 14/24,408 strain, sharing 32.1~53.4% similarity with other FAdV strains in the genus Aviadenovirus. Infected duck embryos died within 3–5 dpi, but no deaths occurred in the infected ducks. Strain WHRS could cause egg drop syndrome in ducks, accompanied by clinical signs similar to those of natural infections. Overall, strain WHRS is lethal to duck embryos and causes egg drop syndrome in breeder ducks.

Structure and expression identification of Cherry Valley duck IRF8

Interferon regulatory factor 8 (IRF8) is also known as interferon (IFN) consensus sequence binding protein (ICSBP), which plays an important role in IFN signal transduction. In this study, we cloned the full-length coding sequence of Cherry Valley duck IRF8 (duIRF8) and analyzed its structure. In addition, we tested the distribution of IRF8 in the tissues of healthy Cherry Valley ducks, and the changes in IRF8 expression levels in the tissues after virus infection. The results show that the open reading frame (ORF) of IRF8 is 1293 bp, encodes 430 amino acids, and have 3 conserved domains: the N-terminal DBD domain, the C-terminal IAD domain, and the NLS domain. Besides, from the analysis of the phylogenetic tree, it can be known that the duIRF8 has the highest homology with the anser cygnoides, and has less homology with the fish. Analyzing the distribution level of IRF8 in the tissues, it is found that the expression level of IRF8 in the liver of Cherry Valley duck is the highest. However, after infection with duck Tambusu virus, novel duck reovirus, and duck plague virus, the expression of IRF8 in the spleen and brain all showed up-regulation. These data indicate that IRF8 is involved in the host's innate immune response against virus in Cherry Valley duck.

Novel duck reovirus exhibits pathogenicity to specific pathogen-free chickens by the subcutaneous route

To study the pathogenicity of new duck reovirus (NDRV) to chickens, eighty 3-day-old SPF chickens were equally divided into two groups. The experimental group was inoculated with a NDRV challenge strain of 100 μL (10^-5.00 ELD₅₀/0.1 mL) by the subcutaneous (s.c.) route, and the control group was inoculated with 100 μL of sterile phosphate-buffered saline (PBS) by the same route. In the experimental group, chickens exhibited introflexion of claws, performing of splits, stunting syndrome, weight loss and death. Gross lesions such as enlargement and yellowish-white focal necroses were observed in the liver and spleen. Microscopic changes were typical including varying degrees of hepatocyte steatosis and necrosis, splenic lymphocyte necrosis, interstitial pneumonia. Viral loads were detected in lung, liver, heart, spleen, duodenum, burse and kidney. The liver and spleen viral loads remained a much higher level and maintained for a longer time, suggesting that these tissues might be the target organs. In summary, NDRV can cause systemic infections and death in chickens, which indicated that chickens may be infected by NDRV in poultry production.

Identification, cloning, and characterization of Cherry Valley duck CD4 and its antiviral immune responses

CD4 protein is a single chain transmembrane glycoprotein and has a broad functionality beyond cell-mediated immunity. In this study, we cloned the full-length coding sequence (CDS) of duck CD4 (duCD4) and analyzed its sequence and structure, and expression levels in several tissues. It consists of 1,449 nucleotides and encodes a 482 amino acid protein. The putative protein of duCD4 consisted of an N-terminal signal peptide, three immunoglobulins and one immunoglobulins-like domain in its central, one terminal transmembrane region, and a C-terminal domain of the CD4 T cell receptor. The duCD4 also has the typical signature “CXC” of CD4s. The multiple sequence alignment suggests duCD4 has four potential N-glycosylation sites and the phylogenetic analysis suggests duCD4 shares greater similarity with avian than other vertebrates. Quantitative real-time PCR analysis showed that duCD4 mRNA transcripts are widely distributed in the healthy Cherry Valley duck, and the highest level in the thymus. During the virus infection, the obvious change of duCD4 expression was observed in the spleen, lung and brain, which suggesting that duCD4 could be involved in the host's immune response to multiple types of viruses. Our research studied the characterization, tissue distribution, and antiviral immune responses of duCD4.

Genomic sequences and pathogenic characteristics of two variant duck reoviruses associated with spleen necrosis

Emerging variant novel duck reovirus (NDRV) strains that cause spleen swelling and necrosis have seriously threatened the waterfowl industry since 2017. However, there is no report about the complete genomic sequence of emerging variant strains isolated from Cherry valley ducks. In this study, we acquired the complete genome sequences of two variant NDRV strains, SD19/6201 and SD19/6202, and analyzed their genetic and evolutionary relationship with other orthoreoviruses. The phylogenetic analysis of σC showed that all the Chinese NDRVs were clustered into two distinct branches. The SD19/6201 strain located in branch I with most of the Chinese NDRVs, while SD19/6202 was clustered in branch II with significantly different from the existing strains. Within the branch I, the NDRVs isolated in 2017 and thereafter clustered in a new subgroup. Comparison analysis of σC amino acid sequences indicated that ten amino acid differences were found between SD19/6201 and SD19/6202. Apart from the SD19/6201 and SD19/6202 strains, isolates in 2017 and thereafter had specific mutations at residues 132A, 138R, 158H, and 258A. These two NDRV strains showed different pathogenicity in SPF duck embryos and ducks. The viral loads in the spleen of infected ducks were significantly higher than those of other organs, which might be the reason why NDRV could cause obvious spleen necrosis in ducks. This study will help us to formulate effective prevention and control strategies against NDRV and enrich our understanding of the intra- and inter-species relationships of orthoreoviruses.

Rapid and visual detection of the emerging novel duck reovirus by using a specific and sensitive reverse transcription recombinase polymerase amplification method

Duck spleen necrosis disease (DSND) caused by Novel Duck Reovirus (NDRV), is an emerging infectious disease that causes severely threaten to duck industry. Currently, the popular conventional RT-PCR technique for detecting NDRV is time consuming. So, it is essential to develop a rapid and accurate molecular diagnosis techniques of the pathogen for the purpose to effective control of the disease. In our study, a simple, rapid and reliable detection method was developed by an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA). The RT-RPA primers were designed targeting the S3 gene of NDRV, and its specificity was verified by testing a series of other waterfowl pathogens. A total of 20 field and experimental samples from infected ducklings were tested by the RT-RPA and compared with the results of the conventional RT-PCR and the quantitative RT-PCR simultaneously. The RT-RPA method could detect as little as 4.14 × 10² copies/μl of the target gene in the sensitivity analysis, which was 10×higher sensitive than the conventional RT-PCR. The major advantage of the RT-RPA method is that it could be performed as an isothermal reaction at 37 ℃ and completed within 20 min. In addition, no cross-reactivity was detected with other waterfowl-origin viruses. Also, the amplified products could be visualized faster, without the gel electrophoresis, by adding the SYBR Green I and observing them under an ultraviolet light. The newly developed RT-RPA method offers a simple, rapid and accurate for rapid detection of NDRV, which especially useful in on-site facilities and resource-limited areas.

Using loop-mediated isothermal amplification for visual detection of porcine parvovirus 7

We developed and optimized a loop-mediated isothermal amplification (LAMP)-based method to detect porcine parvovirus 7 (PPV7). After using three pairs of specific primers to amplify PPV7 isothermally at 62 °C for 40 min, the amplified product was mixed with SYBR Green I, after which the sample turned green. The method detected PPV7 at concentrations as low as 40 copies/μL, and the sensitivity was consistent with that of nested polymerase chain reaction (PCR) analysis, which was tenfold higher than that of conventional PCR. No cross-reactivity occurred with porcine parvovirus 1, porcine circovirus type 3, porcine circovirus type 2, porcine pseudorabies virus, porcine epidemic diarrhea virus, or porcine reproductive and respiratory syndrome virus. Simultaneous analysis of 76 clinical samples was performed using LAMP, conventional PCR, and nested PCR. The results showed that our method is simple, rapid, sensitive, and specific for the rapid diagnosis of PPV7 in pig farms.

SUPPLEMENTARY INFORMATION

The online version of this article (10.1007/s13205-020-02623-5) contains supplementary material, which is available to authorized users.

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.

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

BACKGROUND

In China, Newly emerging duck reovirus (NDRV) variants have been causing major disease problems in cherry valley ducks. NDRV has the potential to cause high morbidity and 5-50% mortality rates. Severe hemorrhagic-necrosis in the liver and spleen were commonly seen in NDRV affected ducks. The availability of upgraded methods for rapid diagnosis of newly emerging DRV variants is crucial for successful DRV infection control and prevention.

RESULTS

In this study, we present a TaqMan-based real-time PCR assay (RT-qPCR) for the detection of NDRV infection. Using the conserved regions within the NDRV genome, we designed the specific primers and probe. The lower limit of detection for NDRV infection was 10 copies/μL (Ct values: 38.3) after the optimization of the RT-qPCR conditions. By cross-checking with other duck viral pathogens, no cross-reactivity was observed confirming the assay was highly specific for the detection of NDRV. Reproducibility of the RT-qPCR was confirmed by intra- and inter-assay variability was less than 2.91%(Intra-assay variability of Ct values: 0.07-1.48%; Interassay variability of Ct values: 0.49-2.91%). This RT-qPCR and conventional PCR (cPCR) detected one hundred and twenty samples of NDRV infection from different regions. The result shows that the positive rates were 94.17 and 84.17% respectively. The detection rate of RT-qPCR rapid detection assay was 10% higher than that of the cPCR method.

CONCLUSION

This research developed a highly sensitive, specific, reproducible and versatile of RT-qPCR for quantitatively detecting NDRV. It can be used to study the pathogenesis and epidemiology investigation of NDRV.

The genomic constellation of a novel duck reovirus strain associated with hemorrhagic necrotizing hepatitis and splenitis in Muscovy ducklings in Fujian, China

The complete sequence of a reovirus, strain NP03 associated with necrotic focus formation in the liver and spleen of Muscovy ducklings in Fujian Province, China in 2009, was determined and compared with sequences of other waterfowl and chicken-origin avian reoviruses (ARVs). Sequencing of the complete genomes of strain NP03 showed that they consisted of 23,418 bp and were divided into 10 segments, ranging from 1191 bp (S4) to 3959 bp (L1) in length, and all segments contained conserved sequences in the 5' non-coding region (GCUUUU) and 3' non-coding region (UCAUC). Pairwise sequence comparisons demonstrated that NP03 strain showed the highest similarity with novel waterfowl origin reoviruses (WRVs). The genome analysis revealed that the S1 segment of novel WRV is a tricistronic gene, encoding the overlapping open reading frames (ORFs) for p10, p18, and σC, similar to the ARV S1 gene, but distinct from classical WRV S4 genome segment, which contained two overlapping ORFs encoding p10 and σC. Phylogenetic analyses of the nucleotide sequences of all 10 segments revealed that NP03 strain was clustered together with other novel WRVs and were distinct from classical WRVs and chicken-origin ARVs. The analyses also showed possible intra-segmental reassortment events in the segments encoding λA, λB, μB, μNS, σA, and σNS between novel and classical WRVs. Potential recombination events detection in segment L1 suggests that NP03 strain may be recombinants of novel WRVs. Based on our genetic analyses, multiple reassortment events, intra-segmental recombination, and accumulation of point mutations have possibly contributed to the emergence of this novel genotype of WRV, identified in China.

Detection of melon necrotic spot virus by one-step reverse transcription loop-mediated isothermal amplification assay

Melon necrotic spot virus (MNSV) can cause significant economic losses due to decreased quality in cucurbit crops. The current study is the first to use reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of MNSV. A set of four LAMP primers was designed based on the coat protein gene sequence of MNSV, and a RT-LAMP reaction was successfully performed for 1 h at 62°C. The results of RT-LAMP showed high specificity for MNSV and no cross-reaction with other viruses. Compared to traditional reverse transcription-PCR (RT-PCR), the RT-LAMP assay was 10³-fold more sensitive in detecting MNSV. Due to its sensitivity, speed and visual assessment, RT-LAMP is appropriate for detecting MNSV in the laboratory.

High-mobility group box 1 protein (HMGB1) from Cherry Valley duck mediates signaling pathways and antiviral activity

High-mobility group box 1 protein (HMGB1) shows endogenous damage-associated molecular patterns (DAMPs) and is also an early warning protein that activates the body's innate immune system. Here, the full-length coding sequence of HMGB1 was cloned from the spleen of Cherry Valley duck and analyzed. We find that duck HMGB1(duHMGB1) is mostly located in the nucleus of duck embryo fibroblast (DEF) cells under normal conditions but released into the cytoplasm after lipopolysaccharide (LPS) stimulation. Knocking-down or overexpressing duHMGB1 had no effect on the baseline apoptosis rate of DEF cells. However, overexpression increased weakly apoptosis after LPS activation. In addition, overexpression strongly activated the IFN-I/IRF7 signaling pathway in DEF cells and significantly increased the transcriptional level of numerous pattern recognition receptors (PRRs), pro-inflammatory cytokines (IL-6, TNF-α), IFNs and antiviral molecules (OAS, PKR, Mx) starting from 48 h post-transfection. Overexpression of duHMGB1 strongly impacted duck virus replication, either by inhibiting it from the first stage of infection for novel duck reovirus (NDRV) and at late stage for duck Tembusu virus (DTMUV) or duck plague virus (DPV), or promoting replication at early stage for DTMUV and DPV infection. Importantly, data from duHMGB1 overexpression and knockdown experiments, time-dependent DEF cells transcriptional immune responses suggest that duHMGB1 and RIG-I receptor might cooperate to promote the expression of antiviral proteins after NDRV infection, as a potential mechanism of duHMGB1-mediated antiviral activity.

Simple and visible detection of duck hepatitis B virus in ducks and geese using loop-mediated isothermal amplification

In this study, loop-mediated isothermal amplification (LAMP) was used to establish a rapid, specific, and visual detection method for duck hepatitis B virus (DHBV). The design and synthesis of 4 specific LAMP primers were based on the conserved gene region of the DHBV genome, and the optimum temperature and time of the LAMP reaction were 63°C and 50 min, respectively. The LAMP assay was confirmed to be specific for DHBV detection and had the same sensitivity as the quantitative PCR assay. A visual detection method for rapid determination of results was developed using a color indicator containing phenol red and cresol red. A color change was produced based on a pH change in the reaction system, indicating a positive reaction. For the detection of samples from ducks and geese, the LAMP method has the advantages of simplicity, high sensitivity and specificity, good visibility, and low cost. Moreover, it is more practical and convenient than PCR-related assays for the clinical detection of DHBV.

Detection of KRAS mutation via ligation-initiated LAMP reaction

KRAS mutations are abnormalities widely found in genomic DNA and circulating tumor DNA (ctDNA) of various types of cancers. Thus, highly sensitive detection of KRAS mutations in genomic DNA is of great significance in disease diagnosis and personalized medicine. Here, we developed a ligation-initiated loop-mediated isothermal amplification (LAMP) assaying method for ultrasensitive detection of KRAS mutation. In the presence of mutant KRAS DNA (mutDNA), the dumbbell-shaped structure (DSS) is formed by the specific ligation of two substrates (SLS1 and SLS2), which act as a template to initiate the following LAMP amplification. Making use of the outstanding specificity of ligation reaction and superior amplification of LAMP, 10 aM mutDNA can be accurately determined. In addition, as low as 0.1% mutDNA can be detected in the presence of a large excess of wild-type KRAS DNA (wtDNA), indicating the high sensitivity and specificity of the method. Furthermore, this strategy has been successfully applied for detection of a KRAS mutation from tissue samples of colorectal cancer patients. Thus, the developed ligation-initiated LAMP fluorescence assaying strategy presents a promising prospect for ultrasensitive detection of mutations.