TaqMan real-time PCR assay based on DNA polymerase gene for rapid detection of Orf infection

Recent advances in diagnostic approaches for orf virus

Orf virus (ORFV), the prototype species of the Parapoxvirus genus, is an important zoonotic virus, causing great economic losses in livestock production. At present, there are no effective drugs for orf treatment. Therefore, it is crucial to develop accurate and rapid diagnostic approaches for ORFV. Over decades, various diagnostic methods have been established, including conventional methods such as virus isolation and electron microscopy; serological methods such as virus neutralization test (VNT), immunohistochemistry (IHC) assay, immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA); and molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and recombinase-aided amplification (RAA) assay. This review provides an overview of currently available diagnostic approaches for ORFV and discusses their advantages and limitations and future perspectives, which would be significantly helpful for ORFV early diagnosis and surveillance to prevent outbreak of orf. KEY POINTS: • Orf virus emerged and reemerged in past years • Rapid and efficient diagnostic approaches are needed and critical for ORFV detection • Novel and sensitive diagnostic methods are required for ORFV detection.

Development of Real-Time PCR Based on A137R Gene for the Detection of African Swine Fever Virus

African swine fever virus (ASFV) can infect domestic pigs and wild boars and causes huge economic losses in global swine industry. Therefore, early diagnosis of ASFV is important for the control and eradication of African swine fever (ASF). In this study, a SYBR Green-based real-time polymerase chain reaction (PCR) assay targeting the viral encoded A137R gene was established for the detection of ASFV infection. For the evaluation of the established real-time PCR, 34 clinical samples were assessed by both the A137R gene-based real-time PCR and OIE-recommended TaqMan PCR. The results showed that 85.29% (29/34) were detected by A137R gene-based real-time PCR, but only 79.41% (27/34) positive using OIE-recommended TaqMan PCR. Moreover, no cross-reaction with other common swine pathogens was found in the A137R gene-based real-time PCR. These results demonstrated that the established real-time PCR assay in this study showed better performance than the OIE-recommended method in detecting ASFV from clinical samples, which could be applied for control and eradication programs of ASF.

Viral Infections in Burn Patients: A State-Of-The-Art Review

Infections that are triggered by the accompanying immunosuppression in patients with burn wounds are very common regardless of age. Among burn patients, the most frequently diagnosed infections include the bacterial ones primarily caused by Pseudomonas aeruginosa or Klebsiella pneumonia, as well as fungal infections with the etiology of Candida spp. or Aspergillus spp. Besides, burn wounds are highly susceptible to viral infections mainly due to the impaired immune responses and defective functions of the immune cells within the wound microenvironment. The most prevalent viruses that invade burn wounds include herpes simplex virus (HSV), cytomegalovirus (CMV), human papilloma virus (HPV), and varicella zoster virus (VZV). Likewise, less prevalent infections such as those caused by the orf virus or Epstein-Barr Virus (EBV) might also occur in immunosuppressed burn patients. Viral infections result in increased morbidity and mortality rates in severely burned patients. Additionally, a positive correlation between the hospitalization duration and the severity of the viral infection has been demonstrated. Viral infections trigger the occurrence of various complications, ranging from mild symptoms to even fatal incidents. Accurate detection of viral infection is of great clinical importance because of the possibility for a quicker introduction of proper treatment therapy and shortening of hospitalization time. The aim of this paper is to provide a comprehensive review of the literature and summarize the findings regarding the most common viral infections in immunosuppressed burn patients.

Laboratory Diagnosis of a NZ7-like Orf Virus Infection and Pathogen Genetic Characterization, Particularly in the VEGF Gene

Orf is a widespread contagious epithelial viral disease found particularly in most sheep breeding countries in the world. Recently, an orf virus (ORFV) strain OV-HLJ05 was isolated from an outbreak in northeast China. Three genes of interest including ORFV011 (B2L), ORFV059 (F1L), and ORFV132 (VEGF) of ORFV, were recruited to identify and genetically characterize this newly isolated virus. Amino acid (aa) sequence compared with the ORFV references listed in GenBank, both B2L and F1L of OV-HLJ05 showed less microheterogeneity from their references. In contrast, the VEGF gene was included in the NZ7-VEGF like group as previously considered by Mercer in 2002. Unexpectedly, further multiple VEGF matches were made, using 34 published sequences from China and India, resulting in 27 strains of the NZ7 members. Based on Karki's report in 2020, NZ7-VEGF like viruses are emerging more and more frequently in these two countries, damaging the Asian sheep industry. Obvious heterogeneity with the NZ2, insertion of two oligopeptides TATI(L)QVVVAI(L) and SSSS(S) motif were found in the NZ7-like VEGF protein. These VEGFs are divided mainly into two types and a significant increase in the number of hydrogen bonds within the NZ7-like VEGF dimers was observed. The NZ7-like ORFV apparently favors the goat as a host and an emphasis on this in future epidemiological and pathological studies should be considered, focusing on the NZ7-like virus.

Establishment and application of a TaqMan-based one-step real-time RT-PCR for the detection of novel goose-origin astrovirus

The outbreak of an infectious disease characterized by severe symptom of gout has set great threat to several major goose-producing regions in China since December 2016. The causative agent for the novel infection has been identified was a novel goose-origin astrovirus (GoAstV). Lack of effective detection methods indeed hinders further research, as well as prevention and control of GoAstV. Keep this in mind, a TaqMan-based one-step real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay for rapid detection of GoAstV was developed. Primers and probe were targeting the capsid protein gene sequence (ORF2). The method is capable of detecting quite low number of targeting nucleic acid as low as 10 copies/μL. What's more, it is also of great specificity and repeatability for GoAstV detection. No cross-activity was found with other goose-origin viruses. The assay had excellent intra-assay and inter-assay repeatability with the coefficient of variation (CV) value from 0.48% to 0.99%. A total of 340 GoAstV specimens from different regions of China were used in this study to verify the feasibility and effectiveness of this method in clinical diagnosis. The results indicated that qRT-PCR is a highly sensitive, specific and repeatable method for quantitative detection of GoAstV, which can be used to detect this virus, thereby facilitating epidemiological investigations of gout in goslings.

Poxviral E3L ortholog (Viral Interferon resistance gene) of orf viruses of sheep and goats indicates species-specific clustering with heterogeneity among parapoxviruses

Orf is a contagious disease posing a serious threat to animal and human health. E3L is one of the evolutionarily acquired immunomodulatory proteins present in orf virus (ORFV) and is responsible for conferring resistance to interferons among poxviruses. Genetic analysis of ORFV isolates of different geographical regions including Indian subcontinent targeting viral interferon resistance (VIR) gene (a homolog of vaccinia virus E3L gene) revealed a high percentage of identity among themselves and other ORFV isolates at both nt and aa levels as compared to low identity among parapoxviruses (PPVs). Phylogenetic analysis showed species-specific clustering among PPVs along with sub-clusters based on host species of origin among ORFVs infecting sheep and goats. Conserved amino acids in N-terminal Z-DNA binding domain and C-terminal ds RNA binding domain of VIR proteins of PPVs corresponding to ORFV VIR positions namely N37, Y41, P57, and W59 (necessary for Z-DNA binding) and E116, F127, F141, and K160 (necessary for dsRNA binding) were found. Further, the predicted protein characteristics and homology model of VIR protein of ORFV showed high structural conservation among poxviruses. This study on E3L genetic analysis of ORFV isolates may provide a better understanding of the molecular epidemiology of circulating strains in India and neighboring countries. Also, E3L deleted or mutated ORFV may be an as vaccine candidate and/or compounds blocking E3L may prove as an effective method for treating broad spectrum poxviral infections, suggesting a wider application in control of poxvirus infections.

TaqMan-based real-time quantitative fluorescence PCR for detection of Orf virus

Contagious ecthyma, also known as scabby mouth or Orf, is a zoonosis, which is caused by the Orf virus (ORFV). Human contact with infected animals can cause cutaneous lesions. To prevent and control ORFV effectively, rapid detection method is very important and highly needed. Real-time quantitative fluorescence PCR (qPCR) assay is considered as a rapid techonology to detect ORFV, and has been used for clinical diagnosis and epidemiological investigation. In present study, we developed a TaqMan-based qPCR assay for detection of ORFV. Beacon Designer 7.9 was used to design specific primers and probes were based on the ORFV020 gene sequence of the virus (GenBank Accession No. KF666563.1). The method had no cross-reactions with other common bacteria and viruses, was highly specific; the sensitivity test result showed that it could detect 10 copies of ORFV genomic DNA, and was more sensitive than conventional PCR. Both intra- and inter-variabilities were less than 2%, indicating the high stability and repeatability of the method. Additionally, 99 clinical samples from sheep and goats with suspected contagious ecthyma were tested using the developed assay and conventional PCR. The results showed that the developed assay was more sensitive and faster than conventional PCR. It can be concluded that the assay was suitable for routine detection of the ORFV and the epidemiological investigation.

Molecular evidence and phylogenetic analysis of orf virus isolates from outbreaks in Tripura state of North-East India

This study describes the first confirmed report of contagious ecthyma in Black Bengal goats from Tripura state, a North-Eastern state of India situated at the Indo-Bangladesh border. Outbreaks were characterized by the high rates of morbidity (58-67%), low mortality (8-10%) and case fatality (11-15%). The etiology of the outbreaks was confirmed as orf virus (ORFV) by standard virological/serological and molecular techniques including sequence analysis of B2L, a major envelop protein gene of genus Parapoxvirus. Sequence and phylogenetic analysis based on B2L gene of ORFV isolates from Tripura revealed that they were closely related to each other and also to other Indian isolates, in particular to ORFV-Shahjahanpur 82/04 isolate from North India. They revealed several specific nucleotide/amino acid substitutions, namely G299A (G100D), G660A, C705T, C795T (N267D) and G872A (R291H) which may be of notable epidemiological significance. This report necessitates the systematic investigation of orf outbreaks in susceptible populations including wild species particularly at transboundary regions by use of rapid diagnostics to control the infection by deploying an effective vaccine/therapeutics and better managemental practices.

Development of multiplex PCR for simultaneous detection and differentiation of six DNA and RNA viruses from clinical samples of sheep and goats

Multiplex reverse transcription-polymerase chain reaction (RT-PCR) and PCR protocols were developed and subsequently evaluated for its effectiveness in detecting simultaneously single and mixed infections in sheep and goats. Specific primers for three DNA viruses and three RNA viruses, including foot and mouth disease virus (FMDV), Bluetongue virus (BTV), peste des petits ruminants virus (PPRV), sheeppox virus (SPPV), goatpox virus (GTPV) and orf virus (ORFV) were used for testing procedure. A single nucleic acid extraction protocol was adopted for the simultaneous extraction of both RNA and DNA viruses. The multiplex PCR consisted with two-step procedure which included reverse transcription of RNA virus and multiplex PCR of viral cDNA and DNA. The multiplex PCR assay was shown to be sensitive because it could detect at least 100pg of viral genomic DNA or RNA from a mixture of six viruses in a reaction. The assay was also highly specific in detecting one or more of the same viruses in various combinations in specimens. Thirty seven clinical samples collected from sheep and goats were detected among forty three samples tested by both uniplex and multiplex PCR, showing highly identification. As results of the sensitivity and specificity, the multiplex PCR is a useful approach for clinical diagnosis of mixed infections of DNA and RNA viruses in sheep and goats with a reaction.

Functional characterization of recombinant major envelope protein (rB2L) of orf virus

Orf, or contagious ecthyma, a highly contagious transboundary disease of sheep and goats, is caused by a double-stranded DNA virus (ORFV) belonging to the genus Parapoxvirus of the family Poxviridae. The ORFV genome encodes the major envelope proteins B2L and F1L, which have been found to be highly immunogenic and have multiple functional characteristics. In order to investigate the functional properties of the B2L protein, in this study, the B2L gene of ORFV strain 59/05, encoding recombinant mature B2L (aa ₁M-D₃₃₄), was produced as a fusion protein in Escherichia coli. The functional characteristics of purified rB2L fusion protein (~60 kDa) were evaluated in vivo and in vitro, showing that this protein had lipase and immunomodulatory activities. Immunization trials involving laboratory animals (mice, rabbits and guinea pigs) using either constant or graded doses of rB2L fusion protein with or without adjuvants (FCA, alum) as well as co-administration with candidate rErns-Ag protein of classical swine fever virus (CSFV) indicated that the rB2L protein is immunogenic and has immunomodulatory properties. This study shows the potential utility of the rB2L protein as a safe and novel adjuvant in veterinary vaccine formulations.

A loop-mediated isothermal amplification assay for rapid and sensitive detection of bovine papular stomatitis virus

Bovine papular stomatitis virus (BPSV) causes pustular cutaneous disease in cattle worldwide. This paper describes the development of a specific loop-mediated isothermal amplification (LAMP) assay to detect BPSV which did not cross-react with other parapoxviruses. To assess analytical sensitivity of this LAMP assay, DNA was extracted from serially diluted BPSV from which the infectious titer was determined by a novel assay based on calf kidney epithelial cells. The LAMP assay had equivalent analytical sensitivity to quantitative PCR, and could detect as few as 86 copies of viral DNA per reaction. These results suggest that the assay is a specific and sensitive technique to rapidly diagnose bovine papular stomatitis in domestic animals.

Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

Background

Orf virus (ORFV) is the causative agent of Orf (also known as contagious ecthyma or contagious papular dermatitis), a severe infectious skin disease in goats, sheep and other ruminants. The rapid detection of ORFV is of great importance in disease control and highly needed. A isothermal molecular diagnostic approach, termed recombinase polymerase amplification (RPA), is considered as an novel and rapid alternative techonology to PCR assay.

Results

In the present study, a novel fluorescent probe based on RPA assay (ORFV exo RPA assay) was developed. The developed ORFV exo RPA assay was capable of as low as 100 copies of ORFV DNA /reaction and was highly specific, with no cross-reaction with closely related viruses (capripox virus, foot-and-mouth disease virus or peste des petits ruminants virus). Further assessment with clinical samples showed that the developed ORFV exo RPA assay has good correlation with qPCR assays for detection of ORFV.

Conclusions

These results suggest that the developed ORFV exo RPA assay is suitable for rapid detection of ORFV.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-015-0440-z) contains supplementary material, which is available to authorized users.

Rapid detection of contagious ecthyma by loop-mediated isothermal amplification and epidemiology in Jilin Province China

The aim of this experiment was to develop a loop-mediated isothermal amplification (LAMP) assay and to research the recent epidemiology of contagious ecthyma in Jilin Province, China, using the assay. A LAMP assay targeting a highly conserved region of the F1L gene was developed to detect contagious ecthyma virus (CEV). Three hundred and sixty-five cases from 64 flocks in 9 different areas of Jilin Province, China, from 2011 to 2014 were tested using the LAMP assay. The results showed that the sensitivity of the LAMP assay was 100 copies of the standard plasmid, which is 100-fold higher than the sensitivity of PCR. No cross-reactivity was observed with capripoxvirus, fowlpox virus, foot-and-mouth disease virus serotype O, foot-and-mouth disease virus serotype Asia I and bluetongue virus. The average positive rate was 19.73% (72/365), and the positive rate was highest in lambs aged 1–6 months. Our results demonstrated that CEV infection was very widespread in the flocks of Jilin Province and that the LAMP assay allows for easy, rapid, accurate and sensitive detection of CEV infection.

Development and comparative evaluation of loop mediated isothermal amplification (LAMP) assay for simple visual detection of orf virus in sheep and goats

A loop-mediated isothermal amplification (LAMP) assay targeting DNA Pol gene was optimized and evaluated for the rapid detection of orf virus in clinical samples. The LAMP assay was found to be specific and sensitive. The detection rate of LAMP (89.3%) was better than PCR (67.9%) and comparable to real-time PCR (91.1%) in clinical samples by gel electrophoresis and visual detection methods. This LAMP assay is simple and does not rely upon any special equipment and could be employed in clinical diagnosis and epidemiological survey of orf infection.

TaqMan based real-time duplex PCR for simultaneous detection and quantitation of capripox and orf virus genomes in clinical samples

A rapid and sensitive TaqMan based real-time duplex PCR (drt-PCR) assay for simultaneous detection, differentiation and quantitation of Capripoxvirus (CaPV) and Orf virus (ORFV) DNA, was optimized targeting the highly conserved DNA polymerase genes of these virus genomes. Two pairs of oligonucleotide primers and two hybridization probes labeled with Cy5/BHQ1 and Hex/BHQ1 for CaPV and ORFV, respectively, were used in the drt-PCR assay. The assay was found to be specific only to targeted viruses and did not react with buffalopox virus (BPXV), camelpox virus (CMLV) (Orthopoxviruses) and cDNA of Peste des petits ruminants virus and bluetongue virus, the other common viruses of sheep and goats. The detection limit of the assay was 20 copies for each of the standard plasmid and 35fg of viral genomic DNA for CaPV and ORFV, respectively, in a single and mixed virus population. Both intra-(0.49-4.6% and 0.7-3.7%) and inter-(0.6-2.35% and 0.27-2.1%) assay variations of drt-PCR for CaPV and ORFV DNA were within the acceptable limits, implying high reproducibility and repeatability of the assay. Further, the diagnostic specificity and the sensitivity of the assay was assessed using known virus isolates of sheeppox virus (SPPV), goatpox virus (GTPV) and ORFV and the clinical specimens from sheep and goats. The developed drt-PCR assay was able to detect, differentiate, quantify simultaneously and also to identity mixed infections of CaPV and ORFV in sheep and goats.

In vitro RNA interference targeting the DNA polymerase gene inhibits orf virus replication in primary ovine fetal turbinate cells

Orf, which is caused by orf virus (ORFV), is distributed worldwide and is endemic in most sheep- and/or goat-raising countries. RNA interference (RNAi) pathways have emerged as important regulators of virus-host cell interactions. In this study, the specific effect of RNAi on the replication of ORFV was explored. The application of RNA interference (RNAi) inhibited the replication of ORFV in cell culture by targeting the ORF025 gene of ORFV, which encodes the viral polymerase. Three small interfering RNA (siRNA) (named siRNA704, siRNA1017 and siRNA1388) were prepared by in vitro transcription. The siRNAs were evaluated for antiviral activity against the ORFV Jilin isolate by the observation of cytopathic effects (CPE), virus titration, and real-time PCR. After 48 h of infection, siRNA704, siRNA1017 and siRNA1388 reduced virus titers by 59- to 199-fold and reduced the level of viral replication by 73-89 %. These results suggest that these three siRNAs can efficiently inhibit ORFV genome replication and infectious virus production. RNAi targeting of the DNA polymerase gene is therefore potentially useful for studying the replication of ORFV and may have potential therapeutic applications.

Multiplex PCR for simultaneous detection and differentiation of sheeppox, goatpox and orf viruses from clinical samples of sheep and goats

A multiplex polymerase chain reaction (mPCR) was developed and evaluated for detection of pox viral infections simultaneously using clinical samples from sheep and goats. Specific primers for three pox viruses of sheep and goats including sheeppox virus (SPPV), goatpox virus (GTPV) and orf virus (ORFV) were designed targeting conserved sequences of the DNA binding phosphoprotein (I3L) coding gene of Capripoxvirus (CaPV) and the DNA polymerase (E9L) gene of parapoxvirus for identification of these viruses. The mPCR assay was found to be sensitive for detecting as low as 350 pg of viral genomic DNA or 10(2) copies of standard plasmid of individual targets; and 10(3) copies of plasmid in a mixture of two or three viruses. The assay was specific for detecting one or more of the viruses in various combinations from clinical specimens. Two hundred and thirty five (n=235) clinical samples from sheep and goats received from different geographical regions of the country for diagnosis of pox infection were evaluated by developed uniplex and mPCR assays. The assay had improved diagnostic sensitivity and specificity over to in-use laboratory diagnostic methods and can be useful for clinical differential diagnosis of these infections in sheep and goats.

Coinfection by Vaccinia virus and an Orf virus–like parapoxvirus in an outbreak of vesicular disease in dairy cows in midwestern Brazil

The current report describes an outbreak of vesicular disease affecting dairy cows in midwestern Brazil in which a coinfection with 2 poxviruses— Vaccinia virus (VACV) and a parapoxvirus—was demonstrated. Milking cows presented vesicles, painful reddish or whitish papules, and scabby proliferative lesions in the teats and udder, in a clinical course of approximately 10–21 days. Histologically, multifocal areas of moderate to severe acanthosis, spongiosis, hypergranulosis, and parakeratotic or orthokeratotic hyperkeratosis with adjacent focally extensive ulcers were observed in the epidermis. Rounded eosinophilic inclusion bodies were observed in the cytoplasm of epithelial cells of areas with acanthosis or necrosis. Moderate inflammatory infiltrate of lymphocytes, plasma cells, neutrophils, and macrophages were observed in some dermal areas. Two people milking the affected cows developed lesions on the hands, painful papules which progressed to ulcerative and scabby lesions in 4–7 days. Electron microscopy of scabs from 1 cow revealed the concomitant presence of orthopoxvirus and parapoxvirus particles. Scabs from 2 cows were positive by polymerase chain reaction for the parapoxvirus B2L gene; 1 of the scabs was also positive for the VACV vgf gene. Nucleotide sequencing of the B2L amplicon revealed a similarity of 96–99% with Orf virus (ORFV) and lower identity with Pseudocowpox virus (92–95%) and Bovine papular stomatitis virus (85–86%). Nucleotide sequencing of a region of parapoxvirus DNA polymerase gene revealed a high similarity (98–100%) with ORFV sequences. Thus, an unusual coinfection with VACV and a parapoxvirus, likely ORFV, was demonstrated in the outbreak.

Taqman real-time PCR assay based on ORFV024 gene for rapid detection of orf infection

In this study, a TaqMan real-time polymerase chain reaction (PCR) assay was developed to detect and quantify orf virus (ORFV) DNA in infected cell culture and clinical samples. Primers and probes were designed to amplify an 87 bp fragment DNA based on the sequence of ORFV024 gene encoding an NF-κB inhibitor of orf virus. The assay was highly specific and sensitive for ORFV DNA and no cross-reactions were detected with any other poxviruses; the sensitivity was 5 fg or 15 copies of ORFV genomic DNA. Both intra- (1.490 ± 1.261%) and inter-assay (1.958 ± 0.568%) variabilities were within the acceptable range, indicating the high efficiency and reproducibility of the assay. Further, the assay has shown a relative diagnostic sensitivity and specificity of 100%, when compared to B2L gene-based semi-nested PCR. The assay is simple, rapid, specific and sensitive with a wide potential for rapid field diagnosis of orf in sheep and goats.

Rapid detection of orf virus by loop-mediated isothermal amplification based on the DNA polymerase gene

At present, there are no effective antiviral treatments available for contagious ecthyma, and rapid diagnosis is therefore critical for effective control of the disease. Recently, the invention of a novel LAMP technique that can rapidly amplify nucleic acids with high specificity and sensitivity under isothermal conditions has overcome some of the deficiencies of nucleic acid-based diagnostic tests and has made on-site diagnosis possible. To establish a flexible loop-mediated isothermal amplification (LAMP) assay for the rapid detection of orf virus, two pairs of primers, including outer primers F3/B3 and inner primers FIP/BIP, were designed to amplify the DNA polymerase gene. Optimal time and temperature conditions for LAMP were found to be 45 min and 62 °C, respectively. The LAMP assay was shown to be specific, with no cross-reactivity with sheeppox virus, goatpox virus, avian molluscum roup virus or vesicular stomatitis virus. Additionally, the sensitivity of the LAMP method was similar to that of real-time PCR and demonstrated greater sensitivity than a conventional polymerase chain reaction (PCR) assay. To assess the utility of LAMP in the detection of orf virus in clinical samples, a total of 35 samples collected from orf virus-infected sheep and goats were tested using the optimized LAMP assay, real-time PCR, and conventional PCR. Of the samples, 26 were found to be positive by LAMP, and 25 (74.3 %) were positive by real-time PCR, whereas only 18 (51.4 %) were positive by conventional PCR. Our results have shown that the LAMP assay developed in this study can be used for the rapid detection of orf virus.