title: Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays.
abstract: BACKGROUND
  Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP) and/or oropharyngeal (OP) swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens.
  
  
  METHODS
  We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Positivity for a specific virus was defined as detection of viral nucleic acid in either swab.
  
  
  RESULTS
  Of 2,331 paired NP/OP specimens, 1,402 (60.1%) were positive for at least one virus, and 393 (16.9%) were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01) and 2009 pandemic influenza A (H1N1) virus (91.2% vs. 70.4%, p<0.01). NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02), parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01), and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01). The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2) virus, parainfluenza virus 1, or respiratory syncytial virus.
  
  
  CONCLUSIONS
  The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.
authors: U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
authors: Curi
authors: C
authors: Kim
authors: Jamal A
authors: JA
authors: Ahmed
authors: Rachel B
authors: RB
authors: Eidex
authors: Raymond
authors: R
authors: Nyoka
authors: Lilian W
authors: LW
authors: Waiboci
authors: Dean
authors: D
authors: Erdman
authors: Adan
authors: A
authors: Tepo
authors: Abdirahman S
authors: AS
authors: Mahamud
authors: Wamburu
authors: W
authors: Kabura
authors: Margaret
authors: M
authors: Nguhi
authors: Philip
authors: P
authors: Muthoka
authors: Wagacha
authors: W
authors: Burton
authors: Robert F
authors: RF
authors: Breiman
authors: M Kariuki
authors: MK
authors: Njenga
authors: Mark A
authors: MA
authors: Katz
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D005260:Female; D006801:Humans; D008297:Male; D009305:Nasopharynx / Q000821:virology*; D009960:Oropharynx / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000821:virology*; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology