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
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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
- 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
- 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
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3B
Description: Differential microbial abundance between non-COVID controls and COVID-19 infected patients
Abundance in Group 1: increased abundance in COVID-19 patients
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 3B
Description: Differential microbial abundance between non-COVID controls and COVID-19 infected patients
Abundance in Group 1: decreased abundance in COVID-19 patients
NCBI | Quality Control | Links |
---|---|---|
unclassified Lachnospiraceae | ||
Neisseria sp. | ||
Anaerostipes hadrus | ||
Corynebacterium sp. | ||
Staphylococcus haemolyticus | ||
Prevotella disiens |
Revision editor(s): Claregrieve1
Experiment 2
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)
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4b
Description: Differential microbial abundance between COVID-19 patients with high viral load and patients with low viral load
Abundance in Group 1: increased abundance in COVID-19 patients with high viral load
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 4b
Description: Differential microbial abundance between COVID-19 patients with high viral load and patients with low viral load
Abundance in Group 1: decreased abundance in COVID-19 patients with high viral load
Revision editor(s): Claregrieve1