Fig 1.
Flow chart of the study.
Table 1.
Patient characteristics at the time of nasopharyngeal swab sampling.
Fig 2.
Relationship between SARS-CoV-2 characteristics and the severity of COVID-19 disease.
(A) Relationship between SARS-CoV-2 viral loads measured in naso-pharyngeal swabs (NPS) with RT-qPCR or metagenomics. (B) Comparison of SARS-CoV-2 viral loads measured by metagenomics in NPS in the three groups of patients. (C) Phylogenetic analysis of full-length SARS-CoV-2 genome sequences from the three groups (indicated by different colors). *p<0.05; **p<0.01.
Table 2.
Bacterial, viral, fungal and parasite coinfections in nasopharyngeal swabs from the 104 patients, classified according to the severity of COVID-19 and their pathogenic capacity.
Fig 3.
Relationship between naso-pharyngeal swab transcriptomics and the severity of COVID-19 disease.
(A) CXCR2 receptor pathway. (B) CXCR3/CCR6 pathway. *p<0.05; **p<0.01.
Fig 4.
Receiver operating characteristic (ROC) curves of CXCR2 (A) and CXCR3 (B) panel predictive values on the severity of COVID-19 disease. The CXCR2 panel included normalized transcript counts for CXCL1, IL8, CXCL5 and CXCR2. The CXCR3 panel included normalized transcript counts for CXCL10, CXCL11, CXCL9, CXCR3, GZMB, CCR6 and CCL20. TP: true positive; FP: false positive.
Fig 5.
Transcriptomic analyses of olfactory receptors and the ACE2 SARS-CoV-2 receptor.
(A) Individual expression of olfactory receptors in the three groups of patients. Each colored circle represents a distinct olfactory receptor differentially transcribed across the three groups (including OR10A7, OR10C1, OR10Q1, OR10V1, OR11A1, OR11H1, OR11L1, OR12D2, OR14K1, OR1I1, OR1J2, OR1L8, OR1M1, OR1Q1, OR2AE1, OR2AT4, OR2B11, OR2F1, OR2G6, OR2T10, OR2V1, OR2W3, OR4D1, OR4K1, OR4M1, OR4Q3, OR51T1, OR52L1, OR52M1, OR52W1, OR56A4, OR6B1, OR6B2, OR6X1, OR8B2, OR8B3 and OR9G1). (B) Expression of the angiotensin-converting enzyme-2 (ACE2) transcript, the SARS-CoV-2 entry receptor, in the three groups of patients. *p<0.05; **p<0.01.
Table 3.
Association between clinical factors and biomarker gene expression (n = 93).
aOR indicate adjusted odds ratio. Significant associations (p <0.05) are in bold.
Table 4.
Multivariate analysis assessing the prognostic value of biomarker gene expression on 30-day mortality in ICU patients (N = 44, 17 deaths).