Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Metatranscriptome Analysis of Nasopharyngeal Swabs Demonstrated Unprecedented Species Diversity

Michaela Hyblova
* ORCID logo ,
Dominik Hadzega
,
Klaudia Babisova
,
Patrik Krumpolec
,
Andrej Gnip
,
Peter Sabaka
ORCID logo ,
Stefan Lassan
,
Gabriel Minarik
Version 1 : Received: 6 June 2023 / Approved: 7 June 2023 / Online: 7 June 2023 (08:23:07 CEST)

A peer-reviewed article of this Preprint also exists.

Hyblova, M.; Hadzega, D.; Babisova, K.; Krumpolec, P.; Gnip, A.; Sabaka, P.; Lassan, S.; Minarik, G. Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity. Microorganisms 2023, 11, 1804. Hyblova, M.; Hadzega, D.; Babisova, K.; Krumpolec, P.; Gnip, A.; Sabaka, P.; Lassan, S.; Minarik, G. Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity. Microorganisms 2023, 11, 1804.

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 performed a multifocus shotgun analysis to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We compared the microbiome of healthy people versus those with varying degrees of COVID-19 severity. We observed a significant increase in the diversity of microbial species in patients with COVID-19 regardless of disease severity. Some bacterial phyla, such as Actinobacteria, are significantly more abundant in healthy people than in infected people, whereas Bacteroides are less abundant in the latter. Infected people, regardless of severity and symptoms, have the same proportional representation of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteriales the same. 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, Molluscum Contagiosum Virus, 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.

Keywords

metatranscriptome; microbiome; SARS-CoV-2; virome

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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