Accuracy of antigen and nucleic acid amplification testing on saliva and naopharyngeal samples for detection of SARS-CoV-2 in ambulatory care

Background: Nasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the current standard diagnostic test for of coronavirus disease 2019 (COVID-19). However, the NAAT technique is lengthy and nasopharyngeal sampling requires trained personnel. Saliva NAAT represents an interesting alternative but diagnostic performances vary widely between studies. Objective: To assess the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as compared to nasopharyngeal NAAT. Design: Prospective participant enrollment from 19 October through 18 December 2020. Setting: Two community COVID-19 screening centers in Paris, France. Participants: 1452 ambulatory children and adults referred for SARS-CoV-2 testing. Interventions: NAAT on a saliva sample (performed with three different protocols for pre-processing, amplification and detection of SARS-CoV-2) and Ag testing on a nasopharyngeal sample. Measurements: Performance of saliva NAAT and nasopharyngeal Ag testing. Results: Overall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was of 94% (95% CI, 86% to 98%), 23% (CI, 14% to 35%), 94% (CI, 88% to 97%) and 96% (CI, 91% to 99%) for the nasopharyngeal Ag test and the three different protocols of saliva NAAT, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals. Limitations: Few children (n=122, 8%) were included. Conclusion: In the ambulatory setting, diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT seems similar to that of nasopharyngeal NAAT, subject to strict compliance with specific pre-processing and amplification protocols. Registration number: NCT04578509 Funding Sources: French Ministry of Health and the Assistance Publique-Hopitaux de Paris Foundation.

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A 30-Min Nucleic Acid Amplification Point-of-Care Test for Genital Chlamydia trachomatis Infection in Women: A Prospective, Multi-center Study of Diagnostic Accuracy

EBioMedicine ◽

10.1016/j.ebiom.2017.12.029 ◽

2018 ◽

Vol 28 ◽

pp. 120-127 ◽

Cited By ~ 12

Author(s):

E.M. Harding-Esch ◽

E.C. Cousins ◽

S.-L.C. Chow ◽

L.T. Phillips ◽

C.L. Hall ◽

...

Keyword(s):

Nucleic Acid ◽

Chlamydia Trachomatis ◽

Diagnostic Accuracy ◽

Point Of Care ◽

Nucleic Acid Amplification ◽

Chlamydia Trachomatis Infection ◽

Point Of Care Test ◽

Multi Center Study ◽

Center Study

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Paper-Based All-in-One Origami Microdevice for Nucleic Acid Amplification Testing for Rapid Colorimetric Identification of Live Cells for Point-of-Care Testing

Analytical Chemistry ◽

10.1021/acs.analchem.9b01263 ◽

2019 ◽

Vol 91 (17) ◽

pp. 11013-11022 ◽

Cited By ~ 8

Author(s):

Phuoc Tung Trieu ◽

Nae Yoon Lee

Keyword(s):

Nucleic Acid ◽

Point Of Care ◽

Nucleic Acid Amplification ◽

Live Cells ◽

Point Of Care Testing ◽

Nucleic Acid Amplification Testing

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A simple check valve for microfluidic point of care diagnostics

Lab on a Chip ◽

10.1039/c6lc01104g ◽

2016 ◽

Vol 16 (22) ◽

pp. 4436-4444 ◽

Cited By ~ 9

Author(s):

C. S. Ball ◽

R. F. Renzi ◽

A. Priye ◽

R. J. Meagher

Keyword(s):

Nucleic Acid ◽

Point Of Care ◽

Check Valve ◽

Nucleic Acid Amplification ◽

Nucleic Acid Amplification Testing ◽

Point Of Care Diagnostics

Laser cut microfluidic check valves enable staged reagent delivery, pumping, and point of care nucleic acid amplification testing.

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1346. Ruling out TB in New York City: Are Two NAATs (Nucleic Acid Amplification Testing) Enough?

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.1210 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S487-S488

Author(s):

William G Greendyke ◽

Janett Pike ◽

Lilibeth V Andrada ◽

Krystal Balzer ◽

Thelesha Gray ◽

...

Keyword(s):

New York ◽

New York City ◽

Nucleic Acid ◽

Diagnostic Accuracy ◽

York City ◽

Median Number ◽

Nucleic Acid Amplification ◽

Pulmonary Tb ◽

Nucleic Acid Amplification Testing ◽

Smear Negative

Abstract Background Prompt diagnosis of pulmonary Mycobacterium tuberculosis (TB) infection can prevent nosocomial exposure. However, sputum smears are insensitive, and turnaround time for cultures can take weeks. Rapid diagnostics, such as nucleic acid amplification testing (NAAT), on respiratory specimens of patients suspected to have TB can improve diagnostic accuracy. Current practice at our institution is to obtain ≥ 3 NAATs in high-risk patients prior to discontinuing airborne isolation, but some studies have suggested that 2 negative NAATs may be sufficient. We conducted a retrospective study of patients at our institution diagnosed with TB. Methods The study was conducted at an academic adult hospital, an academic pediatric hospital, and a community hospital in New York City. Line lists of positive cultures for TB and positive NAATs from 2014 to mid-2018 were obtained from microbiology. Chart review was performed. Patient demographics, comorbidities, and radiographic findings were collected. Concordance between culture results and NAATs was evaluated. Incidence of inpatient TB exposure was noted. Results 82 cases of TB were found in the study period (see Figure 1). 45 cases were new inpatient diagnoses of pulmonary TB. The most common presenting symptoms were cough (69%), weight loss (49%), and fever (42%, see Table 1). 38/45 (84%) of patients were originally from a country other than the United States. 43/45 (96%) of patients had abnormal lung imaging. Cavitary disease was seen in 29%; other upper lobe disease was seen in 42%. Among smear-negative pulmonary TB cases, NAAT was positive in 11/16 (69%) of patients. Within this subgroup, the sensitivity of one NAAT was 41% when compared with culture. In smear-negative, NAAT-positive patients, NAATs were fully concordant with cultures in 4/11 patients (36%, see Table 2). The median number of positive NAATs was 1; the median number of positive cultures was 2. Five patients with pulmonary TB had negative NAATs altogether (median = 3); 2/5 resulted in TB exposure investigations after airborne precautions were discontinued following NAAT results. Overall, 13/45 (28%) of new diagnoses resulted in an exposure investigation. Conclusion Obtaining ≥ 3 NAATs in patients suspected of pulmonary TB improved diagnostic accuracy compared with obtaining 2 or fewer. Disclosures All authors: No reported disclosures.

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A 30-minute nucleic acid amplification point-of-care test for genitalChlamydia trachomatisinfection in women: a prospective, multi-centre study of diagnostic accuracy

10.1101/196675 ◽

2017 ◽

Author(s):

EM Harding-Esch ◽

EC Cousins ◽

S-LC Chow ◽

LT Phillips ◽

CL Hall ◽

...

Keyword(s):

Nucleic Acid ◽

Diagnostic Accuracy ◽

Clinical Pathways ◽

Point Of Care ◽

Specific Treatment ◽

Nucleic Acid Amplification ◽

Clinical Samples ◽

Multi Centre Study ◽

Predictive Values ◽

Significant Difference

ABSTRACTBackgroundRapid Point-Of-Care Tests (POCTs) forChlamydia trachomatis(CT) may reduce onward transmission and reproductive sexual health (RSH) sequelae by reducing turnaround times between diagnosis and treatment. The io®single module system (Atlas Genetics Ltd) runs clinical samples through a microfluidic CT cartridge, delivering results in 30 minutes. We evaluated its performance on female genital samples in four UK Genito-Urinary Medicine (GUM)/RSH clinics.MethodsProspective diagnostic accuracy study, using BD ProbeTec CT/GC assay as the routine clinic nucleic acid amplification test (NAAT) as the initial comparator test, and the QIAgen Artus CT assay to resolve discrepancies. In these instances, the reference standard was defined as the resolved result when two out of three assay results concurred. Female participants aged ≥16 provided additional-to-routine self-collected vulvovaginal swabs. Samples were tested fresh with the io®CT assay within 7 days of collection, or were frozen at −80°C for later testing. Participant clinical, demographic and behavioural characteristics were collected to assess risk factors associated with CT infection.ResultsOf 785 participants recruited, final analyses were conducted on 709 (90.3%). CT prevalence was 7.2% (51/709) overall. Sensitivity, specificity, positive and negative predictive values of the io®CT assay were, respectively, 96.1% (95% Confidence Interval (CI): 86.5-99.5), 97.7% (95%CI: 96.3-98.7), 76.6% (95%CI: 64.3-86.2) and 99.7% (95%CI: 98.9-100). There was no significant difference in performance measures between fresh and frozen samples, or between symptomatic and asymptomatic participants (p>0.05). The only risk factor associated with CT infection was being a sexual contact of an individual with CT.ConclusionsThe io®CT-assay is the only 30-minute, fully automated, high-performing NAAT currently CE-marked for CT diagnosis in women, making it a highly promising diagnostic to enable specific treatment, initiation of partner notification and appropriately intensive health promotion at the point of care. Future research is required to evaluate acceptability by clinicians and patients in GUM/RSH clinics, impact on clinical pathways and patient management, and cost-effectiveness.

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