Carlos Grijalva
Last active: 7/27/2018

Concordance between RT-PCR-based detection of respiratory viruses from nasal swabs collected for viral testing and nasopharyngeal swabs collected for bacterial testing.

Grijalva CG, Griffin MR, Edwards KM, Johnson M, Gil AI, Ver√°stegui H, Lanata CF, Williams JV
J Clin Virol. 2014 60 (3): 309-12

PMID: 24875136 · PMCID: PMC4055503 · DOI:10.1016/j.jcv.2014.04.011

BACKGROUND - Epidemiologic studies of respiratory infections frequently rely on separate sample collections for the detection of bacteria and viruses. The requirement for two specimens presents cost, logistical, and acceptability challenges.

OBJECTIVES - To determine the agreement in detection of respiratory viruses using RT-PCR between two different types of samples collected on the same day: nasal swabs preserved in viral transport medium (NS) and nasopharyngeal swabs preserved in skim milk-tryptone-glucose-glycerol [STGG] medium (NP), the current standard for pneumococcal colonization studies.

STUDY DESIGN - Paired NS and NP samples were collected between May 2009 and September 2011 as part of the RESPIRA-PERU study, a large prospective cohort of Andean children <3 years of age. NS samples used polyester swabs and viral transport medium whereas NP samples used rayon wire-handled swabs and STGG medium. Samples were tested for influenza, human metapneumovirus (MPV), respiratory syncytial virus (RSV), human rhinovirus (HRV), parainfluenza virus 3 (PIV3) and adenovirus (ADV) using real-time RT-PCR. We calculated the agreement, and compared cycle thresholds (CT) between NP and NS samples.

RESULTS - Among 226 paired NP-NS samples, we observed very high agreement with a Kappa statistic ranging from 0.71 for ADV to 0.97 for MPV. CT values were similar for both strategies.

CONCLUSIONS - NP samples preserved in STGG provide a simple and reliable strategy for identification of both pneumococcus and respiratory viruses. This single specimen collection strategy could be used for epidemiologic studies, especially in resource-limited settings. Furthermore, archived NP-STGG specimens from previous studies could be reliably tested by RT-PCR for viruses.

Copyright © 2014 Elsevier B.V. All rights reserved.

MeSH Terms (8)

Bacteria Humans Nasopharynx Reproducibility of Results Respiratory Tract Infections Reverse Transcriptase Polymerase Chain Reaction Sensitivity and Specificity Viruses

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