New method for the visual detection of human respiratory syncytial virus using reverse transcription loop-mediated amplification

Microfluidic-based virus detection methods for respiratory diseases

With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.

A mismatch-tolerant RT-quantitative PCR: application to broad-spectrum detection of respiratory syncytial virus

Quantitative PCR (qPCR) is widely used to detect viruses. However, mismatches occurring in the 3'-end of the primers reduce amplification efficiency of qPCR and limit its capacity in detection of highly variable viruses. Here, we reported a mismatch-tolerant RT-qPCR with a small amount of additional high-fidelity DNA polymerase for simultaneous detection of RSV-A and RSV-B. The novel assay had higher amplification efficiency for various variants forming mismatches with the primers than the conventional RT-qPCR, and showed good specificity and sensitivity. It demonstrated a good correlation coefficient with a commercial RSV detection kit and had relatively lower Ct values than the kit for 16 of 20 RSV-positive samples. The mismatch-tolerant qPCR technique is a promising approach for sensitive detection of highly variable viruses.

Evaluation of a loop-mediated isothermal amplification method for rapid detection of human respiratory syncytial virus in children with acute respiratory infection

Introduction: Human respiratory syncytial virus (hRSV) is the most frequent cause of acute respiratory infection of the lower respiratory tract in children under the age of five. The development of molecular techniques able to identify hRSV is one of the current challenges in the field of clinical research. Objective: To evaluate the ability of an isothermal amplification method to rapidly detect hRSV in children with acute respiratory infection. Materials and methods: We collected 304 nasopharyngeal swab samples from children with symptoms of acute respiratory infection who attended the emergency unit at Hospital de la Universidad del Norte in Barranquilla from April, 2016, to July, 2017. After extracting viral RNA from the samples, we evaluated the ability of the reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) M assay to rapidly detect hRSVA and hRSVB compared to other molecular techniques: quantitative PCR (qPCR), reverse transcriptase-LAMP L assay, and as a standard, the multiplex nested reverse transcriptase polymerase chain reaction (nested RT-PCR). Results: The RT-LAMP M assay had a sensitivity of 93.59% and a specificity of 92.92%, and a concordance of 0.83 ± 0.036 as compared with the nested RT-PCR test. While the Kappa index of the RT-LAMP M assay was higher than the values for the RT-LAMP L assay and the qPCR, the values of the latter two methods were in agreement (0.75 ± 0.043 and 0.71 ± 0.045, respectively). Conclusion: Due to the shorter running times, lower costs and better performance of the RT-LAMP M assay, it can be considered as a useful clinical tool for the detection of RSVA.

Development of a duplex reverse transcription recombinase-aided amplification assay for respiratory syncytial virus incorporating an internal control

Human respiratory syncytial virus (RSV) is a common viral pathogen that causes lower respiratory tract infections in infants and children globally. In this study, we developed a duplex reverse transcription recombinase-aided amplification (duplex-rtRAA) assay containing an internal control in a single closed tube for the detection of human RSV. The internal control in the amplification effectively eliminated false-negative results and ensured the accuracy of the duplex-rtRAA system. We first developed and evaluated a universal singleplex-rtRAA assay for RSV. The sensitivity of this assay for RSV was determined as 4.4 copies per reaction, and the specificity was 100%. Next, a duplex-rtRAA assay with an internal control was established. The sensitivity of the duplex-rtRAA assay approached 5.0 copies per reaction, and no cross-reaction with other common respiratory viruses was observed. The two detection methods (singleplex-rtRAA and duplex-rtRAA) developed in this study were used to test 278 clinical specimens, and the results showed absolute consistency with RSV RT-qPCR analysis, demonstrating 100% diagnostic sensitivity and specificity. These data indicate that the duplex-rtRAA has great potential for the rapid detection of RSV with a high sensitivity.

Development of a reverse transcription recombinase polymerase amplification assay for rapid detection of human respiratory syncytial virus

Respiratory syncytial virus (RSV) is one of the most important causative agents that causing respiratory tract infection in children and associated with high morbidity and mortality. A diagnostic method would be a robust tool for identification of RSV infection, especially in the resource-limited settings. Recombinase polymerase amplification (RPA) is a novel isothermal amplification technique which has been widely employed to detect human/animal pathogens. In present study, a probe-based reverse transcription RPA (RT-RPA) assay was established for the detection of RSV. The primers and probe were designed based on the sequences of the conserved nucleocapsid (N) gene. The minimal detection limit of the RT-RPA assay for the detection of RSV B was 19 copies of RNA molecules at 95% probability, whereas the detection limit for RSV A was 10⁴ copies molecule. The assay was RSV-specific since it had no non-specific reactions with other common human pathogens. The clinical performance of the RT-RPA assay was validated using 188 nasopharyngeal aspirates (NPAs). The nucleic acid extraction of the samples was performed by use of the magnetic bead-based kit which didn't require the heavy and expensive centrifuge. The coincidence rates between RT-RPA and qRT-PCR for the clinical samples was 96%, indicating the RT-RPA assay had good diagnostic performance on clinical samples. The real-time RT-RPA assay combined with the manual genome extraction method make it potential to detect clinical samples in field, providing a possible solution for RSV diagnosis in remote rural areas in developing countries.

Risk of respiratory syncytial virus infection in preterm infants: reviewing the need for prevention

Premature infants are at substantial risk for a spectrum of morbidities that are gestational age dependent. Respiratory syncytial virus (RSV) infection is most common in the first two years of life with the highest burden in children aged <6 months. Preterm infants ≤35 weeks' gestation are handicapped by incomplete immunological and pulmonary maturation and immature premorbid lung function with the added risk of bronchopulmonary dysplasia. Superimposed RSV infection incites marked neutrophilic airway inflammation and innate immunological responses that further compromise normal airway modeling. This review addresses the epidemiology and burden of RSV disease, focusing on the preterm population. Risk factors that determine RSV-disease severity and hospitalization and the impact on healthcare resource utilization and potential long-term respiratory sequelae are discussed. The importance of disease prevention and the evidence-based rationale for prophylaxis with palivizumab is explored, while awaiting the development of a universal vaccine.