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As the SARS‐CoV‐2 virus spread throughout the world, millions of positive cases of COVID‐19 were registered and, even though there are millions of people already vaccinated against SARS‐CoV‐2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS‐CoV‐2 molecular testing availability, we evaluated the diagnostic accuracy of self‐collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit to detect SARS‐CoV‐2. We also created a colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS‐CoV‐2, as another strategy to increase the availability of molecular testing in community‐based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS‐CoV‐2 on the 7500 Fast Dx RT‐PCR using the TaqPath RT‐PCR COVID‐19 molecular test. Data was interpreted by the COVID‐19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene‐Biomarks' SARS‐CoV‐2 Rapid Colorimetric LAMP LDT and the TaqPath RT‐PCR COVID‐19 test. Our results suggest that self‐collected saliva is superior to nasal and urine samples for COVID‐19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT‐PCR tests for the detection of SARS‐CoV‐2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics. [ABSTRACT FROM AUTHOR]

• α-diversity and evenness were higher in nasal lavage compared to nose swabs. • Only microbiome in nasal lavage correlated with upper airway inflammation. • Abundance of Moraxella was associated with higher inflammation in the upper airways. Cystic fibrosis (CF) is characterized by highly viscous mucus obstructing the lower and upper airways, chronic neutrophil inflammation and infection resulting not only in lung destruction but also in paranasal sinus involvement. The pathogenesis of CF-associated chronic rhinosinusitis (CRS) is still not well understood, and it remains unclear how the microbiome in the upper airways (UAW) influences paranasal sinus inflammation. In a cross-sectional study in pediatric patients with CF under stable disease conditions, we examined the microbiome in relation to inflammation by comparing nasal swabs (NS) and nasal lavage (NL) as two UAW sampling methods. The microbiota structure of both NS and NL was determined by 16S rRNA gene amplicon sequencing. In addition, pro-inflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α) and proteases (SLPI, TIMP-1, NE/A1-AT complex) as well as neutrophil elastase activity were measured in NL. Simultaneous NS and NL samples were collected from 36 patients with CF (age range: 7 – 19 years). The microbiome of NS samples was shown to be significantly lower in α-diversity and evenness compared to NL samples. NS samples were particularly found to be colonized with Staphylococcus species. NL microbiome was shown to correlate much better with the sinonasal inflammation status than NS microbiome. Especially the detection of Moraxella in NL was associated with increased inflammatory response. Our results show that the NL microbiome reflects sinonasal inflammation better than NS and support NL as a promising tool for simultaneous assessment of the UAW microbiome and inflammation in children with CF. [ABSTRACT FROM AUTHOR]

Background Respiratory viral shedding is incompletely characterized by existing studies due to the lack of longitudinal nasal sampling and limited inclusion of healthy/asymptomatic children. We describe characteristics associated with prolonged virus detection by polymerase chain reaction (PCR) in a community-based birth cohort. Methods Children were followed from birth to 2 years of age in the PREVAIL cohort. Weekly nasal swabs were collected and tested using the Luminex Respiratory Pathogen Panel. Weekly text surveys were administered to ascertain the presence of acute respiratory illnesses defined as fever and/or cough. Maternal reports and medical chart abstractions identified healthcare utilization. Prolonged virus detection was defined as a persistently positive test lasting ≥4 weeks. Factors associated with prolonged virus detection were assessed using mixed effects multivariable logistic regression. Results From a sub-cohort of 101 children with ≥70% weekly swabs collected, a total of 1489 viral infections were detected. Prolonged virus detection was found in 23.4% of viral infections overall, 39% of bocavirus infections, 33% of rhinovirus/enterovirus infections, 14% of respiratory syncytial virus (RSV) A infections, and 7% of RSV B infections. No prolonged detection was found for influenza virus A or B, coronavirus 229E or HKU1, and parainfluenza virus 2 or 4 infections. First-lifetime infection with each virus, and co-detection of another respiratory virus were significantly associated with prolonged detection, while symptom status, child sex, and child age were not. Conclusions Prolonged virus detection was observed in 1 in 4 viral infections in this cohort of healthy children and varied by pathogen, occurring most often for bocavirus and rhinovirus/enterovirus. Evaluating the immunological basis of how viral co-detections and recurrent viral infections impact duration of virus detection by PCR is needed to better understand the dynamics of prolonged viral shedding. [ABSTRACT FROM AUTHOR]

Abstract As the SARS‐CoV‐2 virus spread throughout the world, millions of positive cases of COVID‐19 were registered and, even though there are millions of people already vaccinated against SARS‐CoV‐2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS‐CoV‐2 molecular testing availability, we evaluated the diagnostic accuracy of self‐collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit to detect SARS‐CoV‐2. We also created a colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS‐CoV‐2, as another strategy to increase the availability of molecular testing in community‐based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS‐CoV‐2 on the 7500 Fast Dx RT‐PCR using the TaqPath RT‐PCR COVID‐19 molecular test. Data was interpreted by the COVID‐19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene‐Biomarks' SARS‐CoV‐2 Rapid Colorimetric LAMP LDT and the TaqPath RT‐PCR COVID‐19 test. Our results suggest that self‐collected saliva is superior to nasal and urine samples for COVID‐19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT‐PCR tests for the detection of SARS‐CoV‐2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.

Isolation of high quality and quantity genomic DNA is essential for molecular studies. It is crucial to select a non-invasive and straightforward technique to ensure the efficient collection of DNA, particularly at the farm level. The aim of this study was to determine if nasal swabs are an appropriate biological matrix to obtain good quality genomic DNA suitable for SNP genotyping. In this study, two biological matrices (blood and nasal swabs) were evaluated and compared for the isolation of genomic DNA obtained from 15 female Texel sheep. DNA quality and quantity were assessed using spectrophotometry and gel electrophoreses. Genotype concordance rates were used for comparison. Results showed that the highest concentration mean was obtained from blood samples (159.14 ng/µl), while from nasal swab samples the concentration mean was lower (130.12 ng/µl), but the difference was non-significant. Regarding purity, DNA obtained from nasal swabs presented a higher A260/A280 ratio (1.96), while the one obtained from blood samples was 1.90. Total DNA yield obtained from blood samples (15.91 µg) was significantly higher than the one obtained from nasal swabs (6.51). Blood and nasal swab genotyping concordance rates were high (mean = 0.984). In conclusion, our results indicate that nasal swabs can yield good quality DNA; however, the DNA extraction protocol should be optimized.

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for the detection of SARS-CoV-2, which we validated and applied to detect the virus in feline samples. The present study describes the application of the nested PCR test in parallel with LAMP for the detection of the virus in 427 nasopharyngeal and oropharyngeal human samples taken between October 2020 and January 2022. Of the swabs tested, there were 43 positives, accounting for 10.1% of all samples tested, with the negatives numbering 382, i.e., 89.5%, and there were 2 (0.4%) invalid ones. The nPCR results confirmed those obtained by using LAMP, with results concordant in both methods. Nasal swabs tested using nPCR confirmed the results of oropharyngeal and nasopharyngeal swab samples tested using LAMP and nPCR. The focus of the discussion is on the two techniques: the actual practical application of the laboratory-developed assays and the diagnostic value of nasal samples. The nPCR used is a reliable and sensitive technique for the detection of SARS-CoV-2 in nasopharyngeal, oropharyngeal, and nasal swab samples. However, it has some disadvantages related to the duration of the entire process, as well as a risk of contamination. Experiments were performed to demonstrate the infectivity of the virus from the positive isolates in vitro. A discrepancy was reported between direct and indirect methods of testing the virus and accounting for its ability to cause infection in vitro. [ABSTRACT FROM AUTHOR]

Usage of self‐screening tests has become increasingly relevant in public health perspective for early detection of SARS‐CoV‐2 infection in the transitioning era of the COVID‐19 pandemic into an endemic. This study was designed to compare the diagnostic accuracy of self‐conducted and health professional‐conducted SARS‐CoV‐2 rapid antigen tests (Ag‐RDTs) and whether the sample was taken from anterior nasal or nasal mid‐turbinate. Eligible comparative Ag‐RDTs accuracy studies were retrieved from electronic databases systematically, in accordance with PRISMA. Selected studies were assessed for risk of bias using QUADAS‐2 and QUADAS‐C. In total, we selected five out of 1952 studies retrieved using the keywords. The overall sensitivity for the self‐collected nasal swab method and healthcare worker‐collected nasopharyngeal swab method was 79% (95% CI 68–87; I2 = 62%) and 83% (95% CI 75–89; I2 = 32%), respectively, which was not statistically different (p = 0.499). Nasal mid‐turbinate swabs have a significantly higher sensitivity compared to anterior nasal swabs (p < 0.01). Both sampling methods represent high and comparable specificity values of 98% (95% CI 97–99; I2 = 0%) and 99% (95% CI 98–99; I2 = 0%). Positive predictive value (range 90%–99%) and negative predictive value (range 87%–98%) were equivalent for both methods. Our findings indicated the accuracy of self‐collected Ag‐RDT on nasal swabs was comparable to those performed by healthcare worker‐collected on nasopharyngeal swabs. Self‐collected Ag‐RDT could be considered as a transmission prevention method in the transition of COVID‐19 pandemic. [ABSTRACT FROM AUTHOR]

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for the detection of SARS-CoV-2, which we validated and applied to detect the virus in feline samples. The present study describes the application of the nested PCR test in parallel with LAMP for the detection of the virus in 427 nasopharyngeal and oropharyngeal human samples taken between October 2020 and January 2022. Of the swabs tested, there were 43 positives, accounting for 10.1% of all samples tested, with the negatives numbering 382, i.e., 89.5%, and there were 2 (0.4%) invalid ones. The nPCR results confirmed those obtained by using LAMP, with results concordant in both methods. Nasal swabs tested using nPCR confirmed the results of oropharyngeal and nasopharyngeal swab samples tested using LAMP and nPCR. The focus of the discussion is on the two techniques: the actual practical application of the laboratory-developed assays and the diagnostic value of nasal samples. The nPCR used is a reliable and sensitive technique for the detection of SARS-CoV-2 in nasopharyngeal, oropharyngeal, and nasal swab samples. However, it has some disadvantages related to the duration of the entire process, as well as a risk of contamination. Experiments were performed to demonstrate the infectivity of the virus from the positive isolates in vitro. A discrepancy was reported between direct and indirect methods of testing the virus and accounting for its ability to cause infection in vitro.

Background: Testing for SARS-CoV-2 is essential to provide early COVID-19 treatment for people at high risk of severe illness and to limit the spread of infection in society. Proper upper respiratory specimen collection is the most critical step in the diagnosis of the SARS-CoV-2 virus in public settings, and throat swabs were the preferred specimens used for mass testing in many countries during the COVID-19 pandemic. However, there is still a discussion about whether throat swabs have a high enough sensitivity for SARS-CoV-2 diagnostic testing, as previous studies have reported a large variability in the sensitivity from 52% to 100%. Many previous studies exploring the diagnostic accuracy of throat swabs lack a detailed description of the sampling technique, which makes it difficult to compare the different diagnostic accuracy results. Some studies perform a throat swab by only collecting specimens from the posterior oropharyngeal wall, while others also include a swab of the palatine tonsils for SARS-CoV-2 testing. However, studies suggest that the palatine tonsils could have a tissue tropism for SARS-CoV-2 that may improve the SARS-CoV-2 detection during sampling. This may explain the variation of sensitivity reported, but no clinical studies have yet explored the differences in sensitivity and patient discomfort whether the palatine tonsils are included during the throat swab or not., Objective: The objective of this study is to examine the sensitivity and patient discomfort of a throat swab including the palatine tonsils compared to only swabbing the posterior oropharyngeal wall in molecular testing for SARS-CoV-2., Methods: We will conduct a randomized controlled study to compare the molecular detection rate of SARS-CoV-2 by a throat swab performed from the posterior oropharyngeal wall and the palatine tonsils (intervention group) or the posterior oropharyngeal wall only (control group). Participants will be randomized in a 1:1 ratio. All participants fill out a baseline questionnaire upon enrollment in the trial, examining their reason for being tested, symptoms, and previous tonsillectomy. A follow-up questionnaire will be sent to participants to explore the development of symptoms after testing., Results: A total of 2315 participants were enrolled in this study between November 10, 2022, and December 22, 2022. The results from the follow-up questionnaire are expected to be completed at the beginning of 2024., Conclusions: This randomized clinical trial will provide us with information about whether throat swabs including specimens from the palatine tonsils will improve the diagnostic sensitivity for SARS-CoV-2 molecular detection. These results can, therefore, be used to improve future testing recommendations and provide additional information about tissue tropism for SARS-CoV-2., Trial Registration: ClinicalTrials.gov NCT05611203; https://clinicaltrials.gov/study/NCT05611203., International Registered Report Identifier (irrid): DERR1-10.2196/47446., (©Benedikte Hartvigsen, Kathrine Kronberg Jakobsen, Thomas Benfield, Niels Tobias Gredal, Annette Kjær Ersbøll, Mathias Waldemar Grønlund, Henning Bundgaard, Mikkel Porsborg Andersen, Nina Steenhard, Christian von Buchwald, Tobias Todsen. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 12.06.2024.)