Direct detection of SARS-CoV-2 antisense and sense genomic RNA in human saliva by semi-autonomous fluorescence in situ hybridization: A proxy for contagiousness?

Use of high-resolution fluorescence in situ hybridization for fast and robust detection of SARS-CoV-2 RNAs

Early, rapid, and accurate diagnostic tests play critical roles not only in the identification/management of individuals infected by SARS-CoV-2, but also in fast and effective public health surveillance, containment, and response. Our aim has been to develop a fast and robust fluorescence in situ hybridization (FISH) detection method for detecting SARS-CoV-2 RNAs by using an HEK 293 T cell culture model. At various times after being transfected with SARS-CoV-2 E and N plasmids, HEK 293 T cells were fixed and then hybridized with ATTO-labeled short DNA probes (about 20 nt). At 4 h, 12 h, and 24 h after transfection, SARS-CoV-2 E and N mRNAs were clearly revealed as solid granular staining inside HEK 293 T cells at all time points. Hybridization time was also reduced to 1 h for faster detection, and the test was completed within 3 h with excellent results. In addition, we have successfully detected 3 mRNAs (E mRNA, N mRNA, and ORF1a (-) RNA) simultaneously inside the buccal cells of COVID-19 patients. Our high-resolution RNA FISH might significantly increase the accuracy and efficiency of SARS-CoV-2 detection, while significantly reducing test time. The method can be conducted on smears containing cells (e.g., from nasopharyngeal, oropharyngeal, or buccal swabs) or smears without cells (e.g., from sputum, saliva, or drinking water/wastewater) for detecting various types of RNA viruses and even DNA viruses at different timepoints of infection.

Advances in Viral Aquatic Animal Disease Knowledge: The Molecular Methods' Contribution

Aquaculture is the fastest-growing food-producing sector, with a global production of 122.6 million tonnes in 2020. Nonetheless, aquatic animal production can be hampered by the occurrence of viral diseases. Furthermore, intensive farming conditions and an increasing number of reared fish species have boosted the number of aquatic animals' pathogens that researchers have to deal with, requiring the quick development of new detection and study methods for novel unknown pathogens. In this respect, the molecular tools have significantly contributed to investigating thoroughly the structural constituents of fish viruses and providing efficient detection methods. For instance, next-generation sequencing has been crucial in reassignment to the correct taxonomic family, the sturgeon nucleo-cytoplasmic large DNA viruses, a group of viruses historically known, but mistakenly considered as iridoviruses. Further methods such as in situ hybridisation allowed objectifying the role played by the pathogen in the determinism of disease, as the cyprinid herpesvirus 2, ostreid herpesvirus 1 and betanodaviruses. Often, a combination of molecular techniques is crucial to understanding the viral role, especially when the virus is detected in a new aquatic animal species. With this paper, the authors would critically revise the scientific literature, dealing with the molecular techniques employed hitherto to study the most relevant finfish and shellfish viral pathogens.

Evaluation of a fluorescence in situ hybridization (FISH)-based method for detection of SARS-CoV-2 in saliva

The use of a non-invasive fluorescence in situ hybridization (FISH)-based method on saliva for the detection of SARS-CoV-2 is evaluated in a proof-of-concept study and thereafter utilized in an outpatient setting with the Biotrack-MED® analyzer. For a proof-of-concept study, saliva samples were obtained from 28 persons with mild or moderate COVID-19-related symptoms who were tested RT-PCR positive or negative for SARS-CoV-2. In an outpatient setting, 972 individual saliva samples were utilized. All saliva samples were FISHed with a Cy3-labeled SARS-CoV-2-specific DNA probe and were analyzed manually by fluorescence microscopy (proof-of-concept) or with the SARS-CoV-2 application of the Biotrack-MED® analyzer, a semi-autonomous multi-sample filter cytometer. The proof-of-concept study showed a sensitivity of 96.0% and a specificity of 98.5% and is therefore comparable to the RT-PCR analysis of nasopharyngeal swabs. The outpatient setting showed a sensitivity of 90.9% and a specificity of 94.5% and seems therefore a valid assay for the detection of SARS-CoV-2 in individuals that are healthy, mild or moderate symptomatic. In conclusion, the method evaluated in this study, the FISH-based SARS-CoV-2 application of the Biotrack-MED® analyzer, is a sensitive and reliable assay for the detection of SARS-CoV-2 in the general population.

Utilization of rapid antigen tests for screening SARS-CoV-2 prior to dental treatment

Potential aerosols containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles can be generated during dental treatment. Hence, patient triage is essential to prevent the spread of SARS-CoV-2 in dental clinical settings. The present study described the use of rapid antigen tests for SARS-CoV-2 screening prior to dental treatment in an academic dental clinical setting in Thailand during the pandemic. The opinions of dental personnel toward the use of rapid antigen test screening prior to dental treatment were also assessed. From August 25 to October 3, 2021, dental patients who were expected to receive aerosols generating dental procedures were requested to screen for SARS-CoV-2 using a rapid antigen test before their treatment. A total of 7,618 cases completed the screening process. The average was 212 cases per day. Only five patients (0.07%) were positive for SARS-CoV-2 in the rapid antigen screening tests. All positive cases exhibited mild symptoms. For the questionnaire study, experienced dental personnel frequently and consistently agreed with the use of the rapid antigen test for SARS-CoV-2 screening, which made them feel safer during their patient treatment. However, implementing rapid antigen tests for SARS-CoV-2 may increase the total time spent on a dental appointment. In conclusion, a rapid antigen test could detect the infected individual prior to dental treatment. However, the specificity of rapid antigen tests for SARS-CoV-2 must be taken into account for consideration as a screening process before dental treatment. The enhanced infection control protocols in dental treatment must be consistently implemented.

Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward

Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.