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RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients

ABSTRACT: RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients

PROVIDER: PRJNA774978 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16596311_1.fastq.gz	Fastqsanger.gz
	SRR16596311_2.fastq.gz	Fastqsanger.gz
	SRR16596312_1.fastq.gz	Fastqsanger.gz
	SRR16596312_2.fastq.gz	Fastqsanger.gz
	SRR16596313_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients

Project description:We used total RNA of nasopharyngeal swabs from COVID-19 patients to identify their gene expression profile. Multiple biological process were significantly enriched in either asymptomatic or mildly symptomatic patients. These significantly expressed genes were suggested to contribute to the severity of the disease. We also performed metagenomics analysis to identify differences in the microbiome profile of the two groups of patients.

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RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.

Project description:ObjectivesThe characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients.MethodsA ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data.ResultsBoth groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients.ConclusionA reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.

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