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

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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): WikiWorks, Peace Sandy, Claregrieve1

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 Epipharynx,Nasal part of pharynx,Nasenrachenraum,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

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

Curated date: 2021/07/10

Curator: Claregrieve1

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

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

NCBI	Quality Control	Links
Anaerococcus sp.
Brevundimonas sp.
Campylobacter hominis
Corynebacterium imitans
Corynebacterium sp.
Ezakiella
Granulicatella sp.
Peptoniphilus lacrimalis
Peptoniphilus sp.
Phocaeicola vulgatus
Segatella copri
Sphingobacterium spiritivorum

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

Signature 2

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

Curated date: 2021/07/10

Curator: Claregrieve1

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

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, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

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)

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

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

Curated date: 2021/07/10

Curator: Claregrieve1

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

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, WikiWorks

Signature 2