Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays

• Published in: PloS one Vol. 6; no. 6; p. e21610
• Main Authors: Kim, Curi, Ahmed, Jamal A, Eidex, Rachel B, Nyoka, Raymond, Waiboci, Lilian W, Erdman, Dean, Tepo, Adan, Mahamud, Abdirahman S, Kabura, Wamburu, Nguhi, Margaret, Muthoka, Philip, Burton, Wagacha, Breiman, Robert F, Njenga, M Kariuki, Katz, Mark A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.06.2011; Public Library of Science (PLoS)
• Subjects: Adenoviruses; Adolescent; Avian flu; Cell culture; Child; Child, Preschool; Comparative analysis; Diagnosis; Disease control; Disease prevention; Female; Humans; Illnesses; Immunoassay; Infections; Influenza; Influenza A; Influenza B; Male; Medical diagnosis; Medical laboratories; Medical research; Medicine; Nasopharynx - virology; Nucleic acids; Oropharynx - virology; Pandemics; Parainfluenza; Patients; Polymerase chain reaction; Public health; Real time; Real-Time Polymerase Chain Reaction - methods; Respiratory diseases; Respiratory syncytial virus; Respiratory Tract Infections - diagnosis; Respiratory Tract Infections - virology; Reverse transcription; Sanitation; Sensitivity; Surveillance systems; Swine flu; Transcription (Genetics); Viral infections; Virology; Virus Diseases - diagnosis; Virus Diseases - virology; Viruses; Atlanta Georgia; Georgia; Kenya; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0021610

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. 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. 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. 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.