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An Age Dependent Pharyngeal Microbiota Signature Associated with SARS-CoV-2 Infection
12 Pages Posted: 30 Apr 2020More...
Background: One of the most striking aspects of the novel Corona Virus Disease 2019 (COVID-19) is the highly variable course of the disease, with the risk for a severe outcome increasing with age. As there is evidence for a role of the pharyngeal microbiota (PM) in susceptibility to other respiratory viral diseases, and their severity, the aim of this study was to identify specific PM associated with the presence or absence of SARS-CoV-2.
Methods: Throat swabs from 46 SARS-CoV-2 PCR positive and 89 SARS-CoV-2 PCR negative patients, presented at the Admiraal de Ruyter Hospital (Goes, The Netherlands) in the second half of March 2020, were used for microbial profiling. DNA was isolated and subjected to IS-pro, a rapid standardized microbiota analysis technique that differentiates bacterial species by length polymorphisms of the 16S-23S rDNA region combined by phylum specific sequence polymorphisms of the 16S rDNA.
Findings: A distinct homogeneous microbial cluster was found that contained a low percentage of positive SARS-CoV-2 PCR positive samples (25%). Remaining samples showed a less uniform microbiota and were almost twice as likely to be positive (25% vs 47%, p=0,008). The homogeneous cluster with low SARS-CoV-2 positivity was linearly less common with increasing age.
Interpretation: We found evidence for an association of the composition of the pharyngeal microbiota with SARS-CoV-2 infection. The observed age-dependency of the PM profile occurrence may explain the enhanced susceptibility of the elderly to COVID-19.
Funding Statement: Participating hospitals did not receive funding, inBiome provided microbiota analysis and data analysis. All parties had access to study data and were involved in all aspects of the study.
Declaration of Interests: Dr. Budding reports other from inBiome, during the conduct of the study; other from inBiome, outside the submitted work; In addition, Dr. Budding has a patent microbial community analysis (1) issued, a patent microbial community analysis (2) pending, and a patent Respiratory infectious disease triage pending. Dr. Sieswerda has nothing to disclose. Dr. Wintermans has nothing to disclose. Dr. Bos reports personal fees from InBiome, during the conduct of the study; personal fees from InBiome, outside the submitted work.
Ethics Approval Statement: The study was considered not to need ethical approval by the Brabant Medical Ethics Committee, Tilburg, the Netherlands (NW2020-30), as the study was retrospectively performed on residual sample material.
Keywords: pharyngeal microbiota; microbiota; microbiome; COVID19; SARS-CoV-2; coronavirus; IS-pro; diagnostics
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