A clinic-based direct real-time fluorescent reverse transcription loop-mediated isothermal amplification assay for influenza virus

Nanoparticle-Based Lateral Flow Biosensors Integrated With Loop-Mediated Isothermal Amplification for the Rapid and Visual Diagnosis of Hepatitis B Virus in Clinical Application

Hepatitis B virus (HBV) infection remains one of the major public health issues worldwide. Developing a rapid, sensitive, specific, easy-to-operate, and cost-saving approach for the diagnosis of HBV is essential for its therapy and prevention. Here, we first devised a novel approach, termed “loop-mediated isothermal amplification integrated with a nanoparticle-based lateral flow biosensor (LAMP-LFB),” for the detection of HBV in clinical application. The results indicated that a set of LAMP primers based on the S gene were valid for the establishment of HBV-LAMP-LFB. The optimal HBV-LAMP can be carried out at a constant temperature of 65°C for 40 min. The whole detection process, including HBV genomic DNA preparation (∼10 min), LAMP (40 min), and LFB reading (within 2 min), can be accomplished within 60 min. The limit of detection of the HBV-LAMP-LFB assay was 7.5 IU per test. The specificity of this assay was one hundred percent, and there was no cross-reactivity with other pathogens. Hence, these results indicated that the HBV-LAMP-LFB assay established in the current study is a sensitive, rapid, specific, visual, simple, and cost-saving method for the screening of HBV agents. More importantly, the HBV-LAMP-LFB has remarkable potential to develop a point-of-care testing in clinical application, especially in resource-scarce regions.

Isothermal amplification and fluorescent detection of SARS-CoV-2 and SARS-CoV-2 variant virus in nasopharyngeal swabs

The COVID-19 pandemic caused by the SARS-CoV-2 is a serious health threat causing worldwide morbidity and mortality. Real-time reverse transcription PCR (RT-qPCR) is currently the standard for SARS-CoV-2 detection. Although various nucleic acid-based assays have been developed to aid the detection of SARS-CoV-2 from COVID-19 patient samples, the objective of this study was to develop a diagnostic test that can be completed in 30 minutes without having to isolate RNA from the samples. Here, we present an RNA amplification detection method performed using reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions to achieve specific, rapid (30 min), and sensitive (<100 copies) fluorescent detection in real-time of SARS-CoV-2 directly from patient nasopharyngeal swab (NP) samples. When compared to RT-qPCR, positive NP swab samples assayed by fluorescent RT-LAMP had 98% (n = 41/42) concordance and negative NP swab samples assayed by fluorescent RT-LAMP had 87% (n = 59/68) concordance for the same samples. Importantly, the fluorescent RT-LAMP results were obtained without purification of RNA from the NP swab samples in contrast to RT-qPCR. We also show that the fluorescent RT-LAMP assay can specifically detect live virus directly from cultures of both SARS-CoV-2 wild type (WA1/2020), and a SARS-CoV-2 B.1.1.7 (alpha) variant strain with equal sensitivity to RT-qPCR. RT-LAMP has several advantages over RT-qPCR including isothermal amplification, speed (<30 min), reduced costs, and similar sensitivity and specificity.

Detection of swine influenza virus in nasal specimens by reverse transcription-loop-mediated isothermal amplification (RT-LAMP)

Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which provides results to the growers after some time which is generally too late to intercede in disease control. Moreover, current diagnostic assays are time-consuming, typically costly, and require skilled technical expertise. We have instituted a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay based on conserved regions of the SIV matrix (M) gene and H1N1 hemagglutinin (HA) sequences. The RT-LAMP assay was optimized to use both colorimetric and fluorescent endpoints and was validated. The M and HA RT-LAMP assays have a limit-of-detection (LOD) sensitive to 11 and 8-log-fold dilutions of viral RNA, respectively, and are capable of discriminating between H1 and H3 strains of SIV. Additionally, the RT-LAMP assay was optimized for direct amplification of SIV from field samples without the need for viral RNA isolation. The direct RT-LAMP detected >86 % of qRT-PCR validated SIV samples, and >66 % of negative samples when spiked with viral RNA or SIV. The diagnostic RT-LAMP assay is a rapid, sensitive, specific, and cost-effective method for the detection of SIV in herds substantially aiding diagnosis and surveillance.