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

Autor: Bronson C. Wessinger, Suman R. Das, Seesandra V. Rajagopala, Kyle Kimura, Christian Rosas-Salazar, Meghan H. Shilts, Britton A. Strickland, Justin H. Turner, Veerain Gupta, Hunter M. Brown, Michael H. Freeman
Rok vydání: 2020
Předmět:
0301 basic medicine
Male
URT
Upper respiratory tract
viruses
Respiratory System
coronavirus
microbiome
nasal
medicine.disease_cause
nasopharynx
RT-qPCR
Quantitative reverse transcription PCR
SARS-CoV-2
Severe acute respiratory syndrome coronavirus-2
RNA
Ribosomal
16S
Prevotella
Immunology and Allergy
Coronavirus
COVID-19
Coronavirus disease 2019
biology
Microbiota
ASV
Amplicon sequence variant
Biodiversity
Amplicon
Middle Aged
Viral Load
medicine.anatomical_structure
Staphylococcus haemolyticus
Respiratory virus
Female
Viral load
Adult
030106 microbiology
Immunology
Article
CT
Cycle threshold
03 medical and health sciences
Species Specificity
medicine
LRT
Lower respiratory tract
Humans
Microbiome
rRNA
Ribosomal ribonucleic acid
Pandemics
Host Microbial Interactions
SARS-CoV-2
COVID-19
IQR
Interquartile range
biology.organism_classification
respiratory
Virology
16S rRNA sequencing
030104 developmental biology
airway
Case-Control Studies
Respiratory tract
Zdroj: The Journal of Allergy and Clinical Immunology
Journal of Allergy and Clinical Immunology
ISSN: 1097-6825
Popis: Background Little is known about the relationships between SARS-CoV-2, the respiratory virus responsible for the ongoing COVID-19 pandemic, and the upper respiratory tract (URT) microbiome. Objective Our objectives were 1) to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults, and 2) 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 ⍺-diversity, β-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 (β linear regression coefficient=7.53, 95%CI=0.17-14.89, p=0.045). In differential abundance testing, 9 amplicon sequence variants (ASVs) were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified ASV 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 ASVs were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19. Conclusion 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.
Capsule Summary: In our study, we found substantial differences in the upper respiratory tract microbiome between SARS-CoV-2-infected and -uninfected adults. Furthermore, we show that the SARS-CoV-2 viral load is associated with the upper respiratory tract microbiome during COVID-19.
Databáze: OpenAIRE
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