Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from saliva

Three-way junction structure-mediated reverse transcription-free exponential amplification reaction for pathogen RNA detection

Since RNA is an important biomarker of many infectious pathogens, RNA detection of pathogenic organisms is crucial for disease diagnosis and environmental and food safety. By simulating the base mismatch during DNA replication, this study presents a novel three-way junction structure-mediated reverse transcription-free exponential amplification reaction (3WJ-RTF-EXPAR) for the rapid and sensitive detection of pathogen RNA. The target RNA served as a switch to initiate the reaction by forming a three-way junction (3WJ) structure with the ex-trigger strand and the ex-primer strand. The generated trigger strand could be significantly amplified through EXPAR to open the stem-loop structure of the molecular beacon to emit fluorescence signal. The proofreading activity of Vent DNA polymerase, in combination with the unique structure of 2+1 bases at the 3'-end of the ex-primer strand, could enhance the role of target RNA as a reaction switch to reduce non-specific amplification and ensure excellent specificity to differentiate target pathogen from those causing similar symptoms. Furthermore, detection of target RNA showed a detection limit of 1.0×104 copies/mL, while the time consumption was only 20 min, outperforming qRT-LAMP and qRT-PCR, the most commonly used RNA detection methods in clinical practice. All those indicates the great application prospects of this method in clinical diagnostic.

The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

Despite its prominence in early scientific records, the usefulness of saliva as a respiratory specimen has been de-emphasised over the past century. However, due to its low cost and reliance on specific supply chains and the non-invasive nature of its collection, its benefits over swab-based specimens are again becoming increasingly recognised. These benefits were highlighted over the course of the COVID-19 pandemic, where saliva emerged as a more practical, clinically non-inferior sample type for the detection of SARS-CoV-2 and saw numerous saliva-based diagnostic tests approved for clinical use. Looking forward, as saliva uniquely contains both respiratory secretions and immunological components, it has potentially wide applications, ranging from clinical diagnostics to post-vaccine disease burden and immunity surveillance. This Personal View seeks to summarise the existing evidence for the use of saliva in detecting respiratory pathogens, beyond SARS-CoV-2, as well as detailing methodological factors that can influence sample quality and thus, clinical utility.

Salivary SARS-CoV-2 RNA for diagnosis of COVID-19 patients: a systematic revisew and meta-analysis of diagnostic accuracy

Accurate, self-collected, and non-invasive diagnostics are critical to perform mass-screening diagnostic tests for COVID-19. This systematic review with meta-analysis evaluated the accuracy, sensitivity, and specificity of salivary diagnostics for COVID-19 based on SARS-CoV-2 RNA compared with the current reference tests using a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS). An electronic search was performed in seven databases to find COVID-19 diagnostic studies simultaneously using saliva and NPS/OPS tests to detect SARS-CoV-2 by RT-PCR. The search resulted in 10,902 records, of which 44 studies were considered eligible. The total sample consisted of 14,043 participants from 21 countries. The accuracy, specificity, and sensitivity for saliva compared with the NPS/OPS was 94.3% (95%CI= 92.1;95.9), 96.4% (95%CI= 96.1;96.7), and 89.2% (95%CI= 85.5;92.0), respectively. Besides, the sensitivity of NPS/OPS was 90.3% (95%CI= 86.4;93.2) and saliva was 86.4% (95%CI= 82.1;89.8) compared to the combination of saliva and NPS/OPS as the gold standard. These findings suggest a similarity in SARS-CoV-2 RNA detection between NPS/OPS swabs and saliva, and the association of both testing approaches as a reference standard can increase by 3.6% the SARS-CoV-2 detection compared with NPS/OPS alone. This study supports saliva as an attractive alternative for diagnostic platforms to provide a non-invasive detection of SARS-CoV-2.

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.

A Qualitative Evaluation of the Barriers and Enablers for Implementation of an Asymptomatic SARS-CoV-2 Testing Service at the University of Nottingham: A Multi-Site Higher Education Setting in England

Asymptomatic testing for SARS-CoV-2 RNA has been used to prevent and manage COVID-19 outbreaks in university settings, but few studies have explored their implementation. The aim of the study was to evaluate how an accredited asymptomatic SARS-CoV-2 testing service (ATS) was implemented at the University of Nottingham, a multi-campus university in England, to identify barriers and enablers of implementation and to draw out lessons for implementing pandemic response initiatives in higher education settings. A qualitative interview study was conducted with 25 ATS personnel between May and July 2022. Interviews were conducted online, audio-recorded, and transcribed. Participants were asked about their experience of the ATS, barriers and enablers of implementation. Transcripts were thematically analysed. There were four overarching themes: (1) social responsibility and innovation, (2) when, how and why people accessed testing, (3) impact of the ATS on the spread of COVID-19, and (4) lessons learned for the future. In establishing the service, the institution was seen to be valuing its community and socially responsible. The service was viewed to be broadly successful as a COVID-19 mitigation approach. Challenges to service implementation were the rapidly changing pandemic situation and government advice, delays in service accreditation and rollout to staff, ambivalence towards testing and isolating in the target population, and an inability to provide follow-up support for positive cases within the service. Facilitators included service visibility, reduction in organisational bureaucracy and red tape, inclusive leadership, collaborative working with regular feedback on service status, flexibility in service delivery approaches and simplicity of saliva testing. The ATS instilled a perception of early 'return to normality' and impacted positively on staff feelings of safety and wellbeing, with wider benefits for healthcare services and local communities. In conclusion, we identified common themes that have facilitated or hindered the implementation of a SARS-CoV-2 testing service at a university in England. Lessons learned from ATS implementation will inform future pandemic response interventions in higher education settings.

Progress in Biosensors for the Point-of-Care Diagnosis of COVID-19

Coronavirus disease 2019 (COVID-19) is a highly virulent infection that has caused a pandemic since 2019. Early diagnosis of the disease has been recognized as one of the important approaches to minimize the pathological impact and spread of infection. Point-of-care tests proved to be substantial analytical tools, and especially lateral flow immunoassays (lateral flow tests) serve the purpose. In the last few years, biosensors have gained popularity. These are simple but highly sensitive and accurate analytical devices composed from a selective molecule such as an antibody or antigen and a sensor platform. Biosensors would be an advanced alternative to current point-of-care tests for COVID-19 diagnosis and standard laboratory methods as well. Recent discoveries related to point-of-care diagnostic tests for COVID-19, the development of biosensors for specific antibodies and specific virus parts or their genetic information are reviewed.