Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity

Author:

Hyblova Michaela1ORCID,Hadzega Dominik1,Babisova Klaudia1,Krumpolec Patrik1,Gnip Andrej1,Sabaka Peter2ORCID,Lassan Stefan3,Minarik Gabriel1

Affiliation:

1. Medirex Group Academy, 949 05 Nitra, Slovakia

2. Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, 814 99 Bratislava, Slovakia

3. Department of Pneumology and Ftizeology I, University Hospital in Bratislava, 831 01 Bratislava, Slovakia

Abstract

The recent global emergence of the SARS-CoV-2 pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We conducted a comprehensive shotgun analysis targeting multiple aspects to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We conducted a comparative analysis of the microbiome between healthy individuals and those with varying degrees of COVID-19 severity, including a total of 151 participants. Our findings revealed a noteworthy increase in microbial species diversity among patients with COVID-19, irrespective of disease severity. Specifically, our analysis revealed a significant difference in the abundance of bacterial phyla between healthy individuals and those infected with COVID-19. We found that Actinobacteria, among other bacterial phyla, showed a notably higher abundance in healthy individuals compared to infected individuals. Conversely, Bacteroides showed a lower abundance in the latter group. Infected people, regardless of severity and symptoms, have the same proportional representation of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteriales. In addition to SARS-CoV-2 and numerous phage groups, we identified sequences of clinically significant viruses such as Human Herpes Virus 1, Human Mastadenovirus D, and Rhinovirus A in several samples. Analyses were performed retrospectively, therefore, in the case of SARS-CoV-2 various WHO variants such as Alpha (B.1.1.7), Delta (B.1.617.2), Omicron (B.1.1.529), and 20C strains are represented. Additionally, the presence of specific virus strains has a certain effect on the distribution of individual microbial taxa.

Funder

OP Integrated Infrastructure

Publisher

MDPI AG

Subject

Virology,Microbiology (medical),Microbiology

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