tetano
Editor, Senior Moderator
J Allergy Clin Immunol
. 2021 Feb 9;S0091-6749(21)00177-9.
doi: 10.1016/j.jaci.2021.02.001. Online ahead of print.
SARS-CoV-2 Infection and Viral Load are Associated with the Upper Respiratory Tract Microbiome
Christian Rosas-Salazar[SUP] 1 [/SUP], Kyle S Kimura[SUP] 2 [/SUP], Meghan H Shilts[SUP] 3 [/SUP], Britton A Strickland[SUP] 4 [/SUP], Michael H Freeman[SUP] 2 [/SUP], Bronson C Wessinger[SUP] 5 [/SUP], Veerain Gupta[SUP] 5 [/SUP], Hunter M Brown[SUP] 3 [/SUP], Seesandra V Rajagopala[SUP] 3 [/SUP], Justin H Turner[SUP] 6 [/SUP], Suman R Das[SUP] 7 [/SUP]
Affiliations
Abstract
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.
Keywords: 16S rRNA sequencing; COVID-19; SARS-CoV-2; airway; coronavirus; microbiome; nasal; nasopharynx; respiratory.
. 2021 Feb 9;S0091-6749(21)00177-9.
doi: 10.1016/j.jaci.2021.02.001. Online ahead of print.
SARS-CoV-2 Infection and Viral Load are Associated with the Upper Respiratory Tract Microbiome
Christian Rosas-Salazar[SUP] 1 [/SUP], Kyle S Kimura[SUP] 2 [/SUP], Meghan H Shilts[SUP] 3 [/SUP], Britton A Strickland[SUP] 4 [/SUP], Michael H Freeman[SUP] 2 [/SUP], Bronson C Wessinger[SUP] 5 [/SUP], Veerain Gupta[SUP] 5 [/SUP], Hunter M Brown[SUP] 3 [/SUP], Seesandra V Rajagopala[SUP] 3 [/SUP], Justin H Turner[SUP] 6 [/SUP], Suman R Das[SUP] 7 [/SUP]
Affiliations
- PMID: 33577896
- PMCID: PMC7871823
- DOI: 10.1016/j.jaci.2021.02.001
Abstract
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.
Keywords: 16S rRNA sequencing; COVID-19; SARS-CoV-2; airway; coronavirus; microbiome; nasal; nasopharynx; respiratory.