Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort

Abstract

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus's effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.

Fig. 1

Experimental workflow. Summary of the experimental workflow applied to generate transcriptomic datasets originated by RNA extracted from nasopharyngeal swabs in the Campania cohort.

Fig. 2

Analysis of RNA gene expression profiles between 1st and 3rd wave (a) Summary of demographics and other patients’ features of recruited cases in this cohort. (b) Volcano plot summarizing transcripts changes comparing 1st vs 3rd period. Green Dot and Red Dot show down- and up-regulated genes, respectively. According to the adjusted p-values (FDR) threshold of 0.05, transcripts associated with insignificant expression values are reported in grey. The dotted line (threshold) represents the cut-off (p-value ≤ 0.01). (c) Bar chart showing statistically significant pathway, according to IPA, of differentially expressed genes between 1st vs 3rd pandemic waves in Campania. (d) Bar chart showing the differentially expressed genes biotype detected in the analysis, divided into protein-coding (blue) and non-coding (orange) genes.

Fig. 3

Quality controls of the experimental procedure. (a) Bar chart showing the Ct value associated with each patient distributed in three different waves (orange: 1st period, blue: 2nd period, grey: 3rd period. (b) Coverage plot showing the reads coverage along gene body. All transcripts for all samples were scaled to 100 nt length and the number of reads covering each nucleotide position was reported as coverage ranged from 0 (jade-green) to 1 (pink).