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.

Evaluation of Direct Detection Protocols for Poliovirus from Stool Samples of Acute Flaccid Paralysis Patients.

Polio surveillance in the Global Polio Eradication Initiative has been conducted with virus isolation from stool samples of acute flaccid paralysis (AFP) cases. Under the current biorisk management/regulations, challenges arise in the timelines of the report, sensitivity of the test and containment of poliovirus (PV) isolates. In the present study, we evaluated protocols of previously reported direct detection (DD) methods targeting the VP1 or VP4-VP2 regions of the PV genome in terms of sensitivity and sequencability. An optimized protocol targeting the entire-capsid region for the VP1 sequencing showed a high sensitivity (limit of detection = 82 copies of PV genome) with a simpler and faster reaction than reported ones (i.e., with the addition of all the primers at the start of the reaction, the RT-PCR reaction finishes within 2.5 h). The DD methods targeting the VP1 region detected PV in 60 to 80% of PV-positive stool samples from AFP cases; however, minor populations of PV strains in the samples with virus mixtures were missed by the methods. Sequencability of the DD methods was primarily determined by the efficiency of the PCRs for both Sanger and nanopore sequencing. The DD method targeting the VP4-VP2 region showed higher sensitivity than that targeting the VP1 region (limit of detection = 25 copies of PV genome) and successfully detected PV from all the stool samples examined. These results suggest that DD methods are effective for the detection of PV and that further improvement of the sensitivity is essential to serve as an alternative to the current polio surveillance algorithm.