Analysis of Factors Causing False-Negative Real-Time Polymerase Chain Reaction Results in Oropharyngeal and Nasopharyngeal Swabs of Patients With COVID-19

Abstract

Objectives: To analyze factors regarding patient characteristics, sampling techniques, and coronavirus disease 2019 (COVID-19) specific manifestations that may cause false-negative reverse-transcription polymerase chain reaction (RT-PCR). Materials and Methods: A cross-sectional study was conducted. For the diagnosis of COVID-19, patients with RT-PCR test positive in the first nasopharyngeal and oropharyngeal swabs were accepted as true positive, and patients with negative 3 consecutive swab results were considered true negative. Those who had a negative initial swab were considered false negatives if they subsequently tested positive on the second or third swab. Demographic data of the patients, the onset of the disease, presence of nasal septal deviation, presence of epistaxis, the clinician (otolaryngologist/other physicians [OP]) who collected the samples, and medical treatments for laryngopharyngeal reflux, allergic respiratory diseases, allergic rhinitis, which include proton pump inhibitors and nasal steroids (NS), were documented. The analysis of dependent variables was performed with the chi-square test. Binary logistic regression was performed for significant variables. Results: A total of 399 patients were included in the study, and 357 (89.5%) patients were detected as positive after 2 or 3 consecutive RT-PCR tests. The presence of ageusia, anosmia, and collecting the samples within 7 days following the onset of symptoms were determined as significant factors for positive RT-PCR results ( P = <.001; odds ratio [OR] = 6.2, 5.8, 11.6, respectively). The profession of the clinician (OP), NS use, and the presence of epistaxis were detected as significant factors for the false-negative RT-PCR results ( P < .001; OR = 2.3, 3.1, 8.7, respectively). Conclusions: Patient- and/or sample-related factors can affect RT-PCR results of possible COVID-19 cases. The presence of these factors can easily be determined in cases with high clinical suspicion and negative RT-PCR results. The presence of ageusia, anosmia, early sampling (<7days), and appropriate collection of swabs decrease false-negative RT-PCR results.