Head-to-head comparison of nasal and nasopharyngeal sampling using SARS-CoV-2 rapid antigen testing in Lesotho

• DOI: 10.1371/journal.pone.0278653
• Publication Date: 2023-03-02T18:34:39Z
• Authors: Niklaus D. Labhardt; Lucia González Fe...; Bulemba Katende; Josephine Muhairwe; Moniek Bresser; Alain Amstutz; Tracy R. Glass; Morten Ruhwald; Jilian A. Sacks; Camille Escadafal; Mathabo Mareka; Sekhele M. Mooko; Margaretha de Vos; Klaus Reither
• Keywords: Adult; Male; Radiology, Nuclear Medicine and Imaging; Epidemiology; Science; Infectious disease (medical specialty); Nose; FOS: Health sciences; Diagnostic Methods for COVID-19 Detection; Filter (signal processing); 03 medical and health sciences; Head (geology); Nasopharynx; Virology; Health Sciences; Epidemiology and Pathogenesis of Respiratory Viral Infections; Pathology; Humans; Disease; Child; Biology; 0303 health sciences; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Q; R; COVID-19; Paleontology; Applications of Deep Learning in Medical Imaging; Sampling (signal processing); 16. Peace & justice; Computer science; 3. Good health; Lesotho; Coronavirus disease 2019 (COVID-19); Infectious Diseases; Medicine; Female; Computer vision; Research Article

Objectives To assess the real-world diagnostic performance of nasal and nasopharyngeal swabs for SD Biosensor STANDARD Q COVID-19 Antigen Rapid Diagnostic Test (Ag-RDT).

Methods Individuals ≥5 years with COVID-19 compatible symptoms or history of exposure to SARS-CoV-2 presenting at hospitals in Lesotho received two nasopharyngeal and one nasal swab. Ag-RDT from nasal and nasopharyngeal swabs were performed as point-of-care on site, the second nasopharyngeal swab used for polymerase chain reaction (PCR) as the reference standard.

Results Out of 2198 participants enrolled, 2131 had a valid PCR result (61% female, median age 41 years, 8% children), 84.5% were symptomatic. Overall PCR positivity rate was 5.8%. The sensitivity for nasopharyngeal, nasal, and combined nasal and nasopharyngeal Ag-RDT result was 70.2% (95%CI: 61.3–78.0), 67.3% (57.3–76.3) and 74.4% (65.5–82.0), respectively. The respective specificity was 97.9% (97.1–98.4), 97.9% (97.2–98.5) and 97.5% (96.7–98.2). For both sampling modalities, sensitivity was higher in participants with symptom duration ≤ 3days versus ≤ 7days. Agreement between nasal and nasopharyngeal Ag-RDT was 99.4%.

Conclusions The STANDARD Q Ag-RDT showed high specificity. Sensitivity was, however, below the WHO recommended minimum requirement of ≥ 80%. The high agreement between nasal and nasopharyngeal sampling suggests that for Ag-RDT nasal sampling is a good alternative to nasopharyngeal sampling.