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

Curi Kim; Jamal A Ahmed; Rachel B Eidex; Raymond Nyoka; Lilian W Waiboci; Dean Erdman; Adan Tepo; Abdirahman S Mahamud; Wamburu Kabura; Margaret Nguhi; Philip Muthoka; Wagacha Burton; Robert F Breiman; M Kariuki Njenga; Mark A Katz

doi:10.1371/journal.pone.0021610

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

Journal article

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

Curi Kim, Jamal A Ahmed, Rachel B Eidex, Raymond Nyoka, Lilian W Waiboci, Dean Erdman, Adan Tepo, Abdirahman S Mahamud, Wamburu Kabura, Margaret Nguhi, …

PloS one, Vol.6(6), pp.e21610-e21610

2011

DOI: https://doi.org/10.1371/journal.pone.0021610

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https://hdl.handle.net/2376/109377

PMCID: PMC3128075

PMID: 21738731

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Abstract

Humans

Real-Time Polymerase Chain Reaction - methods

Child, Preschool

Male

Virus Diseases - virology

Respiratory Tract Infections - diagnosis

Oropharynx - virology

Virus Diseases - diagnosis

Nasopharynx - virology

Adolescent

Female

Respiratory Tract Infections - virology

Child

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.

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Title: Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays
Creators: Curi Kim - U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
Jamal A Ahmed
Rachel B Eidex
Raymond Nyoka
Lilian W Waiboci
Dean Erdman
Adan Tepo
Abdirahman S Mahamud
Wamburu Kabura
Margaret Nguhi
Philip Muthoka
Wagacha Burton
Robert F Breiman
M Kariuki Njenga
Mark A Katz
Publication Details: PloS one, Vol.6(6), pp.e21610-e21610
Academic Unit: Paul G. Allen School for Global Animal Health
Publisher: United States
Identifiers: 99900546921001842
Language: English
Resource Type: Journal article