Comparison of Nasopharyngeal and Oropharyngeal Swabs for the Diagnosis of Eight Respiratory Viruses by Real-Time Reverse Transcription-PCR Assays

Abstract

BackgroundMany 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.MethodsWe 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.ResultsOf 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.ConclusionsThe 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.

Etiology of Pediatric Fever in Western Kenya: A Case–Control Study of Falciparum Malaria, Respiratory Viruses, and Streptococcal Pharyngitis

“…The samples were then tested via real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) using the AgPath-ID One-Step RT-PCR Kit (Applied Biosystems, Carlsbad, CA) for eight viral pathogens (adenovirus, influenza A and B viruses, hMPV, PIV 1-3, and RSV) as previously described. 20 For purposes of immediate patient care, thick and thin blood smears were prepared and stained with 5% Giemsa and read by a laboratory technician. PCR was subsequently performed on whole blood from all patients who provided a whole blood sample (N = 401) using a real-time PCR assay targeting the P. falciparum lactate dehydrogenase (pfldh) gene on genomic DNA (gDNA) extracted from whole blood using Chelex-100 (Sigma-Aldrich, St. Louis, MI).…”

Respiratory syncytial virus and adenovirus in acute lower respiratory infections in hospitalized infants and children

“…However, using both swabs adds costs and patient discomfort. Results from a recent study suggest that a single-swab, whether oropharyngeal or nasopharyngeal could be acceptable for respiratory disease surveillance [23]. For the preceeding reasons and the relative scarcity of our population sample, our results should be interpreted with caution.…”

“…Sampling could influence the frequency of detection of RSV and HAdV [23]. Recently it has been reported that oropharyngeal swabs were more sensitive than nasopharyngeal swabs for detecting HAdV whereas com-parable for detecting RSV [23].…”

Detección de virus parainfluenza en pacientes inmunocomprometidos e inmunocompetentes atendidos en un hospital terciario de la Ciudad de São Paulo, Brasil

“…Las muestras fueron procesadas utilizando protocolos publicados anteriormente 7 . La RT-qPCR (RPC en tiempo real) para los cuatro 8 ; para el VPI-3 se utilizó partidores y sondas específicas para este de acuerdo a Kim, 2011 9 . Las curvas estándares específicas para determinar el límite de detección se llevó a cabo mediante la clonación de los productos de VPI RPC usando kit comercial (TOPO PCR Cloning, Life Technologies, Carlsbad, USA®).…”