Application of recombinase polymerase amplification method for rapid detection of infectious laryngotracheitis virus

Infectious laryngotracheitis is a significant respiratory disease of chickens that causes huge economic losses due to high morbidity and mortality and reduced egg production. A real-time recombinase polymerase amplification (RPA) assay was developed to accurately detect ILTV. The specific probe and primer sets were carefully designed and screened. The real-time RPA assay was carried out at 39 °C for 30 min, and results were obtained within 15 min. The results of the specificity assay showed no fluorescence signals with other avian-related viruses. The sensitivity of the assay was 1 × 10² copies/μL. The low CV value showed that the assay was reproducible. A total of 115 clinical samples were tested using the real-time RPA assay and the real-time PCR assay in parallel; the coincidence rates of the two detection methods were 100%. The results indicated that the real-time RPA assay is a specific, sensitive, rapid, and useful tool for epidemiological studies and clinical diagnosis, especially in the field and in resource-poor areas.     

重组酶介导的蓝氏贾第鞭毛虫特异性等温核酸扩增方法的建立及评价

目的　建立基于重组酶介导的等温扩增技术（RAA）的蓝氏贾第鞭毛虫核酸检测方法,并评价其检测敏感性和特异性。方法　选择蓝氏贾第鞭毛虫β?贾第素（β?giardin）基因作为检测靶基因,设计、合成特异性检测引物及荧光探针,建立荧光RAA检测体系。分别以不同拷贝数的重组质粒（含β?giardin基因靶序列）和不同浓度蓝氏贾第鞭毛虫基因组DNA为模板进行荧光RAA扩增,评价其检测敏感性;分别以蓝氏贾第鞭毛虫、日本血吸虫、华支睾吸虫、微小隐孢子虫、似蚓蛔线虫、沙门氏菌及志贺氏菌基因组DNA为模板进行扩增,评价其检测特异性。结果　成功建立了蓝氏贾第鞭毛虫荧光RAA检测方法,其可在等温（39 ℃）条件下实现对靶基因片段的快速、特异性扩增（20 min内）。分别以重组质粒和蓝氏贾第鞭毛虫基因组DNA为模板,该方法的检测敏感性可达102拷贝/μL和1 pg/μL;以日本血吸虫、华支睾吸虫、微小隐孢子虫、似蚓蛔线虫、沙门氏菌及志贺氏菌基因组DNA为模板的RAA检测结果均为阴性,具备较好特异性。结论　建立了一种操作简便、敏感、特异的可用于蓝氏贾第鞭毛虫核酸检测的荧光RAA方法。     

基于重组酶介导核酸等温扩增反应的曼氏血吸虫 基因检测方法的建立

目的　建立一种可用于曼氏血吸虫特异性基因片段检测的重组酶介导的核酸等温扩增方法（Recombinase?aided amplification, RAA）。方法　以曼氏血吸虫121 bp高重复基因片段作为靶序列,根据RAA反应原理设计、合成引物及荧光探针,建立并优化荧光RAA法反应体系。分别以不同拷贝数的含121 bp基因片段的重组质粒及不同浓度曼氏血吸虫基因组DNA为模板进行荧光RAA法扩增,评价该方法的敏感性;分别以日本和埃及血吸虫虫卵、十二指肠钩虫虫卵、华支睾吸虫囊蚴基因组DNA为模板进行荧光RAA法检测,评价其特异性。结果　建立的荧光RAA法可在39 ℃、20 min内特异性扩增曼氏血吸虫基因组DNA。以重组质粒为模板,荧光RAA法最低可检出的质粒拷贝数为10拷贝/μL;以基因组DNA为模板,荧光RAA法最低可检测浓度为0.1 fg/μL。以日本血吸虫虫卵、埃及血吸虫虫卵、十二指肠钩虫虫卵、华支睾吸虫囊蚴基因组DNA为模板进行荧光RAA法检测,结果均为阴性。结论　成功建立了一种可用于曼氏血吸虫DNA检测的荧光RAA法,该方法反应快捷、操作简便,敏感性和特异性均较好。     

Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay

Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.     

重组酶介导的隐孢子虫属特异性等温核酸扩增 方法的建立及评价

目的　建立一种可用于隐孢子虫检测的重组酶介导的等温核酸扩增（RAA）方法,并对其检测敏感性和特异性进行评价。方法　以隐孢子虫属特异性18S rRNA核酸序列作为检测靶标,采用Amplfix软件设计、合成引物及荧光检测探针,构建并优化RAA荧光反应体系;分别以不同拷贝数的含18S rRNA靶序列的重组质粒、不同浓度隐孢子虫卵囊基因组DNA及不同数量隐孢子虫卵囊基因组DNA为模板进行RAA荧光法检测,以评价其敏感性;分别以隐孢子虫卵囊、蓝氏贾第鞭毛虫包囊、日本血吸虫虫卵、似蚓蛔线虫虫卵、华支睾吸虫虫卵、沙门氏菌、志贺氏菌基因组DNA为模板进行RAA荧光法检测,以评价其特异性。结果　成功建立了隐孢子虫检测RAA法,该方法可在39 ℃、20 min内得到隐孢子虫属18S rRNA基因片段的有效扩增。以不同拷贝数的含18S rRNA靶序列的重组质粒、不同浓度隐孢子虫卵囊基因组DNA及不同数量隐孢子虫卵囊基因组DNA为模板,该方法最低检出限分别为102拷贝/μL、1 pg/μL和1个/50 μL;以蓝氏贾第鞭毛虫包囊、日本血吸虫虫卵、似蚓蛔线虫虫卵、华支睾吸虫虫卵、沙门氏菌、志贺氏菌基因组DNA为模板的荧光RAA扩增结果均为阴性。结论　成功建立了一种可用于检测隐孢子虫卵囊DNA的RAA法,该方法操作简便、反应快速,敏感性和特异性均较好。     

Development and comparative evaluation of real-time PCR and real-time RPA assays for detection of tilapia lake virus

Tilapia lake virus (TiLV) is a newly emerged pathogen responsible for high mortality and economic losses in the global tilapia industry. Early and accurate diagnosis is an important priority for TiLV disease control. In order to evaluate the methodology in the molecular diagnosis of TiLV, we compared newly developed quantitative real-time PCR (qPCR) and real-time recombinase polymerase amplification (real-time RPA) assays regarding their sensitivities, specificities and detection effect on clinical samples. Real-time RPA amplified the target pathogen in less than 30 min at 39 °C with a detection limit of 620 copies, while qPCR required about 60 min with a detection limit of 62 copies. Both assays were specific for TiLV and there were no cross-reactions observed with other common fish pathogens. The assays were validated using 35 tissue samples from clinically infected and 60 from artificially infected animals. The sensitivities for the real-time RPA and qPCR assays were 93.33 and 100%, respectively, and the specificity was 100% for both. Both methods have their advantages and can play their roles in different situations. The qPCR is more suitable for quantitative analysis and accurate detection of TiLV in a diagnostic laboratory, whereas real-time RPA is more suitable for the diagnosis of clinical diseases and preliminary screening for TiLV infection in poorly equipped laboratories as well as in fish farms.     

重组酶聚合酶扩增技术在寄生虫快速检测中的应用

重组酶聚合酶扩增（recombinase polymerase amplification, RPA）是一种新型核酸等温扩增技术,具有特异性强、灵敏度高、恒温反应、操作简单和耗时短等优点。该技术自2006年面世以来,被逐渐应用于医学、食品安全、公共卫生和农业生产等领域。寄生虫病不仅会影响人畜健康,还阻碍经济发展,带来严重的社会问题。对寄生虫病实现准确而快速的诊断有助于推进该类疾病的治疗进程,最大程度降低危害。本文综述了RPA技术的反应原理、反应条件以及在寄生虫快速检测方面的应用,分析RPA技术在原虫、吸虫和线虫检测中的敏感性和特异性。在原虫检测方面,RPA技术较为成熟,它的灵敏度明显优于传统的检测方法。在吸虫检测方面,RPA技术的敏感性和特异性等于或优于传统的检测技术。RPA技术在线虫检测方面的灵敏度优于聚合酶链式反应。此外,本文还对该技术在寄生虫病防疫工作的应用前景进行了展望。     

Development of a recombinase polymerase amplification fluorescence assay to detect feline coronavirus

Feline coronavirus (FCoV) is classified into two pathotypes: the avirulent feline enteric coronavirus (FECV), and the virulent feline infectious peritonitis virus (FIPV). Rapid pathogen detection, which is efficient and convenient, is the best approach for early confirmatory diagnosis. In this study, we first developed and evaluated a rapid recombinase polymerase amplification (RPA) detection method for FCoV that can detect FCoV within 15 min at 39 °C. The detection limit of that assay was 233 copies/μL DNA molecules per reaction. The specificity was high: it did not cross-react with canine distemper virus (CDV), canine coronavirus (CCoV), canine adenovirus (CAV), feline calicivirus (FCV), feline herpesvirus (FHV), or feline parvovirus (FPV). This assay was evaluated using 42 clinical samples (30 diarrhea samples and 12 ascites samples). The coincidence rate between FCoV-RPA and RT-qPCR for detection in clinical samples was 95.2%. In summary, FCoV-RPA analysis provides an efficient, rapid, and sensitive detection method for FCoV.