Dataset Information

Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study.

ABSTRACT: We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collected specimens to determine adequacy, defined as Cycle threshold less than 38. Overall, staff- and participant-collected specimens were 99.9% and 96.4% adequate, respectively. Participant-collected midturbinate specimens were 95.2% adequate in year one, increasing to 97.2% in year two with anterior nasal collection. The mean human ribonuclease P Cycle threshold for participant-collected specimens was 31.18 in year one and 28.48 in year two. The results from this study suggest that community-based participant collection of respiratory specimens is comparable to staff-collected oropharyngeal specimens, is feasible, and may be optimal with anterior nasal collection.

SUBMITTER: Arnold MT

PROVIDER: S-EPMC7540885 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study.

Arnold Mitchell T MT Temte Jonathan L JL Barlow Shari K SK Bell Cristalyne J CJ Goss Maureen D MD Temte Emily G EG Checovich Mary M MM Reisdorf Erik E Scott Samantha S Guenther Kyley K Wedig Mary M Shult Peter P Uzicanin Amra A

PloS one 20201007 10

We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collec ...[more]

PMID: 33027284

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Project description:The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).

Project description:ImportanceSelf- or health care worker (HCW)-collected nasal swab specimens are the preferred sampling method to perform rapid antigen testing for COVID-19, but it is debated whether throat specimens can improve test sensitivity.ObjectiveTo compare the diagnostic accuracy of self- and HCW-collected nasal vs throat swab specimens for COVID-19 rapid antigen testing.Design, setting, and participantsThis per-protocol multicenter randomized clinical trial was conducted from February 15 through March 25, 2022. The participants, individuals aged 16 years or older requesting a COVID-19 test for diagnostic or screening purposes, had 4 specimens collected for individual testing at 1 of 2 urban COVID-19 outpatient test centers in Copenhagen, Denmark.InterventionsParticipants were randomized 1:1 to self-collected or HCW-collected nasal and throat swab specimens for rapid antigen testing. Additional HCW-collected nasal and throat swab specimens for reverse transcriptase-polymerase chain reaction (RT-PCR) were used as the reference standard.Main outcomes and measuresThe primary outcome was sensitivity to diagnose COVID-19 of a self- vs HCW-collected nasal and throat specimen for rapid antigen testing compared with RT-PCR.ResultsOf 2941 participants enrolled, 2674 (90.9%) had complete test results and were included in the final analysis (1535 [57.4%] women; median age, 40 years [IQR, 28-55 years]); 1074 (40.2%) had COVID-19 symptoms, and 827 (30.9%) were positive for SARS-CoV-2 by RT-PCR. Health care worker-collected throat specimens had higher mean sensitivity than HCW-collected nasal specimens for rapid antigen testing (69.4% [95% CI, 65.1%-73.6%] vs 60.0% [95% CI, 55.4%-64.5%]). However, a subgroup analysis of symptomatic participants found that self-collected nasal specimens were more sensitive than self-collected throat specimens for rapid antigen testing (mean sensitivity, 71.5% [95% CI, 65.3%-77.6%] vs 58.0% [95% CI, 51.2%-64.7%]; P < .001). Combining nasal and throat specimens increased sensitivity for HCW- and self-collected specimens by 21.4 and 15.5 percentage points, respectively, compared with a single nasal specimen (both P < .001).Conclusions and relevanceThis randomized clinical trial found that a single HCW-collected throat specimen had higher sensitivity for rapid antigen testing for SARS-CoV-2 than a nasal specimen. In contrast, the self-collected nasal specimens had higher sensitivity than throat specimens for symptomatic participants. Adding a throat specimen to the standard practice of collecting a single nasal specimen could improve sensitivity for rapid antigen testing in health care and home-based settings.Trial registrationClinicalTrials.gov Identifier: NCT05209178.

Project description:Since December 2019, SARS-CoV-2 infection has been still rapidly spreading, resulting in a pandemic, followed by an increasing number of cases in countries throughout the world. The severity of the disease depends on the patient's overall medical condition but no appropriate markers are available to establish the prognosis of the patients. We performed a 16S rRNA gene sequencing, revealing an altered composition of the nasal/oropharyngeal (NOP) microbiota in 21 patients affected by COVID-19, paucisymptomatic or in an Intensive Care Unit (ICU), as compared to 10 controls negative for COVID-19 or eight affected by a different Human Coronavirus (HKU, NL63 and OC43). A significant decrease in Chao1 index was observed when patients affected by COVID-19 (in ICU) were compared to paucisymptomatic. Furthermore, patients who were in ICU, paucisymptomatic or affected by other Coronaviruses all displayed a decrease in the Chao1 index when compared to controls, while Shannon index significantly decreased only in patients under ICU as compared to controls and paucisymptomatic patients. At the phylum level, Deinococcus-Thermus was present only in controls as compared to SARS-CoV-2 patients admitted to ICU, paucisymptomatic or affected by other coronaviruses. Candidatus Saccharibacteria (formerly known as TM7) was strongly increased in negative controls and SARS-CoV-2 paucisymptomatic patients as compared to SARS-CoV-2 ICU patients. Other modifications were observed at a lower taxonomy level. Complete depletion of Bifidobacterium and Clostridium was exclusively observed in ICU SARS-CoV-2 patients, which was the only group characterized by the presence of Salmonella, Scardovia, Serratia and Pectobacteriaceae. In conclusion, our preliminary results showed that nasal/oropharyngeal microbiota profiles of patients affected with SARS-CoV-2 may provide valuable information in order to facilitate the stratification of patients and may open the way to new interventional strategies in order to ameliorate the outcome of the patients.

Dataset Information

Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study.

Publications

Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study.

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