SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2021/07/10
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy
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
- Asymptomatic uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Symptomatic, mild to moderate COVID-19 patients
- 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
- 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
Signature 1
Source: Figure 3B
Description: Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. 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.
Abundance in Group 1: increased abundance in Symptomatic, mild to moderate COVID-19 patients
Revision editor(s): Claregrieve1, Peace Sandy
Signature 2
Source: Figure 3B
Description: Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. 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.
Abundance in Group 1: decreased abundance in Symptomatic, mild to moderate COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes hadrus | ||
| Corynebacterium sp. | ||
| Neisseria sp. | ||
| Prevotella disiens | ||
| Staphylococcus haemolyticus | ||
| unclassified Lachnospiraceae |
Revision editor(s): Claregrieve1, Peace Sandy
Experiment 2
Curated date: 2021/07/10
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy
Subjects
- 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)
Lab analysis
Statistical Analysis
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
Signature 1
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
Revision editor(s): Claregrieve1, Peace Sandy
Signature 2
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
Revision editor(s): Claregrieve1, Peace Sandy
