New insights into upper respiratory microbiota diversity and interplay in patients with COVID-19 depending on the SARS-CoV-2 viral load in the epithelial cells in the nasopharynx

Abstract

Introduction: The effect of SARS-CoV-2 infection on the microbiota of the upper respiratory tract (URT) has yet to be well known, and more attention to this topic is needed.

Objectives: The study aimed to assess the bacterial profile and the possible association between the URT microbiota composition and the SARS-CoV-2 viral load.

Patients and methods: The swabs from the nasopharynx were taken from 60 adult patients infected with SARS-CoV-2 who were divided into three groups based on the quantification cycle (Cq) in PCR: I – Cq ≤31.0 (n = 20; high replication level), II – 31<Cq<38 (n = 20; low replication level), III-Cq higher or equal ≤ 38.0 (n = 20; virus eliminated from the epithelial cells in the nasopharynx). After qPCR, the obtained genetic libraries of 16S rRNA were sequenced using a MiSeq sequencer (Illumina, San Diego, California, USA).

Results: The significantly lower abundance of Prevotella species in the I group was noted compared to the II and III. Akkermansia muciniphila, Faecalibacterium prausnitzii, Fusicatenibacterium saccharivorans, and Bacteroides dorei abundance were characteristic and significantly higher in I compared to II and III groups respectively.

Conclusions: Our study provides important results to explore the linkage between nasopharynx microbiota and virus load in the epithelium cells. The arbitrarily designated division of research groups was reflected in the bacterial microbiota's diversified qualitative and semi-quantitative composition. Patients with low viral replication (group II) and patients who eliminated the SARS-CoV-2 virus from the epithelial cells (group III) formed a less biodiverse group in microbiota community.