SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

卷:147

Article

Rosas-Salazar, Christian¹  Kimura, Kyle S.²  Shilts, Meghan H.³  Strickland, Britton A.^3,4  Freeman, Michael H.²  Wessinger, Bronson C.⁵  Gupta, Veerain⁵  Brown, Hunter M.³  Rajagopala, Seesandra V.³  Turner, Justin H.²  Das, Suman R.^2,3 

[1] Vanderbilt Univ, Med Ctr, Div Allergy Immunol & Pulm Med, Dept Pediat, Nashville, TN 37235 USA

[2] Vanderbilt Univ, Med Ctr, Dept Otolaryngol Head & Neck Surg, 1215 21st Ave South,Med Ctr East,Ste 7209, Nashville, TN 37235 USA

[3] Vanderbilt Univ, Med Ctr, Dept Med, Div Infect Dis, 1161 21st Ave South,Med Ctr North,Ste A2200, Nashville, TN 37232 USA

[4] Vanderbilt Univ, Med Ctr, Dept Pathol Microbiol & Immunol, Nashville, TN USA

[5] Vanderbilt Univ, Sch Med, Nashville, TN 37212 USA

关键词: 16S rRNA sequencing;    coronavirus;    COVID-19;    microbiome;    nasal;    nasopharynx;    respiratory;    SARS-CoV-2;   

DOI  :  10.1016/j.jaci.2021.02.001

来源: Elsevier

【 摘 要 】

Background: Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome. Objective: We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19. Methods: We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the a-diversity, 13-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex. Results: The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (beta linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19. Conclusions: Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.

【 授权许可】

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