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Abstract

The world has experienced several waves of SARS-CoV-2 variants of concern (VoCs) throughout the COVID-19 pandemic since the first cases in December 2019. The Omicron VoC has increased transmission, compared to its predecessors, and can present with sore throat and other cold-like symptoms. Given the predominance of throat symptoms, and previous work demonstrating better sensitivity using antigen-based rapid detection tests when a throat swab is included in the standard nasal sampling, this quality improvement project sought to ensure ongoing suitability of both combined oropharyngeal/nares (OPN) and nasopharyngeal (NP) swab sampling used throughout the pandemic. Consenting participants meeting Public Health testing criteria (mostly symptomatic or a close contact of a known case) were enrolled, and paired NP and OPN swabs were subjected to nucleic acid amplification testing (NAAT). Comparing paired specimens from 392 participants sensitivity of NP swabs was 89.1 % (95 % CI, 78.8–94.9), and that of OPN was 98.4 % (95 % CI: 90.9->99.9) (-value 0.052). This project demonstrated that both NP and combined OPN swabs detected the Omicron variant with similar sensitivity by NAAT, supporting the continued use of either swab collection for SARS-CoV-2 molecular detection.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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/content/journal/jmm/10.1099/jmm.0.001545
2022-06-07
2022-06-25
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References

  1. Bwire GM, Majigo MV, Njiro BJ, Mawazo A. Detection profile of SARS-CoV-2 using RT-PCR in different types of clinical specimens: A systematic review and meta-analysis. J Med Virol 2021; 93:719–725 [View Article] [PubMed]
    [Google Scholar]
  2. LeBlanc JJ, Heinstein C, MacDonald J, Pettipas J, Hatchette TF et al. A combined oropharyngeal/nares swab is A suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2. J Clin Virol 2020; 128:104442 [View Article] [PubMed]
    [Google Scholar]
  3. Patriquin G, Davis I, Heinstein C, MacDonald J, Hatchette TF et al. Exploring alternative swabs for use in SARS-CoV-2 detection from the oropharynx and anterior nares. J Virol Methods 2020; 285:113948 [View Article] [PubMed]
    [Google Scholar]
  4. World Health Organization Tracking SARS-CoV-2 variants; 2022 https://www.who.int/emergencies/what-we-do/tracking-SARS-CoV-2-variants
  5. Collie S, Champion J, Moultrie H, Bekker LG, Gray G. Effectiveness of BNT162b2 Vaccine against Omicron Variant in South Africa. N Engl J Med 2022; 386:494–496 [View Article] [PubMed]
    [Google Scholar]
  6. Araf Y, Akter F, Tang Y-D, Fatemi R, Parvez MSA et al. Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines. J Med Virol 2022; 94:1825–1832 [View Article] [PubMed]
    [Google Scholar]
  7. CDC COVID-19 Response Team SARS-CoV-2 B.1.1.529 (Omicron) Variant - United States, December 1-8, 2021. MMWR Morb Mortal Wkly Rep 2021; 70:1731–1734 [View Article] [PubMed]
    [Google Scholar]
  8. Huang N, Pérez P, Kato T, Mikami Y, Okuda K et al. SARS-CoV-2 infection of the oral cavity and saliva. Nat Med 2021; 27:892–903 [View Article] [PubMed]
    [Google Scholar]
  9. Marais G, Hsiao N, Iranzadeh A, Doolabh D, Enoch A et al. Saliva swabs are the preferred sample for Omicron detection. medRxiv 2021 [View Article]
    [Google Scholar]
  10. Iacobucci G. Covid-19: Runny nose, headache, and fatigue are commonest symptoms of omicron, early data show. BMJ 2021; 375:3103 [View Article] [PubMed]
    [Google Scholar]
  11. Adamson B, Sikka R, Wyllie AL, Premsrirut P. Discordant SARS- CoV- 2 PCR and rapid antigen test results when infectious: a December 2021 occupational case series. medRxiv [Preprint] 2022 [View Article]
    [Google Scholar]
  12. Goodall BL, LeBlanc JJ, Hatchette TF, Barrett L, Patriquin G. Investigating sensitivity of nasal or throat (ISNOT): a combination of both swabs increases sensitivity of SARS-CoV-2 rapid antigen tests. medRxiv [Preprint] 2022 [View Article]
    [Google Scholar]
  13. LeBlanc JJ, Pettipas J, Di Quinzio M, Hatchette TF, Patriquin G. Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: A three-headed comparison on multiple molecular platforms. J Virol Methods 2021; 295:114184 [View Article] [PubMed]
    [Google Scholar]
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