Article Figures & Data
Figures
- FIG 1
Relationships of metatranscriptomic sequencing sample characteristics to sequencing results. (a) Relationship between the proportion of reads mapped to SARS-CoV-2 and the number of reads matched to human sequences. (b to i) Plots of sequencing results against the Ct values of metatranscriptomic sequencing samples. Panels a to f are color coded by severity index values, and panels g to i are color coded by days from onset of symptoms. The severity index was defined on a scale of 1 to 4, as follows: 4, not admitted; 3, admitted; 2, intensive care unit; and 1, required ventilator. Black dots represent samples with unknown onset or severity index values. (b) Relationship of Ct values determined by LDT-RT-PCR to the number of days from symptom onset. (c) Relationship between Ct values and the proportion of total matches of SARS-CoV-2 by CosmosID. (d, g) Relationship between Ct values and the sequencing coverage across the SARS-CoV-2 strain Hu-1 genome. (e, h) Relationship between Ct values and the number of reads analyzed by CosmosID until the first SARS-CoV-2 read was detected. (f, i) Relationship of Ct values to the proportion of SARS-CoV-2 reads present in the sample. Simple linear regression analysis was performed for each set, and the null hypothesis is rejected for panels b to i (P < 0.01), and for each set, R2 is reported.
- FIG 2
Bacterial diversity analysis of metagenomic sequencing results. (a, b, c) Alpha diversity analysis of metagenomic sequencing results. SARS-CoV-2 positivity was determined by LDT-RT-PCR. (a, b) Shannon diversity plot and Chao diversity plot of SARS-CoV-2-negative and -positive samples at the species level. (c) Shannon diversity plot of SARS-CoV-2-negative samples and SARS-CoV-2-positive samples at different periods post-onset of symptoms. (d, e, f) Beta diversity principal-coordinate analysis of metagenomic sequencing results at the species level. (d) Bray-Curtis analysis of bacterial community composition diversity between SARS-CoV-2-negative and SARS-CoV-2-positive samples. (e) Bray-Curtis analysis of bacterial community composition diversity grouped by PCR and sequencing positivity. (f) Bray-Curtis analysis of bacterial diversity in different disease severity groups. (a, b) Wilcoxon rank sum tests were performed between positive and negative SARS-CoV-2 groups for the Shannon diversity index (P = 0.0097) and Chao diversity (P = 0.0082). (c) Wilcoxon rank sum tests were performed between disease onset groups (no significance). (d, f) PERMANOVA tests were performed on Bray-Curtis distance matrices for SARS-CoV-2-positive and -negative groups (P = 0.027) (d) and groups of disease severity (P = 0.022) (f). (e) Pairwise PERMANOVA tests were performed on Bray-Curtis distance matrices between groups defined by SARS-CoV-2 positivity by RT-PCR and sequencing. RT-PCR+/sequencing+ (PCR+/Seq+) versus RT-PCR–/sequencing– (PCR–/Seq–) (P = 0.007); PC1 and -2, principal components 1 and 2. The severity index was defined on a scale of 1 to 4, as follows: 4, not admitted; 3, admitted; 2, intensive care unit; and 1, required ventilator.
- FIG 3
Changes in bacterial microbiome composition in COVID-19 patients. (a, b) Relative abundances of bacteria at the species level in COVID-19-positive and COVID-19-negative samples. (a) Overall relative abundances of bacterial species in COVID-19-positive and COVID-19-negative patients. (b) Relative abundances of bacterial species in individual COVID-19-positive and COVID-19-negative patients, with samples ordered by Ct value determined by LDT-RT-PCR. A Wilcoxon rank sum test was performed on overall relative abundance values for Propionibacteriaceae (*, P = 0.028) and for Corynebacterium accolens (*, P = 0.025).
Tables
- TABLE 1
Suspect COVID-19 sample characteristics and sequencing resultsf
↵a The severity index was defined on a scale of 1 to 4, as follows: 4, not admitted; 3, admitted; 2, intensive care unit; and 1, required ventilator.
↵b Days from onset is defined as the number of days from the initial onset of symptoms until the time of specimen collection.
↵c Putative pathogens causing coinfections are defined as known pathogens, with bacteria having above 50% relative abundance and not considered microbiota.
↵d Suspected COVID-19 specimens that were found to be positive for SARS-CoV-2 by RT-PCR.
↵e Suspected COVID-19 specimens that were found to negative for SARS-CoV-2 by RT-PCR.
↵f Ct, cycle threshold; SD, standard deviation; –, unknown information; No ID, samples that were not identified by CosmosID; NA, not applicable.
- TABLE 2
Patient demographics and clinical characteristics
↵a Self-reported in prespecified fixed categories.
↵b Number of days from onset of symptoms until specimen collection.
↵c The severity index was defined by a 4-point scale: 4, not admitted to hospital; 3, admitted to hospital; 2, admitted to ICU; and 1, required ventilator.
↵d IQR, interquartile range.
TABLE S1
Summary of sequencing reads. Download Table S1, XLSX file, 0.03 MB.
Copyright © 2020 Mostafa et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
TABLE S2
Taxonomic classification matrices for metagenomic and metatranscriptomic data. Download Table S2, XLSX file, 0.3 MB.
Copyright © 2020 Mostafa et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
