Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

  1. Matthew F. Flynn
  2. Martin Kelly
  3. James S. G. Dooley

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Abstract

Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.

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  1. Version published to 10.3390/pathogens10111515
  2. ScreenIT

    SciScore for 10.1101/2020.10.21.20216077: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Cochrane CENTRAL, MEDLINE and Embase were searched, followed by supplemental exploration of reference lists of other reviews for focused optimization of search saturation.
    Cochrane CENTRAL
    suggested: (Cochrane Central Register of Controlled Trials, RRID:SCR_006576)
    MEDLINE
    suggested: (MEDLINE, RRID:SCR_002185)
    Embase
    suggested: (EMBASE, RRID:SCR_001650)
    Data Extraction: The following data were collated onto a Microsoft Excel spreadsheet: Publication year, number of participants, collection type, separate nostrils used, age of population, transport medium, analysis technique, swab type and type and quantity of microbiota detected.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    Sensitivity analysis and McNemars’ test for paired samples were derived using Medcalc and Scistat online statistical software respectively50,51.
    Medcalc
    suggested: (MedCalc, RRID:SCR_015044)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitations of current literature: The Cochrane rapid review protocol proved a portable and efficient mode of prompt evidence synthesis for this timely clinical question, purely with the use of open access freeware. This protocol maintains a moderate degree of quality assessment while removing full search saturation and streamlining study selection and data extraction. As rapid reviews are an evolving methodology, it is unclear the extent to which methodological omissions compromise the saturation of these results71. The clinical application of viral detection is not straightforward. Such techniques detect only pathogen carriage and do not demonstrate fulminant respiratory disease. Variations in viral shedding in the upper respiratory tract include: a shorter time to peak viral concentrations in saliva in SARS-CoV-19 compared to severe acute respiratory syndrome (SARS) (5 days vs 7-10 days), and completed viral shedding of Influenzavirus in adults is only completed around 5-7 days compared to infectivity persisting beyond 10 days in infants72,73,74. The Attributable Fraction, namely the percentage of times a disease is caused by a detected virus ranges from 12% for Rhinovirus to 93% for Respiratory Syncytial Virus75. Thus, even truly reliable results only contribute to a dynamic clinical picture. Need for better understanding of anatomy of the nose in the literature is also called for. “Nasopharyngeal swabs” are not purely so, as the NP cannot be reached except via contact wi...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.10.21.20216077 on medRxiv