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

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-15

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33577896

DOI Digital object identifier for electronic documents.

10.1016/j.jaci.2021.02.001

URI

Authors

Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH, Das SR

Journal

The Journal of allergy and clinical immunology

Year

2021

Keywords:

16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory

BACKGROUND: Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 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 ⍺-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 = .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.

Experiment 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-15

Curated date: 2021/07/10

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy

Differences from previous experiment shown

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-19 patients with low viral load

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 patients with high viral load

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized, with high viral load (quantitative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 38

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: increased

Richness Number of species: increased

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-15

Curated date: 2021/07/10

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy

Source: Figure 4b

Description: Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential abundance testing was conducted using DESeq2 models at the ASV level including age and sex as covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.

Abundance in Group 1: increased abundance in COVID-19 patients with high viral load

NCBI	Quality Control	Links
Anaerococcus sp.
Campylobacter hominis
Corynebacterium sp.
Enterococcus sp.
Faecalibacterium prausnitzii
Peptoniphilus sp.
Segatella copri
unclassified Enterobacteriaceae
unclassified Neisseriaceae

Revision editor(s): Claregrieve1, Peace Sandy

Signature 2

Edit History Delete

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-15

Curated date: 2021/07/10

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy

Source: Figure 4b

Description: Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential abundance testing was conducted using DESeq2 models at the ASV level including age and sex as covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.

Abundance in Group 1: decreased abundance in COVID-19 patients with high viral load

NCBI	Quality Control	Links
Corynebacterium sp.
Dolosigranulum pigrum
Granulicatella elegans
Neisseria sp.
Prevotella disiens
Staphylococcus haemolyticus
Streptococcus sp.
unclassified Acinetobacter
unclassified Stenotrophomonas

Revision editor(s): Claregrieve1, Peace Sandy