Reverse transcription-loop-mediated isothermal amplification for the detection of rodent coronaviruses

Real-time reverse transcription recombinase polymerase amplification for rapid detection of murine hepatitis virus

Murine hepatitis virus (MHV) is a highly infectious murine coronavirus that has a high potential for causing harm to host animals. This study aimed to develop a real-time reverse transcription recombinase polymerase amplification (RT-RPA) method for rapid detection of MHV in laboratory mice.

METHODS

Specific primers and probes for RT-RPA assay were designed targeting the conserved region in the M gene of the MHV reference strain (accession no. FJ6647223) according to the TwistDx manual instructions. The specificity, sensitivity, and reproducibility of the RT-RPA method were evaluated and compared with those of the standard RT-qPCR method. The clinical applicability of this assay was evaluated using 68 field samples.

RESULTS

Amplification using the newly developed RT-RPA assay was completed within 20 min at 37°C, while that using the RT-qPCR method required nearly 60 min. The RT-RPA method exhibited an obvious time-saving advantage. Both RT-RPA and RT-PCR methods had the same limit of detection, which was 4.45 × 101 copies/μL. The specificity was indicated by a lack of cross-reaction with MHV, pneumonia virus of mice, Sendai virus, hantavirus, minute virus of mice, and reovirus type III. The MHV detection rate of RT-RPA assays was 13.63% (9/66) and RT-qPCR assays was 15.15% (10/66). Cohen's "kappa" (κ) analysis results exhibited a very good agreement between two methods with the value of κ ≥ 0.750(since κ = 0.939) and p < 0.0005 (since p = 0.000).

CONCLUSION

The RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of MHV in laboratory mice and has significant potential for application in laboratories.

Development of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Detecting Feline Coronavirus

Simple Summary

Feline coronavirus infecting domestic cats can cause feline infectious peritonitis (FIP), a fatal infectious disease. Several relevant clinical diagnoses and molecular methods are complicated and often ambiguous for veterinarians. In this work developed a rapid, sensitive, specific, and easy-to-visualize colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with a novel LAMP primer set that has high specificity was developed using neutral red as an indicator dye. This proposed procedure could reliably detect FCoV RNA from effusion fluids comparable to the conventional PCR method. Considering these advantages, the RT-LAMP developed here has great potential on FIP-associated FCoV surveillance. Together with other sophisticated molecular diagnostic tools, this method can further be exploited in clinical laboratories to inspect suspected cats with effusive FIP.

Abstract

Feline infectious peritonitis (FIP) is a worldwide fatal disease caused by a mutant feline coronavirus (FCoV). Simple and efficient molecular detection methods are needed. Here, sensitive, specific, rapid, and reliable colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed to detect the ORF1a/1b gene of FCoV from cats with suspected FIP using neutral red as an indicator. Novel LAMP primers were specifically designed based on the gene of interest. The isothermal assay could visually detect FCoV at 58 °C for 50 min. The RT-LAMP assay was highly specific and had no cross-reactivity with other related feline viruses. The detection limit of FCoV detection by RT-LAMP was 20 fg/µL. A blind clinical test (n = 81) of the developed RT-LAMP procedure was in good agreement with the conventional PCR method. In the light of its performance specificity, sensitivity, and easy visualization, this neutral-red-based RT-LAMP approach would be a fruitful alternative molecular diagnostic tool for veterinary inspection of FCoV when combined with nucleotide sequencing or specific PCR to affirm the highly virulent FIP-associated FCoV.

Basic reproduction numbers of three strains of mouse hepatitis viruses in mice

Mouse hepatitis virus (MHV) is a murine coronavirus and one of the most important pathogens in laboratory mice. Although various strains of MHV have been isolated, they are generally excreted in the feces and transmitted oronasally via aerosols and contaminated bedding. In this study, we attempted to determine the basic reproduction numbers (R₀) of three strains of MHV to improve our understanding of MHV infections in mice. Five‐week‐old female C57BL/6J mice were inoculated intranasally with either the Y, NuU, or JHM variant strain of MHV and housed with two naïve mice. After 4 weeks, the presence or absence of anti‐MHV antibody in the mice was determined by ELISA. We also examined the distribution of MHV in the organs of Y, NuU, or JHM variant‐infected mice. Our data suggest that the transmissibility of MHV is correlated with viral growth in the gastrointestinal tract of infected mice. To the best of our knowledge, this is the first report to address the basic reproduction numbers among pathogens in laboratory animals.

Reverse transcriptase loop-mediated isothermal amplification for the detection of feline coronavirus

The Feline coronavirus (FCoV) is the etiological agent of feline infectious peritonitis (FIP), a lethal disease of felids. The role of molecular methods is controversial for the diagnosis of FIP, while essential for the identification of the shedders. Thus, a fast and inexpensive method for the detection of FCoV could be beneficial, especially in multicat environments. A reverse transcription loop mediated isothermal amplification (RT-LAMP) assay was developed. RNA extraction and RT-nPCR for FCoV were performed on thirty-two samples (11 faeces, 9 blood, 8 effusions, and 4 lymph nodes) collected from 27 cats. Six RT-LAMP primers were designed from the same conserved region of RT-nPCR, and the assay was run at 63°C for one hour. Results were evaluated through both agarose gel run and hydroxynapthol blue (HNB) dye and then compared with RT-nPCR results for the assessment of sensitivity and specificity. The overall specificity was 100%, but the sensitivity was 50% and 54.5% for agarose gel and HNB respectively. Therefore, RT-LAMP seems optimal to confirm the presence of the virus, but not applicable to exclude it.

Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia-Retinoic Acid Receptor α mRNA

BACKGROUND

Acute promyelocytic leukemia (APL) is a disease characterized by expression of Promyelocytic Leukemia-Retinoic Acid Receptor α (PML-RARα) chimeric mRNA. Although APL is curable, early death due to hemorrhage is a major problem. Here, we report the development of a simple and rapid diagnostic method for APL based on reverse transcription loop-mediated isothermal amplification (RT-LAMP).

METHODS

An RT-LAMP primer set was designed to detect three types of PML-RARα mRNA in a single reaction. Serial dilutions of plasmid DNA containing bcr1, bcr2, or bcr3 PML-RARα sequences and RNA extracted from bone marrow aspirates of 6 patients with APL were used to compare the results of RT-LAMP and nested PCR assays.

RESULTS

Plasmid DNA was amplified by RT-LAMP, for which the reaction time was > 4 h shorter and the lower detection limit was higher than for nested RT-PCR. Six of 7 samples tested positive by both methods.

CONCLUSION

We developed an RT-LAMP assay for simple and rapid PML-RARα mRNA detection that may be clinically useful for point-of-care testing and APL diagnosis.

Rapid detection of equine coronavirus by reverse transcription loop-mediated isothermal amplification

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An RT-LAMP assay was developed for the detection of equine coronavirus.

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The RT-LAMP assay was more sensitive than conventional RT-PCR.

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Quantitative RT-PCR was more sensitive than RT-LAMP.

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RT-LAMP allows for rapid and simple detection of equine coronavirus.

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid detection of equine coronavirus (ECoV). This assay was conducted at 60 °C for 40 min. Specificity of the RT-LAMP assay was confirmed using several equine intestinal and respiratory pathogens in addition to ECoV. The novel assay failed to cross-react with the other pathogens tested, suggesting it is highly specific for ECoV. Using artificially synthesized ECoV RNA, the 50% detection limit of the RT-LAMP assay was 10^1.8 copies/reaction. This is a 50-fold greater sensitivity than conventional reverse transcription polymerase chain reaction (RT-PCR) assays, but a 4-fold lower sensitivity than quantitative RT-PCR (qRT-PCR) assays. Eighty-two fecal samples collected during ECoV outbreaks were analyzed. ECoV was detected in 59 samples using the RT-LAMP assay, and in 30 and 65 samples using RT-PCR or qRT-PCR assays, respectively. Although the RT-LAMP assay is less sensitive than qRT-PCR techniques, it can be performed without the need for expensive equipment. Thus, the RT-LAMP assay might be suitable for large-scale surveillance and diagnosis of ECoV infection in laboratories with limited resources.

Detection of murine norovirus by reverse transcription loop-mediated isothermal amplification

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RT-LAMP method with the potential to detect a broad range of MNV was developed.

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Sensitivity of RT-LAMP was 50-fold less than that of TaqMan RT-PCR.

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In a practical diagnostic test, RT-LAMP exhibited 96.4% and 94.7% sensitivity compared with TaqMan RT-PCR and nested RT-PCR.

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In a practical diagnostic test, RT-LAMP exhibited 100% specificity compared with both TaqMan RT-PCR and nested RT-PCR.

Murine norovirus (MNV) has considerable genetical and biological diversity and is recognized worldwide as the most common contaminant in laboratory mouse colonies. This study developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method with the potential to detect a broad range of MNV. RT-LAMP, using a set of five primers containing mixed bases, obtained results under isothermal conditions at 62 °C for 90 min. Sensitivity of RT-LAMP was 50-fold less than that of two-step TaqMan real-time reverse transcription-polymerase chain reaction (TaqMan RT-PCR). Diagnostic performance of RT-LAMP on RNA extracted from mouse fecal specimens was compared with TaqMan RT-PCR and nested RT-PCR. MNV was detected in 54 of 120 mouse fecal specimens by RT-LAMP, and RT-LAMP had an estimated sensitivity and specificity of 96.4% and 100% compared with TaqMan RT-PCR, and 94.7% and 100% compared with nested RT-PCR. RT-LAMP, which does not require expensive instruments, might be useful for the screening of mice actively or persistently infected with MNV.

Wildlife health investigations: needs, challenges and recommendations

In a fast changing world with growing concerns about biodiversity loss and an increasing number of animal and human diseases emerging from wildlife, the need for effective wildlife health investigations including both surveillance and research is now widely recognized. However, procedures applicable to and knowledge acquired from studies related to domestic animal and human health can be on partly extrapolated to wildlife. This article identifies requirements and challenges inherent in wildlife health investigations, reviews important definitions and novel health investigation methods, and proposes tools and strategies for effective wildlife health surveillance programs. Impediments to wildlife health investigations are largely related to zoological, behavioral and ecological characteristics of wildlife populations and to limited access to investigation materials. These concerns should not be viewed as insurmountable but it is imperative that they are considered in study design, data analysis and result interpretation. It is particularly crucial to remember that health surveillance does not begin in the laboratory but in the fields. In this context, participatory approaches and mutual respect are essential. Furthermore, interdisciplinarity and open minds are necessary because a wide range of tools and knowledge from different fields need to be integrated in wildlife health surveillance and research. The identification of factors contributing to disease emergence requires the comparison of health and ecological data over time and among geographical regions. Finally, there is a need for the development and validation of diagnostic tests for wildlife species and for data on free-ranging population densities. Training of health professionals in wildlife diseases should also be improved. Overall, the article particularly emphasizes five needs of wildlife health investigations: communication and collaboration; use of synergies and triangulation approaches; investments for the long term; systematic collection of metadata; and harmonization of definitions and methods.