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Volume 9, Issue 2

Upper respiratory tract microbiota dynamics following COVID-19 in adults Open Access

Abstract

To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75–46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=−13.30; 95 % CI=−21.72 to −4.88; =0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA <0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one ASV, , and one ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family ) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): airway , coronavirus , COVID-19 , microbiota , nasal , respiratory and SARS-CoV-2
Funding
This study was supported by the:
  • National Heart, Lung, and Blood Institute (Award K23HL148638)
    • Principle Award Recipient: ChristianRosas-Salazar
  • Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (Award R21AI149262)
    • Principle Award Recipient: SumanRanjan Das
  • Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (Award R21AI154016)
    • Principle Award Recipient: SumanRanjan Das
  • Centers for Disease Control and Prevention (Award 75D3012110094)
    • Principle Award Recipient: SumanRanjan Das
  • Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (Award R21AI142321)
    • Principle Award Recipient: DasSuman RanjanRosas-SalazarChristian
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2023-02-23
2024-04-23
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Upper respiratory tract microbiota dynamics following COVID-19 in adults
M Gen 9, 000957 (2023); https://doi.org/10.1099/mgen.0.000957
/content/journal/mgen/10.1099/mgen.0.000957
/content/journal/mgen/10.1099/mgen.0.000957
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