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Yasuura M, Nakaya Y, Ashiba H, Fukuda T. Investigation on the applicability of a long-range reverse-transcription quantitative polymerase chain reaction assay for the rapid detection of active viruses. BMC Microbiol 2022; 22:300. [PMID: 36510144 PMCID: PMC9743722 DOI: 10.1186/s12866-022-02723-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Although conventional polymerase chain reaction (PCR) methods are widely used in diagnosis, the titer of the pathogenic virus is difficult to determine based on the PCR. In our prior report, a long-range reverse-transcription quantitative PCR (LR-RT-qPCR) assay was developed to assess the titer of UV-irradiated influenza A virus (IAV) rapidly. In this research, we focused on whether the LR-RT-qPCR assay could evaluate the titer of IAV inactivated by other methods. METHODS IAV was inactivated by: heating at 100 °C for periods ranging from 1 to 15 min, treating with 0.12% sodium hypochlorite for periods ranging from 3 to 30 min, or treating with 70% ethanol for periods ranging from 10 to 30 min. Fifty percent tissue culture infectious dose (TCID50) assay was performed to confirm the efficacy of the inactivation methods, followed by LR-RT-qPCR to investigate the correlation between infectivity and copy number. RESULTS One minute heating, 3 min sodium hypochlorite treatment, or 10 min ethanol treatment was sufficient to deactivate IAV. Changes before and after the inactivations in the copy numbers on LR-RT-qPCR were significantly different among the inactivation methods. Heat-inactivation drastically decreased the copy number to below the cutoff value around 5 copies/μL after 5 min treatment. The inactivation time of heating estimated using LR-RT-qPCR was marginally higher than that determined using TCID50. However, the treatments with sodium hypochlorite or ethanol moderately and minimally affected the copy numbers obtained using LR-RT-qPCR (~ 1 digit or no copy number decrease), respectively. CONCLUSIONS In addition to good applicability in UV-irradiation previously reported, the LR-RT-qPCR method is suitable for evaluating the effect of heat-inactivation on IAV infectivity. However, minor modifications may be made and investigated in the future to reduce the time intervals with TCID50. Although this method is not applicable for the ethanol inactivation, rapid evaluation of the effects of chlorination on IAV can be determined by comparing copy numbers before and after treatment using the LR-RT-qPCR method.
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Affiliation(s)
- Masato Yasuura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Yuki Nakaya
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.,Division of Virology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroki Ashiba
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Takashi Fukuda
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
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Hifumi T, Akioka K, Tanaka T, Miyoshi N. Development of a loop-mediated isothermal amplification (LAMP) assay targeting the mitochondrial cytochrome b gene for the rapid detection of alveolar echinococcosis in hepatic nodules of horses. Vet Parasitol 2021; 299:109573. [PMID: 34521042 DOI: 10.1016/j.vetpar.2021.109573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Alveolar echinococcosis, which is caused by a larval-stage infection of Echinococcus multilocularis, is a zoonosis with public health importance. Recently, alveolar echinococcosis in slaughtered horses has been reported in Japan and Poland. In terms of public health, a highly sensitive and specific diagnostic method is essential for early detection during meat inspection. In this study, the loop-mediated isothermal amplification (LAMP) assay was developed and validated to target the mitochondrial cytochrome b (cob) gene of E. multilocularis. Forty-one hepatic solid nodules obtained from each horse were evaluated based on histopathological examination and cob-targeted PCR and then submitted to the LAMP assay. The optimal condition of the developed LAMP assay was 64℃ for 30 min. The results of the developed LAMP assay were completely consistent with those of cob PCR. In addition, the detection limit for the number of copies of the cob gene was 135 copies/μL in the LAMP assay. These findings suggest that the ability of the LAMP assay developed in this study is equivalent to that of the conventional PCR testing. The LAMP assay developed in this study can be used as an alternative to PCR testing for the routine genetic diagnosis of alveolar echinococcosis in horses.
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Affiliation(s)
- Tatsuro Hifumi
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kohei Akioka
- Kumamoto Prefectural Meat Inspection Center, 1314 Sosaki, Shichijo-machi, Kikuchi, Kumamoto 861-1344, Japan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.
| | - Noriaki Miyoshi
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Abstract
This review briefly describes the virus classification, clinical signs, epidemiology,
diagnosis, disinfection, and vaccines related equine group A rotavirus (RVA) infection.
Equine RVA is one of the most important pathogens causing diarrhoea in foals. The main
transmission route is faecal–oral, and the clinical signs are diarrhoea, fever, lethargy,
and anorexia (decreased suckling). Some human RVA rapid antigen detection kits based on
the principles of the immunochromatographic assay are useful for the diagnosis of equine
RVA infection. The kits are used in daily clinical practice because of their rapidity and
ease of handling. Equine RVA is a non-enveloped virus and is more resistant to
disinfectants than enveloped viruses such as equine influenza virus and equine
herpesvirus. Although amphoteric soaps and quaternary ammonium compounds are commonly used
in veterinary hygiene, they are generally ineffective against equine RVA. Alcohol
products, aldehydes, and chlorine- and iodine-based compounds are effective against equine
RVA. Inactivated vaccines have been used for equine RVA infection in some countries.
Pregnant mares are intramuscularly inoculated with a vaccine, and thus their colostrum has
abundant antibodies against RVA at the time of birth. According to G and P classification
defined in accordance with the VP7 and VP4 genes, respectively, the predominant equine
RVAs circulating in horse populations globally are G3P[12] and G14P[12] equine RVAs, but
the vaccines contain only the G3P[12] equine RVA strain. Ideally, a G14P[12] equine RVA
should be added as a vaccine strain to obtain a better vaccine effect.
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Affiliation(s)
- Manabu Nemoto
- Equine Research Institute, Japan Racing Association, Tochigi 329-0412, Japan
| | - Tomio Matsumura
- Equine Research Institute, Japan Racing Association, Tochigi 329-0412, Japan
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da Silva SJR, Pardee K, Balasuriya UBR, Pena L. Development and validation of a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of ZIKV in patient samples from Brazil. Sci Rep 2021; 11:4111. [PMID: 33602985 PMCID: PMC7893177 DOI: 10.1038/s41598-021-83371-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023] Open
Abstract
We have previously developed and validated a one-step assay based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of the Zika virus (ZIKV) from mosquito samples. Patient diagnosis of ZIKV is currently carried out in centralized laboratories using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which, while the gold standard molecular method, has several drawbacks for use in remote and low-resource settings, such as high cost and the need of specialized equipment. Point-of-care (POC) diagnostic platforms have the potential to overcome these limitations, especially in low-resource countries where ZIKV is endemic. With this in mind, here we optimized and validated our RT-LAMP assay for rapid detection of ZIKV from patient samples. We found that the assay detected ZIKV from diverse sample types (serum, urine, saliva, and semen) in as little as 20 min, without RNA extraction. The RT-LAMP assay was highly specific and up to 100 times more sensitive than RT-qPCR. We then validated the assay using 100 patient serum samples collected from suspected cases of arbovirus infection in the state of Pernambuco, which was at the epicenter of the last Zika epidemic. Analysis of the results, in comparison to RT-qPCR, found that the ZIKV RT-LAMP assay provided sensitivity of 100%, specificity of 93.75%, and an overall accuracy of 95.00%. Taken together, the RT-LAMP assay provides a straightforward and inexpensive alternative for the diagnosis of ZIKV from patients and has the potential to increase diagnostic capacity in ZIKV-affected areas, particularly in low and middle-income countries.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, 50670-420, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, 50670-420, Brazil.
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5
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Quick assessment of influenza a virus infectivity with a long-range reverse-transcription quantitative polymerase chain reaction assay. BMC Infect Dis 2020; 20:585. [PMID: 32762666 PMCID: PMC7407439 DOI: 10.1186/s12879-020-05317-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The polymerase chain reaction (PCR) is commonly used to detect viral pathogens because of its high sensitivity and specificity. However, conventional PCR methods cannot determine virus infectivity. Virus infectivity is conventionally examined with methods such as the plaque assay, even though such assays require several days. Long-range reverse-transcription quantitative PCR (RT-qPCR) has previously been suggested for the rapid assessment of RNA virus infectivity where the loss of infectivity is attributable to genomic fragmentation. METHODS IAV was irradiated with 253.7 nm ultraviolet (UV) rays to induce genomic strand breaks that were confirmed by a full-length RT-PCR assay. The IAV was then subjected to plaque assay, conventional RT-qPCR and long-range RT-qPCR to examine the relationship between infectious titer and copy number. A simple linear regression analysis was performed to examine the correlation between the results of these assays. RESULTS A long-range RT-qPCR assay was developed and validated for influenza A virus (IAV). Although only a few minutes of UV irradiation was required to completely inactivate IAV, genomic RNA remained detectable by the conventional RT-qPCR and the full-length RT-PCR for NS of viral genome following inactivation. A long-range RT-qPCR assay was then designed using RT-priming at the 3' termini of each genomic segment and subsequent qPCR of the 5' regions. UV-mediated IAV inactivation was successfully analyzed by the long-range RT-qPCR assay especially when targeting PA of the viral genome. This was also supported by the regression analysis that the long-range RT-qPCR is highly correlated with plaque assay (Adjusted R2 = 0.931, P = 0.000066). CONCLUSIONS This study suggests that IAV infectivity can be predicted without the infectivity assays. The rapid detection of pathogenic IAV has, therefore, been achieved with this sensing technology.
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da Silva SJR, Pardee K, Pena L. Loop-Mediated Isothermal Amplification (LAMP) for the Diagnosis of Zika Virus: A Review. Viruses 2019; 12:v12010019. [PMID: 31877989 PMCID: PMC7019470 DOI: 10.3390/v12010019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
The recent outbreak of Zika virus (ZIKV) in the Americas and its devastating developmental and neurological manifestations has prompted the development of field-based diagnostics that are rapid, reliable, handheld, specific, sensitive, and inexpensive. The gold standard molecular method for lab-based diagnosis of ZIKV, from either patient samples or insect vectors, is reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The method, however, is costly and requires lab-based equipment and expertise, which severely limits its use as a point-of-care (POC) tool in resource-poor settings. Moreover, given the lack of antivirals or approved vaccines for ZIKV infection, a POC diagnostic test is urgently needed for the early detection of new outbreaks and to adequately manage patients. Loop-mediated isothermal amplification (LAMP) is a compelling alternative to RT-qPCR for ZIKV and other arboviruses. This low-cost molecular system can be freeze-dried for distribution and exhibits high specificity, sensitivity, and efficiency. A growing body of evidence suggests that LAMP assays can provide greater accessibility to much-needed diagnostics for ZIKV infections, especially in developing countries where the ZIKV is now endemic. This review summarizes the different LAMP methods that have been developed for the virus and summarizes their features, advantages, and limitations.
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Affiliation(s)
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada;
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Brazil;
- Correspondence: ; Tel.: +55-81-2123-7849
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Development and Validation of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for Rapid Detection of ZIKV in Mosquito Samples from Brazil. Sci Rep 2019; 9:4494. [PMID: 30872672 PMCID: PMC6418238 DOI: 10.1038/s41598-019-40960-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
The rapid spread of Zika virus (ZIKV) represents a global public health problem, especially in areas that harbor several mosquito species responsible for virus transmission, such as Brazil. In these areas, improvement in mosquito control needs to be a top priority, but mosquito viral surveillance occurs inefficiently in ZIKV-endemic countries. Quantitative reverse transcription PCR (qRT-PCR) is the gold standard for molecular diagnostic of ZIKV in both human and mosquito samples. However, the technique presents high cost and limitations for Point-of-care (POC) diagnostics, which hampers its application for a large number of samples in entomological surveillance programs. Here, we developed and validated a one-step reverse transcription LAMP (RT-LAMP) platform for detection of ZIKV in mosquito samples. The RT-LAMP assay was highly specific for ZIKV and up to 10,000 times more sensitive than qRT-PCR. Assay validation was performed using 60 samples from Aedes aegypti and Culex quinquefasciatus mosquitoes collected in Pernambuco State, Brazil, which is at the epicenter of the Zika epidemic. The RT-LAMP had a sensitivity of 100%, specificity of 91.18%, and overall accuracy of 95.24%. Thus, our POC diagnostics is a powerful and inexpensive tool to monitor ZIKV in mosquito populations and will allow developing countries to establish better control strategies for this devastating pathogen.
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Han C, Niu X, Liu L, Li J, Li J, Yao S, Song X, Gao H, Gao Y, Qi X, Zeng X, Wang Y, Wang X. Development of a loop-mediated isothermal amplification assay for the detection of chicken anemia virus. Poult Sci 2019; 98:1176-1180. [PMID: 30544152 DOI: 10.3382/ps/pey495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Chicken anemia virus (CAV) infection has been reported in various poultry industries worldwide. Since CAV infection is becoming increasingly prevalent, especially in local chickens of China, rapid CAV detection has become essential. The conventional diagnostic methods are time consuming and need special expertise. Therefore, in this study, we developed a specific and sensitive loop-mediated isothermal amplification (LAMP) assay for CAV detection by using multiple sequence alignment of VP2. This assay was performed at 61°C for 1 h, and there was no non-specific reaction to common avian disease viruses. The detection limit was 65 copies of viral DNA; thus, this assay showed similar sensitivity to quantitative polymerase chain reaction (qPCR) but it was more sensitive than conventional PCR. Moreover, this assay was performed using clinical samples. The LAMP assay results were 83.6% correlated to the PCR results of the clinical samples, indicating that this method is an effective tool for the rapid detection of CAV.
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Affiliation(s)
- Chunyan Han
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Niu
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Lanlan Liu
- College of Basic Medical Science, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Jiukuan Li
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,Northeast Agricultural University, 150030, Harbin, China
| | - Jing Li
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Shuai Yao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,Northeast Agricultural University, 150030, Harbin, China
| | - Xiuqing Song
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Honglei Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yulong Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiaole Qi
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiangwei Zeng
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Yongqiang Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiaomei Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
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Wang X, Yin F, Bi Y, Cheng G, Li J, Hou L, Li Y, Yang B, Liu W, Yang L. Rapid and sensitive detection of Zika virus by reverse transcription loop-mediated isothermal amplification. J Virol Methods 2016; 238:86-93. [PMID: 27793644 DOI: 10.1016/j.jviromet.2016.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Zika virus (ZIKV) is an arbovirus that recently emerged and has expanded worldwide, causing a global threat and raising international concerns. Current molecular diagnostics, e.g., real-time PCR and reverse transcription PCR (RT-PCR), are time consuming, expensive, and can only be deployed in a laboratory instead of for field diagnostics. OBJECTIVES This study aimed to develop a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform showing sensitivity, specificity, and more convenience than previous methods, being easily distributed and implemented. METHODS Specific primers were designed and screened to target the entire ZIKV genome. The analytical sensitivity and specificity of the assay were evaluated and compared with traditional PCR and quantitative real-time PCR. Three different simulated clinical sample quick preparation protocols were evaluated to establish a rapid and straightforward treatment procedure for clinical specimens in open field detection. RESULTS The RT-LAMP assay for detection of ZIKV demonstrated superior specificity and sensitivity compared to traditional PCR at the optimum reaction temperature. For the ZIKV RNA standard, the limit of detection was 20 copies/test. For the simulated ZIKV clinical samples, the limit of detection was 0.02 pfu/test, which was one order of magnitude higher than RT-PCR and similar to real-time PCR. The detection limit of simulated ZIKV specimens prepared using a protease quick processing method was consistent with that of samples prepared using commercial nucleic acid extraction kits, indicating that our ZIKV detection method could be used in point-of-care testing. CONCLUSIONS The RT-LAMP assay had excellent sensitivity and specificity for detecting ZIKV and can be deployed together with a rapid specimen processing method, offering the possibility for ZIKV diagnosis outside of the laboratory.
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Affiliation(s)
- Xuan Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fenggui Yin
- College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gong Cheng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lidan Hou
- China Institute of Veterinary Drug Control, Beijing 100081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlong Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baozhi Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Limin Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Thirapanmethee K, Pothisamutyothin K, Nathisuwan S, Chomnawang MT, Wiwat C. Loop-mediated isothermal amplification assay targeting the blaCTX-M9 gene for detection of extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Microbiol Immunol 2015; 58:655-65. [PMID: 25284314 DOI: 10.1111/1348-0421.12205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 09/18/2014] [Accepted: 09/30/2014] [Indexed: 11/26/2022]
Abstract
Extended-spectrum β-lactamases (ESBLs) produced by Enterobacteriaceae are one of the resistance mechanisms to most β-lactam antibiotics. ESBLs are currently a major problem in both hospitals and community settings worldwide. Rapid and reliable means of detecting ESBL-producing bacteria is necessary for identification, prevention and treatment. Loop-mediated isothermal amplification (LAMP) is a technique that rapidly amplifies DNA with high specificity and sensitivity under isothermal conditions. This study was aimed to develop a convenient, accurate and inexpensive method for detecting ESBL-producing bacteria by a LAMP technique. ESBLs-producing Escherichia coli and Klebsiella pneumoniae were isolated from a tertiary hospital in Bangkok, Thailand and reconfirmed by double-disk synergy test. A set of four specific oligonucleotide primers of LAMP for detection of bla(CTX-M9) gene was designed based on bla(CTX-M9) from E. coli (GenBank Accession No. AJ416345). The LAMP reaction was amplified under isothermal temperature at 63°C for 60 min. Ladder-like patterns of band sizes from 226 bp of the bla(CTX-M9) DNA target was observed. The LAMP product was further analyzed by restriction digestion with MboI and TaqI endonucleases. The fragments generated were approximately 168, 177 and 250 bp in size for MboI digestion and 165, 193, 229, 281 and 314 bp for TaqI digestion, which is in agreement with the predicted sizes. The sensitivity of the LAMP technique to bla(CTX-M9) was greater than that of the PCR method by at least 10,000-fold. These results showed that the LAMP primers specifically amplified only the bla(CTX-M9) gene. Moreover, the presence of LAMP amplicon was simply determined by adding SYBR Green I in the reaction. In conclusion, this technique for detection of ESBLs is convenient, reliable and easy to perform routinely in hospitals or laboratory units in developing countries.
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Otto PH, Rosenhain S, Elschner MC, Hotzel H, Machnowska P, Trojnar E, Hoffmann K, Johne R. Detection of rotavirus species A, B and C in domestic mammalian animals with diarrhoea and genotyping of bovine species A rotavirus strains. Vet Microbiol 2015. [DOI: 10.1016/j.vetmic.2015.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Abstract
The gastrointestinal system of horses is affected by a large variety of inflammatory infectious and noninfectious conditions. The most prevalent form of gastritis is associated with ulceration of the pars esophagea. Although the diagnostic techniques for alimentary diseases of horses have improved significantly over the past few years, difficulties still exist in establishing the causes of a significant number of enteric diseases in this species. This problem is compounded by several agents of enteric disease also being found in the intestine of clinically normal horses, which questions the validity of the mere detection of these agents in the intestine.
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Affiliation(s)
- Francisco A Uzal
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California Davis, 105 West Central Avenue, San Bernardino, CA 92409, USA.
| | - Santiago S Diab
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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13
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Nemoto M, Morita Y, Niwa H, Bannai H, Tsujimura K, Yamanaka T, Kondo T. Rapid detection of equine coronavirus by reverse transcription loop-mediated isothermal amplification. J Virol Methods 2015; 215-216:13-6. [PMID: 25682750 PMCID: PMC7113660 DOI: 10.1016/j.jviromet.2015.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/08/2023]
Abstract
An RT-LAMP assay was developed for the detection of equine coronavirus. The RT-LAMP assay was more sensitive than conventional RT-PCR. Quantitative RT-PCR was more sensitive than RT-LAMP. 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 101.8 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.
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Affiliation(s)
- Manabu Nemoto
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan.
| | - Yoshinori Morita
- Tokachi Draft Horse Clinic, Nishi 13, Minami 9-1, Obihiro, Hokkaido 080-0023, Japan
| | - Hidekazu Niwa
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Hiroshi Bannai
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Koji Tsujimura
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Takashi Yamanaka
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
| | - Takashi Kondo
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan
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Experimental inoculation of equine coronavirus into Japanese draft horses. Arch Virol 2014; 159:3329-34. [PMID: 25139547 PMCID: PMC7087042 DOI: 10.1007/s00705-014-2205-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/13/2014] [Indexed: 11/02/2022]
Abstract
Recently, outbreaks associated with equine coronavirus (ECoV) have occurred in Japan and the United States. While ECoV is likely to be pathogenic to horses, it has not been shown that experimental inoculation of horses with ECoV produces clinical signs of disease. In this study, we inoculated three Japanese draft horses with an ECoV-positive diarrheic fecal sample to confirm infection after inoculation and to investigate the clinical course and virus shedding patterns of ECoV. Virus neutralization tests showed that all three horses became infected with ECoV. Two of the three horses developed clinical signs similar to those observed during ECoV outbreaks, including fever, anorexia, and gastrointestinal dysfunction. All horses excreted a large amount of virus into their feces for more than 9 days after inoculation regardless of the presence or absence of clinical signs, which suggests that feces are an important source of ECoV infection. ECoV was also detected in nasal swabs from all horses, suggesting that respiratory transmission of ECoV may occur. Both symptomatic horses developed viremia, while the asymptomatic horse did not. White blood cell counts and serum amyloid A concentrations changed relative to the clinical condition of the inoculated horses; these may be useful markers for monitoring the clinical status of horses infected with ECoV. This is the first report of induction of clinical signs of ECoV infection in horses by experimental inoculation. These clinical and virological findings should aid further investigation of the pathogenesis of ECoV.
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Xie L, Xie Z, Zhao G, Liu J, Pang Y, Deng X, Xie Z, Fan Q, Luo S. A loop-mediated isothermal amplification assay for the visual detection of duck circovirus. Virol J 2014; 11:76. [PMID: 24775810 PMCID: PMC4013541 DOI: 10.1186/1743-422x-11-76] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/25/2014] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Liji Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Guangyuan Zhao
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Jiabo Liu
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Yaoshan Pang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Xianwen Deng
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Zhiqin Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Qing Fan
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
| | - Sisi Luo
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, 530001 Nanning, China
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Detection of new bunyavirus RNA by reverse transcription-loop-mediated isothermal amplification. J Clin Microbiol 2013; 52:531-5. [PMID: 24478484 DOI: 10.1128/jcm.01813-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is a newly emerging and epidemic infectious disease in central and northeast China. It is caused by New Bunyavirus and carries an average 12% case fatality rate. Early and rapid detection is critical for prevention and control of New Bunyavirus infection, since no vaccine or antiviral drugs are currently available, and prevention requires careful attention to control of the suspected tick vector. In this study, a simple and sensitive reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed for rapid detection of New Bunyavirus. The detection limit of the RT-LAMP assay was approximately 10(3) 50% tissue culture infective doses/ml of New Bunyavirus in culture supernatants, and no cross-reactive amplification of other viruses known to cause similar clinical manifestations was observed. The assay was further evaluated using 138 specimens from clinically suspected SFTS and 40 laboratory-proven hantavirus infection with fever and renal syndrome patients, and the assay exhibited 97% agreement compared to real-time RT-PCR and conventional RT-PCR. Using real-time RT-PCR as the diagnostic gold standard, RT-LAMP was 99% sensitive and 100% specific. The RT-LAMP assay could become a useful alternative in clinical diagnosis of SFTS caused by New Bunyavirus, especially in resource-limited hospitals or rural clinics of China.
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Papp H, Matthijnssens J, Martella V, Ciarlet M, Bányai K. Global distribution of group A rotavirus strains in horses: a systematic review. Vaccine 2013; 31:5627-33. [PMID: 23994380 DOI: 10.1016/j.vaccine.2013.08.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/01/2013] [Accepted: 08/13/2013] [Indexed: 11/19/2022]
Abstract
Group A rotavirus (RVA) is a major cause of diarrhea and diarrhea-related mortality in foals in parts of the world. In addition to careful horse farm management, vaccination is the only known alternative to reduce the RVA associated disease burden on horse farms. The precise evaluation of vaccine effectiveness against circulating strains needs enhanced surveillance of equine RVAs in areas where vaccine is already available or vaccine introduction is anticipated. Therefore, we undertook the overview of relevant information on epidemiology of equine RVA strains through systematic search of public literature databases. Our findings indicated that over 99% of equine RVA strains characterized during the past three decades belonged to two common genotypes, G3P[12] and G14P[12], whereas most of the minority equine RVA strains were probably introduced from a heterologous host by interspecies transmission. These baseline data on RVA strains in horses shall contribute to a better understanding of the spatiotemporal dynamics of strain prevalence in vaccinated and non-vaccinated herds.
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Affiliation(s)
- Hajnalka Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary.
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Bailey KE, Gilkerson JR, Browning GF. Equine rotaviruses--current understanding and continuing challenges. Vet Microbiol 2013; 167:135-44. [PMID: 23932076 PMCID: PMC7117381 DOI: 10.1016/j.vetmic.2013.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/04/2013] [Accepted: 07/07/2013] [Indexed: 11/20/2022]
Abstract
Equine rotaviruses were first detected in foals over 30 years ago and remain a major cause of infectious diarrhoea in foals. During this time, there has been substantial progress in the development of sensitive methods to detect rotaviruses in foals, enabling surveillance of the genotypes present in various horse populations. However, there has been limited epidemiological investigation into the significance of these circulating genotypes, their correlation with disease and the use of vaccination in these animal populations. Our knowledge of the pathogenesis of rotavirus infection in foals is based on a limited number of studies on a small number of foals and, therefore, most of our understanding in this area has been extrapolated from studies in other species. Questions such as the concentrations of rotavirus particles shed in the faeces of infected foals, both with and without diarrhoea, and factors determining the presence or absence of clinical disease remain to be investigated, as does the relative and absolute efficacy of currently available vaccines. The answer to these questions may help direct research into the development of more effective control measures.
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Affiliation(s)
- Kirsten E Bailey
- Centre for Equine Infectious Diseases, Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Antibody response in vaccinated pregnant mares to recent G3BP[12] and G14P[12] equine rotaviruses. Acta Vet Scand 2012; 54:63. [PMID: 23130609 PMCID: PMC3523035 DOI: 10.1186/1751-0147-54-63] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 11/01/2012] [Indexed: 11/25/2022] Open
Abstract
Background Both the G3P[12] and the G14P[12] type of equine group A rotavirus (RVA) have recently become predominant in many countries, including Japan. G3 types are classified further into G3A and G3B. The G3A viruses have been circulating in Europe, Australia, and Argentina, and the G3B viruses have been circulating in Japan. However, only an inactivated vaccine containing a single G3BP[12] strain is commercially available in Japan. To assess the efficacy of the current vaccine against recently circulating equine RVA strains, we examined antibody responses in pregnant mares to recent G3BP[12] and G14P[12] strains by virus neutralization test. Findings After vaccination in five pregnant mares, the geometric mean serum titers of virus-neutralizing antibody to recent G3BP[12] strains increased 5.3- to 7.0-fold and were similar to that against homologous vaccine strain. Moreover, antibody titers to recent G14P[12] strains were also increased 3.0- to 3.5-fold. Conclusions These results suggest that inoculation of mares with the current vaccine should provide foals with virus-neutralizing antibodies against not only the G3BP[12] but also the G14P[12] RVA strain via the colostrum.
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Mehle N, Ravnikar M. Plant viruses in aqueous environment - survival, water mediated transmission and detection. WATER RESEARCH 2012; 46:4902-17. [PMID: 22871317 DOI: 10.1016/j.watres.2012.07.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/12/2012] [Accepted: 07/15/2012] [Indexed: 05/09/2023]
Abstract
The presence of plant viruses outside their plant host or insect vectors has not been studied intensively. This is due, in part, to the lack of effective detection methods that would enable their detection in difficult matrixes and in low titres, and support the search for unknown viruses. Recently, new and sensitive methods for detecting viruses have resulted in a deeper insight into plant virus movement through, and transmission between, plants. In this review, we have focused on plant viruses found in environmental waters and their detection. Infectious plant pathogenic viruses from at least 7 different genera have been found in aqueous environment. The majority of the plant pathogenic viruses so far recovered from environmental waters are very stable, they can infect plants via the roots without the aid of a vector and often have a wide host range. The release of such viruses from plants can lead to their dissemination in streams, lakes, and rivers, thereby ensuring the long-distance spread of viruses that otherwise, under natural conditions, would remain restricted to limited areas. The possible sources and survival of plant viruses in waters are therefore discussed. Due to the widespread use of hydroponic systems and intensive irrigation in horticulture, the review is focused on the possibility and importance of spreading viral infection by water, together with measures for preventing the spread of viruses. The development of new methods for detecting multiple plant viruses at the same time, like microarrays or new generation sequencing, will facilitate the monitoring of environmental waters and waters used for irrigation and in hydroponic systems. It is reasonable to expect that the list of plant viruses found in waters will thereby be expanded considerably. This will emphasize the need for further studies to determine the biological significance of water-mediated transport.
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Affiliation(s)
- Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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Xie Z, Fan Q, Liu J, Pang Y, Deng X, Xie Z, Liji X, Khan MI. Reverse transcription loop-mediated isothermal amplification assay for rapid detection of Bovine Rotavirus. BMC Vet Res 2012; 8:133. [PMID: 22894568 PMCID: PMC3599620 DOI: 10.1186/1746-6148-8-133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 06/29/2012] [Indexed: 11/27/2022] Open
Abstract
Background Bovine rotavirus (BRV) infection is common in young calves. This viral infection causes acute diarrhea leading to death. Rapid identification of infected calves is essential to control BRV successfully. Therefore development of simple, highly specific, and sensitive detection method for BRV is needed. Results A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed and optimized for rapid detection of BRV. Specific primer sets were designed to target the sequences of the VP6 gene of the neonatal calf diarrhea virus (NCDV) strain of BRV. The RT-LAMP assay was performed in a water bath for 60 minutes at 63°C, and the amplification products were visualized either directly or under ultraviolet light. This BRV specific RT-LAMP assay could detect 3.32 copies of subtype A BRV. No cross-reactions were detected with other bovine pathogens. The ability of RT-LAMP to detect bovine rotavirus was further evaluated with 88 bovine rectal swab samples. Twenty-nine of these samples were found to be positive for BRV using RT-LAMP. The BRV-specific-RT-LAMP results were also confirmed by real-time RT-PCR assay. Conclusions The bovine rotavirus-specific RT-LAMP assay was highly sensitive and holds promise as a prompt and simple diagnostic method for the detection of group A bovine rotavirus infection in young calves.
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Affiliation(s)
- Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, 51 You Ai Road, Nanning, Guangxi, 530001, China.
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Mukhopadhyay HK, Amsaveni S, Matta SL, Antony PX, Thanislass J, Pillai RM. Development and evaluation of loop-mediated isothermal amplification assay for rapid and sensitive detection of canine parvovirus DNA directly in faecal specimens. Lett Appl Microbiol 2012; 55:202-9. [PMID: 22748120 PMCID: PMC7197762 DOI: 10.1111/j.1472-765x.2012.03284.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aims: To develop a specific and highly sensitive loop‐mediated isothermal amplification (LAMP) technique for the rapid detection of canine parvovirus (CPV) DNA directly in suspected faecal samples of dogs by employing a simple method of template preparation. Methods and Results: LAMP reaction was developed by designing two sets of outer and inner primers, which target a total of six distinct regions on VP2 gene of CPV. The template DNA was prepared by a simple boiling and chilling method. Of the 140 faecal samples screened by the developed LAMP and the conventional PCR assays, 104 samples (74·28%) were found positive by LAMP, whereas 81 samples (57·85%) were found positive by PCR. The specificity of the LAMP assay was tested by cross‐examination of common pathogens of dogs and further confirmed by sequencing. The detection limit of the LAMP was 0·0001 TCID50 ml−1, whereas the detection limit of the PCR was 1000 TCID50 ml−1. Conclusions: The developed LAMP assay detects CPV DNA in faecal specimens directly within an hour by following a simple and rapid boiling and chilling method of template preparation. The result also shows that the developed LAMP assay is specific and highly sensitive in detecting CPV. Significance and Impact of the Study: The result indicates the potential usefulness of LAMP which is a simple, rapid, specific, highly sensitive and cost‐effective field‐based method for direct detection of CPV from the suspected faecal samples of dogs.
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Affiliation(s)
- H K Mukhopadhyay
- Department of Veterinary Microbiology, Rajiv Gandhi College of Veterinary and Animal Sciences, Puducherry, India.
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Nemoto M, Yamanaka T, Bannai H, Tsujimura K, Kondo T, Matsumura T. Development of a reverse transcription loop-mediated isothermal amplification assay for H7N7 equine influenza virus. J Vet Med Sci 2012; 74:929-31. [PMID: 22362254 DOI: 10.1292/jvms.11-0541] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting H7N7 equine influenza virus (EIV). The detection limit of the RT-LAMP assay was a virus dilution of 10(-4), which was 10 times more sensitive than that of Espline Influenza A&B-N and the same as that of reverse transcription polymerase chain reaction. The RT-LAMP assay specifically amplified H7N7 EIV strains but did not amplify several pathogens related to equine respiratory disease including H3N8 EIV strains. Because it provides ease of manipulation, the RT-LAMP assay is suitable for large-scale surveillance for H7N7 EIV. In addition, the combination of the H3N8 RT-LAMP assay, which was developed previously, with the H7N7 RT-LAMP assay should be useful to discriminate between H3N8 and H7N7 EIVs in clinical laboratories.
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Affiliation(s)
- Manabu Nemoto
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan.
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Hobo S, Niwa H, Oku K. Development and application of loop-mediated isothermal amplification methods targeting the seM gene for detection of Streptococcus equi subsp. equi. J Vet Med Sci 2011; 74:329-33. [PMID: 22032896 DOI: 10.1292/jvms.11-0317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) constitutes a potentially valuable diagnostic tool for rapid diagnosis of contagious diseases. In this study, we developed a novel LAMP method (seM-LAMP) to detect the seM gene of Streptococcus equi subsp. equi (S. equi), the causative agent of strangles in equids. The seM-LAMP successfully amplified the target sequence of the seM gene at 63°C within 60 min. The sensitivity of the seM-LAMP was slightly lower than the 2nd reaction of the seM semi-nested PCR. To evaluate the species specificity of the seM-LAMP, we tested 100 S. equi and 189 non-S. equi strains. Significant amplification of the DNA originating from S. equi was observed within 60 min incubation, but no amplification of non-S. equi DNA occurred. The results were identical to those of seM semi-nested PCR. To investigate the clinical usefulness of the methods, the seM-LAMP and the seM semi-nested PCR were used to screen 590 nasal swabs obtained during an outbreak of strangles. Both methods showed that 79 and 511 swabs were S. equi positive and negative, respectively, and the results were identical to those of the culture examination. These results indicate that the seM-LAMP is potentially useful for the reliable routine diagnosis of Streptococcus equi subsp. equi infections.
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Affiliation(s)
- Seiji Hobo
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, Shimotsuke-shi, Tochigi 329–0412, Japan.
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Development and evaluation of a reverse transcription loop-mediated isothermal amplification assay for H3N8 equine influenza virus. J Virol Methods 2011; 178:239-42. [PMID: 21907240 DOI: 10.1016/j.jviromet.2011.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 07/20/2011] [Accepted: 07/25/2011] [Indexed: 11/22/2022]
Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) was applied to the detection of equine influenza virus (EIV). Because equine influenza is caused currently by EIV of the H3H8 subtype, the RT-LAMP primer set was designed to target the hemagglutinin gene of this subtype. The detection limit of the RT-LAMP assay was a virus dilution of 10(-5); which was 10(3) times more sensitive than the Espline Influenza A&B-N test and 10 times more sensitive than a reverse transcription polymerase chain reaction (RT-PCR) assay. The specificity of the RT-LAMP assay was examined by using several equine pathogens and nasal swabs collected from horses with fever in 2010 after EIV was eradicated in Japan. No cross-reactions were observed. Using 100 nasal swabs collected from horses with fever during an EIV outbreak in 2007, the RT-LAMP assay detected EIV in 52 samples, whereas the Espline test and the RT-PCR assay detected EIV in only 17 and 41 samples, respectively. These results indicate that the RT-LAMP assay is specific for EIV and more sensitive than the Espline test and the RT-PCR assay. Because it provides high sensitivity and ease of manipulation without the need for a thermal cycler or gel electrophoresis, the RT-LAMP assay should be applicable for laboratory diagnosis of EIV.
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Gutiérrez-Aguirre I, Steyer A, Banjac M, Kramberger P, Poljšak-Prijatelj M, Ravnikar M. On-site reverse transcription-quantitative polymerase chain reaction detection of rotaviruses concentrated from environmental water samples using methacrylate monolithic supports. J Chromatogr A 2010; 1218:2368-73. [PMID: 21040925 DOI: 10.1016/j.chroma.2010.10.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/01/2010] [Accepted: 10/12/2010] [Indexed: 11/25/2022]
Abstract
Rotaviruses are the leading cause of gastroenteritis in children and they exist widely in water environments. Ingestion of 10-100 viral particles is enough to initiate disease, what calls for extremely sensitive detection methods. In this study we have confirmed the validity of a recently published method for rotavirus concentration and detection based on the combination of methacrylate monoliths and real-time reverse transcription-quantitative PCR (RT-qPCR). The method was used to concentrate rotaviruses from different tap water and environmental water samples collected in Slovenia within years 2007 and 2009. The performance of virus concentration using monolithic supports was improved in comparison to the one of tangential ultrafiltration upon application of both methods on a range of environmental samples. Several samples were successfully concentrated on-site after successful adaptation of the method to field requirements. In such on-site format, the combination of concentration using CIM and detection using RT-qPCR detected as low as 30 rotavirus particles/ml, spiked in an environmental water sample.
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Affiliation(s)
- Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
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Nemoto M, Hata H, Higuchi T, Imagawa H, Yamanaka T, Niwa H, Bannai H, Tsujimura K, Kondo T, Matsumura T. Evaluation of rapid antigen detection kits for diagnosis of equine rotavirus infection. J Vet Med Sci 2010; 72:1247-50. [PMID: 20453452 DOI: 10.1292/jvms.10-0064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluated antigen detection kits for human rotavirus with regard to their usefulness for diagnosing equine rotavirus infection. Limiting dilution analyses showed that of the seven kits investigated the Dipstick `Eiken' Rota (Dipstick) had the highest sensitivity to two serotypes of equine rotavirus. The Dipstick did not cross-react with several equine intestinal pathogens. An investigation using 249 fecal samples indicated that the sensitivity of the Dipstick was 81.9% and 47.3%, and its specificity was 98.2% and 99.0%, and its concordance rate was 92.8% and 68.3%, compared with values obtained using reverse transcription polymerase chain reaction and reverse transcription loop-mediated isothermal amplification, respectively. Although a negative result does not preclude the possibility of equine rotavirus infection, the Dipstick would be useful as routine test for diagnosing equine rotavirus infection in daily clinical practice because of its ease of handling.
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Affiliation(s)
- Manabu Nemoto
- Epizootic Research Center, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
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