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A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients.

Author(s): Ek P, Böttiger B, Dahlman D, Hansen KB, Nyman M, Nilsson AC

Publication: Infect Dis (Lond), 2019, Vol. 51, Page 241-248

PubMed ID: 30760088 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared the diagnosis of respiratory viruses by real-time PCR using oropharyngeal specimens to nasopharyngeal specimens. Patient discomfort with both collection methods was also assessed. Specimens were collected from 98 patients aged ≥18 years presenting with acute onset of cough, sore throat, dyspnoea, and/or rhinitis at the emergency department of Skåne University Hospital in Malmo, Sweden. A nasopharyngeal specimen was obtained as standard protocol by a nurse inserting a flocked nylon swab into the nasopharynx and rotating it twice. The same nurse then inserted a new swab into the oropharynx and stroked it twice on the back of the oropharyngeal wall. Swabs were put in separate sterile test tubes containing saline solution and frozen at -20°C until analysis. RNA was extracted using the MagNA Pure 96 system. Influenza AH1, AH3, and B; human metapneumovirus (hMPV); and respiratory syncytial virus (RSV) were detected using a multiplex real-time RT-PCR assay. Differences in viral load were determined by comparison of Ct values with differences >3 cycles considered significant. Patients were asked to rate discomfort during specimen collection for each method using an arbitrary rating scale of 1–4 (1=no discomfort and 4=intolerable discomfort).

   Summary of Findings:

   Respiratory viruses were detected by real-time RT-PCR in 58 patients (10 influenza AH1, 13 influenza AH3, 13 influenza B, 7 hMPV, and 6 RSV) with the same virus being detected in both nasopharyngeal and oropharyngeal specimens in 42/58 patients (72%), a virus detected in the nasopharynx but not in the oropharynx in 10 patients (2 influenza AH1, 5 influenza AH3, and 3 influenza B), and in the oropharynx but not in the nasopharynx in 6 patients (3 influenza AH1, 1 influenza B, and 2 hMPV). There was no statistically significant difference in viral detection rate between the nasopharyngeal and oropharyngeal specimens but using both specimen types significantly increased viral detection rate (P=0.031). Ct values for viral RNA were lower in the nasopharyngeal specimen than the matched oropharyngeal specimen in 38 of the 55 patients in which CT values were available (11 influenza AH1, 12 influenza AH3, 7 influenza B, 4 RSV, and 4 hMPV) and were lower in the oropharyngeal specimen for 7/55 patients (3 influenza AH1, 1 influenza AH3, 1 influenza B, 1 RSV, and 1 hMPV). There was no significant difference (<3 cycles) in Ct values for viral RNA between specimen collection types in 10 patients (5 influenza AH1, 4 influenza B, and 1 hMPV). For the 10 patients considered virus positive only in the nasopharyngeal specimen, the viral load was considered high (Ct value <30) in six cases and low (Ct value ≥35) in four cases. For the six patients considered virus positive based only on the oropharyngeal specimen, the viral load was considered high in two specimens, medium high (Ct value 30–35) in one specimen, and low in three specimens. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling (P<0.001) with 47 patients (57%) reporting mild or no discomfort from nasopharyngeal sampling and 75 (91%) rating the discomfort from the oropharyngeal sampling as non-existent or mild.

   Biospecimens

   • Cell - Nasopharynx

   Preservative Types

   • Frozen

   Diagnoses:

   • Other diagnoses

   Platform:

   Analyte	Technology Platform
   RNA	Real-time qRT-PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Nasopharynx Oropharynx

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