Loop-mediated isothermal amplification for the detection of goose circovirus

TaqMan-probe-based multiplex real-time RT-qPCR for simultaneous detection of GoAstV, GPV, and GoCV

Goose astrovirus (GoAstV), goose parvovirus (GPV), and goose circovirus (GoCV) infections have similar symptoms, such as severe diarrhea, and cause serious economic losses to the goose industry globally. Therefore, it is necessary to develop a rapid and accurate method for the differential diagnosis of the 3 viruses. In this study, a TaqMan probe-based multiplex reverse transcription-qualitative polymerase chain reaction (RT-qPCR) method was established and optimized for simultaneous detection of the three viruses. Three pairs of specific primers and probes were designed considering the conserved sequences of ORF2, VP3, and Rep of GoAstV, GPV, and GoCV, respectively. Singleplex real-time RT-qPCR detected a minimum of 10 copies of these genes, while multiplex real-time RT-qPCR detected a minimum of 100 copies. The correlation coefficients exceeded 0.99, and the amplification efficiency was 80 to 100%. The assay had high sensitivity, specificity, and repeatability. In 85 tissue samples, GoAstV and GPV were the main pathogens and demonstrated co-infection. This assay provides a rapid, efficient, specific, and sensitive tool for the detection of GoAstV, GPV, and GoCV. This can facilitate disease management and epidemiological surveillance.

Optimization and application of loop-mediated isothermal amplification technique for sex identification in red-whiskered bulbul (Pycnonotus jocosus)

The red‐whiskered bulbul (Pycnonotus jocosus) is a popular avian species in Thailand and many other countries. The red‐whiskered bulbul has a high economic value, but breeding is challenging since sex identification is difficult. The PCR method is now used for sex identification. However, PCR amplification and post‐PCR analysis necessitate the use of a laboratory equipped with specialized scientific instruments, which is inconvenient for field operations. This research describes a method for amplification of DNA samples using the loop‐mediated isothermal amplification (LAMP) approach, which is a molecular biology methodology for isothermal amplification that is extremely sensitive, fast, and easy for post‐LAMP product visualization. Herein, total of 23 blood samples were collected and DNA was extracted. Two sets of LAMP primers were designed for CHD‐Z and CHD‐W genes. The colorimetric assay was used to investigate the best conditions for LAMP reactions and post‐LAMP product visualization. LAMP reactions for sex identification were compared to traditional PCR in terms of sensitivity and specificity. LAMP reactions were found to be 10‐fold more sensitive than PCR at 1 ng of DNA. When compared to electrophoresis analysis, the visualization with colorimetric assay using GelRed® and SYTO™ 9 was 100% accurate. The optimal LAMP condition tested simple DNA extracted from bird feathers using the HotSHOT technique. The result showed that the optimal condition could distinguish the sex of red‐whiskered bulbuls totally and accurately. A powerful method for red‐whiskered bulbul sex identification is demonstrated in this study, which can be used in field studies because it is quick and easy to perform, has high sensitivity, and does not require advanced scientific equipment.

Development of a Simple DNA Extraction Method and Candida Pan Loop-Mediated Isothermal Amplification Assay for Diagnosis of Candidemia

To reduce the morbidity and mortality of candidemia patients through rapid treatment, the development of a simple, rapid molecular diagnostic method that is based on nucleic acid extraction and is superior to conventional methods for detecting Candida in the blood is necessary. We developed a multiplex Candida Pan/internal control (IC) loop-mediated isothermal amplification (LAMP) assay and a simple DNA extraction boiling protocol using Chelex-100 that could extract yeast DNA in blood within 20 min. The Chelex-100/boiling method for DNA extraction showed comparable efficiency to that of the commercial QIAamp UCP Pathogen Mini Kit using Candida albicans qPCR. In addition, the Candida Pan/IC LAMP assay showed superior sensitivity to that of general Candida Pan and species qPCRs against clinical DNA samples extracted with the QIAamp UCP Pathogen Mini Kit and Chelex-100/boiling method. The Candida Pan/IC LAMP assay followed by Chelex-100/boiling-mediated DNA extraction showed high sensitivity (100%) and specificity (100%) against clinical samples infected with Candida. These results suggest that the Candida Pan/IC LAMP assay could be used as a rapid molecular diagnostic test for candidemia.

Loop-Mediated Isothermal Amplification (LAMP) as a Promising Point-of-Care Diagnostic Strategy in Avian Virus Research

Simple Summary

Many of the existing screening methods of avian viruses depend on clinical symptoms and pathological gross examinations that still necessitate confirmatory microscopic testing. Confirmation of a virus is often conducted at centralized laboratories that are well-equipped with instruments for virus isolation, hemagglutinin inhibition, virus neutralization, ELISA, PCR and qPCR. These assays are known for their great accuracy and sensitivity, and hence are set as standard practices. Nevertheless, limitations arise due to the time, cost and on-site applicability. As the technology progresses, molecular diagnostics should be more accessible to isolated areas and even practicable for use by non-skilled personnel such as farmers and private breeders. One of the point-of-care diagnostic strategies to consider for such matters is loop-mediated isothermal amplification (LAMP).

Abstract

Over the years, development of molecular diagnostics has evolved significantly in the detection of pathogens within humans and their surroundings. Researchers have discovered new species and strains of viruses, while mitigating the viral infections that occur, owing to the accessibility of nucleic acid screening methods such as polymerase chain reaction (PCR), quantitative (real-time) polymerase chain reaction (qPCR) and reverse-transcription qPCR (RT-qPCR). While such molecular detection methods are widely utilized as the benchmark, the invention of isothermal amplifications has also emerged as a reliable tool to improvise on-field diagnosis without dependence on thermocyclers. Among the established isothermal amplification technologies are loop-mediated isothermal amplification (LAMP), recombinant polymerase amplification (RPA), strand displacement activity (SDA), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA) and rolling circle amplification (RCA). This review highlights the past research on and future prospects of LAMP, its principles and applications as a promising point-of-care diagnostic method against avian viruses.

A SYBR Green I-based real-time polymerase chain reaction assay for detection and quantification of canine bufavirus

Canine bufavirus (CBuV) was first discovered in puppies in Italy in 2016, and subsequent studies have reported its possible relationship with acute enteritis. Currently, there is no specific and quantitative detection method for CBuV. This study examined the conserved NS1 gene and used a pair of specific primers to establish a direct SYBR Green I-based real-time quantitative polymerase chain reaction (qPCR) method for the detection and quantification of CBuV. In the sensitivity experiment, the detection limit of SYBR Green I-based real-time qPCR was 4.676 × 10¹ copies/μL and that of conventional PCR (cPCR) was 4.676 × 10³ copies/μL. Furthermore, the qPCR method did not detect other viruses in dogs, indicating good specificity. The intra-assay coefficient of variation was 0.07-0.55% and the inter-assay coefficient of variation was 0.03-0.11%, indicating good repeatability. In clinical sample testing, the detection rate of qPCR was 5.0% (6/120), higher than that of cPCR (2.5%, 3/120). In addition, the samples that tested CBuV-positive in this experiment were all from dogs with acute enteritis. In summary, the SYBR Green I-based qPCR method established in this study has good sensitivity, specificity, and reproducibility for clinical sample detection and can also assist in future research on CBuV.

A TaqMan-based quantitative real-time PCR assay for identification of the goose circovirus

Goose circovirus (GoCV) is a potential immunosuppressive virus that poses a great hazard to the goose industry and has been shown to be widely distributed throughout China. We have established a fast, sensitive and highly specific TaqMan real-time quantitative PCR detection method for this virus. Specific primers and probes were designed against the conserved regions of the genomic GoCV Rep gene. The results showed that the assay was highly specific and sensitive for GoCV and did not cross-react with other non-targeted waterfowl viruses. The established method will be helpful for epidemiological detection and may be effective in the prevention and control of the disease.

Elaboration of Triplex PCR for Detection of Selected Viral Infections in Waterfowl

Introduction

Viral infections are the greatest threat to waterfowl and cause significant economic losses. Diagnosis and differentiation of three goose viruses is difficult in the field and often requires laboratory confirmation. Therefore, the aim of the study was to develop a triplex PCR and optimise its parameters for simultaneous detection of DNA of goose parvovirus (GPV), goose polyomavirus (GHPV), and goose circovirus (GoCV).

Material and Methods

The DNA of viruses isolated from field cases from the National Veterinary Research Institute’s own collection was used for the study. The primer attachment temperature, the number of reaction cycles, and the Taq DNA polymerase and Mg²⁺ concentrations were optimised. The sensitivity and specificity of this triplex PCR was also determined.

Results

Based on the obtained results, triplex PCR parameters were optimised for simultaneous detection of DNA of GPV, GHPV, and GoCV in one sample. The following PCR products of the expected size were obtained: GPV DNA of 806 bp, GoCV DNA of 571 bp, and GHPV DNA of 180 bp.

Conclusion

The developed triplex PCR method proved to be useful for simultaneous detection of infections with three waterfowl viruses and will be used in relevant laboratory diagnostics.

Loop-Mediated Isothermal Amplification (LAMP) for Detection of Ureaplasma diversum from Cervico-vaginal Swab of Buffaloes

The main plan of the current study was to develop a rapid, robust, and field-applicable loop-mediated isothermal amplification (LAMP) assay for the detection of Ureaplasma diversum. A strain-specific 16S rRNA gene of Ureaplasma diversum was used for detection which was cloned, sequenced, and characterized earlier. LAMP results were visualized within 90 min with the naked eye. Cervico-vaginal swabs of 50 buffaloes were randomly collected from Livestock Research Center of NDRI as per the Institute Animal ethics guidelines. Out of 50 cervico-vaginal swab samples collected randomly, 34 were found positive with LAMP while 16 samples were negative. Conventional PCR results showed the same result. Therefore, the accuracy of the developed LAMP was about 100%. The developed LAMP assay can also be used to screen the animals for Ureaplasma diversum infection in cervico-vaginal swab. However, further study is needed to assess sensitivity and accuracy towards their detection and their relationship in disease diagnosis.

Development and comparative evaluation of different LAMP and PCR assays for coprological diagnosis of feline tritrichomonosis

The protozoan parasite Tritrichomonas foetus may cause severe diarrhea in cats all over the world. In order to evaluate the methodology in coprological molecular diagnosis of feline tritrichomonosis, we compared previously published ("old") and newly developed ("novel") loop-mediated isothermal amplification (LAMP) (targeted to the T. foetus β-tubulin and the elf1α 1 gene, respectively) as well as an old conventional and an old and novel real-time PCR (all targeted to overlapping regions of T. foetus rDNA) assays regarding their diagnostic sensitivities and specificities. Here, the novel real-time PCR yielded the best methodical performance in that a sensitivity with a detection limit of <0.1 trophozoites (corresponding to ca.<0.13 trophozoites per mg feces) and a maximal specificity for diagnosis of Tritrichomonas spp. was achieved. The other test systems exhibited either an approximately 10-times lower sensitivity (<1 trophozoite corresponding to ca.<1.3 trophozoites per mg feces) (conventional PCR and both LAMP assays) or a lower specificity (old real-time PCR). Conversely, the diagnostic performance assessed with clinical fecal samples from cats demonstrated identical sensitivities (8 of 20 samples tested were positive) for the novel PCR and both LAMP assays. Diagnostic sensitivities were significantly higher than those found for the old real-time (5 positive samples) and conventional PCR (6 positive samples), respectively. Accordingly, our data suggested the novel PCR and both LAMP assays to be well suited molecular tools for direct (i.e. without including an in vitro cultivation step) coprological diagnosis of tritrichomonosis in cats. Interestingly, relative high (novel LAMP, 7 positive samples) to at least moderate (old LAMP, 6 positive samples and 1 sample with equivocal score) diagnostic sensitivities were also achieved by testing clinical samples upon simple visual inspection of colorimetric changes during the LAMP amplification reactions. Accordingly, both LAMP assays may serve as practical molecular tools to perform epidemiological studies on feline (and bovine as well as porcine) tritrichomonosis under simple laboratory conditions.

Loop-mediated isothermal amplification (LAMP) approach for detection of heat-resistant Talaromyces flavus species

Talaromyces flavus is a soilborne fungus that can contaminate fruits. It constitutes serious influence on heat-processed food spoilage, as T. flavus belongs to the heat-resistant fungi group, which are able to survive the pasteurization process. Moreover T. flavus has been reported to be capable of mycotoxigenicity, therefore they have a serious threat to human health. To maintain the safety of food production, sensitive method for T. flavus detection was developed. The loop mediated amplification, abbreviated LAMP, reactions were designed as specific for detection of DNA replication licensing factor gene of T. flavus. The specificity of assay was confirmed by use of 5 T. flavus strains and 35 other fungal isolates. The achieved limit of detection was 1fg of T. flavus genomic DNA and 64 ascospores in 1 g of strawberry fruits or soil samples.

Loop-Mediated Isothermal Amplification on Crude DNA as a Point-of-Care Test for the Diagnosis of Mycoplasma-Related Vaginitis During Early Pregnancy

Background

Mycoplasma-related vaginitis gradually has been growing as a threat in adults-genitourinary infection contributes to funisitis, spontaneous abortion, and low birth weight. Until now, use of loop-mediated isothermal amplification (LAMP) to detect Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), or Mycoplasma genitalium (MG) has been reported by some researchers. However, previous studies focused on purified DNA as the template for LAMP assay, which is usually extracted via commercial kit.

Methods

We developed a LAMP assay for rapid detection of UU, MH, and MG genital mycoplasmas using a simple boiling method for DNA extraction, in a cohort of pregnant women with mycoplasma-related vaginitis. We monitored amplicons with the naked eye using SYBR Green I.

Results

The cohort in our study showed a prevalence of 22.6% in pregnant women, as detected by UU-LAMP assay. Compared to the polymerase chain reaction (PCR) test with purified DNA, the sensitivity of the UU-LAMP in clinical specimens with crude DNA was 87.5% (95% confidence interval [CI], 64.6%->99.9). For crude DNA specimens, UU-LAMP was more sensitive and reliable than PCR, with a higher agreement rate (96.8%) and Youden index value (0.88).

Conclusions

As a point-of-care test, LAMP is a useful, specific, and efficient way to detect genital mycoplasmas in resource-limited settings, especially for crude DNA.

Epidemiological investigation of H9 avian influenza virus, Newcastle disease virus, Tembusu virus, goose parvovirus and goose circovirus infection of geese in China

To deepen the knowledge about epidemic prevalence in the goose breeding field, a triplex PCR assay was established, and 478 samples were collected from scaled goose farms in 11 provinces in China. The results of this epidemiological investigation showed that incidence rates of H9 avian influenza and goose circovirus were the highest among five infectious diseases that were evaluated. In addition, the triplex PCR assay established remarkable sensitivity, rapidity and versatility compared to other diagnostic methods. Dual infection comprised a large proportion of the co-infections in the field, of which the combinations of H9/Tembusu, H9/goose circovirus and goose circovirus/Tembusu co-infected cases were more common. Epidemics were more severe in winter and spring. Additionally, significant differences in the prevalence of these infectious diseases were observed in association with different age groups. In addition, phylogenetic analysis, determined by the neighbour-joining method, was carried out to investigate the evolution of these viruses during the study period. For the most part, virus strains isolated during the study were consistent with most goose-origin strains isolated from the Chinese mainland over the past few years. However, mutations were observed between isolated H9 avian influenza virus strains and sequences available from GenBank, which should draw much attention.

The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen

The results of detection and identification of Bacillus anthracis strains in loop-mediated isothermal DNA amplification (LAMP) reaction performed under optimized conditions with original primers and thermostable DNA polymerase are presented. Reproducible LAMP-based detection of chromosomal and plasmid DNA targets specific for B. anthracis strains has been demonstrated. No cross reactions with DNA from bacterial strains of other species of the B. cereus group were detected. The development of tests for anthrax-pathogen detection based on the optimized reaction of loop isothermal DNA amplification is planned. These tests will be convenient for clinical studies and field diagnostics due to the absence of requirements for sophisticated equipment.

Cross-priming amplification targeting the coagulase gene for rapid detection of coagulase-positive Staphylococci

AIMS

To develop and evaluate cross-priming amplification (CPA) combined with immuno-blotting for the detection of coagulase-positive Staphylococci including Staphylococcus aureus.

METHODS AND RESULTS

Twenty-four sets of cross and detection primers were designed according to four sequences of coagulase gene in Staph. aureus. The most specific primer pair was screened out for the next amplification and interaction. The specificity was evaluated in a total of 53 species of Staph. aureus and non-Staph. aureus. Two red lines indicating positive were always observed on the BioHelix Express strip for 12 subspecies of Staph. aureus. In contrast, only one signal line showing negative results was detected in all of non-Staph. aureus samples. The limit of detection (LOD) of CPA was 3·6 ± 2·7 fg for the genomic DNA, which is about 100 and 10 times sensitive than those of PCR and loop-mediated isothermal amplification respectively. For the pure culture of Staph. aureus and milk powders, the LODs of CPA were about 1·34 CFU per reaction and 5·2 ± 3·7 CFU per 100 g of milk powder respectively. The CPA method was also successfully applied to evaluate the contamination of Staph. aureus in 318 samples of daily food.

CONCLUSIONS

CPA is a very sensitive and rapid method to detect Staph. aureus by simple laboratory instrument.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first report on the application of the CPA with immuno-blotting for detection of coagulase-positive Staphylococci including Staph. aureus.

Two methods for increased specificity and sensitivity in loop-mediated isothermal amplification

The technique of loop-mediated isothermal amplification (LAMP) utilizes four (or six) primers targeting six (or eight) regions within a fairly small segment of a genome for amplification, with concentration higher than that used in traditional PCR methods. The high concentrations of primers used leads to an increased likelihood of non-specific amplification induced by primer dimers. In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay.

Development of a rapid assay to detect the jellyfish Cyanea nozakii using a loop-mediated isothermal amplification method

Blooms of the harmful jellyfish Cyanea nozakii, which are a severe nuisance to fisheries and tourisms, frequently occur in the northern East China Sea, Yellow Sea, and Bohai Sea. To provide early warning of this species, a simple and effective molecular method for identifying C. nozakii was developed using the loop-mediated isothermal amplification method (LAMP). The LAMP assay is highly specific and uses a set of four primers that target six different regions on the mitochondrial cytochrome c oxidase subunit I (COI) gene of C. nozakii. The amplification conditions, including the dNTP and betaine concentrations, the inner primer to outer primer concentration ratio, reaction time and temperature, were optimized. The LAMP assay amplified DNA extracted from tissue samples of C. nozakii but did not amplify DNA from other common scyphozoans and hydrozoans collected in the same region. In addition, the LAMP assay was more sensitive than conventional PCR. Therefore, the established LAMP assay is a sensitive, specific, fast, and easily performed method for detection of C. nozakii at different stages in their life cycle.

Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification

Mycoplasma synoviae (MS) remains a serious concern in production of poultry and affects world production of chickens and turkeys. Loop-mediated isothermal amplification (LAMP) of DNA has been recently used for the identification of different economically important avian pathogens. The aim of this study was to develop LAMP for simple and inexpensive detection of MS strains in poultry using specifically designed primers targeting hemagglutin A (vlh) gene. The assay was conducted in a water bath for 1 h at 63 °C. The results were visualized after addition of SYBR Green(®) fluorescent dye. LAMP was specific exclusively for MS without cross-reactivity with other Mycoplasma species. The sensitivity of LAMP was determined as 10(-1) CFU/ml and was 1,000 times higher than MS-specific polymerase chain reaction. LAMP assay was conducted on 18 MS field strains to ensure its reliability and usefulness. This is the first report on LAMP development and application for the rapid detection of MS isolated from chickens. This simple method may be applied by diagnostic laboratories without access to expensive equipment.

Loop-mediated isothermal amplification (LAMP) assays for rapid detection and differentiation of Nosema apis and N. ceranae in honeybees

Nosemosis is a contagious disease of honeybees (Apis mellifera) manifested by increased winter mortality, poor spring build-up and even the total extinction of infected bee colonies. In this paper, loop-mediated isothermal amplifications (LAMP) were used for the first time to identify and differentiate N. apis and N. ceranae, the causative agents of nosemosis. LAMP assays were performed at a constant temperature of 60 °C using two sets of six species-specific primers, recognising eight distinct fragments of 16S rDNA gene and GspSSD polymerase with strand displacement activity. The optimal time for LAMP and its Nosema species sensitivity and specificity were assessed. LAMP only required 30 min for robust identification of the amplicons. Ten-fold serial dilutions of total DNA isolated from bees infected with microsporidia were used to determine the detection limit of N. apis and N. ceranae DNAs by LAMP and standard PCR assays. LAMP appeared to be 10(3) -fold more sensitive than a standard PCR in detecting N. apis and N. ceranae. LAMP methods developed by us are highly Nosema species specific and allow to identify and differentiate N. apis and N. ceranae.

Occurrence of reovirus infection in Muscovy ducks (Cairina moschata) in south western Poland

During the summer 2012 an incidence of high mortality, above 44 percent, in two flocks of Muscovy ducklings in Poland was noted. The clinical signs included considerable weight loss and inability to walk.

During the post-mortem evaluations dehydration and enteritis, gouty kidneys as well as hemorrhagic liver and spleen lesions were found. The laboratory diagnosis included agar gel precipitation assay (AGP) as well as polymerase chain reaction (PCR) or reverse transcription PCR for the presence of goose parvovirus (GPV), duck circovirus (DuCV), duck reovirus (DRV) and avian reovirus (ARV). Interestingly, the examinations performed by AGP showed partial reactivity of liver homogenates from Muscovy ducklings with chicken S1133 antiserum. The presence of duck reovirus RNA was also detected by real-time RT-PCR targeting the chicken reovirus sigma NS fragment, while the sequencing showed major similarity to chicken S1133, 1733, GX/2010/1 and TARV-MN2 reovirus strains. The virus sequence was also related to a previously isolated TH11 strain from Muscovy ducks in China.

Further study is needed in order to explain the particular epidemiology of the reovirus infection of Muscovy ducklings

A loop-mediated isothermal amplification assay for the visual detection of duck circovirus

BACKGROUND

Duck circovirus (DuCV) infection in farmed ducks is associated with growth problems or retardation syndromes. Rapid identification of DuCV infected ducks is essential to control DuCV effectively. Therefore, this study aims to develop of an assay for DuCV to be highly specific, sensitive, and simple without any specialized equipment.

METHODS

A set of six specific primers was designed to target the sequences of the Rep gene of DuCV, and A loop-mediated isothermal amplification (LAMP) assay were developed and the reaction conditions were optimized for rapid detection of DuCV.

RESULTS

The LAMP assay reaction was conducted in a 62°C water bath condition for 50 min. Then the amplification products were visualized directly for color changes. This LAMP assay is highly sensitive and able to detect twenty copies of DuCV DNA. The specificity of this LAMP assay was supported by no cross-reaction with other duck pathogens.

CONCLUSION

This LAMP method for DuCV is highly specific and sensitive and can be used as a rapid and direct diagnostic assay for testing clinical samples.