An Ultra-Rapid Real-Time RT-PCR Method Using PCR1100 for Detecting Human Orthopneumovirus

Rapid multiplex real-time PCR assay using a portable device for the detection of oral pathogens

Colonization by several oral pathogens and the onset of oral diseases, such as dental caries and periodontal diseases, are closely related. Therefore, the analysis of pathogens in oral specimens would be helpful for the risk assessment of oral diseases. We developed a rapid multiplex real-time polymerase chain reaction (PCR) method using a portable device and newly designed probe/primer sets to detect the oral pathogens Streptococcus mutans, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The theoretical minimum detectable cell numbers of S. mutans, P. gingivalis, T. denticola, and T. forsythia were 1, 1, 4, and 3, respectively. The multiplex real-time PCR system simultaneously detected the colonization of S. mutans and P. gingivalis in human saliva. These results suggest that the multiplex real-time PCR system may be useful for the risk assessment of oral diseases.

Rapid and sensitive on-site detection of SARS-CoV-2 RNA from environmental surfaces using portable laboratory devices

IMPORTANCE

This study presents the development of a highly sensitive on-site method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA on various surfaces, including doorknobs and tables. Identifying SARS-CoV-2 RNA on these surfaces can be crucial in guiding decision-making for implementing non-pharmaceutical interventions, such as zoning strategies, improving ventilation, maintaining physical distancing, and promoting increased hand hygiene practices. Moreover, the on-site detection system can facilitate the swift initiation of mitigation responses in non-laboratory settings, including long-term care facilities and schools. The protocols established in this study offer a comprehensive approach for achieving both sensitivity and rapidity in on-site SARS-CoV-2 RNA detection. Furthermore, since the RT-qPCR assay serves as the gold standard for detecting viral RNAs, the developed protocol holds potential for application to other viruses, including enteroviruses and noroviruses.

Development of a duplex real-time RT-PCR assay for the detection and identification of two subgroups of human metapneumovirus in a single tube

Human metapneumovirus (hMPV) is a common cause of respiratory infections in children. Many genetic diagnostic assays have been developed, but most detect hMPV regardless of the subgroup. In this study, we developed a real-time RT-PCR assay that can detect and identify the two major subgroups of hMPV (A and B) in one tube. Primers and probes were designed based on the sequences of recent clinical isolates in Japan. The assay showed comparable analytical sensitivity to a previously reported real-time RT-PCR assay and specific reactions to hMPV subgroups. The assay also showed no cross-reactivity to clinical isolates of 19 species of other respiratory viruses. In a validation assay using post-diagnosed clinical specimens, 98% (167/170) positivity was confirmed for the duplex assay, and the three specimens not detected were of low copy number. The duplex assay also successfully distinguished the two major subgroups for all 12 clinical specimens, for which the subgroup had already been determined by genomic sequencing analysis. The duplex assay described here will contribute to the rapid and accurate identification and surveillance of hMPV infections.

Development of a Real-Time RT-PCR System Applicable for Rapid and Pen-Side Diagnosis of Foot-and-Mouth Disease Using a Portable Device, PicoGene® PCR1100

Foot-and-mouth disease (FMD) is a highly contagious viral vesicular disease, causing devastating losses to the livestock industry. A diagnostic method that enables quick decisions is required to control the disease, especially in FMD-free countries. Although conventional real-time reverse transcription polymerase chain reaction (RT-PCR) is a highly sensitive method widely used for the diagnosis of FMD, a time lag caused by the transport of samples to a laboratory may allow the spread of FMD. Here, we evaluated a real-time RT-PCR system using a portable PicoGene PCR1100 device for FMD diagnosis. This system could detect the synthetic FMD viral RNA within 20min with high sensitivity compared with a conventional real-time RT-PCR. Furthermore, the Lysis Buffer S for crude nucleic extraction improved the viral RNA detection of this system in a homogenate of vesicular epithelium samples collected from FMD virus-infected animals. Furthermore, this system could detect the viral RNA in crude extracts prepared using the Lysis Buffer S from the vesicular epithelium samples homogenized using a Finger Masher tube, which allows easy homogenization without any equipment, with a high correlation compared to the standard method. Thus, the PicoGene device system can be utilized for the rapid and pen-side diagnosis of FMD. (199 words).

Evaluation of a real-time mobile PCR device (PCR 1100) for the detection of the rabies gene in field samples

BACKGROUND

The Philippines is ranked among the top countries with 200-300 annual deaths due to rabies. Most human rabies cases have been reported in remote areas, where dog surveillance is inadequate. Therefore, a strategy to effectively improve surveillance in remote areas will increase the number of detections. Detecting pathogens using portable real-time reverse transcription-polymerase chain reaction (RT-PCR) has the potential to be accepted in these areas. Thus, we aimed to develop an assay to detect the rabies virus (RABV) genome by combining the robust primer system LN34 with the PicoGene PCR1100 portable rapid instrument targeting RABV RNA (PCR1100 assay).

METHODS

Procedures were optimised using an LN34 primer/probe set, KAPA3G Plant PCR Kit (KAPA Biosystems), FastGene Scriptase II (NIPPON Genetics), and an artificial positive control RNA.

RESULTS

Positive control RNA showed an analytical limit of detection of 10 copies/µL without false positivity, generating results in approximately 32 min. Compared to dFAT or RT-qPCR using field samples, the sensitivity and specificity of the PCR1100 assay were 100%, and even lower copy numbers (approximately 10 copies/µL) were detected.

CONCLUSIONS

This study demonstrated that the developed assay can detect rabies RNA in field samples. Because dog-mediated rabies is endemic in remote areas, the rapidity, mobility, and practicality of the PCR1100 assay as well as the high sensitivity of the LN34 system make it an ideal tool for the confirmation of rabies in these areas.

Improving the Detection Sensitivity of a New Rapid Diagnostic Technology for Severe Acute Respiratory Syndrome Coronavirus 2 Using a Trace Amount of Saliva

The early diagnosis and isolation of infected individuals with coronavirus disease 2019 (COVID-19) remain important. Although quantitative polymerase chain reaction (qPCR) testing is considered the most accurate test available for COVID-19 diagnosis, it has some limitations, such as the need for specialized laboratory technicians and a long turnaround time. Therefore, we have established and reported a rapid diagnostic method using a small amount of saliva as a sample using a lightweight mobile qPCR device. This study aimed to improve the existing method and increase the detection sensitivity and specificity. The detection specificity of CDC N1 and N2 was examined by improving qPCR reagents and polymerase chain reaction conditions for the previously reported method. Furthermore, the feasibility of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA was examined using both the previous method and the improved method in patients with COVID-19. The results showed that the improved method increased the specificity and sensitivity. This improved method is useful for the rapid diagnosis of SARS-CoV-2.

Practical Validation of United States Centers for Disease Control and Prevention Assays for the Detection of Human Respiratory Syncytial Virus in Pediatric Inpatients in Japan

The World Health Organization initiated a global surveillance system for respiratory syncytial virus (RSV) in 2015, and the pilot surveillance is ongoing. The real-time RT-PCR RSV assays (Pan-RSV and duplex assays) developed by the United States Centers for Disease Control and Prevention are applied as the standard assays. To introduce these as standard assays in Japan, their practicality was evaluated using 2261 specimens obtained from pediatric inpatients in Japan, which were collected from 2018 to 2021. Although the Pan-RSV and duplex assays had similar analytical sensitivities, they yielded 630 (27.9%) and 786 (34.8%) RSV-positive specimens, respectively (p < 0.001). Although sequencing analysis showed mismatches in the reverse primer used in the Pan-RSV assay, these mismatches did not affect its analytical sensitivity. The analysis of read numbers of RSV isolates from air−liquid interface culture of human bronchial/tracheal epithelial cells showed that the duplex assay had a greater number of reads than did the Pan-RSV assay. Therefore, the duplex assay has superior detection performance compared with the Pan-RSV assay, but the two assays have similar analytical sensitivities.

Feasibility of Rapid Diagnostic Technology for SARS-CoV-2 Virus Using a Trace Amount of Saliva

Containment of SARS-CoV-2 has become an urgent global issue. To overcome the problems of conventional quantitative polymerase chain reaction (qPCR) tests, we verified the usefulness of a mobile qPCR device that utilizes mouthwash to obtain a saliva sample with the aim of developing a rapid diagnostic method for SARS-CoV-2. First, we examined whether anyone could easily operate this device. Then, we examined whether RNA in the mouthwash could be detected in a short time. In addition, we investigated whether it was possible to diagnose SARS-CoV-2 infection using mouthwash obtained from COVID-19 patients undergoing hospitalization. The results revealed that all subjects were able to complete the operation properly without error. In addition, RNase P was detected in the mouthwash without pretreatment. The average detection time was 18 min, which is significantly shorter than conventional qPCR devices. Furthermore, this device detected SARS-CoV-2 in the mouthwash of a COVID-19 patient undergoing hospitalization. The above findings verified the efficacy of this diagnostic method, which had a low risk of infection, was technically simple, and provided stable results. Therefore, this method is useful for the rapid detection of SARS-CoV-2.

Performance evaluation of real-time RT-PCR assays for detection of severe acute respiratory syndrome coronavirus-2 developed by the National Institute of Infectious Diseases, Japan

Soon after the December 2019 outbreak of coronavirus disease 2019 in Wuhan, China, a protocol for real-time RT-PCR assay detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) was established by the National Institute of Infectious Diseases (NIID) in Japan. The protocol used Charité's nucleocapsid (Sarbeco-N) and NIID's nucleocapsid (NIID-N2) assays. During the following months, SARS-CoV-2 spread causing a global pandemic, and a variety of SARS-CoV-2 sequences were registered to public databases, such as the Global Initiative on Sharing All Influenza Data (GISAID). In this study, we evaluated the newly developed S2 assay (NIID-S2) to replace the Sarbeco-N assay and the performance of NIID-N2 and NIID-S2 assays, referring mismatches in the primer/probe targeted region. We found the analytical sensitivity and specificity of the NIID-S2 set were comparable to the NIID-N2 assay, and the detection rate for clinical specimens was identical to that of the NIID-N2 assay. Furthermore, among available sequences (approximately 192,000), the NIID-N2 and NIID-S2 sets had 2.6% and 1.2% mismatched sequences, respectively, although most of these mismatches did not affect the amplification efficiency, with the exception of the 3' end of the NIID-N2 forward primer. These findings indicate that the previously developed NIID-N2 assay remains suitable for the detection SARS-CoV-2 with support of the newly developed NIID-S2 set.

An Ultra-Rapid Real-Time RT-PCR Method Using the PCR1100 to Detect Severe Acute Respiratory Syndrome Coronavirus-2

The disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Wuhan, China, in December 2019, has rapidly spread worldwide. SARS-CoV-2 is usually detected via real-time reverse-transcription polymerase chain reaction (RT-PCR). However, the increase in specimen load in institutions/hospitals necessitates a simpler detection system. Here, we present an ultra-rapid, real-time RT-PCR assay for SARS-CoV-2 detection using PCR1100 device. Although PCR1100 tests only one specimen at a time, the amplification period is less than 20 min and the sensitivity and specificity match those of conventional real-time RT-PCR performed on large instruments. The method is potentially helpful when daily multiple SARS-CoV-2 testing is needed, for example to confirm virus-free status prior to patient discharge.