Abstract
BackgroundThe upper respiratory tract (URT) is the portal of entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-CoV-2 likely interacts with the URT microbiome. However, understanding of the associations between the URT microbiome and the severity of coronavirus disease 2019 (COVID-19) is still limited.ObjectiveOur primary objective was to identify URT microbiome signature/s that consistently changed over a spectrum of COVID-19 severity.MethodsUsing data from 103 adult participants from two cities in the United States, we compared the bacterial load and the URT microbiome between five groups: 20 asymptomatic SARS-CoV-2-negative participants, 27 participants with mild COVID-19, 28 participants with moderate COVID-19, 15 hospitalized patients with severe COVID-19, and 13 hospitalized patients in the ICU with very severe COVID-19.ResultsURT bacterial load, bacterial richness, and within-group microbiome composition dissimilarity consistently increased as COVID-19 severity increased, while the relative abundance of an amplicon sequence variant (ASV), Corynebacterium_unclassified.ASV0002, consistently decreased as COVID-19 severity increased.ConclusionsWe observed that the URT microbiome composition significantly changed as COVID-19 severity increased. The URT microbiome could potentially predict which patients may be more likely to progress to severe disease or be modified to decrease severity. However, further research in additional longitudinal cohorts is needed to better understand how the microbiome affects COVID-19 severity.
Highlights
The upper respiratory tract (URT) microbiome is an important contributor to respiratory health (Man et al, 2017)
The URT microbiome is an important contributor to respiratory health (Man et al, 2017), impacts the severity of other respiratory viruses, and can influence acute immune response (Ederveen et al, 2018; Shilts et al, 2020), and the URT is a major portal of entry for this virus (Gallo et al, 2020)
To better understand how the URT microbiome could impact COVID-19 severity and outcomes, our study showed that URT bacterial load, richness, and within-group dissimilarity increased, while the relative abundance of a Corynebacterium amplicon sequence variant (ASV) decreased, as COVID19 severity increased
Summary
The upper respiratory tract (URT) microbiome is an important contributor to respiratory health (Man et al, 2017). Understanding of the association of the URT microbiome with clinical outcomes related to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)—the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic—is limited, despite the URT being a major portal of entry for this virus (Gallo et al, 2020). While previous research has focused mostly on comparing the respiratory microbiome during COVID-19 to uninfected controls (De Maio et al, 2020; Shen et al, 2020; Zhang et al, 2020; Haiminen et al, 2021; Maes et al, 2021; Nardelli et al, 2021; Rosas-Salazar et al, 2021; Xu et al, 2021), studies examining the association between the URT microbiome and COVID-19 severity have been limited far (Mostafa et al, 2020; Hernández-Terán et al, 2021; Li et al, 2021; Merenstein et al, 2021; Rueca et al, 2021; Ventero et al, 2021). Understanding of the associations between the URT microbiome and the severity of coronavirus disease 2019 (COVID-19) is still limited
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