Development of a loop-mediated isothermal amplification assay for rapid detection of iridovirus in the Chinese giant salamander

Development of a droplet digital PCR assay for the sensitive detection of iridovirus in Andrias davidianus

Chinese giant salamander iridovirus (GSIV) is the first known and causative viral pathogen in Andrias davidianus. Developing a sensitive, accurate and specific assay to detect GSIV in samples is essential to prevent the further spread of the pathogen. In this study, we established a droplet digital PCR (ddPCR) assay that targeted the mcp gene of GSIV, enabling rapid and quantitative detection of the virus. We determined that the optimal annealing temperature, primer concentration and probe concentration were 57.1°C, 50 nM and 500 nM, respectively. We analysed the specificity and sensitivity of the ddPCR assay and found that five common aquatic animal viruses, including Cyprinid herpesvirus 2 (CyHV-2), infectious spleen and kidney necrosis virus (ISKNV), Koi herpesvirus (KHV) and Carp Edema Virus (CEV) displayed negative results based on this GSIV ddPCR assay. The assay can detect GSIV with the lowest detection limit of 3.7 copies per reaction. To evaluate the sensitivity and accuracy of the ddPCR assay, we tested different infected tissue samples with both the ddPCR and TaqMan real-time PCR assays. Our results showed that the ddPCR assay detected GSIV in all samples with 100% positivity, while the TaqMan real-time PCR assay detected GSIV in only 82.1% of samples. The established ddPCR method provided several advantages in detecting GISV, including high sensitivity, high precision and absolute quantification, making it a powerful tool for detection of possible and potential GSIV infection, even in samples with low viral load.

Development of a droplet digital PCR method for the sensitive detection and quantification of largemouth bass ranavirus

Largemouth bass ranavirus (LMBRaV), also known as largemouth bass virus (LMBV), is a high mortality pathogen in largemouth bass. A rapid, sensitive, specific and convenient diagnosis method is an urgent requirement for the prevention of virus transmission. In the present study, a droplet digital PCR (ddPCR) method based on the major capsid protein (mcp) gene was established to detect and quantify the virus genome copy number. Oligonucleotide primers were designed based on the LMBRaV mcp gene sequence. The specificity and sensitivity of ddPCR assay were analysed. The other aquatic virus including Chinese giant salamander iridovirus (GSIV), Cyprinid herpesvirus II (CyHV-2) and infectious spleen and kidney necrosis virus could not be detected by LMBRaV ddPCR assay. The detection limit of ddPCR assay was 2 ± 0.37 copies/μl DNA sample. And this ddPCR assay had great repeatability and reproducibility. In clinical diagnosis of 50 largemouth bass, 43 positive samples were detected by ddPCR, whereas only 34 positive samples were detected by quantitative PCR (qPCR). This LMBRaV detection assay provided a specific and sensitive method for the rapid diagnosis of LMBRaV infection in largemouth bass as well as quantification of the virus load.

Choice of molecular assay determines ranavirus detection probability and inferences about prevalence and occurrence

Ranaviruses are emerging pathogens that can cause morbidity, mortality and population declines in ectothermic hosts; however, there is no standardized approach to diagnostics. Here, we compared the inter-assay variation and intra-assay precision among 2 commonly used quantitative PCRs (qPCRs), a conventional and a nested PCR assay (used as a gold standard), using laboratory-propagated ranavirus (FV3 and CMTV) and field-collected samples. A qPCR assay ('Leung') detected viral DNA in dilutions 2 orders of magnitude lower than other assays regardless of the viral lineage of the cultured isolate (FV3/CMTV). The second qPCR ('Brunner') was slightly more sensitive than the conventional PCR ('Mao' assay). For field samples, the Leung qPCR detected all known positives, while the Mao assay PCR only detected 2.5% of the positive samples. Amplicon sequences from the 2 conventional PCRs were shown to be useful for inferring viral lineage. Inaccurate results will bias estimates of the distribution and prevalence of ranaviruses, and together these findings emphasize that molecular assays should be chosen carefully in the context of study aims.

High pathogen prevalence in an amphibian and reptile assemblage at a site with risk factors for dispersal in Galicia, Spain

Ranaviruses are agents of disease, mortality and population declines in ectothermic vertebrates and emergences have been repeatedly linked to human activities. Ranaviruses in the common midwife toad ranavirus lineage are emerging in Europe. They are known to be severe multi-host pathogens of amphibians and can also cause disease in reptiles. Recurrent outbreaks of ranavirus disease and mortality affecting three species have occurred at a small reservoir in north-west Spain but no data were available on occurrence of the pathogen in the other amphibian and reptile species present or at adjacent sites. We sampled nine species of amphibians and reptiles at the reservoir and nearby sites and screened for ranavirus presence using molecular methods. Our results show infection with ranavirus in all nine species, including first reports for Hyla molleri, Pelophylax perezi, Rana iberica, and Podarcis bocagei. We detected ranavirus in all four local sites and confirmed mass mortality incidents involving Lissotriton boscai and Triturus marmoratus were ongoing. The reservoir regularly hosts water sports tournaments and the risks of ranavirus dispersal through the translocation of contaminated equipment are discussed.

Rapid diagnosis of largemouth bass ranavirus in fish samples using the loop-mediated isothermal amplification method

Largemouth bass ranavirus (LMBV) has been recognized as the causative pathogen responsible for infectious skin ulcerative syndrome in cultured largemouth bass in China. A fast and simple LMBV detection method is urgently needed. Here, a loop-mediated isothermal amplification (LAMP) assay was established for the detection of this virus using primers targeting the major capsid protein gene of LMBV. The amplification conditions were optimized; the assay was specific for the diagnosis of LMBV, as there was no cross-reactivity with other four Iridoviridae viruses (large yellow croaker iridovirus, Singapore grouper iridovirus, tiger frog virus, and soft-shelled turtle iridovirus), grass carp reovirus, white spot syndrome virus, or healthy largemouth bass. The sensitivity of the LAMP assay was found to be 8.55 × 10¹ copies/μL of LMBV DNA, which was 10-fold higher than that of the conventional PCR. Application of the LAMP assay was evaluated using 10 clinical samples, and the results indicated the reliability of the test as a rapid, field diagnostic tool for LMBV detection. Thus, the simplicity and nearly instrument-free LAMP method provides an alternative for rapid and sensitive detection of LMBV and has great potential for early diagnosis of LMBV infection in the farm.

Rapid detection of giant salamander iridovirus by cross-priming amplification

Giant salamander iridovirus (GSIV) belongs to the epizootic genus Ranavirus, and is the cause of epidemic diseases associated with high mortality and great losses to artificial breeding and farming. Here, we established a simple, accurate, and reliable cross-priming amplification (CPA) method to detect GSIV. The CPA assay targets the major caspid protein gene of the GSIV genome to design crossing primer pairs, and the reaction conditions were optimized, including optimal concentrations of the primers, betaine, dNTPs, Mg²⁺, and Bst DNA polymerase, and reaction conditions. The sensitivity was shown to be 10 times higher than that of conventional polymerase chain reaction (PCR), and the specificity was 100%. The results were identified on nucleic acid strips within 3-5 min. Application of the CPA and PCR to 54 samples of giant salamander showed a positive rate of 72.22% and 74.07%, respectively, demonstrating high coincidence (94.44%, kappa = 8.7, P < 0.0001). The sensitivity of the CPA assay was 97.50% and the specificity was 92.86%. Thus, the CPA assay is as effective as conventional PCR, but with added practical advantages of simplicity and an almost instrument-free platform, which will be useful for both laboratories and giant salamander farms.

Iridoviral infection can be reduced by UCHL1-loaded exosomes from the testis of Chinese giant salamanders (Andrias davidianus)

Chinese giant salamander iridovirus (CGSIV) is a large double-stranded DNA virus that infects Chinese giant salamanders (CGSs) and is responsible for a high mortality rate of CGSs under certain conditions. It is generally believed that CGSIV is a horizontally transmitting virus that affects lower vertebrates. Exosomes from tissues and cells affect the mechanism of viral infections. UCHL1, a deubiquitinating enzyme, is indirectly involved in virus propagation via cytokine and chemokine suppression. In our study, a few CGSIVs were detected in the testis of the special symptom CGSs using PCR and immunofluorescence analysis. The exosomes originating in the testicular fluid was isolated and identified using the Nanosight NS300 system and scanning electron microscopy. The UCHL1-loaded exosomes may resist CGSIV entry by fusing with and remodeling CGSIV. UCHL1 in the primary testicular fibroblasts was maintained at a stable level to inhibit the infection and replication of CGSIV by secreting and sorting exosomes. These data provided a new insight into CGSIV being a type of horizontally transmitting virus.

In vitro antiviral efficacy of moroxydine hydrochloride and ribavirin against grass carp reovirus and giant salamander iridovirus

Moroxydine hydrochloride (Mor) and ribavirin (Rib) have been reported to exhibit multi-antiviral activities against DNA and RNA viruses, but their antiviral activities and pharmacologies have seldom been studied in aquaculture. This paper has selected 3 aquatic viruses including a double-stranded RNA virus (grass carp reovirus, GCRV), a single-stranded RNA virus (spring viraemia of carp virus, SVCV) and a DNA virus (giant salamander iridovirus, GSIV) for antiviral testing. The results showed that Mor and Rib can effectively control the infection of GCRV and GSIV in respective host cells. Further study was undertaken to explore the antivirus efficiencies and pharmacological mechanisms of Mor and Rib on GCRV and GSIV in vitro. Briefly, compounds showed over 50% protective effects at 15.9 µg ml-1 except for the group of GSIV-infected epithelioma papulosum cyprinid (EPC) cells treated with Mor. Moreover, Mor and Rib blocked the virus-induced cytopathic effects and apoptosis in host cells to keep the normal cellular structure. The expression of VP1 (GCRV) and major capsid protein (MCP; GSIV) gene was also significantly inhibited in the virus-infected cells when treated with Mor and Rib. Cytotoxicity assay verified the 2 compounds had no toxic effects on grass carp ovary (GCO) cells and EPC cells at ≤96 µg ml-1. In conclusion, these results indicated that exposing GCRV-infected GCO cells and GSIV-infected EPC cells to Mor and Rib could elicit significant antiviral responses, and the 2 compounds have been shown to be promising agents for viral control in the aquaculture industry.

Autophagy and apoptosis induced by Chinese giant salamander (Andrias davidianus) iridovirus (CGSIV)

The outbreak of Chinese Giant Salamander (Andrias davidianus, CGS) Iridovirus (CGSIV) caused massive death of CGSs. However, some CGSs with low level of CGSIV usually could survive. In our study, major capsid protein (MCP) DNA replicates of CGSIV in shedding skin were employed to assess the relative content of CGSIV in the living CGSs by qPCR. Furthermore, the examinations of autophagy and apoptosis in CGSs in vivo and in the primary renal cells in vitro were performed, respectively. The results showed that the relative contents of CGSIV in the shedding skin could reflect those in liver, spleen, and kidney of the CGSs. In these tissues of the CGSs with low-level replicates of CGSIV, there were not obviously macroscopic lesions. But the irregularly-shaped vesicles perhaps involving in autophagosome were observed by transmission electron microscopy (TEM). The LC3B protein displayed uneven distribution by Immunohistochemistry and the level mRNA of Atg5 was higher in these tissues than that in the tissues of healthy CGSs using qRT-PCR. Meanwhile, the apoptosis also appeared in these tissues by TUNEL staining and higher level mRNA of type I IFN were detected in these tissues using qRT-PCR. Further, both the expression level of LC3B II protein and Atg5 mRNA increased significantly at 2h after the virus infected the primary renal cells from the health CGSs in vitro. In addition, apoptosis and type I IFN mRNA began to increase significantly at 4h after the virus infected the renal cells. It was suggested that autophagy may be a pivotal role for survival of CGSIV in the CGSs during early infection and the rapid proliferation of CGSIV could be inhibited by innate immune response and apoptosis.

Transcriptomic analysis of the host response to an iridovirus infection in Chinese giant salamander, Andrias davidianus

The emergence of an infectious viral disease caused by the Chinese giant salamander iridovirus (GSIV) has led to substantial economic losses. However, no more molecular information is available for the understanding of the mechanisms associated with virus–host interaction. In this study, de novo sequencing was used to obtain abundant high-quality ESTs and investigate differentially-expressed genes in the spleen of Chinese giant salamanders that were either infected or mock infected with GSIV. Comparative expression analysis indicated that 293 genes were down-regulated and 220 genes were up-regulated. Further enrichment analysis showed that the most enriched pathway is “complement and coagulation cascades”, and significantly enriched diseases include “inherited thrombophilia”, “immune system diseases”, “primary immunodeficiency”, “complement regulatory protein defects”, and “disorders of nucleotide excision repair”. Additionally, 30 678 simple sequence repeats (SSRs) from all spleen samples, 26 355 single nucleotide polymorphisms (SNPs) from the spleens of uninfected animals and 36 070 SNPs from the spleens of infected animals were detected. The large amount of variation was specific for the Chinese giant salamanders that were infected with GSIV. The results reported herein provided significant and new EST information that could contribute greatly in investigations into the molecular functions of immune genes in the Chinese giant salamander.

Cloning, sequence analysis and expression profiles of Toll-like receptor 7 from Chinese giant salamander Andrias davidianus

The Chinese giant salamander, Andrias davidianus, is the largest extant amphibian species in the world, which is of significance due to its specific position in the evolutionary history of vertebrates. Currently, limited information about the innate immune system of this animal is known. In this study, the toll-like receptor 7 (TLR7), designated CgsTLR7, was cloned from Chinese giant salamander, A. davidianus. The full-length cDNA of CgsTLR7 is 3747 bp, with an open reading frame of 3150 bp, encoding 1049 amino acids. The TLR family motifs, including the leucine-rich repeat (LRR) and Toll/interleukin (IL)-1 receptor (TIR) domain are conserved in CgsTLR7, which includes 19 LRRs and a TIR domain. The predicted amino acid sequence of CgsTLR7 has 71%, 65%, 63% and 55% identity with turtle, chicken, human and fugu TLR7 homologues, respectively. Phylogenetic analysis showed that CgsTLR7 is closest to that of frog TLR7 among the examined species. Quantitative real-time PCR analysis revealed broad expression of CgsTLR7 in tissues from apparently healthy Chinese giant salamanders with the highest expression in the liver and the lowest expression in the intestine. The mRNA expression was up-regulated and reached a peak level in the kidney, liver and spleen at 12 h, 24 h and 48 h after infecting the animals with the giant salamander iridovirus (GSIV), respectively. These results suggest that CgsTLR7 has a conserved gene structure and might play an important role in immune regulation against viral infections in the Chinese giant salamander.